Bioinformatics

 

Mission

The mission of the Bioinformatics Core is to apply and develop cutting-edge computational and statistical methods that support ongoing research projects within Vitalant Research Institute (VRI) and external collaborators.  Current research focus includes metagenomic viral discovery, genomics of HIV pathogenesis and persistence, statistical methods on detection and evaluation of blood-borne infections.  The Bioinformatics Core also offers consultation on general computing, data visualization, statistical modeling and machine learning for collaborators. Xutao Deng, PhD, is the Head of the Bioinformatics Core.  Dr. Deng earned his BS degree from the University of Science & Technology of China, his MS & PhD degrees in information science from the College of Information Science & Technology at the University of Nebraska and completed his Post-doc training in bioinformatics at UCLA.  Dr. Deng has extensive experience in bioinformatics and biostatistics and has published more than 80 papers since 2005.

Director: Xutao Deng

Xutao Deng, Ph.D.

Vitalant Research Institute
360 Spear Street, Suite 200
San Francisco, CA 94105

Phone: (415) 749 - 6606 ext.331

Bioinformatics consultation support
We provide consultation on study design and sample size calculation for array or deep-sequencing-based genomics studies. We have in-house computational pipelines built for metagenomic viral discovery, RNASeq quantification, exome sequencing and whole genome sequencing for variants detection using GATK, Affymetrix & Illumina expression array and SNP chips, GWAS, digital PCR analysis, mass spectrometry and biomarker discovery. We also provide general statistical consultation, supervised and unsupervised machine learning, data visualization and graphing services.

Computing support
We are equipped with a state-of-the-art computing cluster hosted and maintained by the IT department of Vitalant, Arizona. The cluster currently contains 36 servers with a total of 700 cores and 2TB RAM. The cluster is capable of processing most of our deep-sequencing projects and is available to our investigators and collaborators. For additional processing power, we have access to Amazon cloud that is available on a pay-per-use basis.

Publications in NLM's PubMed

Selected Publications

Deng X, Geng H, Ali HH. Joint learning of gene functions--a Bayesian network model approach. J Bioinform Comput Biol. 2006 Apr;4(2):217-39. PubMed PMID: 16819781.

Deng X Geng H, Ali HH. Cross-platform analysis of cancer biomarkers: a Bayesian network approach to incorporating mass spectrometry and microarray data. Cancer Inform. 2007 Apr 29;3:183-202. PubMed PMID: 19455243; PubMed Central PMCID: PMC2675834.

Deng X, Xu J, Wang C. Improving the power for detecting overlapping genes from multiple DNA microarray-derived gene lists. BMC Bioinformatics. 2008 May 28;9 Suppl 6:S14. PubMed PMID: 18541049; PubMed Central PMCID: PMC2423437.

Deng X, Campagne F. Introduction to the development and validation of predictive biomarker models from high-throughput data sets. Methods Mol Biol. 2010;620:435-70. PubMed PMID: 20652515.

Figueroa ME, Lugthart S, Li Y, Erpelinck-Verschueren C, Deng X, et al. DNA methylation signatures identify biologically distinct subtypes in acute myeloid leukemia. Cancer Cell. 2010 Jan 19;17(1):13-27. PubMed PMID: 20060365; NIHMSID: NIHMS255838; PubMed Central PMCID: PMC3008568.

Shi L, Campbell G, Jones WD, Campagne F, Wen Z, Deng X, et al. The MicroArray Quality Control (MAQC)-II study of common practices for the development and validation of microarray-based predictive models. Nat Biotechnol. 2010 Aug;28(8):827-38. PubMed PMID: 20676074; NIHMSID: NIHMS235927; PubMed Central PMCID: PMC3315840.

Deng X. SeqGene: a comprehensive software solution for mining exome- and transcriptome- sequencing data. BMC Bioinformatics. 2011 Jun 29;12:267. PubMed PMID: 21714929; PubMed Central PMCID: PMC3148209.

Jackman RP, Deng X, Bolgiano D, Lebedeva M, Heitman JW, et al. Low-level HLA antibodies do not predict platelet transfusion failure in TRAP study participants. Blood. 2013 Apr 18;121(16):3261-6; quiz 3299. PubMed PMID: 23393051; PubMed Central PMCID: PMC3630837.

Li L, Deng X, Linsuwanon P, Bangsberg D, Bwana MB, et al. AIDS alters the commensal plasma virome. J Virol. 2013 Oct;87(19):10912-5. PubMed PMID: 23903845; PubMed Central PMCID: PMC3807392.

Deng X, Sabino EC, Cunha-Neto E, Ribeiro AL, Ianni B, et al. Genome wide association study (GWAS) of Chagas cardiomyopathy in Trypanosoma cruzi seropositive subjects. PLoS One. 2013 Nov 20;8(11):e79629. PubMed PMID: 24324551; PubMed Central PMCID: PMC3854669.

Danesh A, Inglis HC, Jackman RP, Wu S, Deng X, et al. Exosomes from red blood cell units bind to monocytes and induce proinflammatory cytokines, boosting T-cell responses in vitro. Blood. 2014 Jan 30;123(5):687-96. PubMed PMID: 24335232; PubMed Central PMCID: PMC3907755.

Ng TF, Chen LF, Zhou Y, Shapiro B, Stiller M, et al. Preservation of viral genomes in 700-y-old caribou feces from a subarctic ice patch. Proc Natl Acad Sci USA. 2014 Nov 25;111(47):16842-7. PubMed PMID: 25349412; PubMed Central PMCID: PMC4250163.

Abdel-Mohsen M, Wang C, Strain MC, Lada SM, Deng X, et al. Select host restriction factors are associated with HIV persistence during antiretroviral therapy. AIDS. 2015 Feb 20;29(4):411-20. PubMed PMID: 25602681; NIHMSID: NIHMS675382; PubMed Central PMCID: PMC4385712.

Deng X, Naccache SN, Ng T, Federman S, Li L, et al. An ensemble strategy that significantly improves de novo assembly of microbial genomes from metagenomic next-generation sequencing data. Nucleic Acids Res. 2015 Apr 20;43(7):e46. PubMed PMID: 25586223; PubMed Central PMCID: PMC4402509.

Ferreira LR, Ferreira FM, Nakaya HI, Deng X, Cândido DD, et al. Blood Gene Signatures of Chagas disease Cardiomyopathy with or without ventricular dysfunction. J Infect Dis. 2016 Dec 21;PubMed PMID: 28003350.

Xutao Deng, Ph.D.

Vitalant Research Institute
360 Spear Street, Suite 200
San Francisco, CA 94105

Phone: (415) 749 - 6606 ext.331

Bioinformatics consultation support
We provide consultation on study design and sample size calculation for array or deep-sequencing-based genomics studies. We have in-house computational pipelines built for metagenomic viral discovery, RNASeq quantification, exome sequencing and whole genome sequencing for variants detection using GATK, Affymetrix & Illumina expression array and SNP chips, GWAS, digital PCR analysis, mass spectrometry and biomarker discovery. We also provide general statistical consultation, supervised and unsupervised machine learning, data visualization and graphing services.

Computing support
We are equipped with a state-of-the-art computing cluster hosted and maintained by the IT department of Vitalant, Arizona. The cluster currently contains 36 servers with a total of 700 cores and 2TB RAM. The cluster is capable of processing most of our deep-sequencing projects and is available to our investigators and collaborators. For additional processing power, we have access to Amazon cloud that is available on a pay-per-use basis.

Publications in NLM's PubMed

Selected Publications

Deng X, Geng H, Ali HH. Joint learning of gene functions--a Bayesian network model approach. J Bioinform Comput Biol. 2006 Apr;4(2):217-39. PubMed PMID: 16819781.

Deng X Geng H, Ali HH. Cross-platform analysis of cancer biomarkers: a Bayesian network approach to incorporating mass spectrometry and microarray data. Cancer Inform. 2007 Apr 29;3:183-202. PubMed PMID: 19455243; PubMed Central PMCID: PMC2675834.

Deng X, Xu J, Wang C. Improving the power for detecting overlapping genes from multiple DNA microarray-derived gene lists. BMC Bioinformatics. 2008 May 28;9 Suppl 6:S14. PubMed PMID: 18541049; PubMed Central PMCID: PMC2423437.

Deng X, Campagne F. Introduction to the development and validation of predictive biomarker models from high-throughput data sets. Methods Mol Biol. 2010;620:435-70. PubMed PMID: 20652515.

Figueroa ME, Lugthart S, Li Y, Erpelinck-Verschueren C, Deng X, et al. DNA methylation signatures identify biologically distinct subtypes in acute myeloid leukemia. Cancer Cell. 2010 Jan 19;17(1):13-27. PubMed PMID: 20060365; NIHMSID: NIHMS255838; PubMed Central PMCID: PMC3008568.

Shi L, Campbell G, Jones WD, Campagne F, Wen Z, Deng X, et al. The MicroArray Quality Control (MAQC)-II study of common practices for the development and validation of microarray-based predictive models. Nat Biotechnol. 2010 Aug;28(8):827-38. PubMed PMID: 20676074; NIHMSID: NIHMS235927; PubMed Central PMCID: PMC3315840.

Deng X. SeqGene: a comprehensive software solution for mining exome- and transcriptome- sequencing data. BMC Bioinformatics. 2011 Jun 29;12:267. PubMed PMID: 21714929; PubMed Central PMCID: PMC3148209.

Jackman RP, Deng X, Bolgiano D, Lebedeva M, Heitman JW, et al. Low-level HLA antibodies do not predict platelet transfusion failure in TRAP study participants. Blood. 2013 Apr 18;121(16):3261-6; quiz 3299. PubMed PMID: 23393051; PubMed Central PMCID: PMC3630837.

Li L, Deng X, Linsuwanon P, Bangsberg D, Bwana MB, et al. AIDS alters the commensal plasma virome. J Virol. 2013 Oct;87(19):10912-5. PubMed PMID: 23903845; PubMed Central PMCID: PMC3807392.

Deng X, Sabino EC, Cunha-Neto E, Ribeiro AL, Ianni B, et al. Genome wide association study (GWAS) of Chagas cardiomyopathy in Trypanosoma cruzi seropositive subjects. PLoS One. 2013 Nov 20;8(11):e79629. PubMed PMID: 24324551; PubMed Central PMCID: PMC3854669.

Danesh A, Inglis HC, Jackman RP, Wu S, Deng X, et al. Exosomes from red blood cell units bind to monocytes and induce proinflammatory cytokines, boosting T-cell responses in vitro. Blood. 2014 Jan 30;123(5):687-96. PubMed PMID: 24335232; PubMed Central PMCID: PMC3907755.

Ng TF, Chen LF, Zhou Y, Shapiro B, Stiller M, et al. Preservation of viral genomes in 700-y-old caribou feces from a subarctic ice patch. Proc Natl Acad Sci USA. 2014 Nov 25;111(47):16842-7. PubMed PMID: 25349412; PubMed Central PMCID: PMC4250163.

Abdel-Mohsen M, Wang C, Strain MC, Lada SM, Deng X, et al. Select host restriction factors are associated with HIV persistence during antiretroviral therapy. AIDS. 2015 Feb 20;29(4):411-20. PubMed PMID: 25602681; NIHMSID: NIHMS675382; PubMed Central PMCID: PMC4385712.

Deng X, Naccache SN, Ng T, Federman S, Li L, et al. An ensemble strategy that significantly improves de novo assembly of microbial genomes from metagenomic next-generation sequencing data. Nucleic Acids Res. 2015 Apr 20;43(7):e46. PubMed PMID: 25586223; PubMed Central PMCID: PMC4402509.

Ferreira LR, Ferreira FM, Nakaya HI, Deng X, Cândido DD, et al. Blood Gene Signatures of Chagas disease Cardiomyopathy with or without ventricular dysfunction. J Infect Dis. 2016 Dec 21;PubMed PMID: 28003350.

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