BioMed Central | Members | Stanford University

Submit a manuscript Register Contact us

Institution search

Search by institution name/city

Members

Australia (21)
Austria (6)
Belgium (2)
Brazil (4)
Burkina Faso (1)
Canada (27)
Central African Republic (1)
China (3)
Cyprus (3)
Czech Republic (1)
Denmark (1)
Ethiopia (1)
Finland (6)
France (6)
Germany (48)
Ghana (3)
Greece (1)
Hong Kong (2)
Hungary (1)
India (7)
Ireland (1)
Israel (1)
Italy (13)
Japan (1)
Kenya (2)
Korea, South (1)
Lebanon (1)
Lithuania (1)
Luxembourg (1)
Madagascar (1)
Malaysia (3)
Mexico (1)
Morocco (2)
Netherlands (10)
New Zealand (1)
Nigeria (2)
Norway (3)
Poland (1)
Portugal (1)
Romania (1)
South Africa (6)
Spain (14)
Sweden (9)
Switzerland (10)
Taiwan (3)
Tanzania (2)
Thailand (1)
Trinidad and Tobago (1)
Uganda (1)
United Kingdom (41)
United States of America (153)

Advertisement

Supporter Member - Stanford University

Die Luft der Freiheit weht

http://www.stanford.edu/

Research staff and students at Stanford University:

Do you realize that you will get a 15% discount on the article-processing charges of all research articles accepted for publication in journals published by BioMed Central, Chemistry Central and SpringerOpen? Read more information about publishing your articles with us.

Work published with BioMed Central, Chemistry Central and SpringerOpen by researchers at Stanford University

Display/download options Articles per page: 25 | 50 | 100

Display options

Editor's summary Citation

Download options

Send
To

	1.	Research 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 \| Editor’s summary Machine learning analysis of ENCODE data for 100 transcription factors reveals six classes of genomic regions
	2.	Research 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 \| Editor’s summary Models for linking gene expression with chromatin features vary according to cellular context and RNA measurement method
	3.	Software 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
	4.	Method 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 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.	Open letter An encyclopedia of mouse DNA elements (Mouse ENCODE) John A Stamatoyannopoulos, Michael Snyder, Ross Hardison, Bing Ren, Thomas Gingeras, David M Gilbert, Mark Groudine, Michael Bender, Rajinder Kaul, Theresa Canfield, Erica Giste, Audra Johnson, Mia Zhang, Gayathri Balasundaram, Rachel Byron, Vaughan Roach, Peter J Sabo, Richard Sandstrom, A Sandra Stehling, Robert E Thurman, Sherman M Weissman, Philip Cayting, Manoj Hariharan, Jin Lian, Yong Cheng, Stephen G Landt, Zhihai Ma, Barbara J Wold, Job Dekker et al. Genome Biology 2012, 13:418 (13 August 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary The Mouse ENCODE Consortium is applying the same experimental pipelines developed for human ENCODE to annotate the mouse genome
	7.	Study protocol 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
	8.	Research Engineered cell-cell communication via DNA messaging Monica E Ortiz, Drew Endy Journal of Biological Engineering 2012, 6:16 (7 September 2012) Abstract \| Full text \| PDF \| PubMed
	9.	Research Transcriptional profiling of lncRNAs 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 \| Provisional PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Transcript sequencings from 64 solid tumours of 17 diagnostic classes reveals cancer-specific lncRNAs
	10.	Forum 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 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.	Comment Are we training pit bulls to review our manuscripts? Virginia Walbot Journal of Biology 2009, 8:24 (9 March 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| 4 comments \| Editor’s summary Virginia Walbot accepts some of the blame for remorselessly negative reviewers, and suggests a training program for graduate students and post docs that will deliver a fairer assessment of manuscripts.
	13.	Research article Anti-NMDA-receptor antibody detected in encephalitis, schizophrenia, and narcolepsy with psychotic features Ko Tsutsui, Takashi Kanbayashi, Keiko Tanaka, Shuken Boku, Wakako Ito, Jun Tokunaga, Akane Mori, Yasuo Hishikawa, Tetsuo Shimizu, Seiji Nishino BMC Psychiatry 2012, 12:37 (8 May 2012) Abstract \| Full text \| PDF \| PubMed
	14.	Research article Deciphering neo-sex and B chromosome evolution by the draft genome of Drosophila albomicans Qi Zhou, Hong-mei Zhu, Quan-fei Huang, Li Zhao, Guo-jie Zhang, Scott W Roy, Beatriz Vicoso, Zhao-lin Xuan, Jue Ruan, Yue Zhang, Ruo-ping Zhao, Chen Ye, Xiu-qing Zhang, Jun Wang, Wen Wang, Doris Bachtrog BMC Genomics 2012, 13:109 (22 March 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Analysis of the genome of Drosophila albomicans, shows the extremely young neo-sex chromosomes already have an accumulation of excess deleterious mutations and the B chromosomes have an origin in sex chromosome-autosome fusion.
	15.	Software BioWarehouse: a bioinformatics database warehouse toolkit Thomas J Lee, Yannick Pouliot, Valerie Wagner, Priyanka Gupta, David WJ Stringer-Calvert, Jessica D Tenenbaum, Peter D Karp BMC Bioinformatics 2006, 7:170 (23 March 2006) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central
	16.	Research article GC-Content Normalization for RNA-Seq Data Davide Risso, Katja Schwartz, Gavin Sherlock, Sandrine Dudoit BMC Bioinformatics 2011, 12:480 (17 December 2011) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary The combination of three different strategies for GC-content normalization of RNA-seq data leads to more accurate estimations of gene expression levels and fold-changes, making statistical inference of differential expression less prone to false discoveries.
	17.	Research article The effect of a cold beverage during an exercise session combining both strength and energy systems development training on core temperature and markers of performance Danielle LaFata, Amanda Carlson-Phillips, Stacy T Sims, Elizabeth M Russell Journal of the International Society of Sports Nutrition 2012, 9:44 (19 September 2012) Abstract \| Full text \| PDF \| PubMed
	18.	Research article Gene expression patterns associated with blood-feeding in the malaria mosquito Anopheles gambiae Ali N Dana, Young S Hong, Marcia K Kern, Maureen E Hillenmeyer, Brent W Harker, Neil F Lobo, James R Hogan, Patricia Romans, Frank H Collins BMC Genomics 2005, 6:5 (14 January 2005) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Expression patterns of genes affected by the female malaria mosquito's physiological responses to blood feeding are defined.
	19.	Opinion Q & A: the Snyderome Michael Snyder Genome Biology 2012, 13:147 (16 March 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Michael Snyder answers Genome Biology's questions on the human and professional stories underlying his Snyderome integrative omics project
	20.	Review 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
	21.	Opinion Categorization of humans in biomedical research: genes, race and disease Neil Risch, Esteban Burchard, Elad Ziv, Hua Tang Genome Biology 2002, 3:comment2007-comment2007.12 (1 July 2002) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A debate has arisen regarding the validity of racial/ethnic categories for biomedical and genetic research. An epidemiologic perspective on the issue of human categorization in biomedical and genetic research strongly supports the continued use of self-identified race and ethnicity.
	22.	Commentary How do miRNAs mediate translational repression? Shuo Gu, Mark A Kay Silence 2010, 1:11 (7 May 2010) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central
	23.	Research Systems-level analysis of age-related macular degeneration reveals global biomarkers and phenotype-specific functional networks Aaron M Newman, Natasha B Gallo, Lisa S Hancox, Norma J Miller, Carolyn M Radeke, Michelle A Maloney, James B Cooper, Gregory S Hageman, Don H Anderson, Lincoln V Johnson, Monte J Radeke Genome Medicine 2012, 4:16 (24 February 2012) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Comparative transcriptome profiling of eye specimens, integrated with functionally enriched protein network analysis reveals candidate drug targets for treating age-related macular degeneration.
	24.	Opinion The real cost of sequencing: higher than you think! Andrea Sboner, Xinmeng Mu, Dov Greenbaum, Raymond K Auerbach, Mark B Gerstein Genome Biology 2011, 12:125 (25 August 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The sharp decrease in the cost of 'data generation' has not been matched by a comparable decrease in the cost of the computational infrastructure required to mine the data
	25.	Research Population-specificity of human DNA methylation Hunter B Fraser, Lucia L Lam, Sarah M Neumann, Michael S Kobor Genome Biology 2012, 13:R8 (9 February 2012) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Measurement of TSS-proximal DNA methylation in CEU and YRI genomes reveals significant population specificity