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Work published with BioMed Central, Chemistry Central and SpringerOpen by researchers at The Jackson Laboratory

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1.

Review   Open Access

The role of mouse strain differences in the susceptibility to fibrosis: a systematic review

Louise Walkin, Sarah E Herrick, Angela Summers, Paul E Brenchley, Catherine M Hoff, Ron Korstanje, Peter J Margetts Fibrogenesis & Tissue Repair 2013, 6:18 (25 September 2013)

Abstract | Full text | PDF

2.

Review   Open Access

Proprotein convertases in high-density lipoprotein metabolism

Seungbum Choi, Ron Korstanje Biomarker Research 2013, 1:27 (18 September 2013)

Abstract | Full text | PDF

3.

Database   Open Access

The mouse pathology ontology, MPATH; structure and applications

Paul N Schofield, John P Sundberg, Beth A Sundberg, Colin McKerlie, Georgios V Gkoutos Journal of Biomedical Semantics 2013, 4:18 (13 September 2013)

Abstract | Provisional PDF | PubMed

4.

Research   Open Access

Glial scaffold required for cerebellar granule cell migration is dependent on dystroglycan function as a receptor for basement membrane proteins

Huy Nguyen, Adam P Ostendorf, Jakob S Satz, Steve Westra, Susan E Ross-Barta, Kevin P Campbell, Steven A Moore Acta Neuropathologica Communications 2013, 1:58 (6 September 2013)

Abstract | Full text | PDF

5.

Methodology article   Open Access Highly Accessed

Ontology based molecular signatures for immune cell types via gene expression analysis

Terrence F Meehan, Nicole A Vasilevsky, Christopher J Mungall, David S Dougall, Melissa A Haendel, Judith A Blake, Alexander D Diehl BMC Bioinformatics 2013, 14:263 (30 August 2013)

Abstract | Full text | PDF | PubMed

6.

Short Report   Open Access

EMAP/EMAPA ontology of mouse developmental anatomy: 2013 update

Terry F Hayamizu, Michael N Wicks, Duncan R Davidson, Albert Burger, Martin Ringwald, Richard A Baldock Journal of Biomedical Semantics 2013, 4:15 (26 August 2013)

Abstract | Provisional PDF | PubMed

7.

Database   Open Access

The Vertebrate Trait Ontology: a controlled vocabulary for the annotation of trait data across species

Carissa A Park, Susan M Bello, Cynthia L Smith, Zhi-Liang Hu, Diane H Munzenmaier, Rajni Nigam, Jennifer R Smith, Mary Shimoyama, Janan T Eppig, James M Reecy Journal of Biomedical Semantics 2013, 4:13 (9 August 2013)

Abstract | Provisional PDF | PubMed

8.

Methodology article   Open Access

Dovetailing biology and chemistry: integrating the Gene Ontology with the ChEBI chemical ontology

David P Hill, Nico Adams, Mike Bada, Colin Batchelor, Tanya Z Berardini, Heiko Dietze, Harold J Drabkin, Marcus Ennis, Rebecca E Foulger, Midori A Harris, Janna Hastings, Namrata S Kale, Paula de Matos, Christopher J Mungall, Gareth Owen, Paola Roncaglia, Christoph Steinbeck, Steve Turner, Jane Lomax BMC Genomics 2013, 14:513 (29 July 2013)

Abstract | Full text | PDF | PubMed

9.

Research   Open Access

Decreased APOE-containing HDL subfractions and cholesterol efflux capacity of serum in mice lacking Pcsk9

Seungbum Choi, Aleksandra Aljakna, Ujala Srivastava, Blake R Peterson, Bin Deng, Annik Prat, Ron Korstanje Lipids in Health and Disease 2013, 12:112 (24 July 2013)

Abstract | Full text | PDF | PubMed | Cited on BioMed Central

10.

Research   Open Access

Intratumoral localization and activity of 17β-hydroxysteroid dehydrogenase type 1 in non-small cell lung cancer: a potent prognostic factor

Mohit K Verma, Yasuhiro Miki, Keiko Abe, Takashi Suzuki, Hiromichi Niikawa, Satoshi Suzuki, Takashi Kondo, Hironobu Sasano Journal of Translational Medicine 2013, 11:167 (9 July 2013)

Abstract | Full text | PDF | PubMed

11.

Research   Open Access

Deficiency of complement component 5 ameliorates glaucoma in DBA/2J mice

Gareth R Howell, Ileana Soto, Margaret Ryan, Leah C Graham, Richard S Smith, Simon WM John Journal of Neuroinflammation 2013, 10:76 (27 June 2013)

Abstract | Full text | PDF | PubMed

12.

Research   Open Access

DNA binding specificities of the long zinc-finger recombination protein PRDM9

Timothy Billings, Emil D Parvanov, Christopher L Baker, Michael Walker, Kenneth Paigen, Petko M Petkov Genome Biology 2013, 14:R35 (24 April 2013)

Abstract | Full text | PDF | PubMed |  Editor’s summary

A detailed analysis of DNA binding by PRDM9, the zinc finger protein that determines recombination hotspots in mammals

13.

Research   Open Access

Brain involvement in Alström syndrome

Valentina Citton, Angela Favaro, Vera Bettini, Joseph Gabrieli, Gabriella Milan, Nella Augusta Greggio, Jan D Marshall, Jürgen K Naggert, Renzo Manara, Pietro Maffei Orphanet Journal of Rare Diseases 2013, 8:24 (13 February 2013)

Abstract | Full text | PDF | PubMed

14.

Research article   Open Access

Notch2 is required in somatic cells for breakdown of ovarian germ-cell nests and formation of primordial follicles

Jingxia Xu, Thomas Gridley BMC Biology 2013, 11:13 (13 February 2013)

Abstract | Full text | PDF | PubMed

15.

Research article   Open Access

Effect of the myostatin locus on muscle mass and intramuscular fat content in a cross between mouse lines selected for hypermuscularity

Stefan Kärst, Eva M Strucken, Armin O Schmitt, Alexandra Weyrich, Fernando PM de Villena, Hyuna Yang, Gudrun A Brockmann BMC Genomics 2013, 14:16 (16 January 2013)

Abstract | Full text | PDF | PubMed

16.

Correspondence   Open Access Highly Accessed

ISA-TAB-Nano: A Specification for Sharing Nanomaterial Research Data in Spreadsheet-based Format

Dennis G Thomas, Sharon Gaheen, Stacey L Harper, Martin Fritts, Fred Klaessig, Elizabeth Hahn-Dantona, David Paik, Sue Pan, Grace A Stafford, Elaine T Freund, Juli D Klemm, Nathan A Baker BMC Biotechnology 2013, 13:2 (14 January 2013)

Abstract | Full text | PDF | PubMed

17.

Research article   Open Access

Genetic variation in hippocampal microRNA expression differences in C57BL/6 J X DBA/2 J (BXD) recombinant inbred mouse strains

Michael J Parsons, Christina Grimm, Jose L Paya-Cano, Cathy Fernandes, Lin Liu, Vivek M Philip, Elissa J Chesler, Wilfried Nietfeld, Hans Lehrach, Leonard C Schalkwyk BMC Genomics 2012, 13:476 (13 September 2012)

Abstract | Full text | PDF | PubMed | Cited on BioMed Central

18.

Research   Open Access

Sequencing and characterization of the FVB/NJ mouse genome

Kim Wong, Suzannah Bumpstead, Louise Van Der Weyden, Laura G Reinholdt, Laurens G Wilming, David J Adams, Thomas M Keane Genome Biology 2012, 13:R72 (23 August 2012)

Abstract | Full text | PDF | PubMed | Cited on BioMed Central |  Editor’s summary

The genome of the FVB/NJ mouse is sequenced, revealing variants specific to this strain

19.

Research article   Open Access

Concept annotation in the CRAFT corpus

Michael Bada, Miriam Eckert, Donald Evans, Kristin Garcia, Krista Shipley, Dmitry Sitnikov, William A Baumgartner, K Cohen, Karin Verspoor, Judith A Blake, Lawrence E Hunter BMC Bioinformatics 2012, 13:161 (9 July 2012)

Abstract | Full text | PDF | PubMed

20.

Proceedings   Open Access

A systematic comparison of genome-scale clustering algorithms

Jeremy J Jay, John D Eblen, Yun Zhang, Mikael Benson, Andy D Perkins, Arnold M Saxton, Brynn H Voy, Elissa J Chesler, Michael A Langston BMC Bioinformatics 2012, 13(Suppl 10):S7 (25 June 2012)

Abstract | Full text | PDF | PubMed

21.

Research   Open Access

The genomic landscape shaped by selection on transposable elements across 18 mouse strains

Christoffer Nellåker, Thomas M Keane, Binnaz Yalcin, Kim Wong, Avigail Agam, T Grant Belgard, Jonathan Flint, David J Adams, Wayne N Frankel, Chris P Ponting Genome Biology 2012, 13:R45 (15 June 2012)

Abstract | Full text | PDF | PubMed | Cited on BioMed Central |  Editor’s summary

A comprehensive catalog of transposable elements across 18 mouse strains, and a subsequent analysis of selection acting on these transposable elements

22.

Methodology article   Open Access

Discovery of novel variants in genotyping arrays improves genotype retention and reduces ascertainment bias

John P Didion, Hyuna Yang, Keith Sheppard, Chen-Ping Fu, Leonard McMillan, Fernando de Villena, Gary A Churchill BMC Genomics 2012, 13:34 (19 January 2012)

Abstract | Full text | PDF | PubMed | Cited on BioMed Central

23.

Software   Open Access Highly Accessed

Improving ontologies by automatic reasoning and evaluation of logical definitions

Sebastian Köhler, Sebastian Bauer, Chris J Mungall, Gabriele Carletti, Cynthia L Smith, Paul Schofield, Georgios V Gkoutos, Peter N Robinson BMC Bioinformatics 2011, 12:418 (27 October 2011)

Abstract | Full text | PDF | PubMed | Cited on BioMed Central

24.

Research   Open Access

BioCreative III interactive task: an overview

Cecilia N Arighi, Phoebe M Roberts, Shashank Agarwal, Sanmitra Bhattacharya, Gianni Cesareni, Andrew Chatr-aryamontri, Simon Clematide, Pascale Gaudet, Michelle Giglio, Ian Harrow, Eva Huala, Martin Krallinger, Ulf Leser, Donghui Li, Feifan Liu, Zhiyong Lu, Lois J Maltais, Naoaki Okazaki, Livia Perfetto, Fabio Rinaldi, Rune Sætre, David Salgado, Padmini Srinivasan, Philippe E Thomas, Luca Toldo, Lynette Hirschman, Cathy H Wu BMC Bioinformatics 2011, 12(Suppl 8):S4 (3 October 2011)

Abstract | Full text | PDF | PubMed

25.

Database   Open Access Highly Accessed

The representation of protein complexes in the Protein Ontology (PRO)

Carol J Bult, Harold J Drabkin, Alexei Evsikov, Darren Natale, Cecilia Arighi, Natalia Roberts, Alan Ruttenberg, Peter D'Eustachio, Barry Smith, Judith A Blake, Cathy Wu BMC Bioinformatics 2011, 12:371 (19 September 2011)

Abstract | Full text | PDF | PubMed |  Editor’s summary

ProComp is a component of the Protein Ontology (PRO) database for implementing a logical and consistent representation of protein complexes, and facilitates robust annotation of variations in composition and function contexts within and between species

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