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Monica Nicolau is a project scientist at the University of California, Davis studying computational systems biology, topological data analysis, and the mathematical analysis of complex networks from omics, biomedical, and single cell data. She has over 30 years of experience in research mathematics, computational biology, and applied statistics. Her software tools DSGA and PAD are used for disease-specific genomic analysis and identifying disease progression changes from microarray data.
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Jerry S. Chen, a PhD graduate, recently published an article in the PLOS Computational Biology Journal along with SDSU faculty Joseph Mahaffy and Robert Zeller. The article, titled "An Expanded Notch-Delta Model Exhibiting Long-Range Patterning and Incorporating MicroRNA Regulation," was featured on the journal cover. The article contributed to an expanded mathematical model that explains irregular patterning in marine invertebrates based on experimental data and building upon classical Notch-Delta models. The SDSU Computational Science program has graduated 11 students from its quantitative biology PhD and master's programs, with another 6 currently enrolled.
The Clinical Genome Conference 2014
This year's 3rd Annual TCGC: The Clinical Genome Conference, held June 10-12, 2014 in San Francisco, is a three-day event that weaves together the science of sequencing and the business of implementing genomics in the clinic. It uniquely illustrates the mutual influence of those areas and the need to therefore consider the needs, challenges and opportunities of both - from next-generation sequencing and variant interpretation to insurance reimbursement and electronic health records - throughout the entire research process.Learn more at http://www.clinicalgenomeconference.com
cv1
Benjamin E. Deonovic is a Ph.D. candidate in Biostatistics at the University of Iowa, expected to graduate in May 2017. His research interests include Bayesian modeling, MCMC, and statistical methods applied to genomics and bioinformatics. He has published papers on haplotype phasing and allele-specific expression using hybrid sequencing data, and has presented his research at several conferences. Deonovic has worked as a research assistant at the University of Iowa on projects involving genetic association studies, pathway analysis, and joint modeling of sequencing data.
Curriculum vita
Margaret Colón is a PhD student at Michigan State University studying comparative medicine and integrative biology. She received her bachelor's degree in applied microbiology from Universidad del Este. Her research focuses on the effects of postnatal mercury exposure on nerve membrane proteins. She has worked as a graduate assistant studying this topic since 2010 under Dr. William Atchison. She has presented her research at several conferences and received multiple awards and fellowships.
MseqDR consortium: a grass-roots effort to establish a global resource aimed ...
MseqDR consortium: a grass-roots effort to establish a global resource aimed ...Human Variome Project
The success of whole exome sequencing (WES) for highly heterogeneous disorders, such as mitochondrial disease, is limited by substantial technical and bioinformatics challenges to correctly identify and prioritize the extensive number of sequence variants present in each patient. The likelihood of success can be greatly improved if a large cohort of patient data is assembled in which sequence variants can be systematically analysed, annotated, and interpreted relative to known phenotype. This effort has engaged and united more than 100 international mitochondrial clinicians, researchers, and bioinformaticians in the Mitochondrial Disease Sequence Data Resource (MSeqDR) consortium that formed in June 2012 to identify and prioritize the specific WES data analysis needs of the global mitochondrial disease community. Through regular web-based meetings, we have familiarized ourselves with existing strengths and gaps facing integration of MSeqDR with public resources, as well as the major practical, technical, and ethical challenges that must be overcome to create a sustainable data resource. We have now moved forward toward our common goal by establishing a central data resource (http://mseqdr.org/) that has both public access and secure web-based features that allow the coherent compilation, organization, annotation, and analysis of WES and mtDNA genome data sets generated in both clinical- and research-based settings of suspected mitochondrial disease patients. The most important aims of the MSeqDR consortium are summarized in the MSeqDR portal within the Consortium overview sections. Consortium participants are organized in 3 working groups that include (1) Technology and Bioinformatics; (2) Phenotyping, databasing, IRB concerns and access; and (3) Mitochondrial DNA specific concerns. The online MSeqDR resource is organized into discrete sections to facilitate data deposition and common reannotation, data visualization, data set mining, and access management. With the support of the United Mitochondrial Disease Foundation (UMDF) and the NINDS/NICHD U54 supported North American Mitochondrial Disease Consortium (NAMDC), the MSeqDR prototype has been built. Current major components include common data upload and reannotation using a novel HBCR based annotation tool that has also been made publicly available through the website, MSeqDR GBrowse that allows ready visualization of all public and MSeqDR specific data including labspecific aggregate data visualization tracks, MSeqDR-LSDB instance of nearly 1250 mitochondrial disease and mitochodnrial localized genes that is based on the Locus Specific Database model, exome data set mining in individuals or families using the GEM.app tool, and Account & Access Management. Within MSeqDR GBrowse it is now possible to explore data derived from MitoMap, HmtDB, ClinVar, UCSC-NumtS, ENCODE, 1000 genomes, and many other resources that bioinformaticians recruited to the project are organizing.Corbitt_Thesis
This document provides a curriculum vitae and dissertation abstract for Paul Timothy Corbitt. Corbitt earned a PhD in applied physics from the University of Maryland, Baltimore County in 2014. His dissertation consisted of two projects using mathematical models. The first project used models from nuclear physics to analyze epidemiological data related to schizophrenia. The second project created a novel mathematical model to relate white matter lesion development to aging, diabetes, and hypertension using data from a Mexican-American population. The curriculum vitae details Corbitt's educational background and research experience, including publications and presentations.
AI in translational medicine webinar
Dr. Dennis Wang discusses possible ways to enable ML methods to be more powerful for discovery and to reduce ambiguity within translational medicine, allowing data-informed decision-making to deliver the next generation of diagnostics and therapeutics to patients quicker, at lowered costs, and at scale.
The talk by Dr. Dennis Wang was followed by a panel discussion with Mr. Albert Wang, M. Eng., Head, IT Business Partner, Translational Research & Technologies, Bristol-Myers Squibb.
BIOLCHI CV 2016 GSK
Alessia Biolchi is seeking a position as a scientist. She has over 15 years of experience in vaccine research and development working with pathogens in BSL3 laboratories. Her skills include immunoassays, clinical trial support, data management, and project management. She has a Biology Degree from the University of Bologna and professional training in communication, presentation, and project management skills.
Romain Banchereau - Resume
Romain Banchereau is a computational biologist and translational immunologist focused on analyzing immune cell populations and transcriptional profiles from human disease cohorts. He has expertise in genomics analysis of blood and immune cells from infectious and autoimmune disease patients. Through bioinformatics analysis, he identifies biomarkers for disease diagnosis, prognosis, and response to treatment. He currently works as a research associate applying these skills to study lupus, juvenile arthritis, and complications during pregnancy with SLE.
Oleg kogan resume aug 2015
Oleg Kogan has strong skills in mathematical modeling, analysis, and computational modeling. He has expertise in nonlinear dynamics, statistical physics, and other fields. His strength is reducing complex problems to simple analytical models. He has worked as a computational scientist developing reduced-order models and as a postdoctoral researcher studying disease dynamics, jammed systems, and nonequilibrium fluctuations. He has published several papers in these areas and presented his work at major physics conferences.
RESUME_RHOWTON_02FEB2017
Rozarina Md Yusof Howton has extensive education and experience in various areas of science including medical physics, bioengineering, data science, and teaching. She holds a Master's degree in Medical Physics and Bioengineering from University College London and has undertaken continuing education in machine learning, programming, and languages. Her experience includes work as a private tutor, data analyst, science teacher, finance intern, and postgraduate research using optical tomography for imaging the neonatal brain. She has published papers and presented research at conferences on this topic.
Resume
Jasmine Lucas is a recent graduate of Michigan State University with a B.Sc. in Biochemistry and Molecular Biology. As an undergraduate, she conducted research studying RNA interactions in trypanosomes and held several leadership roles in STEM organizations on campus. She has experience with various lab techniques and coordinating outreach programs to engage K-12 students in science.
Brandon Plante Resume
Brandon Plante has extensive experience in cell culture and data analysis from experimental results. He has a M.Sc. in Biomedical Sciences from Iowa State University where he examined the effectiveness of novel compounds to reduce microglial activation. Prior to his graduate studies, Plante gained research experience as an undergraduate student at Saint John's University synthesizing novel boronic acid compounds. He also has medical and emergency response experience from his roles as an EMT, medical assistant, and security officer. Plante is skilled in laboratory techniques including cell culture, fluorescence microscopy, and RT-qPCR as well as data analysis and communication skills.
08 Vannucci, Marina
Marina Vannucci is a professor of statistics and co-director of a biostatistics graduate program at Rice University. Her research interests include Bayesian modeling, variable selection, nonparametric functional estimation, and wavelet-based statistical models. She applies these methods to problems in bioinformatics, chemometrics, and engineering. She has advised many students and collaborates with researchers at hospitals and cancer centers.
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MseqDR consortium: a grass-roots effort to establish a global resource aimed ...
MseqDR consortium: a grass-roots effort to establish a global resource aimed ...
nicolau_BioSketch
- 1. Monica Nicolau, PhD Project Scientist Topological Molecular Biology Group Department of Molecular and Cell Biology University of California, Davis Research Interests: Computational systems biology, topological data analysis, geometric transformations of large data, bioinformatics and applied statistics with focus on mathematical analysis of complex networks originating as omic, biomedical, and single cell data. Appointments: 2015-present Project Scientist, Molecular and Cell Biology, University of California, Davis. 2013-2015 Research Associate, Microbiology Immunology/Baxter, Stanford Medicine. 2010-2015 Research Associate, Center for Cancer Systems Biology, Stanford Medicine. 2006-2013 Research Associate, Mathematics, Stanford University. 2004-2006 Research Associate, Surgery, Stanford School of Medicine. 2003-2004 Visiting Assis Prof. Research, Surgery, Stanford School of Medicine. 1999-2003 Visiting Scholar, Genetics, Stanford School of Medicine. 1998-2004 Assis Research Statistician, Statistics, University of California, Berkeley. 1986-1996 Assis Professor, Mathematics, University of Illinois, Urbana-Champaign. 1988-1989 Visiting Assis Professor, Mathematics, SUNY at Albany (on leave from Univ. of Illinois) 1986-1987 Lecturer, Mathematics, UC Berkeley. Partially supported by NSF mnicolau AT ucdavis DOT edu Research mathematician: computational systems biology; complex networks; big data BIOSKETCH In the News: After Surgery, Predicting a Speedy Recovery The New York Times Sept. 2014 Studying the shape of data using topology Princeton Institute for Advanced Studies Newsletter August 2013 Rising chances for research The Paly Voice May 2012 Turning numbers into shapes offers potential medical benefits Science News Prime Oct. 2011 Stanford scientists identify protein involved in fast spreading cancers Stanford Cancer Institute Research News June 2006 Nicolau specializes in solving knotty problems Illini News Nov. 1989 Software: DSGA Disease-Specific Genomic Analysis : R-Code package for extracting the disease-relevant component of microarray data. Publication: Nicolau et al - Bioinformatics 2007 PAD Progression Analysis of Disease : combined R-Code and Matlab package for identifying gradual progression changes in microarray data from disease. Publication: Nicolau et al - Proc Natl Acad Sci U S A. 2011 I bring a computational focus to the study of the complex data generated in systems biology. I am particularly interested in developing hands-on algorithms to simplify and elucidate the structure of the complex networks underlying data, with the goal to generate concrete results in a range of systems biology problems including immunology, cancer biology and DNA packing. My background, combines research in the mathematics of high dimensional spaces, applied statistics and genomics. Education: Early Education Graduated Bronx High School of Science BA in Mathematics Barnard College, Columbia University Magna Cum Laude; Kohn Undergraduate Mathematics prize; Senior Mathematics prize. Professional Education PhD in Mathematics Rutgers University PhD thesis award NSF/USNCM at International Congress of Mathematics ICM86 Postdoctoral Fellow in Mathematics UC Berkeley NIH/NHGRI Mentored Research Scientist Development Grant K01 Statistics: UC Berkeley & Genetics: Stanford Medicine.