Hot off the presses! May 31 PLoS

The May 31 issue of the PLoS is now up on Pubget (About PLoS): if you're at a subscribing institution, just click the link in the latest link at the home page. (Note you'll only be able to get all the PDFs in the issue if your institution subscribes to Pubget.)

Latest Articles Include:

• Tsetse Flies Rely on Symbiotic Wigglesworthia for Immune System Development
  - PLoS 9(5):e1001070 (2011)
  

Hot off the presses! Jun 01 Nat Meth

The Jun 01 issue of the Nat Meth is now up on Pubget (About Nat Meth): if you're at a subscribing institution, just click the link in the latest link at the home page. (Note you'll only be able to get all the PDFs in the issue if your institution subscribes to Pubget.)

Latest Articles Include:

• Mapping the money
  - Nat Meth 8(6):437 (2011)
  Nature Methods | Editorial Mapping the money Journal name:Nature MethodsVolume: 8,Page:437Year published:(2011)DOI:doi:10.1038/nmeth.1623Published online27 May 2011 Improving search tools for NIH grants will increase the transparency of US government–sponsored research and aid those seeking funding. View full text Additional data
• The author file
  - Nat Meth 8(6):439 (2011)
  Nature Methods | Editorial Mapping the money Journal name:Nature MethodsVolume: 8,Page:437Year published:(2011)DOI:doi:10.1038/nmeth.1623Published online27 May 2011 Improving search tools for NIH grants will increase the transparency of US government–sponsored research and aid those seeking funding. View full text Additional data
• Color blindness
  - Nat Meth 8(6):441 (2011)
  Article preview View full access options Nature Methods | This Month Color blindness * Bang Wong1Journal name:Nature MethodsVolume: 8,Page:441Year published:(2011)DOI:doi:10.1038/nmeth.1618Published online27 May 2011 Since my first column on color coding1 appeared, we have received a number of e-mails asking us to highlight the issue of color blindness. One of those correspondences was published in the October 2010 issue2. Here I offer guidelines to make graphics accessible to those with color vision deficiencies. Color blindness affects a substantial portion of the human population. Protanopia and deuteranopia, the two most common forms of inherited color blindness, are red-green color vision defects caused by the absence of red or green retinal photoreceptors, respectively. In individuals of Northern European ancestry, as many as 8 percent of men and 0.5 percent of women experience the common form of red-green color blindness3. If a submitted manuscript happens to go to three male reviewers of Northern European descent, the chance that at least one will be color blind is 22 percent. Picking colors suitable for color-blind readers not only enhances accessibility but also is good graphic design practice. For example, the Ishihara color vision test intentionally relies only on color hue to create contrast, as evident when the image is converted to grayscale (Fig. 1a). In general, colors will be easier to distinguish when they vary in lightness and saturation as well as hue (Fig. 1b). The palette of eight colors shown in Figure 2 has good overall variability and can be differentiated by individuals with red-green color blindness. Figure 1: Ishihara color-vision test plate. () Viewers with normal color vision should see the numeral '6′. () Changing lightness of background improves contrast. * Full size image (260 KB) * Figures index * Next figure Figure 2: Colors optimized for color-blind individuals. P and D indicate simulated colors as seen by individuals with protanopia and deuteranopia, respectively. Figures at a glance * Figure 1: Ishihara color-vision test plate. () Viewers with normal color vision should see the numeral '6′. () Changing lightness of background improves contrast. * Figure 2: Colors optimized for color-blind individuals. P and D indicate simulated colors as seen by individuals with protanopia and deuteranopia, respectively. * Figure 3: Red-green color coding in an immunofluorescent image. () Conventional color coding is difficult for individuals with red-green color blindness (protanopia or deuteranopia) to discriminate. () Replacing red with magenta (top) or green with turquoise (bottom) improves visibility for such individuals. Source image from reference 4. Article preview Read the full article * Instant access to this article: US$32 Buy now * Subscribe to Nature Methods for full access: Subscribe * Personal subscribers: Log in Additional access options: * Login via Athens * Login via your Institution * Purchase a site license * Use a document delivery service * British Library Document Supply Centre * Infotrieve * Thompson ISI Document Delivery * You can also request this document from your local library through inter-library loan services. Author information Article tools * Full text * Print * Email * Download PDF * Download citation * Order reprints * Rights and permissions * Share/bookmark * Connotea * CiteULike * Facebook * Twitter * Delicious * Digg Affiliations * Bang Wong is the creative director of the Broad Institute of the Massachusetts Institute of Technology & Harvard and an adjunct assistant professor in the Department of Art as Applied to Medicine at The Johns Hopkins University School of Medicine. Author Details * Bang Wong Search for this author in: * NPG journals * PubMed * Google Scholar Additional data * Journal home * Current issue * For authors * Subscribe * E-alert sign up * RSS feed Science jobs from naturejobs * Gene Ontology Developer / Curator * European Bioinformatics Institute (EBI) * Cambridge, United Kingdom * Post-doctoral Scientist (m / f) * Boehringer Ingelheim RCV Vienna * Vienna, Austria * Vienna International Post-Doctoral Training in Molecular Life Sciences * Max F. Perutz Laboratories * Wien, Austria * Post a free job * More science jobs Open innovation challenges * Upload Your Compound Libraries! Deadline:Jan 20 2013Reward:See Details As part of our improved Novel Molecules Challenge (NMC) procedure, you may now upload to InnoCenti… * Novel Chemical Derivatives of Bicarbonate Deadline:Jun 02 2011Reward:$20,000 USD The Seeker desires suggestions for novel chemical derivatives of bicarbonate that are water-insolu… * Powered by: * More challenges Top content Emailed * Defining pluripotency Nature Methods 28 Oct 2010 * Light tools Nature Methods 20 Dec 2010 * Visualizing a one-way protein encounter complex by ultrafast single-molecule mixing Nature Methods 06 Feb 2011 * Enzymatic assembly of DNA molecules up to several hundred kilobases Nature Methods 12 Apr 2009 * Fluorescence protease protection of GFP chimeras to reveal protein topology and subcellular localization Nature Methods 17 Feb 2006 View all Downloaded * Fast, three-dimensional super-resolution imaging of live cells Nature Methods 08 May 2011 * Rapid three-dimensional isotropic imaging of living cells using Bessel beam plane illumination Nature Methods 04 Mar 2011 * Chemically defined conditions for human iPSC derivation and culture Nature Methods 10 Apr 2011 * Mapping and quantifying mammalian transcriptomes by RNA-Seq Nature Methods 30 May 2008 * A quantitative analysis of CLIP methods for identifying binding sites of RNA-binding proteins Nature Methods 15 May 2011 View all Blogged * Two-photon absorption properties of fluorescent proteins Nature Methods 28 Apr 2011 * Chemically defined conditions for human iPSC derivation and culture Nature Methods 10 Apr 2011 * Validation of two ribosomal RNA removal methods for microbial metatranscriptomics Nature Methods 19 Sep 2010 * Microbial community resemblance methods differ in their ability to detect biologically relevant patterns Nature Methods 05 Sep 2010 * Comprehensive comparative analysis of strand-specific RNA sequencing methods Nature Methods 15 Aug 2010 View all * Nature Methods * ISSN: 1548-7091 * EISSN: 1548-7105 * About NPG * Contact NPG * RSS web feeds * Help * Privacy policy * Legal notice * Accessibility statement * Terms * Nature News * Naturejobs * Nature Asia * Nature EducationSearch:Go © 2011 Nature Publishing Group, a division of Macmillan Publishers Limited. All Rights Reserved.partner of AGORA, HINARI, OARE, INASP, CrossRef and COUNTER
• Database of NIH grants using machine-learned categories and graphical clustering
  - Nat Meth 8(6):443-444 (2011)
  Nature Methods | Editorial Mapping the money Journal name:Nature MethodsVolume: 8,Page:437Year published:(2011)DOI:doi:10.1038/nmeth.1623Published online27 May 2011 Improving search tools for NIH grants will increase the transparency of US government–sponsored research and aid those seeking funding. View full text Additional data
• Predicting protein associations with long noncoding RNAs
  - Nat Meth 8(6):444-445 (2011)
  Nature Methods | Editorial Mapping the money Journal name:Nature MethodsVolume: 8,Page:437Year published:(2011)DOI:doi:10.1038/nmeth.1623Published online27 May 2011 Improving search tools for NIH grants will increase the transparency of US government–sponsored research and aid those seeking funding. View full text Additional data
• Perfecting ChR2
  - Nat Meth 8(6):447 (2011)
  Nature Methods | Research Highlights Perfecting ChR2 * Erika PastranaJournal name:Nature MethodsVolume: 8,Page:447Year published:(2011)DOI:doi:10.1038/nmeth0611-447Published online27 May 2011 Two new reports describe variants of channelrhodopsin 2 with improved properties. View full text Subject terms: * Neuroscience Additional data Author Details * Erika Pastrana Search for this author in: * NPG journals * PubMed * Google Scholar
• The right chromophore for the job
  - Nat Meth 8(6):448-449 (2011)
  Nature Methods | Research Highlights The right chromophore for the job * Daniel EvankoJournal name:Nature MethodsVolume: 8,Pages:448–449Year published:(2011)DOI:doi:10.1038/nmeth0611-448aPublished online27 May 2011 A normally undesirable property of chromophores is used in the creation of a genetically encoded tag for correlated light and electron microscopy. View full text Subject terms: * Sensors and probes Additional data Author Details * Daniel Evanko Search for this author in: * NPG journals * PubMed * Google Scholar
• From pseudogenes to proteins
  - Nat Meth 8(6):448-449 (2011)
  Nature Methods | Research Highlights From pseudogenes to proteins * Nicole RuskJournal name:Nature MethodsVolume: 8,Pages:448–449Year published:(2011)DOI:doi:10.1038/nmeth0611-448bPublished online27 May 2011 Combining proteome analysis with genome sequencing improves gene annotation and yields evidence that some genes presumed to be noncoding are actually expressed. View full text Subject terms: * Genomics Additional data Author Details * Nicole Rusk Search for this author in: * NPG journals * PubMed * Google Scholar
• News in brief
  - Nat Meth 8(6):449 (2011)
  Article preview View full access options Nature Methods | Research Highlights News in brief Journal name:Nature MethodsVolume: 8,Page:449Year published:(2011)DOI:doi:10.1038/nmeth0611-449Published online27 May 2011 Genome-wide map of the sixth base Although 5-hyrdoxymethyl-cytosine (5hmC) is thought to be important for genome function in certain cells, a lack of tools has made profiling difficult. Xu et al. used a 5hmC-specific antibody for methylated DNA immunoprecipitation (MeDIP) and found distinct genome-wide 5hmC patterns in the mouse. The researchers saw 5hmC enrichment in gene bodies rather than at promoters and in intergenic regions. They also uncovered a role for the ten-eleven translocation (Tet) family of 5mC hydroxylases. Xu, Y.et al. Mol. Cell. advance online publication (20 April 2011). Article preview Read the full article * FREE access with registration Register now * Already have a Nature.com account? Log in Additional access options: * Login via Athens * Login via your Institution * Purchase a site license * Use a document delivery service * British Library Document Supply Centre * Infotrieve * Thompson ISI Document Delivery * You can also request this document from your local library through inter-library loan services. Additional data
• Directed evolution made easy
  - Nat Meth 8(6):451 (2011)
  Nature Methods | Research Highlights Perfecting ChR2 * Erika PastranaJournal name:Nature MethodsVolume: 8,Page:447Year published:(2011)DOI:doi:10.1038/nmeth0611-447Published online27 May 2011 Two new reports describe variants of channelrhodopsin 2 with improved properties. View full text Subject terms: * Neuroscience Additional data Author Details * Erika Pastrana Search for this author in: * NPG journals * PubMed * Google Scholar
• Resurrected enzymes
  - Nat Meth 8(6):452 (2011)
  Nature Methods | Research Highlights Perfecting ChR2 * Erika PastranaJournal name:Nature MethodsVolume: 8,Page:447Year published:(2011)DOI:doi:10.1038/nmeth0611-447Published online27 May 2011 Two new reports describe variants of channelrhodopsin 2 with improved properties. View full text Subject terms: * Neuroscience Additional data Author Details * Erika Pastrana Search for this author in: * NPG journals * PubMed * Google Scholar
• DNA origami in 3D
  - Nat Meth 8(6):454 (2011)
  Nature Methods | Research Highlights Perfecting ChR2 * Erika PastranaJournal name:Nature MethodsVolume: 8,Page:447Year published:(2011)DOI:doi:10.1038/nmeth0611-447Published online27 May 2011 Two new reports describe variants of channelrhodopsin 2 with improved properties. View full text Subject terms: * Neuroscience Additional data Author Details * Erika Pastrana Search for this author in: * NPG journals * PubMed * Google Scholar
• Microarrays, megasynthesis
  - Nat Meth 8(6):457-460 (2011)
  Nature Methods | Editorial Mapping the money Journal name:Nature MethodsVolume: 8,Page:437Year published:(2011)DOI:doi:10.1038/nmeth.1623Published online27 May 2011 Improving search tools for NIH grants will increase the transparency of US government–sponsored research and aid those seeking funding. View full text Additional data
• Bringing fly brains in line
  - Nat Meth 8(6):461-463 (2011)
  Article preview View full access options Nature Methods | This Month Color blindness * Bang Wong1Journal name:Nature MethodsVolume: 8,Page:441Year published:(2011)DOI:doi:10.1038/nmeth.1618Published online27 May 2011 Since my first column on color coding1 appeared, we have received a number of e-mails asking us to highlight the issue of color blindness. One of those correspondences was published in the October 2010 issue2. Here I offer guidelines to make graphics accessible to those with color vision deficiencies. Color blindness affects a substantial portion of the human population. Protanopia and deuteranopia, the two most common forms of inherited color blindness, are red-green color vision defects caused by the absence of red or green retinal photoreceptors, respectively. In individuals of Northern European ancestry, as many as 8 percent of men and 0.5 percent of women experience the common form of red-green color blindness3. If a submitted manuscript happens to go to three male reviewers of Northern European descent, the chance that at least one will be color blind is 22 percent. Picking colors suitable for color-blind readers not only enhances accessibility but also is good graphic design practice. For example, the Ishihara color vision test intentionally relies only on color hue to create contrast, as evident when the image is converted to grayscale (Fig. 1a). In general, colors will be easier to distinguish when they vary in lightness and saturation as well as hue (Fig. 1b). The palette of eight colors shown in Figure 2 has good overall variability and can be differentiated by individuals with red-green color blindness. Figure 1: Ishihara color-vision test plate. () Viewers with normal color vision should see the numeral '6′. () Changing lightness of background improves contrast. * Full size image (260 KB) * Figures index * Next figure Figure 2: Colors optimized for color-blind individuals. P and D indicate simulated colors as seen by individuals with protanopia and deuteranopia, respectively. Figures at a glance * Figure 1: Ishihara color-vision test plate. () Viewers with normal color vision should see the numeral '6′. () Changing lightness of background improves contrast. * Figure 2: Colors optimized for color-blind individuals. P and D indicate simulated colors as seen by individuals with protanopia and deuteranopia, respectively. * Figure 3: Red-green color coding in an immunofluorescent image. () Conventional color coding is difficult for individuals with red-green color blindness (protanopia or deuteranopia) to discriminate. () Replacing red with magenta (top) or green with turquoise (bottom) improves visibility for such individuals. Source image from reference 4. Article preview Read the full article * Instant access to this article: US$32 Buy now * Subscribe to Nature Methods for full access: Subscribe * Personal subscribers: Log in Additional access options: * Login via Athens * Login via your Institution * Purchase a site license * Use a document delivery service * British Library Document Supply Centre * Infotrieve * Thompson ISI Document Delivery * You can also request this document from your local library through inter-library loan services. Author information Article tools * Full text * Print * Email * Download PDF * Download citation * Order reprints * Rights and permissions * Share/bookmark * Connotea * CiteULike * Facebook * Twitter * Delicious * Digg Affiliations * Bang Wong is the creative director of the Broad Institute of the Massachusetts Institute of Technology & Harvard and an adjunct assistant professor in the Department of Art as Applied to Medicine at The Johns Hopkins University School of Medicine. Author Details * Bang Wong Search for this author in: * NPG journals * PubMed * Google Scholar Additional data * Journal home * Current issue * For authors * Subscribe * E-alert sign up * RSS feed Science jobs from naturejobs * Gene Ontology Developer / Curator * European Bioinformatics Institute (EBI) * Cambridge, United Kingdom * Post-doctoral Scientist (m / f) * Boehringer Ingelheim RCV Vienna * Vienna, Austria * Vienna International Post-Doctoral Training in Molecular Life Sciences * Max F. Perutz Laboratories * Wien, Austria * Post a free job * More science jobs Open innovation challenges * Upload Your Compound Libraries! Deadline:Jan 20 2013Reward:See Details As part of our improved Novel Molecules Challenge (NMC) procedure, you may now upload to InnoCenti… * Novel Chemical Derivatives of Bicarbonate Deadline:Jun 02 2011Reward:$20,000 USD The Seeker desires suggestions for novel chemical derivatives of bicarbonate that are water-insolu… * Powered by: * More challenges Top content Emailed * Defining pluripotency Nature Methods 28 Oct 2010 * Light tools Nature Methods 20 Dec 2010 * Visualizing a one-way protein encounter complex by ultrafast single-molecule mixing Nature Methods 06 Feb 2011 * Enzymatic assembly of DNA molecules up to several hundred kilobases Nature Methods 12 Apr 2009 * Fluorescence protease protection of GFP chimeras to reveal protein topology and subcellular localization Nature Methods 17 Feb 2006 View all Downloaded * Fast, three-dimensional super-resolution imaging of live cells Nature Methods 08 May 2011 * Rapid three-dimensional isotropic imaging of living cells using Bessel beam plane illumination Nature Methods 04 Mar 2011 * Chemically defined conditions for human iPSC derivation and culture Nature Methods 10 Apr 2011 * Mapping and quantifying mammalian transcriptomes by RNA-Seq Nature Methods 30 May 2008 * A quantitative analysis of CLIP methods for identifying binding sites of RNA-binding proteins Nature Methods 15 May 2011 View all Blogged * Two-photon absorption properties of fluorescent proteins Nature Methods 28 Apr 2011 * Chemically defined conditions for human iPSC derivation and culture Nature Methods 10 Apr 2011 * Validation of two ribosomal RNA removal methods for microbial metatranscriptomics Nature Methods 19 Sep 2010 * Microbial community resemblance methods differ in their ability to detect biologically relevant patterns Nature Methods 05 Sep 2010 * Comprehensive comparative analysis of strand-specific RNA sequencing methods Nature Methods 15 Aug 2010 View all * Nature Methods * ISSN: 1548-7091 * EISSN: 1548-7105 * About NPG * Contact NPG * RSS web feeds * Help * Privacy policy * Legal notice * Accessibility statement * Terms * Nature News * Naturejobs * Nature Asia * Nature EducationSearch:Go © 2011 Nature Publishing Group, a division of Macmillan Publishers Limited. All Rights Reserved.partner of AGORA, HINARI, OARE, INASP, CrossRef and COUNTER
• Channeling the data deluge
  - Nat Meth 8(6):463-465 (2011)
  Article preview View full access options Nature Methods | This Month Color blindness * Bang Wong1Journal name:Nature MethodsVolume: 8,Page:441Year published:(2011)DOI:doi:10.1038/nmeth.1618Published online27 May 2011 Since my first column on color coding1 appeared, we have received a number of e-mails asking us to highlight the issue of color blindness. One of those correspondences was published in the October 2010 issue2. Here I offer guidelines to make graphics accessible to those with color vision deficiencies. Color blindness affects a substantial portion of the human population. Protanopia and deuteranopia, the two most common forms of inherited color blindness, are red-green color vision defects caused by the absence of red or green retinal photoreceptors, respectively. In individuals of Northern European ancestry, as many as 8 percent of men and 0.5 percent of women experience the common form of red-green color blindness3. If a submitted manuscript happens to go to three male reviewers of Northern European descent, the chance that at least one will be color blind is 22 percent. Picking colors suitable for color-blind readers not only enhances accessibility but also is good graphic design practice. For example, the Ishihara color vision test intentionally relies only on color hue to create contrast, as evident when the image is converted to grayscale (Fig. 1a). In general, colors will be easier to distinguish when they vary in lightness and saturation as well as hue (Fig. 1b). The palette of eight colors shown in Figure 2 has good overall variability and can be differentiated by individuals with red-green color blindness. Figure 1: Ishihara color-vision test plate. () Viewers with normal color vision should see the numeral '6′. () Changing lightness of background improves contrast. * Full size image (260 KB) * Figures index * Next figure Figure 2: Colors optimized for color-blind individuals. P and D indicate simulated colors as seen by individuals with protanopia and deuteranopia, respectively. Figures at a glance * Figure 1: Ishihara color-vision test plate. () Viewers with normal color vision should see the numeral '6′. () Changing lightness of background improves contrast. * Figure 2: Colors optimized for color-blind individuals. P and D indicate simulated colors as seen by individuals with protanopia and deuteranopia, respectively. * Figure 3: Red-green color coding in an immunofluorescent image. () Conventional color coding is difficult for individuals with red-green color blindness (protanopia or deuteranopia) to discriminate. () Replacing red with magenta (top) or green with turquoise (bottom) improves visibility for such individuals. Source image from reference 4. Article preview Read the full article * Instant access to this article: US$32 Buy now * Subscribe to Nature Methods for full access: Subscribe * Personal subscribers: Log in Additional access options: * Login via Athens * Login via your Institution * Purchase a site license * Use a document delivery service * British Library Document Supply Centre * Infotrieve * Thompson ISI Document Delivery * You can also request this document from your local library through inter-library loan services. Author information Article tools * Full text * Print * Email * Download PDF * Download citation * Order reprints * Rights and permissions * Share/bookmark * Connotea * CiteULike * Facebook * Twitter * Delicious * Digg Affiliations * Bang Wong is the creative director of the Broad Institute of the Massachusetts Institute of Technology & Harvard and an adjunct assistant professor in the Department of Art as Applied to Medicine at The Johns Hopkins University School of Medicine. Author Details * Bang Wong Search for this author in: * NPG journals * PubMed * Google Scholar Additional data * Journal home * Current issue * For authors * Subscribe * E-alert sign up * RSS feed Science jobs from naturejobs * Gene Ontology Developer / Curator * European Bioinformatics Institute (EBI) * Cambridge, United Kingdom * Post-doctoral Scientist (m / f) * Boehringer Ingelheim RCV Vienna * Vienna, Austria * Vienna International Post-Doctoral Training in Molecular Life Sciences * Max F. Perutz Laboratories * Wien, Austria * Post a free job * More science jobs Open innovation challenges * Upload Your Compound Libraries! Deadline:Jan 20 2013Reward:See Details As part of our improved Novel Molecules Challenge (NMC) procedure, you may now upload to InnoCenti… * Novel Chemical Derivatives of Bicarbonate Deadline:Jun 02 2011Reward:$20,000 USD The Seeker desires suggestions for novel chemical derivatives of bicarbonate that are water-insolu… * Powered by: * More challenges Top content Emailed * Defining pluripotency Nature Methods 28 Oct 2010 * Light tools Nature Methods 20 Dec 2010 * Visualizing a one-way protein encounter complex by ultrafast single-molecule mixing Nature Methods 06 Feb 2011 * Enzymatic assembly of DNA molecules up to several hundred kilobases Nature Methods 12 Apr 2009 * Fluorescence protease protection of GFP chimeras to reveal protein topology and subcellular localization Nature Methods 17 Feb 2006 View all Downloaded * Fast, three-dimensional super-resolution imaging of live cells Nature Methods 08 May 2011 * Rapid three-dimensional isotropic imaging of living cells using Bessel beam plane illumination Nature Methods 04 Mar 2011 * Chemically defined conditions for human iPSC derivation and culture Nature Methods 10 Apr 2011 * Mapping and quantifying mammalian transcriptomes by RNA-Seq Nature Methods 30 May 2008 * A quantitative analysis of CLIP methods for identifying binding sites of RNA-binding proteins Nature Methods 15 May 2011 View all Blogged * Two-photon absorption properties of fluorescent proteins Nature Methods 28 Apr 2011 * Chemically defined conditions for human iPSC derivation and culture Nature Methods 10 Apr 2011 * Validation of two ribosomal RNA removal methods for microbial metatranscriptomics Nature Methods 19 Sep 2010 * Microbial community resemblance methods differ in their ability to detect biologically relevant patterns Nature Methods 05 Sep 2010 * Comprehensive comparative analysis of strand-specific RNA sequencing methods Nature Methods 15 Aug 2010 View all * Nature Methods * ISSN: 1548-7091 * EISSN: 1548-7105 * About NPG * Contact NPG * RSS web feeds * Help * Privacy policy * Legal notice * Accessibility statement * Terms * Nature News * Naturejobs * Nature Asia * Nature EducationSearch:Go © 2011 Nature Publishing Group, a division of Macmillan Publishers Limited. All Rights Reserved.partner of AGORA, HINARI, OARE, INASP, CrossRef and COUNTER
• All-in-one live: genes trapped, tagged and conditionally broken
  - Nat Meth 8(6):466-467 (2011)
  Article preview View full access options Nature Methods | This Month Color blindness * Bang Wong1Journal name:Nature MethodsVolume: 8,Page:441Year published:(2011)DOI:doi:10.1038/nmeth.1618Published online27 May 2011 Since my first column on color coding1 appeared, we have received a number of e-mails asking us to highlight the issue of color blindness. One of those correspondences was published in the October 2010 issue2. Here I offer guidelines to make graphics accessible to those with color vision deficiencies. Color blindness affects a substantial portion of the human population. Protanopia and deuteranopia, the two most common forms of inherited color blindness, are red-green color vision defects caused by the absence of red or green retinal photoreceptors, respectively. In individuals of Northern European ancestry, as many as 8 percent of men and 0.5 percent of women experience the common form of red-green color blindness3. If a submitted manuscript happens to go to three male reviewers of Northern European descent, the chance that at least one will be color blind is 22 percent. Picking colors suitable for color-blind readers not only enhances accessibility but also is good graphic design practice. For example, the Ishihara color vision test intentionally relies only on color hue to create contrast, as evident when the image is converted to grayscale (Fig. 1a). In general, colors will be easier to distinguish when they vary in lightness and saturation as well as hue (Fig. 1b). The palette of eight colors shown in Figure 2 has good overall variability and can be differentiated by individuals with red-green color blindness. Figure 1: Ishihara color-vision test plate. () Viewers with normal color vision should see the numeral '6′. () Changing lightness of background improves contrast. * Full size image (260 KB) * Figures index * Next figure Figure 2: Colors optimized for color-blind individuals. P and D indicate simulated colors as seen by individuals with protanopia and deuteranopia, respectively. Figures at a glance * Figure 1: Ishihara color-vision test plate. () Viewers with normal color vision should see the numeral '6′. () Changing lightness of background improves contrast. * Figure 2: Colors optimized for color-blind individuals. P and D indicate simulated colors as seen by individuals with protanopia and deuteranopia, respectively. * Figure 3: Red-green color coding in an immunofluorescent image. () Conventional color coding is difficult for individuals with red-green color blindness (protanopia or deuteranopia) to discriminate. () Replacing red with magenta (top) or green with turquoise (bottom) improves visibility for such individuals. Source image from reference 4. Article preview Read the full article * Instant access to this article: US$32 Buy now * Subscribe to Nature Methods for full access: Subscribe * Personal subscribers: Log in Additional access options: * Login via Athens * Login via your Institution * Purchase a site license * Use a document delivery service * British Library Document Supply Centre * Infotrieve * Thompson ISI Document Delivery * You can also request this document from your local library through inter-library loan services. Author information Article tools * Full text * Print * Email * Download PDF * Download citation * Order reprints * Rights and permissions * Share/bookmark * Connotea * CiteULike * Facebook * Twitter * Delicious * Digg Affiliations * Bang Wong is the creative director of the Broad Institute of the Massachusetts Institute of Technology & Harvard and an adjunct assistant professor in the Department of Art as Applied to Medicine at The Johns Hopkins University School of Medicine. Author Details * Bang Wong Search for this author in: * NPG journals * PubMed * Google Scholar Additional data * Journal home * Current issue * For authors * Subscribe * E-alert sign up * RSS feed Science jobs from naturejobs * Gene Ontology Developer / Curator * European Bioinformatics Institute (EBI) * Cambridge, United Kingdom * Post-doctoral Scientist (m / f) * Boehringer Ingelheim RCV Vienna * Vienna, Austria * Vienna International Post-Doctoral Training in Molecular Life Sciences * Max F. Perutz Laboratories * Wien, Austria * Post a free job * More science jobs Open innovation challenges * Upload Your Compound Libraries! Deadline:Jan 20 2013Reward:See Details As part of our improved Novel Molecules Challenge (NMC) procedure, you may now upload to InnoCenti… * Novel Chemical Derivatives of Bicarbonate Deadline:Jun 02 2011Reward:$20,000 USD The Seeker desires suggestions for novel chemical derivatives of bicarbonate that are water-insolu… * Powered by: * More challenges Top content Emailed * Defining pluripotency Nature Methods 28 Oct 2010 * Light tools Nature Methods 20 Dec 2010 * Visualizing a one-way protein encounter complex by ultrafast single-molecule mixing Nature Methods 06 Feb 2011 * Enzymatic assembly of DNA molecules up to several hundred kilobases Nature Methods 12 Apr 2009 * Fluorescence protease protection of GFP chimeras to reveal protein topology and subcellular localization Nature Methods 17 Feb 2006 View all Downloaded * Fast, three-dimensional super-resolution imaging of live cells Nature Methods 08 May 2011 * Rapid three-dimensional isotropic imaging of living cells using Bessel beam plane illumination Nature Methods 04 Mar 2011 * Chemically defined conditions for human iPSC derivation and culture Nature Methods 10 Apr 2011 * Mapping and quantifying mammalian transcriptomes by RNA-Seq Nature Methods 30 May 2008 * A quantitative analysis of CLIP methods for identifying binding sites of RNA-binding proteins Nature Methods 15 May 2011 View all Blogged * Two-photon absorption properties of fluorescent proteins Nature Methods 28 Apr 2011 * Chemically defined conditions for human iPSC derivation and culture Nature Methods 10 Apr 2011 * Validation of two ribosomal RNA removal methods for microbial metatranscriptomics Nature Methods 19 Sep 2010 * Microbial community resemblance methods differ in their ability to detect biologically relevant patterns Nature Methods 05 Sep 2010 * Comprehensive comparative analysis of strand-specific RNA sequencing methods Nature Methods 15 Aug 2010 View all * Nature Methods * ISSN: 1548-7091 * EISSN: 1548-7105 * About NPG * Contact NPG * RSS web feeds * Help * Privacy policy * Legal notice * Accessibility statement * Terms * Nature News * Naturejobs * Nature Asia * Nature EducationSearch:Go © 2011 Nature Publishing Group, a division of Macmillan Publishers Limited. All Rights Reserved.partner of AGORA, HINARI, OARE, INASP, CrossRef and COUNTER
• Computational methods for transcriptome annotation and quantification using RNA-seq
  - Nat Meth 8(6):469-477 (2011)
  Nature Methods | Editorial Mapping the money Journal name:Nature MethodsVolume: 8,Page:437Year published:(2011)DOI:doi:10.1038/nmeth.1623Published online27 May 2011 Improving search tools for NIH grants will increase the transparency of US government–sponsored research and aid those seeking funding. View full text Additional data
• Next-generation sequencing to generate interactome datasets
  - Nat Meth 8(6):478-480 (2011)
  Nature Methods | Editorial Mapping the money Journal name:Nature MethodsVolume: 8,Page:437Year published:(2011)DOI:doi:10.1038/nmeth.1623Published online27 May 2011 Improving search tools for NIH grants will increase the transparency of US government–sponsored research and aid those seeking funding. View full text Additional data
• Combining quantitative proteomics data processing workflows for greater sensitivity
  - Nat Meth 8(6):481-483 (2011)
  Nature Methods | Editorial Mapping the money Journal name:Nature MethodsVolume: 8,Page:437Year published:(2011)DOI:doi:10.1038/nmeth.1623Published online27 May 2011 Improving search tools for NIH grants will increase the transparency of US government–sponsored research and aid those seeking funding. View full text Additional data
• Analysis of repetitive DNA in chromosomes by flow cytometry
  - Nat Meth 8(6):484-486 (2011)
  Nature Methods | Editorial Mapping the money Journal name:Nature MethodsVolume: 8,Page:437Year published:(2011)DOI:doi:10.1038/nmeth.1623Published online27 May 2011 Improving search tools for NIH grants will increase the transparency of US government–sponsored research and aid those seeking funding. View full text Additional data
• Adaptive informatics for multifactorial and high-content biological data
  - Nat Meth 8(6):487-492 (2011)
  Nature Methods | Editorial Mapping the money Journal name:Nature MethodsVolume: 8,Page:437Year published:(2011)DOI:doi:10.1038/nmeth.1623Published online27 May 2011 Improving search tools for NIH grants will increase the transparency of US government–sponsored research and aid those seeking funding. View full text Additional data
• BrainAligner: 3D registration atlases of Drosophila brains
  - Nat Meth 8(6):493-498 (2011)
  Nature Methods | Editorial Mapping the money Journal name:Nature MethodsVolume: 8,Page:437Year published:(2011)DOI:doi:10.1038/nmeth.1623Published online27 May 2011 Improving search tools for NIH grants will increase the transparency of US government–sponsored research and aid those seeking funding. View full text Additional data
• Fast, three-dimensional super-resolution imaging of live cells
  - Nat Meth 8(6):499-505 (2011)
  Nature Methods | Editorial Mapping the money Journal name:Nature MethodsVolume: 8,Page:437Year published:(2011)DOI:doi:10.1038/nmeth.1623Published online27 May 2011 Improving search tools for NIH grants will increase the transparency of US government–sponsored research and aid those seeking funding. View full text Additional data
• In vivo protein trapping produces a functional expression codex of the vertebrate proteome
  - Nat Meth 8(6):506-512 (2011)
  Nature Methods | Editorial Mapping the money Journal name:Nature MethodsVolume: 8,Page:437Year published:(2011)DOI:doi:10.1038/nmeth.1623Published online27 May 2011 Improving search tools for NIH grants will increase the transparency of US government–sponsored research and aid those seeking funding. View full text Additional data
• Sequence-based identification of 3D structural modules in RNA with RMDetect
  - Nat Meth 8(6):513-519 (2011)
  Nature Methods | Editorial Mapping the money Journal name:Nature MethodsVolume: 8,Page:437Year published:(2011)DOI:doi:10.1038/nmeth.1623Published online27 May 2011 Improving search tools for NIH grants will increase the transparency of US government–sponsored research and aid those seeking funding. View full text Additional data

Hot off the presses! Jun 01 Nat Med

The Jun 01 issue of the Nat Med is now up on Pubget (About Nat Med): if you're at a subscribing institution, just click the link in the latest link at the home page. (Note you'll only be able to get all the PDFs in the issue if your institution subscribes to Pubget.)

Latest Articles Include:

• Standard cooperating procedures
  - Nat Med 43(6):501 (2011)
  Nature Genetics | Editorial Standard cooperating procedures Journal name:Nature GeneticsVolume: 43,Page:501Year published:(2011)DOI:doi:10.1038/ng.853Published online26 May 2011 Community review of proposed standards is a good strategy to broaden consensus on ways to conduct principled, ethical and efficient research. We are pleased to welcome new partners for our Nature Precedings Data Standards initiative and suggest other standards that could be usefully presented as citable preprints. View full text Additional data
• The role of a bioresource research impact factor as an incentive to share human bioresources
  - Nat Med 43(6):503-504 (2011)
  Article preview View full access options Nature Genetics | Correspondence The role of a bioresource research impact factor as an incentive to share human bioresources * Anne Cambon-Thomsen1, 2 * Gudmundur A Thorisson3 * * Laurence Mabile1, 2 * for the BRIF workshop group4 * Affiliations * Corresponding authorJournal name:Nature GeneticsVolume: 43,Pages:503–504Year published:(2011)DOI:doi:10.1038/ng.831Published online26 May 2011 To the Editor: Numerous health research funding institutions have recently expressed their strong will to promote data sharing1 (http://www.wellcome.ac.uk/publichealthdata). As under-lined in a recent editorial in Nature Medicine, an operational approach is needed to achieve this goal2. Bioresources such as biobanks, databases and bioinformatics tools are important elements in this landscape. Bioresources need to be easily accessible to facilitate advancement of research. Besides technical and ethical aspects, a major obstacle for sharing them is the absence of recognition of the effort behind establishing and maintaining such resources. The main objective of proposing a Bioresource Research Impact Factor (BRIF) is to promote the sharing of bioresources by creating a link between their initiators or implementers and the impact of the scientific research using them3. A BRIF would make it possible to trace the quantitative use of a bioresource, the kind of research using it and the efforts o! f the people and institutions that construct it and make it available. In the context of EU projects, a BRIF working group has been set up, including 101 participants so far (http://www.gen2phen.org/groups/brif-bio-resource-impact-factor). The work involves several steps: creating a unique identifier, standardizing bioresource acknowledgment in papers, cataloging bioresource data access and sharing policies, identifying other parameters to take into account, and prototype testing with the help of volunteer bioresources and journal editors. The first BRIF workshop was held in Toulouse, France (January 17–18, 2011), gathering 34 people from ten countries and representing various domains: biobanks, genome databases, epidemiological longitudinal cohorts, bioinformatics, scientific publishing, bibliometry, health law and bioethics (http://precedings.nature.com/collections/brif-workshop-january-2011). The lack of objective measures for the use of bioresources was recognized by all; we focused on shared aims but underlined that each community had specific aspects to consider and resolve. Bioresources need to be identified by a unique digital identifier (ID), ideally through existing mechanisms4. Digital object identifiers (DOIs) may be interesting (http://www.doi.org/). Several issues must be considered, including what to identify (biobank, collection, database, dataset, subset and version), identifier requirements (persistent over time, globally unique, citable) and which international and independent body should be responsible for assigning bioresource IDs. Working subgroups were created to address those questions. Attribution of credit to scientists for different kinds of work (in addition to publications) using researcher IDs was also discussed. The ORCID initiative (http://www.orcid.org/) is building a new contributor ID framework which should, in principle, enable credit to be given to both bioresources and individuals involved in their creation and maintenance. Standardization of citation is necessary but could be combined with existing referencing standards and conventions5, such as citing marker papers, standardized sentences in the materials and methods or acknowledgments sections of papers, co-authorship when justified and including the resource name in the paper title. Specific requirements for citing bioresources are lacking in the Uniform Requirements for Manuscripts Submitted to Biomedical Journals (http://www.icmje.org/urm_main.html, version April 2010) and should be added. In order to enable automated tracking of bioresource use, the bioresource ID should ideally appear in or under the abstract section in order to be visible even without access to the full text of articles. BRIF should not be a citation index only. Factors such as time and domain of bioresources need to be considered in the calculation process and its weighting. Although the BRIF scope could be extended to measure many different aspects of bioresource utilization, including economic implications, it was decided to concentrate first on use and impact in research settings. Access and sharing policies have been developed over the years6. However, the incentivization of bioresources to promote access needs to be balanced with appropriate provisions compatible with all stakeholder interests, that is, proper recognition of scientific contribution and sustainability supported by the capacity for measuring their own resource use and impact. There are no mechanisms in place to measure this impact. Empowering bioresources with tools such as BRIF is therefore urgent. The full impact of bioresources is wider than BRIF, but unique bioresource identifiers and metrics must be established as the first operational step. The present proliferation of ideas, statements and proposals around data sharing from different perspectives and stakeholders1, 2, 3, 7 favors the implementation of tools such as BRIF in order to make data sharing principles operational. Workshop participants and members of the working group urge concerned stakeholders to join our efforts in developing such an instrument. Article preview Read the full article * Instant access to this article: US$18 Buy now * Subscribe to Nature Genetics for full access: Subscribe * Personal subscribers: Log in Additional access options: * Login via Athens * Login via your Institution * Purchase a site license * Use a document delivery service * British Library Document Supply Centre * Infotrieve * Thompson ISI Document Delivery * You can also request this document from your local library through inter-library loan services. Author information Article tools * Full text * Print * Email * Download PDF * Download citation * Order reprints * Rights and permissions * Share/bookmark * Connotea * CiteULike * Facebook * Twitter * Delicious * Digg Affiliations * Inserm, UMR1027, Epidemiology and Analyses in Public Health, Toulouse, France. * Anne Cambon-Thomsen & * Laurence Mabile * Université de Toulouse, Université Paul Sabatier, Toulouse III, UMR 1027, Toulouse, France. * Anne Cambon-Thomsen & * Laurence Mabile * Department of Genetics, University of Leicester, Leicester, UK. * Gudmundur A Thorisson * A full list of members appears at the end of the paper. * the BRIF workshop group * Inserm, UMR1027, Epidemiology and Analyses in Public Health, Toulouse, France. * Sandrine Andrieu, * Anne Cambon-Thomsen, * Laurence Mabile, * Emmanuelle Rial-Sebbag & * Mogens Thomsen * Université de Toulouse, Université Paul Sabatier, Toulouse III, UMR 1027, Toulouse, France. * Sandrine Andrieu, * Anne Cambon-Thomsen, * Laurence Mabile, * Emmanuelle Rial-Sebbag & * Mogens Thomsen * Center for Genomic Regulation, Barcelona, Spain. * Gabrielle Bertier * University of Amsterdam, Department of Philosophy, Amsterdam, The Netherlands. * Martin Boeckhout * Australian Breast Cancer Tissue Bank, University of Sydney, New South Wales, Sydney, Australia. * Jane Carpenter * Inserm, Public Health Institute, Paris, France. * Georges Dagher * Department of Genetics, University of Leicester, Leicester, UK. * Raymond Dalgleish & * Gudmundur A Thorisson * P3G, Montreal, Quebec, Canada. * Mylène Deschênes * 3C-R, Toulouse, France. * Jeanne Hélène di Donato * Laboratorio Diagnosi Pre-Postnatale Malattie Metaboliche, Istituto G. Gaslini, G. Gaslini Institute, Genova, Italy. * Mirella Filocamo * Inserm U1018, Centre for Research in Epidemiology and Population Health, Villejuif, France. * Marcel Goldberg, * Francine Kauffmann & * Marie Zins * Versailles-Saint Quentin University, UMRS 1018, Versailles, France. * Marcel Goldberg & * Marie Zins * European, Middle Eastern and African Society for Biopreservation and Biobanking (ESBB), Aix en Provence, France. * Robert Hewitt * Laboratory of Clinical and Experimental Pathology & Human Biobank, Pasteur Hospital, University of Nice Sophia, Nice, France. * Paul Hofman * Paris Sud University, UMRS 1018, Villejuif, France. * Francine Kauffmann * Estonian Genome Center, University of Tartu, Tartu, Estonia. * Liis Leitsalu & * Andres Metspalu * Laboratorio ImmunoBiología Molecular, Spanish HIV HGM BioBank, Madrid, Spain. * Irene Lomba * Department of Medical Genetics, University of Pécs, Pécs, Hungary. * Bela Melegh * Estonian Genome Center, Institute of Molecular and Cell Biology, University of Tartu, Tartu, Estonia. * Andres Metspalu * Estonian Biocentre, Tartu, Estonia. * Andres Metspalu * Biobusiness Consulting, Inc., Lowell, Massachusetts, USA. * Lisa Miranda * Istituto Superiore di Sanita, Rome, Italy. * Federica Napolitani * World Health Organization, Department of Health Statistics & Informatics, Geneva, Switzerland. * Mikkel Z Oestergaard * National Institute for Cancer Research, Genoa, Italy. * Barbara Parodi * International Prevention Research Institute, Lyon, France. * Markus Pasterk * Fundació IMIM, Barcelona, Spain. * Acacia Reiche * Thomson Reuters, Toulouse, France. * Guillaume Rivalle * Claudius Regaud Institute, Toulouse, France. * Philippe Rochaix * Biomed Central, London, UK. * Guillaume Susbielle * Latvian Biomedical Research and Study Center, Genome Database of Latvian Population [LGDB], Riga, Latvia. * Linda Tarasova * McGill University, Centre of Genomics and Policy, Montreal, Quebec, Canada. * Ma'n H Zawati Consortia * the BRIF workshop group * Anne Cambon-Thomsen, * Gudmundur A Thorisson, * Laurence Mabile * * Named collaborators * Sandrine Andrieu, * Gabrielle Bertier, * Martin Boeckhout, * Anne Cambon-Thomsen, * Jane Carpenter, * Georges Dagher, * Raymond Dalgleish, * Mylène Deschênes, * Jeanne Hélène di Donato, * Mirella Filocamo, * Marcel Goldberg, * Robert Hewitt, * Paul Hofman, * Francine Kauffmann, * Liis Leitsalu, * Irene Lomba, * Laurence Mabile, * Bela Melegh, * Andres Metspalu, * Lisa Miranda, * Federica Napolitani, * Mikkel Z Oestergaard, * Barbara Parodi, * Markus Pasterk, * Acacia Reiche, * Emmanuelle Rial-Sebbag, * Guillaume Rivalle, * Philippe Rochaix, * Guillaume Susbielle, * Linda Tarasova, * Mogens Thomsen, * Gudmundur A Thorisson, * Ma'n H Zawati & * Marie Zins Competing financial interests The authors declare no competing financial interests. Corresponding author Correspondence to: * Anne Cambon-Thomsen Author Details * Anne Cambon-Thomsen Search for this author in: * NPG journals * PubMed * Google Scholar * Gudmundur A Thorisson Search for this author in: * NPG journals * PubMed * Google Scholar * Laurence Mabile Search for this author in: * NPG journals * PubMed * Google Scholar Additional data
• SOX2 and CHD7 cooperatively regulate human disease genes
  - Nat Med 43(6):505-506 (2011)
  Article preview View full access options Nature Genetics | Correspondence The role of a bioresource research impact factor as an incentive to share human bioresources * Anne Cambon-Thomsen1, 2 * Gudmundur A Thorisson3 * * Laurence Mabile1, 2 * for the BRIF workshop group4 * Affiliations * Corresponding authorJournal name:Nature GeneticsVolume: 43,Pages:503–504Year published:(2011)DOI:doi:10.1038/ng.831Published online26 May 2011 To the Editor: Numerous health research funding institutions have recently expressed their strong will to promote data sharing1 (http://www.wellcome.ac.uk/publichealthdata). As under-lined in a recent editorial in Nature Medicine, an operational approach is needed to achieve this goal2. Bioresources such as biobanks, databases and bioinformatics tools are important elements in this landscape. Bioresources need to be easily accessible to facilitate advancement of research. Besides technical and ethical aspects, a major obstacle for sharing them is the absence of recognition of the effort behind establishing and maintaining such resources. The main objective of proposing a Bioresource Research Impact Factor (BRIF) is to promote the sharing of bioresources by creating a link between their initiators or implementers and the impact of the scientific research using them3. A BRIF would make it possible to trace the quantitative use of a bioresource, the kind of research using it and the efforts o! f the people and institutions that construct it and make it available. In the context of EU projects, a BRIF working group has been set up, including 101 participants so far (http://www.gen2phen.org/groups/brif-bio-resource-impact-factor). The work involves several steps: creating a unique identifier, standardizing bioresource acknowledgment in papers, cataloging bioresource data access and sharing policies, identifying other parameters to take into account, and prototype testing with the help of volunteer bioresources and journal editors. The first BRIF workshop was held in Toulouse, France (January 17–18, 2011), gathering 34 people from ten countries and representing various domains: biobanks, genome databases, epidemiological longitudinal cohorts, bioinformatics, scientific publishing, bibliometry, health law and bioethics (http://precedings.nature.com/collections/brif-workshop-january-2011). The lack of objective measures for the use of bioresources was recognized by all; we focused on shared aims but underlined that each community had specific aspects to consider and resolve. Bioresources need to be identified by a unique digital identifier (ID), ideally through existing mechanisms4. Digital object identifiers (DOIs) may be interesting (http://www.doi.org/). Several issues must be considered, including what to identify (biobank, collection, database, dataset, subset and version), identifier requirements (persistent over time, globally unique, citable) and which international and independent body should be responsible for assigning bioresource IDs. Working subgroups were created to address those questions. Attribution of credit to scientists for different kinds of work (in addition to publications) using researcher IDs was also discussed. The ORCID initiative (http://www.orcid.org/) is building a new contributor ID framework which should, in principle, enable credit to be given to both bioresources and individuals involved in their creation and maintenance. Standardization of citation is necessary but could be combined with existing referencing standards and conventions5, such as citing marker papers, standardized sentences in the materials and methods or acknowledgments sections of papers, co-authorship when justified and including the resource name in the paper title. Specific requirements for citing bioresources are lacking in the Uniform Requirements for Manuscripts Submitted to Biomedical Journals (http://www.icmje.org/urm_main.html, version April 2010) and should be added. In order to enable automated tracking of bioresource use, the bioresource ID should ideally appear in or under the abstract section in order to be visible even without access to the full text of articles. BRIF should not be a citation index only. Factors such as time and domain of bioresources need to be considered in the calculation process and its weighting. Although the BRIF scope could be extended to measure many different aspects of bioresource utilization, including economic implications, it was decided to concentrate first on use and impact in research settings. Access and sharing policies have been developed over the years6. However, the incentivization of bioresources to promote access needs to be balanced with appropriate provisions compatible with all stakeholder interests, that is, proper recognition of scientific contribution and sustainability supported by the capacity for measuring their own resource use and impact. There are no mechanisms in place to measure this impact. Empowering bioresources with tools such as BRIF is therefore urgent. The full impact of bioresources is wider than BRIF, but unique bioresource identifiers and metrics must be established as the first operational step. The present proliferation of ideas, statements and proposals around data sharing from different perspectives and stakeholders1, 2, 3, 7 favors the implementation of tools such as BRIF in order to make data sharing principles operational. Workshop participants and members of the working group urge concerned stakeholders to join our efforts in developing such an instrument. Article preview Read the full article * Instant access to this article: US$18 Buy now * Subscribe to Nature Genetics for full access: Subscribe * Personal subscribers: Log in Additional access options: * Login via Athens * Login via your Institution * Purchase a site license * Use a document delivery service * British Library Document Supply Centre * Infotrieve * Thompson ISI Document Delivery * You can also request this document from your local library through inter-library loan services. Author information Article tools * Full text * Print * Email * Download PDF * Download citation * Order reprints * Rights and permissions * Share/bookmark * Connotea * CiteULike * Facebook * Twitter * Delicious * Digg Affiliations * Inserm, UMR1027, Epidemiology and Analyses in Public Health, Toulouse, France. * Anne Cambon-Thomsen & * Laurence Mabile * Université de Toulouse, Université Paul Sabatier, Toulouse III, UMR 1027, Toulouse, France. * Anne Cambon-Thomsen & * Laurence Mabile * Department of Genetics, University of Leicester, Leicester, UK. * Gudmundur A Thorisson * A full list of members appears at the end of the paper. * the BRIF workshop group * Inserm, UMR1027, Epidemiology and Analyses in Public Health, Toulouse, France. * Sandrine Andrieu, * Anne Cambon-Thomsen, * Laurence Mabile, * Emmanuelle Rial-Sebbag & * Mogens Thomsen * Université de Toulouse, Université Paul Sabatier, Toulouse III, UMR 1027, Toulouse, France. * Sandrine Andrieu, * Anne Cambon-Thomsen, * Laurence Mabile, * Emmanuelle Rial-Sebbag & * Mogens Thomsen * Center for Genomic Regulation, Barcelona, Spain. * Gabrielle Bertier * University of Amsterdam, Department of Philosophy, Amsterdam, The Netherlands. * Martin Boeckhout * Australian Breast Cancer Tissue Bank, University of Sydney, New South Wales, Sydney, Australia. * Jane Carpenter * Inserm, Public Health Institute, Paris, France. * Georges Dagher * Department of Genetics, University of Leicester, Leicester, UK. * Raymond Dalgleish & * Gudmundur A Thorisson * P3G, Montreal, Quebec, Canada. * Mylène Deschênes * 3C-R, Toulouse, France. * Jeanne Hélène di Donato * Laboratorio Diagnosi Pre-Postnatale Malattie Metaboliche, Istituto G. Gaslini, G. Gaslini Institute, Genova, Italy. * Mirella Filocamo * Inserm U1018, Centre for Research in Epidemiology and Population Health, Villejuif, France. * Marcel Goldberg, * Francine Kauffmann & * Marie Zins * Versailles-Saint Quentin University, UMRS 1018, Versailles, France. * Marcel Goldberg & * Marie Zins * European, Middle Eastern and African Society for Biopreservation and Biobanking (ESBB), Aix en Provence, France. * Robert Hewitt * Laboratory of Clinical and Experimental Pathology & Human Biobank, Pasteur Hospital, University of Nice Sophia, Nice, France. * Paul Hofman * Paris Sud University, UMRS 1018, Villejuif, France. * Francine Kauffmann * Estonian Genome Center, University of Tartu, Tartu, Estonia. * Liis Leitsalu & * Andres Metspalu * Laboratorio ImmunoBiología Molecular, Spanish HIV HGM BioBank, Madrid, Spain. * Irene Lomba * Department of Medical Genetics, University of Pécs, Pécs, Hungary. * Bela Melegh * Estonian Genome Center, Institute of Molecular and Cell Biology, University of Tartu, Tartu, Estonia. * Andres Metspalu * Estonian Biocentre, Tartu, Estonia. * Andres Metspalu * Biobusiness Consulting, Inc., Lowell, Massachusetts, USA. * Lisa Miranda * Istituto Superiore di Sanita, Rome, Italy. * Federica Napolitani * World Health Organization, Department of Health Statistics & Informatics, Geneva, Switzerland. * Mikkel Z Oestergaard * National Institute for Cancer Research, Genoa, Italy. * Barbara Parodi * International Prevention Research Institute, Lyon, France. * Markus Pasterk * Fundació IMIM, Barcelona, Spain. * Acacia Reiche * Thomson Reuters, Toulouse, France. * Guillaume Rivalle * Claudius Regaud Institute, Toulouse, France. * Philippe Rochaix * Biomed Central, London, UK. * Guillaume Susbielle * Latvian Biomedical Research and Study Center, Genome Database of Latvian Population [LGDB], Riga, Latvia. * Linda Tarasova * McGill University, Centre of Genomics and Policy, Montreal, Quebec, Canada. * Ma'n H Zawati Consortia * the BRIF workshop group * Anne Cambon-Thomsen, * Gudmundur A Thorisson, * Laurence Mabile * * Named collaborators * Sandrine Andrieu, * Gabrielle Bertier, * Martin Boeckhout, * Anne Cambon-Thomsen, * Jane Carpenter, * Georges Dagher, * Raymond Dalgleish, * Mylène Deschênes, * Jeanne Hélène di Donato, * Mirella Filocamo, * Marcel Goldberg, * Robert Hewitt, * Paul Hofman, * Francine Kauffmann, * Liis Leitsalu, * Irene Lomba, * Laurence Mabile, * Bela Melegh, * Andres Metspalu, * Lisa Miranda, * Federica Napolitani, * Mikkel Z Oestergaard, * Barbara Parodi, * Markus Pasterk, * Acacia Reiche, * Emmanuelle Rial-Sebbag, * Guillaume Rivalle, * Philippe Rochaix, * Guillaume Susbielle, * Linda Tarasova, * Mogens Thomsen, * Gudmundur A Thorisson, * Ma'n H Zawati & * Marie Zins Competing financial interests The authors declare no competing financial interests. Corresponding author Correspondence to: * Anne Cambon-Thomsen Author Details * Anne Cambon-Thomsen Search for this author in: * NPG journals * PubMed * Google Scholar * Gudmundur A Thorisson Search for this author in: * NPG journals * PubMed * Google Scholar * Laurence Mabile Search for this author in: * NPG journals * PubMed * Google Scholar Additional data
• Conducting the metabolic syndrome orchestra
  - Nat Med 43(6):506-508 (2011)
  Article preview View full access options Nature Genetics | Correspondence The role of a bioresource research impact factor as an incentive to share human bioresources * Anne Cambon-Thomsen1, 2 * Gudmundur A Thorisson3 * * Laurence Mabile1, 2 * for the BRIF workshop group4 * Affiliations * Corresponding authorJournal name:Nature GeneticsVolume: 43,Pages:503–504Year published:(2011)DOI:doi:10.1038/ng.831Published online26 May 2011 To the Editor: Numerous health research funding institutions have recently expressed their strong will to promote data sharing1 (http://www.wellcome.ac.uk/publichealthdata). As under-lined in a recent editorial in Nature Medicine, an operational approach is needed to achieve this goal2. Bioresources such as biobanks, databases and bioinformatics tools are important elements in this landscape. Bioresources need to be easily accessible to facilitate advancement of research. Besides technical and ethical aspects, a major obstacle for sharing them is the absence of recognition of the effort behind establishing and maintaining such resources. The main objective of proposing a Bioresource Research Impact Factor (BRIF) is to promote the sharing of bioresources by creating a link between their initiators or implementers and the impact of the scientific research using them3. A BRIF would make it possible to trace the quantitative use of a bioresource, the kind of research using it and the efforts o! f the people and institutions that construct it and make it available. In the context of EU projects, a BRIF working group has been set up, including 101 participants so far (http://www.gen2phen.org/groups/brif-bio-resource-impact-factor). The work involves several steps: creating a unique identifier, standardizing bioresource acknowledgment in papers, cataloging bioresource data access and sharing policies, identifying other parameters to take into account, and prototype testing with the help of volunteer bioresources and journal editors. The first BRIF workshop was held in Toulouse, France (January 17–18, 2011), gathering 34 people from ten countries and representing various domains: biobanks, genome databases, epidemiological longitudinal cohorts, bioinformatics, scientific publishing, bibliometry, health law and bioethics (http://precedings.nature.com/collections/brif-workshop-january-2011). The lack of objective measures for the use of bioresources was recognized by all; we focused on shared aims but underlined that each community had specific aspects to consider and resolve. Bioresources need to be identified by a unique digital identifier (ID), ideally through existing mechanisms4. Digital object identifiers (DOIs) may be interesting (http://www.doi.org/). Several issues must be considered, including what to identify (biobank, collection, database, dataset, subset and version), identifier requirements (persistent over time, globally unique, citable) and which international and independent body should be responsible for assigning bioresource IDs. Working subgroups were created to address those questions. Attribution of credit to scientists for different kinds of work (in addition to publications) using researcher IDs was also discussed. The ORCID initiative (http://www.orcid.org/) is building a new contributor ID framework which should, in principle, enable credit to be given to both bioresources and individuals involved in their creation and maintenance. Standardization of citation is necessary but could be combined with existing referencing standards and conventions5, such as citing marker papers, standardized sentences in the materials and methods or acknowledgments sections of papers, co-authorship when justified and including the resource name in the paper title. Specific requirements for citing bioresources are lacking in the Uniform Requirements for Manuscripts Submitted to Biomedical Journals (http://www.icmje.org/urm_main.html, version April 2010) and should be added. In order to enable automated tracking of bioresource use, the bioresource ID should ideally appear in or under the abstract section in order to be visible even without access to the full text of articles. BRIF should not be a citation index only. Factors such as time and domain of bioresources need to be considered in the calculation process and its weighting. Although the BRIF scope could be extended to measure many different aspects of bioresource utilization, including economic implications, it was decided to concentrate first on use and impact in research settings. Access and sharing policies have been developed over the years6. However, the incentivization of bioresources to promote access needs to be balanced with appropriate provisions compatible with all stakeholder interests, that is, proper recognition of scientific contribution and sustainability supported by the capacity for measuring their own resource use and impact. There are no mechanisms in place to measure this impact. Empowering bioresources with tools such as BRIF is therefore urgent. The full impact of bioresources is wider than BRIF, but unique bioresource identifiers and metrics must be established as the first operational step. The present proliferation of ideas, statements and proposals around data sharing from different perspectives and stakeholders1, 2, 3, 7 favors the implementation of tools such as BRIF in order to make data sharing principles operational. Workshop participants and members of the working group urge concerned stakeholders to join our efforts in developing such an instrument. Article preview Read the full article * Instant access to this article: US$18 Buy now * Subscribe to Nature Genetics for full access: Subscribe * Personal subscribers: Log in Additional access options: * Login via Athens * Login via your Institution * Purchase a site license * Use a document delivery service * British Library Document Supply Centre * Infotrieve * Thompson ISI Document Delivery * You can also request this document from your local library through inter-library loan services. Author information Article tools * Full text * Print * Email * Download PDF * Download citation * Order reprints * Rights and permissions * Share/bookmark * Connotea * CiteULike * Facebook * Twitter * Delicious * Digg Affiliations * Inserm, UMR1027, Epidemiology and Analyses in Public Health, Toulouse, France. * Anne Cambon-Thomsen & * Laurence Mabile * Université de Toulouse, Université Paul Sabatier, Toulouse III, UMR 1027, Toulouse, France. * Anne Cambon-Thomsen & * Laurence Mabile * Department of Genetics, University of Leicester, Leicester, UK. * Gudmundur A Thorisson * A full list of members appears at the end of the paper. * the BRIF workshop group * Inserm, UMR1027, Epidemiology and Analyses in Public Health, Toulouse, France. * Sandrine Andrieu, * Anne Cambon-Thomsen, * Laurence Mabile, * Emmanuelle Rial-Sebbag & * Mogens Thomsen * Université de Toulouse, Université Paul Sabatier, Toulouse III, UMR 1027, Toulouse, France. * Sandrine Andrieu, * Anne Cambon-Thomsen, * Laurence Mabile, * Emmanuelle Rial-Sebbag & * Mogens Thomsen * Center for Genomic Regulation, Barcelona, Spain. * Gabrielle Bertier * University of Amsterdam, Department of Philosophy, Amsterdam, The Netherlands. * Martin Boeckhout * Australian Breast Cancer Tissue Bank, University of Sydney, New South Wales, Sydney, Australia. * Jane Carpenter * Inserm, Public Health Institute, Paris, France. * Georges Dagher * Department of Genetics, University of Leicester, Leicester, UK. * Raymond Dalgleish & * Gudmundur A Thorisson * P3G, Montreal, Quebec, Canada. * Mylène Deschênes * 3C-R, Toulouse, France. * Jeanne Hélène di Donato * Laboratorio Diagnosi Pre-Postnatale Malattie Metaboliche, Istituto G. Gaslini, G. Gaslini Institute, Genova, Italy. * Mirella Filocamo * Inserm U1018, Centre for Research in Epidemiology and Population Health, Villejuif, France. * Marcel Goldberg, * Francine Kauffmann & * Marie Zins * Versailles-Saint Quentin University, UMRS 1018, Versailles, France. * Marcel Goldberg & * Marie Zins * European, Middle Eastern and African Society for Biopreservation and Biobanking (ESBB), Aix en Provence, France. * Robert Hewitt * Laboratory of Clinical and Experimental Pathology & Human Biobank, Pasteur Hospital, University of Nice Sophia, Nice, France. * Paul Hofman * Paris Sud University, UMRS 1018, Villejuif, France. * Francine Kauffmann * Estonian Genome Center, University of Tartu, Tartu, Estonia. * Liis Leitsalu & * Andres Metspalu * Laboratorio ImmunoBiología Molecular, Spanish HIV HGM BioBank, Madrid, Spain. * Irene Lomba * Department of Medical Genetics, University of Pécs, Pécs, Hungary. * Bela Melegh * Estonian Genome Center, Institute of Molecular and Cell Biology, University of Tartu, Tartu, Estonia. * Andres Metspalu * Estonian Biocentre, Tartu, Estonia. * Andres Metspalu * Biobusiness Consulting, Inc., Lowell, Massachusetts, USA. * Lisa Miranda * Istituto Superiore di Sanita, Rome, Italy. * Federica Napolitani * World Health Organization, Department of Health Statistics & Informatics, Geneva, Switzerland. * Mikkel Z Oestergaard * National Institute for Cancer Research, Genoa, Italy. * Barbara Parodi * International Prevention Research Institute, Lyon, France. * Markus Pasterk * Fundació IMIM, Barcelona, Spain. * Acacia Reiche * Thomson Reuters, Toulouse, France. * Guillaume Rivalle * Claudius Regaud Institute, Toulouse, France. * Philippe Rochaix * Biomed Central, London, UK. * Guillaume Susbielle * Latvian Biomedical Research and Study Center, Genome Database of Latvian Population [LGDB], Riga, Latvia. * Linda Tarasova * McGill University, Centre of Genomics and Policy, Montreal, Quebec, Canada. * Ma'n H Zawati Consortia * the BRIF workshop group * Anne Cambon-Thomsen, * Gudmundur A Thorisson, * Laurence Mabile * * Named collaborators * Sandrine Andrieu, * Gabrielle Bertier, * Martin Boeckhout, * Anne Cambon-Thomsen, * Jane Carpenter, * Georges Dagher, * Raymond Dalgleish, * Mylène Deschênes, * Jeanne Hélène di Donato, * Mirella Filocamo, * Marcel Goldberg, * Robert Hewitt, * Paul Hofman, * Francine Kauffmann, * Liis Leitsalu, * Irene Lomba, * Laurence Mabile, * Bela Melegh, * Andres Metspalu, * Lisa Miranda, * Federica Napolitani, * Mikkel Z Oestergaard, * Barbara Parodi, * Markus Pasterk, * Acacia Reiche, * Emmanuelle Rial-Sebbag, * Guillaume Rivalle, * Philippe Rochaix, * Guillaume Susbielle, * Linda Tarasova, * Mogens Thomsen, * Gudmundur A Thorisson, * Ma'n H Zawati & * Marie Zins Competing financial interests The authors declare no competing financial interests. Corresponding author Correspondence to: * Anne Cambon-Thomsen Author Details * Anne Cambon-Thomsen Search for this author in: * NPG journals * PubMed * Google Scholar * Gudmundur A Thorisson Search for this author in: * NPG journals * PubMed * Google Scholar * Laurence Mabile Search for this author in: * NPG journals * PubMed * Google Scholar Additional data
• New modifier loci in cystic fibrosis
  - Nat Med 43(6):508-509 (2011)
  Article preview View full access options Nature Genetics | Correspondence The role of a bioresource research impact factor as an incentive to share human bioresources * Anne Cambon-Thomsen1, 2 * Gudmundur A Thorisson3 * * Laurence Mabile1, 2 * for the BRIF workshop group4 * Affiliations * Corresponding authorJournal name:Nature GeneticsVolume: 43,Pages:503–504Year published:(2011)DOI:doi:10.1038/ng.831Published online26 May 2011 To the Editor: Numerous health research funding institutions have recently expressed their strong will to promote data sharing1 (http://www.wellcome.ac.uk/publichealthdata). As under-lined in a recent editorial in Nature Medicine, an operational approach is needed to achieve this goal2. Bioresources such as biobanks, databases and bioinformatics tools are important elements in this landscape. Bioresources need to be easily accessible to facilitate advancement of research. Besides technical and ethical aspects, a major obstacle for sharing them is the absence of recognition of the effort behind establishing and maintaining such resources. The main objective of proposing a Bioresource Research Impact Factor (BRIF) is to promote the sharing of bioresources by creating a link between their initiators or implementers and the impact of the scientific research using them3. A BRIF would make it possible to trace the quantitative use of a bioresource, the kind of research using it and the efforts o! f the people and institutions that construct it and make it available. In the context of EU projects, a BRIF working group has been set up, including 101 participants so far (http://www.gen2phen.org/groups/brif-bio-resource-impact-factor). The work involves several steps: creating a unique identifier, standardizing bioresource acknowledgment in papers, cataloging bioresource data access and sharing policies, identifying other parameters to take into account, and prototype testing with the help of volunteer bioresources and journal editors. The first BRIF workshop was held in Toulouse, France (January 17–18, 2011), gathering 34 people from ten countries and representing various domains: biobanks, genome databases, epidemiological longitudinal cohorts, bioinformatics, scientific publishing, bibliometry, health law and bioethics (http://precedings.nature.com/collections/brif-workshop-january-2011). The lack of objective measures for the use of bioresources was recognized by all; we focused on shared aims but underlined that each community had specific aspects to consider and resolve. Bioresources need to be identified by a unique digital identifier (ID), ideally through existing mechanisms4. Digital object identifiers (DOIs) may be interesting (http://www.doi.org/). Several issues must be considered, including what to identify (biobank, collection, database, dataset, subset and version), identifier requirements (persistent over time, globally unique, citable) and which international and independent body should be responsible for assigning bioresource IDs. Working subgroups were created to address those questions. Attribution of credit to scientists for different kinds of work (in addition to publications) using researcher IDs was also discussed. The ORCID initiative (http://www.orcid.org/) is building a new contributor ID framework which should, in principle, enable credit to be given to both bioresources and individuals involved in their creation and maintenance. Standardization of citation is necessary but could be combined with existing referencing standards and conventions5, such as citing marker papers, standardized sentences in the materials and methods or acknowledgments sections of papers, co-authorship when justified and including the resource name in the paper title. Specific requirements for citing bioresources are lacking in the Uniform Requirements for Manuscripts Submitted to Biomedical Journals (http://www.icmje.org/urm_main.html, version April 2010) and should be added. In order to enable automated tracking of bioresource use, the bioresource ID should ideally appear in or under the abstract section in order to be visible even without access to the full text of articles. BRIF should not be a citation index only. Factors such as time and domain of bioresources need to be considered in the calculation process and its weighting. Although the BRIF scope could be extended to measure many different aspects of bioresource utilization, including economic implications, it was decided to concentrate first on use and impact in research settings. Access and sharing policies have been developed over the years6. However, the incentivization of bioresources to promote access needs to be balanced with appropriate provisions compatible with all stakeholder interests, that is, proper recognition of scientific contribution and sustainability supported by the capacity for measuring their own resource use and impact. There are no mechanisms in place to measure this impact. Empowering bioresources with tools such as BRIF is therefore urgent. The full impact of bioresources is wider than BRIF, but unique bioresource identifiers and metrics must be established as the first operational step. The present proliferation of ideas, statements and proposals around data sharing from different perspectives and stakeholders1, 2, 3, 7 favors the implementation of tools such as BRIF in order to make data sharing principles operational. Workshop participants and members of the working group urge concerned stakeholders to join our efforts in developing such an instrument. Article preview Read the full article * Instant access to this article: US$18 Buy now * Subscribe to Nature Genetics for full access: Subscribe * Personal subscribers: Log in Additional access options: * Login via Athens * Login via your Institution * Purchase a site license * Use a document delivery service * British Library Document Supply Centre * Infotrieve * Thompson ISI Document Delivery * You can also request this document from your local library through inter-library loan services. Author information Article tools * Full text * Print * Email * Download PDF * Download citation * Order reprints * Rights and permissions * Share/bookmark * Connotea * CiteULike * Facebook * Twitter * Delicious * Digg Affiliations * Inserm, UMR1027, Epidemiology and Analyses in Public Health, Toulouse, France. * Anne Cambon-Thomsen & * Laurence Mabile * Université de Toulouse, Université Paul Sabatier, Toulouse III, UMR 1027, Toulouse, France. * Anne Cambon-Thomsen & * Laurence Mabile * Department of Genetics, University of Leicester, Leicester, UK. * Gudmundur A Thorisson * A full list of members appears at the end of the paper. * the BRIF workshop group * Inserm, UMR1027, Epidemiology and Analyses in Public Health, Toulouse, France. * Sandrine Andrieu, * Anne Cambon-Thomsen, * Laurence Mabile, * Emmanuelle Rial-Sebbag & * Mogens Thomsen * Université de Toulouse, Université Paul Sabatier, Toulouse III, UMR 1027, Toulouse, France. * Sandrine Andrieu, * Anne Cambon-Thomsen, * Laurence Mabile, * Emmanuelle Rial-Sebbag & * Mogens Thomsen * Center for Genomic Regulation, Barcelona, Spain. * Gabrielle Bertier * University of Amsterdam, Department of Philosophy, Amsterdam, The Netherlands. * Martin Boeckhout * Australian Breast Cancer Tissue Bank, University of Sydney, New South Wales, Sydney, Australia. * Jane Carpenter * Inserm, Public Health Institute, Paris, France. * Georges Dagher * Department of Genetics, University of Leicester, Leicester, UK. * Raymond Dalgleish & * Gudmundur A Thorisson * P3G, Montreal, Quebec, Canada. * Mylène Deschênes * 3C-R, Toulouse, France. * Jeanne Hélène di Donato * Laboratorio Diagnosi Pre-Postnatale Malattie Metaboliche, Istituto G. Gaslini, G. Gaslini Institute, Genova, Italy. * Mirella Filocamo * Inserm U1018, Centre for Research in Epidemiology and Population Health, Villejuif, France. * Marcel Goldberg, * Francine Kauffmann & * Marie Zins * Versailles-Saint Quentin University, UMRS 1018, Versailles, France. * Marcel Goldberg & * Marie Zins * European, Middle Eastern and African Society for Biopreservation and Biobanking (ESBB), Aix en Provence, France. * Robert Hewitt * Laboratory of Clinical and Experimental Pathology & Human Biobank, Pasteur Hospital, University of Nice Sophia, Nice, France. * Paul Hofman * Paris Sud University, UMRS 1018, Villejuif, France. * Francine Kauffmann * Estonian Genome Center, University of Tartu, Tartu, Estonia. * Liis Leitsalu & * Andres Metspalu * Laboratorio ImmunoBiología Molecular, Spanish HIV HGM BioBank, Madrid, Spain. * Irene Lomba * Department of Medical Genetics, University of Pécs, Pécs, Hungary. * Bela Melegh * Estonian Genome Center, Institute of Molecular and Cell Biology, University of Tartu, Tartu, Estonia. * Andres Metspalu * Estonian Biocentre, Tartu, Estonia. * Andres Metspalu * Biobusiness Consulting, Inc., Lowell, Massachusetts, USA. * Lisa Miranda * Istituto Superiore di Sanita, Rome, Italy. * Federica Napolitani * World Health Organization, Department of Health Statistics & Informatics, Geneva, Switzerland. * Mikkel Z Oestergaard * National Institute for Cancer Research, Genoa, Italy. * Barbara Parodi * International Prevention Research Institute, Lyon, France. * Markus Pasterk * Fundació IMIM, Barcelona, Spain. * Acacia Reiche * Thomson Reuters, Toulouse, France. * Guillaume Rivalle * Claudius Regaud Institute, Toulouse, France. * Philippe Rochaix * Biomed Central, London, UK. * Guillaume Susbielle * Latvian Biomedical Research and Study Center, Genome Database of Latvian Population [LGDB], Riga, Latvia. * Linda Tarasova * McGill University, Centre of Genomics and Policy, Montreal, Quebec, Canada. * Ma'n H Zawati Consortia * the BRIF workshop group * Anne Cambon-Thomsen, * Gudmundur A Thorisson, * Laurence Mabile * * Named collaborators * Sandrine Andrieu, * Gabrielle Bertier, * Martin Boeckhout, * Anne Cambon-Thomsen, * Jane Carpenter, * Georges Dagher, * Raymond Dalgleish, * Mylène Deschênes, * Jeanne Hélène di Donato, * Mirella Filocamo, * Marcel Goldberg, * Robert Hewitt, * Paul Hofman, * Francine Kauffmann, * Liis Leitsalu, * Irene Lomba, * Laurence Mabile, * Bela Melegh, * Andres Metspalu, * Lisa Miranda, * Federica Napolitani, * Mikkel Z Oestergaard, * Barbara Parodi, * Markus Pasterk, * Acacia Reiche, * Emmanuelle Rial-Sebbag, * Guillaume Rivalle, * Philippe Rochaix, * Guillaume Susbielle, * Linda Tarasova, * Mogens Thomsen, * Gudmundur A Thorisson, * Ma'n H Zawati & * Marie Zins Competing financial interests The authors declare no competing financial interests. Corresponding author Correspondence to: * Anne Cambon-Thomsen Author Details * Anne Cambon-Thomsen Search for this author in: * NPG journals * PubMed * Google Scholar * Gudmundur A Thorisson Search for this author in: * NPG journals * PubMed * Google Scholar * Laurence Mabile Search for this author in: * NPG journals * PubMed * Google Scholar Additional data
• Research highlights
  - Nat Med 43(6):511 (2011)
  Article preview View full access options Nature Genetics | Correspondence The role of a bioresource research impact factor as an incentive to share human bioresources * Anne Cambon-Thomsen1, 2 * Gudmundur A Thorisson3 * * Laurence Mabile1, 2 * for the BRIF workshop group4 * Affiliations * Corresponding authorJournal name:Nature GeneticsVolume: 43,Pages:503–504Year published:(2011)DOI:doi:10.1038/ng.831Published online26 May 2011 To the Editor: Numerous health research funding institutions have recently expressed their strong will to promote data sharing1 (http://www.wellcome.ac.uk/publichealthdata). As under-lined in a recent editorial in Nature Medicine, an operational approach is needed to achieve this goal2. Bioresources such as biobanks, databases and bioinformatics tools are important elements in this landscape. Bioresources need to be easily accessible to facilitate advancement of research. Besides technical and ethical aspects, a major obstacle for sharing them is the absence of recognition of the effort behind establishing and maintaining such resources. The main objective of proposing a Bioresource Research Impact Factor (BRIF) is to promote the sharing of bioresources by creating a link between their initiators or implementers and the impact of the scientific research using them3. A BRIF would make it possible to trace the quantitative use of a bioresource, the kind of research using it and the efforts o! f the people and institutions that construct it and make it available. In the context of EU projects, a BRIF working group has been set up, including 101 participants so far (http://www.gen2phen.org/groups/brif-bio-resource-impact-factor). The work involves several steps: creating a unique identifier, standardizing bioresource acknowledgment in papers, cataloging bioresource data access and sharing policies, identifying other parameters to take into account, and prototype testing with the help of volunteer bioresources and journal editors. The first BRIF workshop was held in Toulouse, France (January 17–18, 2011), gathering 34 people from ten countries and representing various domains: biobanks, genome databases, epidemiological longitudinal cohorts, bioinformatics, scientific publishing, bibliometry, health law and bioethics (http://precedings.nature.com/collections/brif-workshop-january-2011). The lack of objective measures for the use of bioresources was recognized by all; we focused on shared aims but underlined that each community had specific aspects to consider and resolve. Bioresources need to be identified by a unique digital identifier (ID), ideally through existing mechanisms4. Digital object identifiers (DOIs) may be interesting (http://www.doi.org/). Several issues must be considered, including what to identify (biobank, collection, database, dataset, subset and version), identifier requirements (persistent over time, globally unique, citable) and which international and independent body should be responsible for assigning bioresource IDs. Working subgroups were created to address those questions. Attribution of credit to scientists for different kinds of work (in addition to publications) using researcher IDs was also discussed. The ORCID initiative (http://www.orcid.org/) is building a new contributor ID framework which should, in principle, enable credit to be given to both bioresources and individuals involved in their creation and maintenance. Standardization of citation is necessary but could be combined with existing referencing standards and conventions5, such as citing marker papers, standardized sentences in the materials and methods or acknowledgments sections of papers, co-authorship when justified and including the resource name in the paper title. Specific requirements for citing bioresources are lacking in the Uniform Requirements for Manuscripts Submitted to Biomedical Journals (http://www.icmje.org/urm_main.html, version April 2010) and should be added. In order to enable automated tracking of bioresource use, the bioresource ID should ideally appear in or under the abstract section in order to be visible even without access to the full text of articles. BRIF should not be a citation index only. Factors such as time and domain of bioresources need to be considered in the calculation process and its weighting. Although the BRIF scope could be extended to measure many different aspects of bioresource utilization, including economic implications, it was decided to concentrate first on use and impact in research settings. Access and sharing policies have been developed over the years6. However, the incentivization of bioresources to promote access needs to be balanced with appropriate provisions compatible with all stakeholder interests, that is, proper recognition of scientific contribution and sustainability supported by the capacity for measuring their own resource use and impact. There are no mechanisms in place to measure this impact. Empowering bioresources with tools such as BRIF is therefore urgent. The full impact of bioresources is wider than BRIF, but unique bioresource identifiers and metrics must be established as the first operational step. The present proliferation of ideas, statements and proposals around data sharing from different perspectives and stakeholders1, 2, 3, 7 favors the implementation of tools such as BRIF in order to make data sharing principles operational. Workshop participants and members of the working group urge concerned stakeholders to join our efforts in developing such an instrument. Article preview Read the full article * Instant access to this article: US$18 Buy now * Subscribe to Nature Genetics for full access: Subscribe * Personal subscribers: Log in Additional access options: * Login via Athens * Login via your Institution * Purchase a site license * Use a document delivery service * British Library Document Supply Centre * Infotrieve * Thompson ISI Document Delivery * You can also request this document from your local library through inter-library loan services. Author information Article tools * Full text * Print * Email * Download PDF * Download citation * Order reprints * Rights and permissions * Share/bookmark * Connotea * CiteULike * Facebook * Twitter * Delicious * Digg Affiliations * Inserm, UMR1027, Epidemiology and Analyses in Public Health, Toulouse, France. * Anne Cambon-Thomsen & * Laurence Mabile * Université de Toulouse, Université Paul Sabatier, Toulouse III, UMR 1027, Toulouse, France. * Anne Cambon-Thomsen & * Laurence Mabile * Department of Genetics, University of Leicester, Leicester, UK. * Gudmundur A Thorisson * A full list of members appears at the end of the paper. * the BRIF workshop group * Inserm, UMR1027, Epidemiology and Analyses in Public Health, Toulouse, France. * Sandrine Andrieu, * Anne Cambon-Thomsen, * Laurence Mabile, * Emmanuelle Rial-Sebbag & * Mogens Thomsen * Université de Toulouse, Université Paul Sabatier, Toulouse III, UMR 1027, Toulouse, France. * Sandrine Andrieu, * Anne Cambon-Thomsen, * Laurence Mabile, * Emmanuelle Rial-Sebbag & * Mogens Thomsen * Center for Genomic Regulation, Barcelona, Spain. * Gabrielle Bertier * University of Amsterdam, Department of Philosophy, Amsterdam, The Netherlands. * Martin Boeckhout * Australian Breast Cancer Tissue Bank, University of Sydney, New South Wales, Sydney, Australia. * Jane Carpenter * Inserm, Public Health Institute, Paris, France. * Georges Dagher * Department of Genetics, University of Leicester, Leicester, UK. * Raymond Dalgleish & * Gudmundur A Thorisson * P3G, Montreal, Quebec, Canada. * Mylène Deschênes * 3C-R, Toulouse, France. * Jeanne Hélène di Donato * Laboratorio Diagnosi Pre-Postnatale Malattie Metaboliche, Istituto G. Gaslini, G. Gaslini Institute, Genova, Italy. * Mirella Filocamo * Inserm U1018, Centre for Research in Epidemiology and Population Health, Villejuif, France. * Marcel Goldberg, * Francine Kauffmann & * Marie Zins * Versailles-Saint Quentin University, UMRS 1018, Versailles, France. * Marcel Goldberg & * Marie Zins * European, Middle Eastern and African Society for Biopreservation and Biobanking (ESBB), Aix en Provence, France. * Robert Hewitt * Laboratory of Clinical and Experimental Pathology & Human Biobank, Pasteur Hospital, University of Nice Sophia, Nice, France. * Paul Hofman * Paris Sud University, UMRS 1018, Villejuif, France. * Francine Kauffmann * Estonian Genome Center, University of Tartu, Tartu, Estonia. * Liis Leitsalu & * Andres Metspalu * Laboratorio ImmunoBiología Molecular, Spanish HIV HGM BioBank, Madrid, Spain. * Irene Lomba * Department of Medical Genetics, University of Pécs, Pécs, Hungary. * Bela Melegh * Estonian Genome Center, Institute of Molecular and Cell Biology, University of Tartu, Tartu, Estonia. * Andres Metspalu * Estonian Biocentre, Tartu, Estonia. * Andres Metspalu * Biobusiness Consulting, Inc., Lowell, Massachusetts, USA. * Lisa Miranda * Istituto Superiore di Sanita, Rome, Italy. * Federica Napolitani * World Health Organization, Department of Health Statistics & Informatics, Geneva, Switzerland. * Mikkel Z Oestergaard * National Institute for Cancer Research, Genoa, Italy. * Barbara Parodi * International Prevention Research Institute, Lyon, France. * Markus Pasterk * Fundació IMIM, Barcelona, Spain. * Acacia Reiche * Thomson Reuters, Toulouse, France. * Guillaume Rivalle * Claudius Regaud Institute, Toulouse, France. * Philippe Rochaix * Biomed Central, London, UK. * Guillaume Susbielle * Latvian Biomedical Research and Study Center, Genome Database of Latvian Population [LGDB], Riga, Latvia. * Linda Tarasova * McGill University, Centre of Genomics and Policy, Montreal, Quebec, Canada. * Ma'n H Zawati Consortia * the BRIF workshop group * Anne Cambon-Thomsen, * Gudmundur A Thorisson, * Laurence Mabile * * Named collaborators * Sandrine Andrieu, * Gabrielle Bertier, * Martin Boeckhout, * Anne Cambon-Thomsen, * Jane Carpenter, * Georges Dagher, * Raymond Dalgleish, * Mylène Deschênes, * Jeanne Hélène di Donato, * Mirella Filocamo, * Marcel Goldberg, * Robert Hewitt, * Paul Hofman, * Francine Kauffmann, * Liis Leitsalu, * Irene Lomba, * Laurence Mabile, * Bela Melegh, * Andres Metspalu, * Lisa Miranda, * Federica Napolitani, * Mikkel Z Oestergaard, * Barbara Parodi, * Markus Pasterk, * Acacia Reiche, * Emmanuelle Rial-Sebbag, * Guillaume Rivalle, * Philippe Rochaix, * Guillaume Susbielle, * Linda Tarasova, * Mogens Thomsen, * Gudmundur A Thorisson, * Ma'n H Zawati & * Marie Zins Competing financial interests The authors declare no competing financial interests. Corresponding author Correspondence to: * Anne Cambon-Thomsen Author Details * Anne Cambon-Thomsen Search for this author in: * NPG journals * PubMed * Google Scholar * Gudmundur A Thorisson Search for this author in: * NPG journals * PubMed * Google Scholar * Laurence Mabile Search for this author in: * NPG journals * PubMed * Google Scholar Additional data
• Principles for the post-GWAS functional characterization of cancer risk loci
  - Nat Med 43(6):513-518 (2011)
  Article preview View full access options Nature Genetics | Correspondence The role of a bioresource research impact factor as an incentive to share human bioresources * Anne Cambon-Thomsen1, 2 * Gudmundur A Thorisson3 * * Laurence Mabile1, 2 * for the BRIF workshop group4 * Affiliations * Corresponding authorJournal name:Nature GeneticsVolume: 43,Pages:503–504Year published:(2011)DOI:doi:10.1038/ng.831Published online26 May 2011 To the Editor: Numerous health research funding institutions have recently expressed their strong will to promote data sharing1 (http://www.wellcome.ac.uk/publichealthdata). As under-lined in a recent editorial in Nature Medicine, an operational approach is needed to achieve this goal2. Bioresources such as biobanks, databases and bioinformatics tools are important elements in this landscape. Bioresources need to be easily accessible to facilitate advancement of research. Besides technical and ethical aspects, a major obstacle for sharing them is the absence of recognition of the effort behind establishing and maintaining such resources. The main objective of proposing a Bioresource Research Impact Factor (BRIF) is to promote the sharing of bioresources by creating a link between their initiators or implementers and the impact of the scientific research using them3. A BRIF would make it possible to trace the quantitative use of a bioresource, the kind of research using it and the efforts o! f the people and institutions that construct it and make it available. In the context of EU projects, a BRIF working group has been set up, including 101 participants so far (http://www.gen2phen.org/groups/brif-bio-resource-impact-factor). The work involves several steps: creating a unique identifier, standardizing bioresource acknowledgment in papers, cataloging bioresource data access and sharing policies, identifying other parameters to take into account, and prototype testing with the help of volunteer bioresources and journal editors. The first BRIF workshop was held in Toulouse, France (January 17–18, 2011), gathering 34 people from ten countries and representing various domains: biobanks, genome databases, epidemiological longitudinal cohorts, bioinformatics, scientific publishing, bibliometry, health law and bioethics (http://precedings.nature.com/collections/brif-workshop-january-2011). The lack of objective measures for the use of bioresources was recognized by all; we focused on shared aims but underlined that each community had specific aspects to consider and resolve. Bioresources need to be identified by a unique digital identifier (ID), ideally through existing mechanisms4. Digital object identifiers (DOIs) may be interesting (http://www.doi.org/). Several issues must be considered, including what to identify (biobank, collection, database, dataset, subset and version), identifier requirements (persistent over time, globally unique, citable) and which international and independent body should be responsible for assigning bioresource IDs. Working subgroups were created to address those questions. Attribution of credit to scientists for different kinds of work (in addition to publications) using researcher IDs was also discussed. The ORCID initiative (http://www.orcid.org/) is building a new contributor ID framework which should, in principle, enable credit to be given to both bioresources and individuals involved in their creation and maintenance. Standardization of citation is necessary but could be combined with existing referencing standards and conventions5, such as citing marker papers, standardized sentences in the materials and methods or acknowledgments sections of papers, co-authorship when justified and including the resource name in the paper title. Specific requirements for citing bioresources are lacking in the Uniform Requirements for Manuscripts Submitted to Biomedical Journals (http://www.icmje.org/urm_main.html, version April 2010) and should be added. In order to enable automated tracking of bioresource use, the bioresource ID should ideally appear in or under the abstract section in order to be visible even without access to the full text of articles. BRIF should not be a citation index only. Factors such as time and domain of bioresources need to be considered in the calculation process and its weighting. Although the BRIF scope could be extended to measure many different aspects of bioresource utilization, including economic implications, it was decided to concentrate first on use and impact in research settings. Access and sharing policies have been developed over the years6. However, the incentivization of bioresources to promote access needs to be balanced with appropriate provisions compatible with all stakeholder interests, that is, proper recognition of scientific contribution and sustainability supported by the capacity for measuring their own resource use and impact. There are no mechanisms in place to measure this impact. Empowering bioresources with tools such as BRIF is therefore urgent. The full impact of bioresources is wider than BRIF, but unique bioresource identifiers and metrics must be established as the first operational step. The present proliferation of ideas, statements and proposals around data sharing from different perspectives and stakeholders1, 2, 3, 7 favors the implementation of tools such as BRIF in order to make data sharing principles operational. Workshop participants and members of the working group urge concerned stakeholders to join our efforts in developing such an instrument. Article preview Read the full article * Instant access to this article: US$18 Buy now * Subscribe to Nature Genetics for full access: Subscribe * Personal subscribers: Log in Additional access options: * Login via Athens * Login via your Institution * Purchase a site license * Use a document delivery service * British Library Document Supply Centre * Infotrieve * Thompson ISI Document Delivery * You can also request this document from your local library through inter-library loan services. Author information Article tools * Full text * Print * Email * Download PDF * Download citation * Order reprints * Rights and permissions * Share/bookmark * Connotea * CiteULike * Facebook * Twitter * Delicious * Digg Affiliations * Inserm, UMR1027, Epidemiology and Analyses in Public Health, Toulouse, France. * Anne Cambon-Thomsen & * Laurence Mabile * Université de Toulouse, Université Paul Sabatier, Toulouse III, UMR 1027, Toulouse, France. * Anne Cambon-Thomsen & * Laurence Mabile * Department of Genetics, University of Leicester, Leicester, UK. * Gudmundur A Thorisson * A full list of members appears at the end of the paper. * the BRIF workshop group * Inserm, UMR1027, Epidemiology and Analyses in Public Health, Toulouse, France. * Sandrine Andrieu, * Anne Cambon-Thomsen, * Laurence Mabile, * Emmanuelle Rial-Sebbag & * Mogens Thomsen * Université de Toulouse, Université Paul Sabatier, Toulouse III, UMR 1027, Toulouse, France. * Sandrine Andrieu, * Anne Cambon-Thomsen, * Laurence Mabile, * Emmanuelle Rial-Sebbag & * Mogens Thomsen * Center for Genomic Regulation, Barcelona, Spain. * Gabrielle Bertier * University of Amsterdam, Department of Philosophy, Amsterdam, The Netherlands. * Martin Boeckhout * Australian Breast Cancer Tissue Bank, University of Sydney, New South Wales, Sydney, Australia. * Jane Carpenter * Inserm, Public Health Institute, Paris, France. * Georges Dagher * Department of Genetics, University of Leicester, Leicester, UK. * Raymond Dalgleish & * Gudmundur A Thorisson * P3G, Montreal, Quebec, Canada. * Mylène Deschênes * 3C-R, Toulouse, France. * Jeanne Hélène di Donato * Laboratorio Diagnosi Pre-Postnatale Malattie Metaboliche, Istituto G. Gaslini, G. Gaslini Institute, Genova, Italy. * Mirella Filocamo * Inserm U1018, Centre for Research in Epidemiology and Population Health, Villejuif, France. * Marcel Goldberg, * Francine Kauffmann & * Marie Zins * Versailles-Saint Quentin University, UMRS 1018, Versailles, France. * Marcel Goldberg & * Marie Zins * European, Middle Eastern and African Society for Biopreservation and Biobanking (ESBB), Aix en Provence, France. * Robert Hewitt * Laboratory of Clinical and Experimental Pathology & Human Biobank, Pasteur Hospital, University of Nice Sophia, Nice, France. * Paul Hofman * Paris Sud University, UMRS 1018, Villejuif, France. * Francine Kauffmann * Estonian Genome Center, University of Tartu, Tartu, Estonia. * Liis Leitsalu & * Andres Metspalu * Laboratorio ImmunoBiología Molecular, Spanish HIV HGM BioBank, Madrid, Spain. * Irene Lomba * Department of Medical Genetics, University of Pécs, Pécs, Hungary. * Bela Melegh * Estonian Genome Center, Institute of Molecular and Cell Biology, University of Tartu, Tartu, Estonia. * Andres Metspalu * Estonian Biocentre, Tartu, Estonia. * Andres Metspalu * Biobusiness Consulting, Inc., Lowell, Massachusetts, USA. * Lisa Miranda * Istituto Superiore di Sanita, Rome, Italy. * Federica Napolitani * World Health Organization, Department of Health Statistics & Informatics, Geneva, Switzerland. * Mikkel Z Oestergaard * National Institute for Cancer Research, Genoa, Italy. * Barbara Parodi * International Prevention Research Institute, Lyon, France. * Markus Pasterk * Fundació IMIM, Barcelona, Spain. * Acacia Reiche * Thomson Reuters, Toulouse, France. * Guillaume Rivalle * Claudius Regaud Institute, Toulouse, France. * Philippe Rochaix * Biomed Central, London, UK. * Guillaume Susbielle * Latvian Biomedical Research and Study Center, Genome Database of Latvian Population [LGDB], Riga, Latvia. * Linda Tarasova * McGill University, Centre of Genomics and Policy, Montreal, Quebec, Canada. * Ma'n H Zawati Consortia * the BRIF workshop group * Anne Cambon-Thomsen, * Gudmundur A Thorisson, * Laurence Mabile * * Named collaborators * Sandrine Andrieu, * Gabrielle Bertier, * Martin Boeckhout, * Anne Cambon-Thomsen, * Jane Carpenter, * Georges Dagher, * Raymond Dalgleish, * Mylène Deschênes, * Jeanne Hélène di Donato, * Mirella Filocamo, * Marcel Goldberg, * Robert Hewitt, * Paul Hofman, * Francine Kauffmann, * Liis Leitsalu, * Irene Lomba, * Laurence Mabile, * Bela Melegh, * Andres Metspalu, * Lisa Miranda, * Federica Napolitani, * Mikkel Z Oestergaard, * Barbara Parodi, * Markus Pasterk, * Acacia Reiche, * Emmanuelle Rial-Sebbag, * Guillaume Rivalle, * Philippe Rochaix, * Guillaume Susbielle, * Linda Tarasova, * Mogens Thomsen, * Gudmundur A Thorisson, * Ma'n H Zawati & * Marie Zins Competing financial interests The authors declare no competing financial interests. Corresponding author Correspondence to: * Anne Cambon-Thomsen Author Details * Anne Cambon-Thomsen Search for this author in: * NPG journals * PubMed * Google Scholar * Gudmundur A Thorisson Search for this author in: * NPG journals * PubMed * Google Scholar * Laurence Mabile Search for this author in: * NPG journals * PubMed * Google Scholar Additional data
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