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Bioinformatics

Research Papers

A temporal precedence based clustering method for gene expression microarray data
By Ritesh Krishna et al. BMC Bioinformatics, January 30, 2010, 11:68, doi:10.1186/1471-2105-11-68

Dissection of a complex transcriptional response using genome-wide transcriptional modelling
By Martino Barenco et al. BMC Bioinformatics, November 17, 2009, 5:327, doi:10.1038/msb.2009.84

Integrin Proteomes Reveal a New Guide for Cell Motility
By Erik H. J. Danen. Science Signaling, Sept. 22, 2009, Vol. 2, Issue 89, p. pe58, DOI: 10.1126/scisignal.289pe58

Bacterial genomic G + C composition-eliciting environmental adaptation
By Scott Manna and Yi-Ping Phoebe Chen. Genomics, Sept. 9, 2009, doi:10.1016/j.ygeno.2009.09.002

Uniqueness, intractability and exact algorithms: Reflections on level-K phylogenetic networks
By Leo van Iersel, et al. Journal of Bioinformatics and Computational Biology, Volume: 7, Issue: 4 (2009) pp. 597-623 DOI: 10.1142/S0219720009004308

The epitope regions of H1-subtype influenza A, with application to vaccine efficacy
By Michael W. Deem and Keyao Pan. Protein Engineering Design and Selection, 2009 22(9):543-546; doi:10.1093/protein/gzp027

RNA-binding proteins in human genetic disease
By Kiven E. Lukong, et al. Trends in Genetics, August 1, 2009, DOI: 10.1007/s10142-009-0115-1

A candidate for Lr19, an exotic gene conditioning leaf rust resistance in wheat
By Andrea Gennaro, et al. Functional and Integrative Genomics, August 2009, DOI: 10.1007/s10142-009-0115-1

Fast model-based estimation of ancestry in unrelated individuals
By David H. Alexander, et al. Genome Research, July 31, 2009, doi:10.1101/gr.094052.109

BSMAP: whole genome Bisulfite Sequence MAPping program
By Yuanxin Xi and Wei Li. BMC Bioinformatics, July 27, 2009, 10:232, doi:10.1186/1471-2105-10-232

The Gene Ontology - Providing a Functional Role in Proteomic Studies
By Emily C. Dimmer, et al. Proteomics, July 17, 2009, doi:10.1002/pmic.200800002

Integrating Sequencing Technologies in Personal Genomics: Optimal Low Cost Reconstruction of Structural Variants
By Jiang Du, et al. PLoS Computational Biology, July 10, 2009, 5(7): e1000432. doi:10.1371/journal.pcbi.1000432

Localization of Type 1 diabetes susceptibility in the ancestral haplotype 18.2 by high density SNP mapping
By Jose Luis Santiago, et al. Genomics, July 8, 2009, doi:10.1016/j.ygeno.2009.06.007

Genome-wide association study identifies three loci associated with melanoma risk
By D. Timothy Bishop, et al. Nature Genetics, July 5, 2009, doi:10.1038/ng.411

Genomic linkage map of the human blood fluke Schistosoma mansoni
By Charles D. Criscione, et al. Genome Biology, June 30, 2009, 10:R71 doi:10.1186/gb-2009-10-6-r71

Critical evaluation of the FANTOM3 non-coding RNA transcripts
By Karl J.V. Nordstr÷m, et al. Genomics, June 9, 2009, doi:10.1016/j.ygeno.2009.05.012

The Impact of Divergence Time on the Nature of Population Structure: An Example from Iceland
By Alkes L. Price, et al. PLoS Genetics, June 5, 2009, 5(6): e1000505. doi:10.1371/journal.pgen.1000505

Sequencing and de novo analysis of a coral larval transcriptome using 454 GSFlx
By Eli Meyer, et al. BMC Genomics, May 12, 2009, 10:219doi:10.1186/1471-2164-10-219

The Genome Sequence of Taurine Cattle: A Window to Ruminant Biology and Evolution
By Christine G. Elsik, et al. Science, April 24, 2009, Vol. 324. no. 5926, pp. 522-528. DOI: 10.1126/science.1169588

A whole-genome assembly of the domestic cow, Bos taurus
By Aleksey V. Zimin, et al. Genome Biology, April 24, 2009, 10:R42. doi:10.1186/gb-2009-10-4-r42

The homology recognition well as an innate property of DNA structure
By Alexei A. Kornyshev and Aaron Wynveen. Proceedings of the National Academy of Sciences, March 9, 2009, 106:4683-4688. doi:10.1073/pnas.0811208106

Sample entropy analysis of cervical neoplasia gene-expression signatures
By Shaleen K Botting, et al. BMC Bioinformatics, Feb. 20, 2009, 10:66. doi:10.1186/1471-2105-10-66

Instability of Plastid DNA in the Nuclear Genome
By Anna E. Sheppard and Jeremy N. Timmis. PLoS Genetics, Jan. 2, 2009, 5(1): e1000323. doi:10.1371/journal.pgen.1000323

2008

Differentiating Protein-Coding and Noncoding RNA: Challenges and Ambiguities
By Marcel E. Dinger, et al. PLoS Computational Biology, Nov. 28, 2008, 4(11): e1000176. doi:10.1371/journal.pcbi.1000176

Environmental Genomics Reveals a Single-Species Ecosystem Deep Within Earth
By Dylan Chivian, et al. Science, Vol. 322. no. 5899 (October 10, 2008), pp. 275 - 278 DOI: 10.1126/science.1155495

Insulin-Like Growth Factor-I Activates Gene Transcription Programs Strongly Associated With Poor Breast Cancer Prognosis
By Chad J. Creighton, et al. Journal of Clinical Oncology, Vol 26, No 25 (September 1), 2008: pp. 4078-4085 DOI: 10.1200/JCO.2007.13.4429

Genetic Determinants of Self Identity and Social Recognition in Bacteria
By Karine A. Gibbs, et al. Science, 11 July 2008: Vol. 321. no. 5886, pp. 256 - 259 DOI: 10.1126/science.1160033.

Phylogeny-Aware Gap Placement Prevents Errors in Sequence Alignment and Evolutionary Analysis
By Ari Löytynoja and Nick Goldman. Science, 20 June 2008: Vol. 320. no. 5883, pp. 1632 - 1635 DOI: 10.1126/science.1158395.

Discovering Sequence Motifs with Arbitrary Insertions and Deletions
By Martin C. Frith, et al. PLoS Computational Biology, PLoS Comput Biol 4(5): e1000071. doi:10.1371/journal.pcbi.1000071 (2008).

Genome sequencing and analysis of the biomass-degrading fungus Trichoderma reesei
By Diego Martinez, et al. Nature Biotechnology, Nature Biotechnology 26, 553 - 560 Published online: 4 May 2008 | doi:10.1038/nbt1403 (2008).

Exon level integration of proteomics and microarray data
By Danny Bitton, et al. BMC Bioinformatics, BMC Bioinformatics 2008, 9:118doi:10.1186/1471-2105-9-118 (2008).

Geographic Patterns of Genome Admixture in Latin American Mestizos
By Sijia Wang, et al. PLoS Genetics, PLoS Genet 4(3): e1000037. doi:10.1371/journal.pgen.1000037 (2008).

Global Analysis of Genetic, Epigenetic and Transcriptional Polymorphisms in Arabidopsis thaliana Using Whole Genome Tiling Arrays
By Xu Zhang, et al. PLoS Genetics, PLoS Genet 4(3): e1000032. doi:10.1371/journal.pgen.1000032 (2008).

Worldwide Human Relationships Inferred from Genome-Wide Patterns of Variation
By Jun Z. Li, et al. Science, Vol. 319. no. 5866, pp. 1100-1104, DOI: 10.1126/science.1153717) (2008).

Evolution of Complex Modular Biological Networks
By Arend Hintze and Christoph Adami. PLoS Computational Biology, PLoS Comput Biol 4(2): e23 doi:10.1371/journal.pcbi.0040023 (2008).

Genome resequencing and genetic variation
By Michael Stratton. Nature Biotechnology, doi:10.1038/nbt0108-65 (2008).

Identification of Host Proteins Required for HIV Infection Through a Functional Genomic Screen
By Abraham L. Brass et al. Science, 10.1126/science.1152725 (2008).

2007

Bioinformatics prediction of HIV coreceptor usage
By Thomas Lengauer et al. Nature Biotechnology, 25:1407-1410 (2007).

Genome-Wide Experimental Determination of Barriers to Horizontal Gene Transfer
By Rotem Sorek et al. Science, 318:1449-1452 (2007).

Genome Organization and Gene Expression Shape the Transposable Element Distribution in the Drosophila melanogaster Euchromatin
By Pierre Fontanillas et al. PLoS Genetics, 3(11): e210 doi:10.1371/journal.pgen.0030210 (2007).

A Bivariate Whole-Genome Linkage Scan Suggests Several Shared Genomic Regions for Obesity and Osteoporosis
By Zi-Hui Tang et al. Journal of Clinical Endocrinology & Metabolism, Vol. 92, No. 7 2751-2757.

Sea Anemone Genome Reveals Ancestral Eumetazoan Gene Repertoire and Genomic Organization
By Nicholas H. Putnam et al. Science, 317:86-94 (2007).

New method for reading DNA sheds light on how cells define themselves
By Mikkelsen et al. Nature via Science Daily, DOI:10.1038/nature06008 (2007).

A Breakthrough for Global Public Health
By Dave D. Chadee et al. Science, 316:1703-1704 (2007).

A New Approach for Using Genome Scans to Detect Recent Positive Selection in the Human Genome
By Tang K et al. PLoS Biology, 5(7): e171 doi:10.1371/journal.pbio.0050171 (2007).

Strain-resolved community proteomics reveals recombining genomes of acidophilic bacteria
By Ian Lo et al. Nature , 446:537-541 (2007).

Genome sequence of the lignocellulose-bioconverting and xylose-fermenting yeast Pichia stipitis
By Thomas W Jeffries et al. Nature Biotechnology, 25:319-326 (2007).

Population-based resequencing of ANGPTL4 uncovers variations that reduce triglycerides and increase HDL
By Stefano Romeo et al. Nature Genetics, 39:513-516 (2007).

The Calyptogena magnifica Chemoautotrophic Symbiont Genome
By I. L. G. Newton et al. Science, 315:998-1000 (2007).

Transition-Transversion Bias Is Not Universal: A Counter Example from Grasshopper Pseudogenes
By Irene Keller et al. PLoS Genetics, 3(2): e22 doi:10.1371/journal.pgen.0030022 (2007).