Careers in Bioinformatics: From the Lab to the Clinic and Beyond

Speakers

Piraye Yurttas Beim, PhD

Celmatix, Inc.

Piraye Yurttas Beim is the Co-Founder and Chief Scientific Officer of Celmatix, Inc., an early stage, venture-backed, biotechnology company based in TriBeCa, New York City. Celmatix is developing the world¹s first non-invasive, genetics-based diagnostic for assessing female egg quality and female infertility. The FertilArray test will be a multi-parametric diagnostic, assaying genetic, phenotypic, and environmental determinants of infertility. This vital personalized information will allow women and their doctors to optimize family planning, fertility preservation, and infertility treatments. Piraye performed her postdoctoral work in the field of mammalian pre-implantation embryology at the Gurdon Institute of the University of Cambridge in the UK and her doctoral work on the molecular and genetic underpinnings of mammalian infertility at Cornell University, Weill Medical College/Sloan Kettering Institute in New York City.

Mgavi E. Brathwaite, MS

Polytechnic Institute of New York University

Mgavi Brathwaite has worked in bioinformatics and genomics for over a decade, and has developed an expertise in sequence analysis. After working at DNAStar, the Columbia University Genome Center, Regeneron, the IBM Watson Center for Computational Biology, and the National Institutes of Health-National Institute on Aging, he took a position at NYU-Polytechnic University, where he currently manages the Masters in Bioinformatics program. He also lectures on Perl with BioPerl, Next Generation Sequence Analysis, and Structural Bioinformatics.

Mgavi has a BS in Chemistry from Lincoln University, an MS in Plant Biotechnology from Tuskegee University, and a pending MS from Iowa State University in Bioinformatics and Computational Biology.

Tamer Chowdbury, MS

Merck & Co.

Tamer Chowdhury is an IT analyst supporting Merck's Clinical Development Platform. He provides end-to-end technical support for a suite of applications enabling patient safety surveillance, electronic data capture, and analysis and reporting of clinical trial data. Tamer has over 12 years of experience with Merck supporting clinical applications as a business analyst, project manager and support lead.

He also leads a Six Sigma initiative to align IT service management framework to business milestones and priorities. Tamer has extensive knowledge in Oracle query tuning, performance improvement, rapid application development and prototyping with Java, R based technologies.

Tamer received his Bachelors degree in Chemical Engineering from the University of Idaho and a Masters degree in Bioinformatics from NYU-Polytechnic Institute. He currently teaches a graduate course at NYU-Poly on microarray gene expression data analysis leveraging BioConductor . Tamer takes an active interest in developing work flow tools to automate statistical analysis, data mining and data visualization to aid translational medicine research.

Zeynep H. Gumus, PhD

Weill Cornell Medical College

Zeynep H. Gumus is a junior faculty member at the level of Instructor jointly appointed at the Institute for Computational Biomedicine and at the Department of Physiology and Biophysics of the Weill Medical College of Cornell University. Her laboratory activities are focused on bringing a mechanistic and functional understanding to biomolecular networks in cancer, cancer prevention and therapeutics, to help better design appropriate cancer preventive agents and anti-cancer drugs. Specifically, she focuses on extracting patterns from high-throughput computational genomics data (RNA-seq, ChIP-seq, whole-genome sequencing, exome-sequencing, microarray, proteomics) by utilizing advanced statistical, optimization and 3D immersive data visualization technologies, as well as network inference technologies to reverse engineer the drivers of perturbation in cancer networks. She received her B.S. degree from Bogazici University in Istanbul, Turkey and both M. A. and Ph.D. degrees from Princeton University. Prior to Cornell, she was a postdoctoral research fellow at University of Pennsylvania School of Medicine. She is the recipient of the Outstanding Young Person in Academic Leadership award from Junior Council International and Schowalter award from Princeton University. Dr. Gumus currently has internship opportunities for enthusiastic students with advanced programming skills in developing immersive data visualization technologies in 3D for cancer research.

Bud Mishra

NYU Courant Institute

Prof. Bud Mishra is a professor of computer science and mathematics at NYU's Courant Institute of Mathematical Sciences, professor of human genetics at Mt. Sinai School of Medicine, and a professor of cell biology at NYU School of Medicine. He founded the NYU/Courant Bioinformatics Group, a multi-disciplinary group working on research at the interface of computer science, applied mathematics, biology, biomedicine and bio/nano-technologies. Prof. Mishra has a degree in Physics from Utkal University, in Electronics and Communication Engineering from IIT, Kharagpur, and MS and PhD degrees in Computer Science from Carnegie-Mellon University. He has industrial experience in Computer Science (Tartan Laboratories, and ATTAP), Finance (Tudor Investment and PRF, LLC), Robotics and Bio- and Nanotechnologies (OpGen, and Bioarrays). He is editor of Molecular Cancer Therapeutics, AMRX (Applied Mathematics Research Exchange), Nanotechnology, Science and Applications, and Transactions on Systems Biology, and author of a textbook on algorithmic algebra and more than two hundred archived publications. He has advised and mentored more than 35 graduate students and post-docs in the areas of computer science, robotics and control engineering, applied mathematics, finance, biology and medicine. He is an inventor of Optical Mapping and Sequencing (SMASH), Array Mapping, Copy-Number Variation Mapping, Model Checker for circuit verification, Robot Grasping and Fixturing devices and algorithms, Reactive Robotics, and Nanotechnology for DNA profiling. He is a fellow of AAAS, IEEE and ACM and a NYSTAR Distinguished Professor (2001). He also holds adjunct professorship at Tata Institute of Fundamental Research in Mumbai, India. From 2001-04, he was a professor at the Watson School of Biological Sciences, Cold Spring Harbor Lab; currently he is a visiting scholar at the Center of Quantitative Biology at CSHL.

Mishra is well-known for his pioneering contributions in creating new disciplines within computer science, mathematics and technologies: In 1983, while a graduate student, Mishra created the first computer-aided-verification tool for hardware using model checking and temporal logic, and showed its utility by fining a timing bug in Seitz’s self-timed FIFO queue element circuit. In 1985, Prof. Mishra (with Robert Tarjan of Princeton) created a new graph-algorithmic paradigm based on Tutte’s theory of bridges and applied it to finding errors (“sneak paths”) in CMOS circuits. In 1987, Mishra (with Jack Schwartz) created first algorithms for grasp planning, which he then extended to deal with fixturing, work-holding and other related applications in manufacturing. He also initiated the field of “Reactive Robitics” (also related to RISC: Reduced Intricacy in Sensing and Control). In 1993, he wrote one of the first text books on “Algorithmic Algebra,” covering various algorithmic questions in symbolic computation. In 1994, he solved (with a constructive upper bound) a problem originally posed by Kronecker in 1890’s and extensively discussed by Hensel. In 1995, he (with David Schwartz and Thomas Anantharaman) created the first single-molecule technologies to accurately map genomes (“Optical Mapping”).

Usman W. Roshan, PhD

New Jersey Insitute of Technology

Usman Roshan is an Associate Professor in the Computer Science Department at the New Jersey Institute of Technology (NJIT). Prior to joining NJIT he was at The University of Texas at Austin where he completed his PhD in Computer Science. He also serves as Director of the Bioinformatics program at NJIT that offers both graduate and undergraduate degrees.
Roshan works in the field of bioinformatics and has published algorithms and software for key problems in this area such as sequence alignment, large-scale phylogeny reconstruction, and analysis of genome wide association studies. Currently he is developing new algorithms for sequence alignment and genome wide association studies using probabilistic and machine learning approaches.