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76.

Method   Open Access Highly Accessed

Estimating enrichment of repetitive elements from high-throughput sequence data

Daniel S Day, Lovelace J Luquette, Peter J Park, Peter V Kharchenko Genome Biology 2010, 11:R69 (28 June 2010)

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

The authors present a method for estimating repetitive sequence content in high-throughput sequencing data, including from ChIP-seq experiments

77.

Review   Open Access

Ankyrin 3: genetic association with bipolar disorder and relevance to disease pathophysiology

Melanie P Leussis, Jon M Madison, Tracey L Petryshen Biology of Mood & Anxiety Disorders 2012, 2:18 (1 October 2012)

Abstract | Full text | PDF | PubMed

78.

Research   Open Access

Community transcriptomics reveals universal patterns of protein sequence conservation in natural microbial communities

Frank J Stewart, Adrian K Sharma, Jessica A Bryant, John M Eppley, Edward F DeLong Genome Biology 2011, 12:R26 (22 March 2011)

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

Analysis of several metagenomic datasets reveals that highly expressed genes are more conserved than less highly expressed ones

79.

Research   Open Access

Genome-wide analysis reveals rapid and dynamic changes in miRNA and siRNA sequence and expression during ovule and fiber development in allotetraploid cotton (Gossypium hirsutum L.)

Mingxiong Pang, Andrew W Woodward, Vikram Agarwal, Xueying Guan, Misook Ha, Vanitharani Ramachandran, Xuemei Chen, Barbara A Triplett, David M Stelly, Z Jeffrey Chen Genome Biology 2009, 10:R122 (4 November 2009)

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

Rapid and dynamic changes in the expression of small RNAs are seen during ovule and fiber development in allotetraploid cotton.

80.

Proceedings   Open Access Highly Accessed

The coastal environment and human health: microbial indicators, pathogens, sentinels and reservoirs

Jill R Stewart, Rebecca J Gast, Roger S Fujioka, Helena M Solo-Gabriele, J Scott Meschke, Linda A Amaral-Zettler, Erika del Castillo, Martin F Polz, Tracy K Collier, Mark S Strom, Christopher D Sinigalliano, Peter DR Moeller, A Fredrick Holland Environmental Health 2008, 7(Suppl 2):S3 (7 November 2008)

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

81.

Research   Open Access Highly Accessed

Echocardiographic AV-interval optimization in patients with reduced left ventricular function

C Melzer, AC Borges, F Knebel, WS Richter, W Combs, G Baumann, H Theres Cardiovascular Ultrasound 2004, 2:30 (17 December 2004)

Abstract | Full text | PDF | PubMed

82.

Research   Open Access

Combined dietary folate, vitamin B-12, and vitamin B-6 intake influences plasma docosahexaenoic acid concentration in rats

Nick van Wijk, Carol J Watkins, Robert J J Hageman, John C W Sijben, Patrick G H J Kamphuis, Richard J Wurtman, Laus M Broersen Nutrition & Metabolism 2012, 9:49 (30 May 2012)

Abstract | Full text | PDF | PubMed

83.

Research   Open Access

Transfer Entropy Estimation and Directional Coupling Change Detection in Biomedical Time Series

Joon Lee, Shamim Nemati, Ikaro Silva, Bradley A Edwards, James P Butler, Atul Malhotra BioMedical Engineering OnLine 2012, 11:19 (13 April 2012)

Abstract | Full text | PDF | PubMed

84.

Research   Open Access Highly Accessed

Genome-wide SNP genotyping highlights the role of natural selection in Plasmodium falciparum population divergence

Daniel E Neafsey, Stephen F Schaffner, Sarah K Volkman, Daniel Park, Philip Montgomery, Danny A Milner, Amanda Lukens, David Rosen, Rachel Daniels, Nathan Houde, Joseph F Cortese, Erin Tyndall, Casey Gates, Nicole Stange-Thomann, Ousmane Sarr, Daouda Ndiaye, Omar Ndir, Soulyemane Mboup, Marcelo U Ferreira, Sandra Moraes, Aditya P Dash, Chetan E Chitnis, Roger C Wiegand, Daniel L Hartl, Bruce W Birren, Eric S Lander, Pardis C Sabeti, Dyann F Wirth Genome Biology 2008, 9:R171 (15 December 2008)

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

An array-based SNP genotyping platform for Plasmodium falciparum is reported together with an analysis of SNP diversity in global population samples.

85.

Methodology article   Open Access Highly Accessed

Assessing statistical significance in causal graphs

Leonid Chindelevitch, Po-Ru Loh, Ahmed Enayetallah, Bonnie Berger, Daniel Ziemek BMC Bioinformatics 2012, 13:35 (20 February 2012)

Abstract | Full text | PDF | PubMed

86.

Methodology   Open Access

BglBricks: A flexible standard for biological part assembly

J Christopher Anderson, John E Dueber, Mariana Leguia, Gabriel C Wu, Jonathan A Goler, Adam P Arkin, Jay D Keasling Journal of Biological Engineering 2010, 4:1 (20 January 2010)

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

87.

Method   Open Access Highly Accessed

Assisted assembly: how to improve a de novo genome assembly by using related species

Sante Gnerre, Eric S Lander, Kerstin Lindblad-Toh, David B Jaffe Genome Biology 2009, 10:R88 (27 August 2009)

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

A method is described for improving low sequence coverage genome assemblies

88.

Research article   Open Access Highly Accessed

Mechanistic studies of Gemcitabine-loaded nanoplatforms in resistant pancreatic cancer cells

Anne-Laure Papa, Sudipta Basu, Poulomi Sengupta, Deboshri Banerjee, Shiladitya Sengupta, Rania Harfouche BMC Cancer 2012, 12:419 (22 September 2012)

Abstract | Full text | PDF | PubMed

89.

Research article   Open Access Highly Accessed

Novel reference genes for quantifying transcriptional responses of Escherichia coli to protein overexpression by quantitative PCR

Kang Zhou, Lihan Zhou, Qing Lim, Ruiyang Zou, Gregory Stephanopoulos, Heng-Phon Too BMC Molecular Biology 2011, 12:18 (23 April 2011)

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

A suite of novel reference genes that are more reliable than commonly used rRNAs, have been selected from a meta-analysis of microarray data for use in quantitative Real-Time PCR experiments in E. coli over-expressing recombinant proteins.

90.

Research   Open Access

Uncertainty in techno-economic estimates of cellulosic ethanol production due to experimental measurement uncertainty

Kristin J Vicari, Sai Tallam, Tatyana Shatova, Koh Joo, Christopher J Scarlata, David Humbird, Edward J Wolfrum, Gregg T Beckham Biotechnology for Biofuels 2012, 5:23 (17 April 2012)

Abstract | Full text | PDF | PubMed

91.

Review   Open Access

Authentic teaching and learning through synthetic biology

Natalie Kuldell Journal of Biological Engineering 2007, 1:8 (27 December 2007)

Abstract | Full text | PDF | PubMed | 1 comment

92.

Research article   Open Access

Serum protein profiles predict coronary artery disease in symptomatic patients referred for coronary angiography

William A LaFramboise, Rajiv Dhir, Lori A Kelly, Patricia Petrosko, John M Krill-Burger, Christin M Sciulli, Maureen A Lyons-Weiler, Uma R Chandran, Aleksey Lomakin, Robert V Masterson, Oscar C Marroquin, Suresh R Mulukutla, Dennis M McNamara BMC Medicine 2012, 10:157 (5 December 2012)

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

Protein biomarkers discriminate between patients lacking significant coronary artery disease from those with the disease and requiring angiography, with long-term benefits including reduced patient exposure to ionization and lower healthcare costs.

93.

Meeting report   Free Highly Accessed

Epigenomics and chromatin dynamics

Veronika Akopian, Michelle M Chan, Kendell Clement, Christina Galonska, Casey A Gifford, Elizabeth Lehtola, Jing Liao, Payman Samavarchi-Tehrani, Camille Sindhu, Zachary D Smith, Alexander M Tsankov, Jamie Webster, Yingying Zhang, Michael J Ziller, Alexander Meissner Genome Biology 2012, 13:313 (24 February 2012)

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

A report on the Joint Keystone Symposium on Epigenomics and Chromatin Dynamics, Keystone, Colorado, 17-22 January 2012

94.

Research   Open Access Highly Accessed

Modeling the cumulative genetic risk for multiple sclerosis from genome-wide association data

Joanne H Wang, Derek Pappas, Philip L De Jager, Daniel Pelletier, Paul IW de Bakker, Ludwig Kappos, Chris H Polman, Lori B Chibnik, David A Hafler, Paul M Matthews, Stephen L Hauser, Sergio E Baranzini, Jorge R Oksenberg Genome Medicine 2011, 3:3 (18 January 2011)

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

A novel genetic profile for multiple sclerosis is enriched for genes involved in such pathways as immune response and nervous system development, providing insights into disease heterogeneity and genetic risk.

95.

Editorial   Open Access

JNER: a forum to discuss how neuroscience and biomedical engineering are reshaping physical medicine & rehabilitation

Paolo Bonato Journal of NeuroEngineering and Rehabilitation 2004, 1:1 (13 October 2004)

Abstract | Full text | PDF | PubMed

96.

Research article   Open Access

Interplay between neural-cadherin and vascular endothelial-cadherin in breast cancer progression

Maryam Rezaei, Katrin Friedrich, Ben Wielockx, Aleksandar Kuzmanov, Antje Kettelhake, Myriam Labelle, Hans Schnittler, Gustavo Baretton, Georg Breier Breast Cancer Research 2012, 14:R154 (6 December 2012)

Abstract | Full text | PDF | PubMed

97.

Method   Open Access Highly Accessed

Automated eukaryotic gene structure annotation using EVidenceModeler and the Program to Assemble Spliced Alignments

Brian J Haas, Steven L Salzberg, Wei Zhu, Mihaela Pertea, Jonathan E Allen, Joshua Orvis, Owen White, C Robin Buell, Jennifer R Wortman Genome Biology 2008, 9:R7 (11 January 2008)

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

EVidenceModeler (EVM) is an automated annotation tool that predicts protein-coding regions, alternatively spliced transcripts and untranslated regions of eukaryotic genes.

98.

Methodology article   Open Access Highly Accessed

Improving the performance of true single molecule sequencing for ancient DNA

Aurelien Ginolhac, Julia Vilstrup, Jesper Stenderup, Morten Rasmussen, Mathias Stiller, Beth Shapiro, Grant Zazula, Duane Froese, Kathleen E Steinmann, John F Thompson, Khaled AS AL-Rasheid, Thomas MP Gilbert, Eske Willerslev, Ludovic Orlando BMC Genomics 2012, 13:177 (10 May 2012)

Abstract | Full text | PDF | PubMed

99.

Mini-Review   Open Access Highly Accessed

Modeling formalisms in Systems Biology

Daniel Machado, Rafael S Costa, Miguel Rocha, Eugénio C Ferreira, Bruce Tidor, Isabel Rocha AMB Express 2011, 1:45 (5 December 2011)

Abstract | Full text | PDF | PubMed

100.

Research   Open Access

Sterol regulatory element binding protein-dependent regulation of lipid synthesis supports cell survival and tumor growth

Beatrice Griffiths, Caroline A Lewis, Karim Bensaad, Susana Ros, Qifeng Zhang, Emma C Ferber, Sofia Konisti, Barrie Peck, Heike Miess, Philip East, Michael Wakelam, Adrian L Harris, Almut Schulze Cancer & Metabolism 2013, 1:3 (23 January 2013)

Abstract | Full text | PDF |  Editor’s summary

Akt/mTORC1 signalling via SREBP was shown to coordinate lipid and protein biosynthesis in both normal and cancer cells, while ablation of this pathway caused ER stress, apoptosis and cell death and prevented tumor growth in a mouse model.

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