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1.

Research   Open Access Highly Accessed

Characterizing the admixed African ancestry of African Americans

Fouad Zakharia, Analabha Basu, Devin Absher, Themistocles L Assimes, Alan S Go, Mark A Hlatky, Carlos Iribarren, Joshua W Knowles, Jun Li, Balasubramanian Narasimhan, Steven Sidney, Audrey Southwick, Richard M Myers, Thomas Quertermous, Neil Risch, Hua Tang Genome Biology 2009, 10:R141 (22 December 2009)

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

Genome-wide SNP analyses reveal the admixed African genetic ancestry of African Americans.

2.

Research   Open Access Highly Accessed

A survey of enabling technologies in synthetic biology

Linda J Kahl, Drew Endy Journal of Biological Engineering 2013, 7:13 (10 May 2013)

Abstract | Full text | PDF | PubMed

3.

Research article   Open Access

Phenotype, donor age and gender affect function of human bone marrow-derived mesenchymal stromal cells

Georg Siegel, Torsten Kluba, Ursula Hermanutz-Klein, Karen Bieback, Hinnak Northoff, Richard Schäfer BMC Medicine 2013, 11:146 (11 June 2013)

Abstract | Provisional PDF | PubMed |  Editor’s summary

Mesenchymal stromal cells have potential for clinical application in regenerative medicine, but have varying functional properties owing to donor age and gender, suggesting that identification of these factors are important for clinical use.

4.

Method   Open Access Highly Accessed

Model-based Analysis of ChIP-Seq (MACS)

Yong Zhang, Tao Liu, Clifford A Meyer, Jérôme Eeckhoute, David S Johnson, Bradley E Bernstein, Chad Nusbaum, Richard M Myers, Myles Brown, Wei Li, X Shirley Liu Genome Biology 2008, 9:R137 (17 September 2008)

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

MACS performs model-based analysis of ChIP-Seq data generated by short read sequencers.

5.

Review   Open Access Highly Accessed

The Stanford Health Assessment Questionnaire: Dimensions and Practical Applications

Bonnie Bruce, James F Fries Health and Quality of Life Outcomes 2003, 1:20 (9 June 2003)

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

6.

Software   Open Access Highly Accessed

The Transcription Factor Encyclopedia

Dimas Yusuf, Stefanie L Butland, Magdalena I Swanson, Eugene Bolotin, Amy Ticoll, Warren A Cheung, Xiao Cindy Zhang, Christopher TD Dickman, Debra L Fulton, Jonathan S Lim, Jake M Schnabl, Oscar HP Ramos, Mireille Vasseur-Cognet, Charles N de Leeuw, Elizabeth M Simpson, Gerhart U Ryffel, Eric W-F Lam, Ralf Kist, Miranda SC Wilson, Raquel Marco-Ferreres, Jan J Brosens, Leonardo L Beccari, Paola Bovolenta, Bérénice A Benayoun, Lara J Monteiro, Helma DC Schwenen, Lars Grontved, Elizabeth Wederell, Susanne Mandrup, Reiner A Veitia et al. Genome Biology 2012, 13:R24 (29 March 2012)

Abstract | Full text | PDF | PubMed | Cited on BioMed Central | 1 comment |  Editor’s summary

A high quality compendium of transcription factor data that allows researchers to add new data via a peer-review system

7.

Research   Open Access

Integrative analysis of the microbiome and metabolome of the human intestinal mucosal surface reveals exquisite inter-relationships

Ian H McHardy, Maryam Goudarzi, Maomeng Tong, Paul M Ruegger, Emma Schwager, John R Weger, Thomas G Graeber, Justin L Sonnenburg, Steve Horvath, Curtis Huttenhower, Dermot PB McGovern, Albert J Fornace, James Borneman, Jonathan Braun Microbiome 2013, 1:17 (5 June 2013)

Abstract | Full text | PDF

8.

Review   Open Access Highly Accessed

Multiplicity of cerebrospinal fluid functions: New challenges in health and disease

Conrad E Johanson, John A Duncan, Petra M Klinge, Thomas Brinker, Edward G Stopa, Gerald D Silverberg Cerebrospinal Fluid Research 2008, 5:10 (14 May 2008)

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

9.

Research article   Open Access

A diagnostic window for the treatment of acute graft-versus-host disease prior to visible clinical symptoms in a murine model

Carina A Bäuerlein, Simone S Riedel, Jeanette Baker, Christian Brede, Ana-Laura Garrote, Martin Chopra, Miriam Ritz, Georg F Beilhack, Stephan Schulz, Robert Zeiser, Paul G Schlegel, Hermann Einsele, Robert S Negrin, Andreas Beilhack BMC Medicine 2013, 11:134 (21 May 2013)

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

Alloreactive T cells are present in the blood 2 weeks before the onset of acute graft-versus-host disease (GVHD) symptoms in a mouse model, suggesting these cells could be measured to allow early diagnosis and timely therapeutic intervention.

10.

Forum   Open Access Highly Accessed

What determines cell size?

Wallace F Marshall, Kevin D Young, Matthew Swaffer, Elizabeth Wood, Paul Nurse, Akatsuki Kimura, Joseph Frankel, John Wallingford, Virginia Walbot, Xian Qu, Adrienne HK Roeder BMC Biology 2012, 10:101 (14 December 2012)

Abstract | Full text | PDF | PubMed | 2 comments |  Editor’s summary

In a Forum article in the Cell geometry series, ten experts in ten different systems explain why it matters what size a cell is, and offer ten different answers on how it is controlled – probably all of them right.

11.

Research   Open Access Highly Accessed

Moving pictures of the human microbiome

J Gregory Caporaso, Christian L Lauber, Elizabeth K Costello, Donna Berg-Lyons, Antonio Gonzalez, Jesse Stombaugh, Dan Knights, Pawel Gajer, Jacques Ravel, Noah Fierer, Jeffrey I Gordon, Rob Knight Genome Biology 2011, 12:R50 (30 May 2011)

Abstract | Full text | PDF | PubMed | Cited on BioMed Central | F1000 Biology |  Editor’s summary

The dynamism of microbiome populations is seen in daily samples from a landmark multi-body site, multi-individual study

12.

Research   Open Access Highly Accessed

Discovery and validation of cell cycle arrest biomarkers in human acute kidney injury

Kianoush Kashani, Ali Al-Khafaji, Thomas Ardiles, Antonio Artigas, Sean M Bagshaw, Max Bell, Azra Bihorac, Robert Birkhahn, Cynthia M Cely, Lakhmir S Chawla, Danielle L Davison, Thorsten Feldkamp, Lui G Forni, Michelle Gong, Kyle J Gunnerson, Michael Haase, James Hackett, Patrick M Honore, Eric AJ Hoste, Olivier Joannes-Boyau, Michael Joannidis, Patrick Kim, Jay L Koyner, Daniel T Laskowitz, Matthew E Lissauer, Gernot Marx, Peter A McCullough, Scott Mullaney, Marlies Ostermann, Thomas Rimmelé et al. Critical Care 2013, 17:R25 (6 February 2013)

Abstract | Full text | PDF | PubMed | Cited on BioMed Central | F1000 Biology |  Editor’s summary

Urine TIMP-2, and IGFBP7, two novel biomarkers for risk stratification of acute kidney injury, have been discovered and validated in more than 1000 critically ill patients. 

13.

Research   Open Access Highly Accessed

Classification of human genomic regions based on experimentally determined binding sites of more than 100 transcription-related factors

Kevin Y Yip, Chao Cheng, Nitin Bhardwaj, James B Brown, Jing Leng, Anshul Kundaje, Joel Rozowsky, Ewan Birney, Peter Bickel, Michael Snyder, Mark Gerstein Genome Biology 2012, 13:R48 (5 September 2012)

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

Machine learning analysis of ENCODE data for 100 transcription factors reveals six classes of genomic regions

14.

Research   Open Access Highly Accessed

Improvements in patient-reported outcomes with apremilast, an oral phosphodiesterase 4 inhibitor, in the treatment of moderate to severe psoriasis: results from a phase IIb randomized, controlled study

Vibeke Strand, David Fiorentino, ChiaChi Hu, Robert M Day, Randall M Stevens, Kim A Papp Health and Quality of Life Outcomes 2013, 11:82 (10 May 2013)

Abstract | Full text | PDF | PubMed

15.

Study protocol   Open Access Highly Accessed

Evaluation of lifestyle interventions to treat elevated cardiometabolic risk in primary care (E-LITE): a randomized controlled trial

Jun Ma, Abby C King, Sandra R Wilson, Lan Xiao, Randall S Stafford BMC Family Practice 2009, 10:71 (12 November 2009)

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

16.

Debate   Open Access

Informing DSM-5: biological boundaries between bipolar I disorder, schizoaffective disorder, and schizophrenia

Victoria E Cosgrove, Trisha Suppes BMC Medicine 2013, 11:127 (14 May 2013)

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

Victoria Cosgrove and Trisha Suppes agree that boundaries between the diagnosis of bipolar disorder I, schizophrenia and schizoaffective disorder are preserved in the DSM-5 criteria, as there is not yet enough data to justify a continuous model of psychosis.

17.

Research   Open Access Highly Accessed

Transcriptional profiling of long non-coding RNAs and novel transcribed regions across a diverse panel of archived human cancers

Alayne L Brunner, Andrew H Beck, Badreddin Edris, Robert T Sweeney, Shirley X Zhu, Rui Li, Kelli Montgomery, Sushama Varma, Thea Gilks, Xiangqian Guo, Joseph W Foley, Daniela M Witten, Craig P Giacomini, Ryan A Flynn, Jonathan R Pollack, Robert Tibshirani, Howard Y Chang, Matt van de Rijn, Robert B West Genome Biology 2012, 13:R75 (28 August 2012)

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

Transcript sequencings from 64 solid tumours of 17 diagnostic classes reveals cancer-specific lncRNAs

18.

Methodology article   Open Access

QualComp: a new lossy compressor for quality scores based on rate distortion theory

Idoia Ochoa, Himanshu Asnani, Dinesh Bharadia, Mainak Chowdhury, Tsachy Weissman, Golan Yona BMC Bioinformatics 2013, 14:187 (8 June 2013)

Abstract | Provisional PDF | PubMed

19.

Research article   Open Access Highly Accessed

Comparative analysis of mycobacterium and related actinomycetes yields insight into the evolution of mycobacterium tuberculosis pathogenesis

Abigail McGuire, Brian Weiner, Sang Park, Ilan Wapinski, Sahadevan Raman, Gregory Dolganov, Matthew Peterson, Robert Riley, Jeremy Zucker, Thomas Abeel, Jared White, Peter Sisk, Christian Stolte, Mike Koehrsen, Robert T Yamamoto, Milena Iacobelli-Martinez, Matthew J Kidd, Andreia M Maer, Gary K Schoolnik, Aviv Regev, James Galagan BMC Genomics 2012, 13:120 (28 March 2012)

Abstract | Full text | PDF | PubMed

20.

Review   Open Access Highly Accessed

Depression and Obstructive Sleep Apnea (OSA)

Carmen M Schröder, Ruth O'Hara Annals of General Psychiatry 2005, 4:13 (27 June 2005)

Abstract | Full text | PDF | PubMed | Cited on BioMed Central | 3 comments

21.

Research   Open Access Highly Accessed

Modeling gene expression using chromatin features in various cellular contexts

Xianjun Dong, Melissa C Greven, Anshul Kundaje, Sarah Djebali, James B Brown, Chao Cheng, Thomas R Gingeras, Mark Gerstein, Roderic Guigó, Ewan Birney, Zhiping Weng Genome Biology 2012, 13:R53 (5 September 2012)

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

Models for linking gene expression with chromatin features vary according to cellular context and RNA measurement method

22.

Research article   Open Access

The mxd operon in Shewanella oneidensis MR-1 is induced in response to starvation and regulated by Arcs/Arca and Bara/Uvry

Jana Müller, Soni Shukla, Kathinka A Jost, Alfred M Spormann BMC Microbiology 2013, 13:119 (27 May 2013)

Abstract | Provisional PDF | PubMed

23.

Review   Open Access Highly Accessed

Hormone-Sensitive Lipase Knockouts

Fredric B Kraemer, Wen-Jun Shen Nutrition & Metabolism 2006, 3:12 (10 February 2006)

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

24.

Research   Open Access

Chimeric antigen receptor containing ICOS signaling domain mediates specific and efficient antitumor effect of T cells against EGFRvIII expressing glioma

Chan-Juan Shen, Yu-Xiu Yang, Ethan Q Han, Na Cao, Yun-Fei Wang, Yi Wang, Ying-Ying Zhao, Li-Ming Zhao, Jian Cui, Puja Gupta, Albert J Wong, Shuang-Yin Han Journal of Hematology & Oncology 2013, 6:33 (9 May 2013)

Abstract | Full text | PDF | PubMed

25.

Research article   Open Access Highly Accessed

Small RNA pyrosequencing in the protozoan parasite Entamoeba histolytica reveals strain-specific small RNAs that target virulence genes

Hanbang Zhang, Gretchen M Ehrenkaufer, Neil Hall, Upinder Singh BMC Genomics 2013, 14:53 (25 January 2013)

Abstract | Full text | PDF | PubMed

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