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Work published with BioMed Central, Chemistry Central and SpringerOpen by researchers at University of California, San Francisco

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26.

Software   Open Access Highly Accessed

CHANCE: comprehensive software for quality control and validation of ChIP-seq data

Aaron Diaz, Abhinav Nellore, Jun S Song Genome Biology 2012, 13:R98 (15 October 2012)

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

A user friendly graphical software package with multiple tools for quality assessment of ChIP-seq data

27.

Research   Open Access Highly Accessed

Analysis of inflammation-related nigral degeneration and locomotor function in DJ-1 −/− mice

Thi A Nguyen, Tamy Frank-Cannon, Terina N Martinez, Kelly A Ruhn, Marian Marvin, Bradford Casey, Isaac Treviño, John J Hong, Matthew S Goldberg, Malú G Tansey Journal of Neuroinflammation 2013, 10:50 (28 April 2013)

Abstract | Full text | PDF | PubMed

28.

Research   Open Access Highly Accessed

Cyclist route choice, traffic-related air pollution, and lung function: a scripted exposure study

Sarah Jarjour, Michael Jerrett, Dane Westerdahl, Audrey de Nazelle, Cooper Hanning, Laura Daly, Jonah Lipsitt, John Balmes Environmental Health 2013, 12:14 (7 February 2013)

Abstract | Full text | PDF | PubMed

29.

Technical advance   Open Access Highly Accessed

The use of mobile phones as a data collection tool: A report from a household survey in South Africa

Mark Tomlinson, Wesley Solomon, Yages Singh, Tanya Doherty, Mickey Chopra, Petrida Ijumba, Alexander C Tsai, Debra Jackson BMC Medical Informatics and Decision Making 2009, 9:51 (23 December 2009)

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

30.

Research article   Open Access Highly Accessed

Epidemiology of breast cancer subtypes in two prospective cohort studies of breast cancer survivors

Marilyn L Kwan, Lawrence H Kushi, Erin Weltzien, Benjamin Maring, Susan E Kutner, Regan S Fulton, Marion M Lee, Christine B Ambrosone, Bette J Caan Breast Cancer Research 2009, 11:R31 (22 May 2009)

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

31.

Research article   Open Access Highly Accessed

What does my patient's coronary artery calcium score mean? Combining information from the coronary artery calcium score with information from conventional risk factors to estimate coronary heart disease risk

Mark J Pletcher, Jeffrey A Tice, Michael Pignone, Charles McCulloch, Tracy Q Callister, Warren S Browner BMC Medicine 2004, 2:31 (24 August 2004)

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

The addition of standard risk factors to the coronary artery calcium score can affect the clinical assessment of coronary heart disease risks.

32.

Method   Open Access Highly Accessed

Haplotype and isoform specific expression estimation using multi-mapping RNA-seq reads

Ernest Turro, Shu-Yi Su, Ângela Gonçalves, Lachlan JM Coin, Sylvia Richardson, Alex Lewin Genome Biology 2011, 12:R13 (10 February 2011)

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

A novel method for estimating isoform-specific expression and allelic imbalance in diploid organisms from RNA-seq data

33.

Research   Open Access

Cerebrospinal fluid neopterin decay characteristics after initiation of antiretroviral therapy

Aylin Yilmaz, Constantin T Yiannoutsos, Dietmar Fuchs, Richard W Price, Kathryn Crozier, Lars Hagberg, Serena Spudich, Magnus Gisslén Journal of Neuroinflammation 2013, 10:62 (10 May 2013)

Abstract | Full text | PDF | PubMed

34.

Research article   Open Access Highly Accessed

Oral health-related cultural beliefs for four racial/ethnic groups: Assessment of the literature

Yogita Butani, Jane A Weintraub, Judith C Barker BMC Oral Health 2008, 8:26 (15 September 2008)

Abstract | Full text | PDF | PubMed

35.

Research   Open Access Highly Accessed

Macrophage imbalance (M1 vs. M2) and upregulation of mast cells in wall of ruptured human cerebral aneurysms: preliminary results

David Hasan, Nohra Chalouhi, Pascal Jabbour, Tomoki Hashimoto Journal of Neuroinflammation 2012, 9:222 (21 September 2012)

Abstract | Full text | PDF | PubMed

36.

Research   Open Access

The effects of intestinal microbial community structure on disease manifestation in IL-10-/- mice infected with Helicobacter hepaticus

Nabeetha A Nagalingam, Courtney J Robinson, Ingrid L Bergin, Kathryn A Eaton, Gary B Huffnagle, Vincent B Young Microbiome 2013, 1:15 (10 May 2013)

Abstract | Full text | PDF

37.

Research article   Open Access Highly Accessed

Co-expression of HER2 and HER3 receptor tyrosine kinases enhances invasion of breast cells via stimulation of interleukin-8 autocrine secretion

Nicola Aceto, Stephan Duss, Gwen MacDonald, Dominique S Meyer, Tim-C Roloff, Nancy E Hynes, Mohamed Bentires-Alj Breast Cancer Research 2012, 14:R131 (12 October 2012)

Abstract | Full text | PDF | PubMed

38.

Review   Open Access

Active microscope stabilization in three dimensions using image correlation

Ryan McGorty, Daichi Kamiyama, Bo Huang Optical Nanoscopy 2013, 2:3 (18 April 2013)

Abstract | Full text | PDF

39.

Commentary   Open Access

Advocacy spurs innovation: promoting synergy between physical and biomedical sciences

Susan Samson, Irene Acerbi, Carole Baas, Valerie Weaver, Hope Rugo EPJ Nonlinear Biomedical Physics 2013, 1:1 (9 May 2013)

Abstract | Full text | PDF

40.

Review   Open Access Highly Accessed

Society for Cardiovascular Magnetic Resonance guidelines for reporting cardiovascular magnetic resonance examinations

W Gregory Hundley, David Bluemke, Jan G Bogaert, Matthias G Friedrich, Charles B Higgins, Mark A Lawson, Michael V McConnell, Subha V Raman, Albert C van Rossum, Scott Flamm, Christopher M Kramer, Eike Nagel, Stefan Neubauer Journal of Cardiovascular Magnetic Resonance 2009, 11:5 (3 March 2009)

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

41.

Research article   Open Access

The effect of depression symptoms and social support on black-white differences in health-related quality of life in early pregnancy: the health status in pregnancy (HIP) study

Li Liu, Rosanna Setse, Ruby Grogan, Neil R Powe, Wanda K Nicholson BMC Pregnancy and Childbirth 2013, 13:125 (3 June 2013)

Abstract | Full text | PDF | PubMed

42.

Software   Open Access Highly Accessed

clusterMaker: a multi-algorithm clustering plugin for Cytoscape

John H Morris, Leonard Apeltsin, Aaron M Newman, Jan Baumbach, Tobias Wittkop, Gang Su, Gary D Bader, Thomas E Ferrin BMC Bioinformatics 2011, 12:436 (9 November 2011)

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

43.

Research   Open Access

Measuring infertility in populations: constructing a standard definition for use with demographic and reproductive health surveys

Maya N Mascarenhas, Hoiwan Cheung, Colin D Mathers, Gretchen A Stevens Population Health Metrics 2012, 10:17 (31 August 2012)

Abstract | Full text | PDF | PubMed

44.

Research article   Open Access

Social determinants of health and seasonal influenza vaccination in adults ≥65 years: a systematic review of qualitative and quantitative data

Jason M Nagata, Isabel Hernández-Ramos, Anand Kurup, Daniel Albrecht, Claudia Vivas-Torrealba, Carlos Franco-Paredes BMC Public Health 2013, 13:388 (25 April 2013)

Abstract | Full text | PDF | PubMed

45.

Research article   Open Access Highly Accessed

Potential for false positive HIV test results with the serial rapid HIV testing algorithm

Steven Baveewo, Moses R Kamya, Harriet Mayanja-Kizza, Robin Fatch, David R Bangsberg, Thomas Coates, Judith A Hahn, Rhoda K Wanyenze BMC Research Notes 2012, 5:154 (19 March 2012)

Abstract | Full text | PDF | PubMed

46.

Research   Open Access

Chromatin accessibility reveals insights into androgen receptor activation and transcriptional specificity

Alok K Tewari, Galip Yardimci, Yoichiro Shibata, Nathan C Sheffield, Lingyun Song, Barry S Taylor, Stoyan G Georgiev, Gerhard A Coetzee, Uwe Ohler, Terrence S Furey, Gregory E Crawford, Phillip G Febbo Genome Biology 2012, 13:R88 (3 October 2012)

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

Androgen receptor binding to the genome occurs by multiple mechanisms and is associated with an increase in chromatin accessibility

47.

Research article   Open Access Highly Accessed

The Ramachandran plots of glycine and pre-proline

Bosco K Ho, Robert Brasseur BMC Structural Biology 2005, 5:14 (16 August 2005)

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

48.

Research article   Open Access Highly Accessed

Impact of hormone receptor status on patterns of recurrence and clinical outcomes among patients with human epidermal growth factor-2-positive breast cancer in the National Comprehensive Cancer Network: a prospective cohort study

Ines Vaz-Luis, Rebecca A Ottesen, Melissa E Hughes, P Kelly Marcom, Beverly Moy, Hope S Rugo, Richard L Theriault, John Wilson, Joyce C Niland, Jane C Weeks, Nancy U Lin Breast Cancer Research 2012, 14:R129 (1 October 2012)

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

Clinical outcomes and patterns of recurrence differ by hormone receptor (HR) status in patients with human epidermal growth factor-2 (HER2)- positive breast cancer, meriting further investigation and consideration in trial design.

49.

Research article   Open Access

Temporal and spatial requirements of Smoothened in ventral midbrain neuronal development

Mianzhi Tang, Sarah X Luo, Vivian Tang, Eric J Huang Neural Development 2013, 8:8 (26 April 2013)

Abstract | Full text | PDF | PubMed

50.

Research article   Open Access Highly Accessed

Encountering abuse in health care; lifetime experiences in postnatal women - a qualitative study

Anne-Mette Schroll, Hanne Kjærgaard, Julie Midtgaard BMC Pregnancy and Childbirth 2013, 13:74 (22 March 2013)

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

Women who previously experienced abuse in healthcare find constructive ways to manage the experience during pregnancy and childbirth, suggesting that healthcare professionals have a unique opportunity to support the reproductive health of these women.

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