227 East 30th Street
New York, NY 10016
Bioinformatics addresses the use of computers for the acquisition, management, and analysis of biological information. The explosion of interest in bioinformatics in the past few years has been driven by the tremendous growth of DNA sequencing technology. Investigators use sequencing techniques for a variety of genomics applications but require bioinformatics skills to support this work.
I act as bioinformatics consultant for NYU Medical Center, collaborating as needed on a wide range of research projects. The extent of these collaborations ranges from a few consultation meetings to co-investigator on NIH grants. I am currently working on projects that include metagenomics (Human Microbiome Project), the genetic variation in hospital isolates of Staph bacteria, de novo genome sequencing of non-model organisms, and analysis of RNA-seq data from a variety of clinical and basic science research projects. Other projects that I have recently worked on include the draft genome of the coffee borer beetle, discovery of human papiloma virus in human tissue DNA samples, and an evolutionary analysis of the mammalian glucosidase gene family.
REST is a hypoxia-responsive transcriptional repressor
Cavadas, Miguel A S; Mesnieres, Marion; Crifo, Bianca; Manresa, Mario C; Selfridge, Andrew C; Keogh, Ciara E; Fabian, Zsolt; Scholz, Carsten C; Nolan, Karen A; Rocha, Liliane M A; Tambuwala, Murtaza M; Brown, Stuart; Wdowicz, Anita; Corbett, Danielle; Murphy, Keith J; Godson, Catherine; Cummins, Eoin P; Taylor, Cormac T; Cheong, Alex. REST is a hypoxia-responsive transcriptional repressor. Scientific reports. 2016 Aug 17;6:31355-31355 (2218892)
Lhx6 and Lhx8 promote palate development through negative regulation of a cell cycle inhibitor gene, p57Kip2
Cesario, Jeffry M; Landin Malt, Andre; Deacon, Lindsay J; Sandberg, Magnus; Vogt, Daniel; Tang, Zuojian; Zhao, Yangu; Brown, Stuart; Rubenstein, John L; Jeong, Juhee. Lhx6 and Lhx8 promote palate development through negative regulation of a cell cycle inhibitor gene, p57Kip2. Human molecular genetics. 2015 Sep 01;24(17):5024-5039 (1625852)
Draft genome of the most devastating insect pest of coffee worldwide: the coffee berry borer, Hypothenemus hampei
Vega, Fernando E; Brown, Stuart M; Chen, Hao; Shen, Eric; Nair, Mridul B; Ceja-Navarro, Javier A; Brodie, Eoin L; Infante, Francisco; Dowd, Patrick F; Pain, Arnab. Draft genome of the most devastating insect pest of coffee worldwide: the coffee berry borer, Hypothenemus hampei. Scientific reports. 2015 Jul 31;5:12525-12525 (1698642)
Cloud-based next-generation sequencing infomatics
Krampis, Konstantinos; Efstathiadis, Efstratios; Brown, Stuart M. Cloud-based next-generation sequencing infomatics IN: Next-generation DNA sequencing informatics. Cold Spring Harbor, New York : Cold Spring Harbor Laboratory Press, 2015 2nd edition. p.361-370 (1681522)
RNA sequencing with next-generation sequencing
Brown, Stuart; Goecks, Jeremy. RNA sequencing with next-generation sequencing IN: Next-generation DNA sequencing informatics. Cold Spring Harbor, New York : Cold Spring Harbor Laboratory Press, 2015 2nd edition. p.273-308 (1671652)