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Work published with BioMed Central, Chemistry Central and SpringerOpen by researchers at University of Texas San Antonio UTSA

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1.

Proceedings   Open Access

A genome-wide cis-regulatory element discovery method based on promoter sequences and gene co-expression networks

Zhen Gao, Ruizhe Zhao, Jianhua Ruan BMC Genomics 2013, 14(Suppl 1):S4 (21 January 2013)

Abstract | Full text | PDF | PubMed

2.

Research   Open Access

Decomposing Kenyan socio-economic inequalities in skilled birth attendance and measles immunization

Carine Van Malderen, Irene Ogali, Anne Khasakhala, Stephen N Muchiri, Corey Sparks, Herman Van Oyen, Niko Speybroeck International Journal for Equity in Health 2013, 12:3 (7 January 2013)

Abstract | Full text | PDF | PubMed

3.

Research   Open Access

A Bayesian decision fusion approach for microRNA target prediction

Dong Yue, Maozu Guo, Yidong Chen, Yufei Huang BMC Genomics 2012, 13(Suppl 8):S13 (17 December 2012)

Abstract | Full text | PDF | PubMed

4.

Research   Open Access

Mathematical modeling of left ventricular dimensional changes in mice during aging

Tianyi Yang, Ying Chiao, Yunji Wang, Andrew Voorhees, Hai-Chao Han, Merry L Lindsey, Yu-Fang Jin BMC Systems Biology 2012, 6(Suppl 3):S10 (17 December 2012)

Abstract | Full text | PDF | PubMed

5.

Research   Open Access

Module-based subnetwork alignments reveal novel transcriptional regulators in malaria parasite Plasmodium falciparum

Hong Cai, Changjin Hong, Jianying Gu, Timothy G Lilburn, Rui Kuang, Yufeng Wang BMC Systems Biology 2012, 6(Suppl 3):S5 (17 December 2012)

Abstract | Full text | PDF | PubMed

6.

Introduction   Open Access

Advances in systems biology: computational algorithms and applications

Yufei Huang, Zhongming Zhao, Hua Xu, Yu Shyr, Bing Zhang BMC Systems Biology 2012, 6(Suppl 3):S1 (17 December 2012)

Abstract | Full text | PDF | PubMed

7.

Introduction   Open Access

Genomics in 2012: challenges and opportunities in the next generation sequencing era

Zhongming Zhao, Yufei Huang, Bing Zhang, Yu Shyr, Hua Xu BMC Genomics 2012, 13(Suppl 8):S1 (17 December 2012)

Abstract | Full text | PDF | PubMed

8.

Research article   Open Access Highly Accessed

Depletion of neutrophils in a protective model of pulmonary cryptococcosis results in increased IL-17A production by gamma/delta T cells

Karen L Wozniak, Jay K Kolls, Floyd L Wormley BMC Immunology 2012, 13:65 (7 December 2012)

Abstract | Full text | PDF | PubMed

9.

Nano Express   Open Access

Morphological, compositional, structural, and optical properties of Si-nc embedded in SiOx films

J. Alberto Luna López, J. Carrillo López, D. E. Vazquez Valerdi, G. Garcia Salgado, A. Ponce Pedraza, T. Diaz Becerril, F. J. Flores Gracia Nanoscale Research Letters 2012, 7:604 (30 October 2012)

Abstract | Provisional PDF | PubMed

10.

Research   Open Access

Mathematical modeling and stability analysis of macrophage activation in left ventricular remodeling post-myocardial infarction

Yunji Wang, Tianyi Yang, Yonggang Ma, Ganesh V Halade, Jianqiu Zhang, Merry L Lindsey, Yu-Fang Jin BMC Genomics 2012, 13(Suppl 6):S21 (26 October 2012)

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

11.

Research   Open Access

A nonparametric Bayesian approach for clustering bisulfate-based DNA methylation profiles

Lin Zhang, Jia Meng, Hui Liu, Yufei Huang BMC Genomics 2012, 13(Suppl 6):S20 (26 October 2012)

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

12.

Research   Open Access

A Steiner tree-based method for biomarker discovery and classification in breast cancer metastasis

Md Jamiul Jahid, Jianhua Ruan BMC Genomics 2012, 13(Suppl 6):S8 (26 October 2012)

Abstract | Full text | PDF | PubMed

13.

Introduction   Open Access

Selected articles from the IEEE International Workshop on Genomic Signal Processing and Statistics (GENSIPS'2011)

Ranadip Pal, Yufei Huang, Yidong Chen BMC Genomics 2012, 13(Suppl 6):S1 (26 October 2012)

Full text | PDF | PubMed | Cited on BioMed Central

14.

Poster presentation   Open Access

Modeling the effects of molecular crowding on cerebellar long term depression

Horace Deans, Fidel Santamaria BMC Neuroscience 2012, 13(Suppl 1):P47 (16 July 2012)

Full text | PDF

15.

Poster presentation   Open Access

Variability of inter-syllable gaps challenges the branched-chain model of sequence production in Bengalese finches

Kristofer E Bouchard, Anand S Kulkarni, Michael S Brainard, Todd W Troyer BMC Neuroscience 2012, 13(Suppl 1):P19 (16 July 2012)

Full text | PDF

16.

Poster presentation   Open Access

Spike threshold dynamics reshape the phase response curve and increase the degree of synchronization among neurons coupled by excitatory synapses

Michael A Farries, Charles J Wilson BMC Neuroscience 2012, 13(Suppl 1):P12 (16 July 2012)

Full text | PDF

17.

Research   Open Access

Transcriptome analysis of the ependymal barrier during murine neurocysticercosis

Pramod Mishra, Judy M Teale Journal of Neuroinflammation 2012, 9:141 (25 June 2012)

Abstract | Full text | PDF | PubMed

18.

Proceedings   Open Access

Genome plasticity and systems evolution in Streptomyces

Zhan Zhou, Jianying Gu, Yong-Quan Li, Yufeng Wang BMC Bioinformatics 2012, 13(Suppl 10):S8 (25 June 2012)

Abstract | Full text | PDF | PubMed

19.

Research article   Open Access

Protease-associated cellular networks in malaria parasite Plasmodium falciparum

Timothy G Lilburn, Hong Cai, Zhan Zhou, Yufeng Wang BMC Genomics 2011, 12(Suppl 5):S9 (23 December 2011)

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

20.

Research article   Open Access Highly Accessed

Bayesian parameter estimation for nonlinear modelling of biological pathways

Omid Ghasemi, Merry L Lindsey, Tianyi Yang, Nguyen Nguyen, Yufei Huang, Yu-Fang Jin BMC Systems Biology 2011, 5(Suppl 3):S9 (23 December 2011)

Abstract | Full text | PDF

21.

Research   Open Access

Loss of the bloom syndrome helicase increases DNA ligase 4-independent genome rearrangements and tumorigenesis in aging Drosophila

Ana Garcia, Robert N Salomon, Alice Witsell, Justine Liepkalns, R Brent Calder, Moonsook Lee, Martha Lundell, Jan Vijg, Mitch McVey Genome Biology 2011, 12:R121 (19 December 2011)

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

Drosophila blm mutants show an increase in genome rearrangements which, surprisingly, are independent of DNA ligase 4

22.

Proceedings   Open Access

Systematic identification of functional modules and cis-regulatory elements in Arabidopsis thaliana

Jianhua Ruan, Joseph Perez, Brian Hernandez, Chengwei Lei, Garry Sunter, Valerie M Sponsel BMC Bioinformatics 2011, 12(Suppl 12):S2 (24 November 2011)

Abstract | Full text | PDF | PubMed

23.

Methodology article   Open Access

SCFIA: a statistical corresponding feature identification algorithm for LC/MS

Jian Cui, Xuepo Ma, Long Chen, Jianqiu Zhang BMC Bioinformatics 2011, 12:439 (11 November 2011)

Abstract | Full text | PDF | PubMed

24.

Research article   Open Access Highly Accessed

Biofilm and planktonic pneumococci demonstrate disparate immunoreactivity to human convalescent sera

Carlos J Sanchez, Brady J Hurtgen, Anel Lizcano, Pooja Shivshankar, Garry T Cole, Carlos J Orihuela BMC Microbiology 2011, 11:245 (2 November 2011)

Abstract | Full text | PDF | PubMed

25.

Research   Open Access Highly Accessed

Comparative genomics of the pathogenic ciliate Ichthyophthirius multifiliis, its free-living relatives and a host species provide insights into adoption of a parasitic lifestyle and prospects for disease control

Robert S Coyne, Linda Hannick, Dhanasekaran Shanmugam, Jessica B Hostetler, Daniel Brami, Vinita S Joardar, Justin Johnson, Diana Radune, Irtisha Singh, Jonathan H Badger, Ujjwal Kumar, Milton Saier, Yufeng Wang, Hong Cai, Jianying Gu, Michael W Mather, Akhil B Vaidya, David E Wilkes, Vidyalakshmi Rajagopalan, David J Asai, Chad G Pearson, Robert C Findly, Harry W Dickerson, Martin Wu, Cindy Martens, Yves Van de Peer, David S Roos, Donna M Cassidy-Hanley, Theodore G Clark Genome Biology 2011, 12:R100 (17 October 2011)

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

The genome of the pathogenic ciliate Ichthyophthirius multifiliis, which causes white spot disease in fish, is presented

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