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Mission

The Tufts Computational Biology Initiative’s mission is to raise awareness, enhance infrastructure, and promote computational biology in a collaborative environment among a diverse group of biologists, clinicians, high throughput technologists, information technology professionals, statisticians, bioinformaticists, and computational biologists at Tufts Medical Center and all Tufts University campuses.

Membership

All of the CBI resources will be available to you whether you are an official CBI member or not. Becoming a member just means that you want to more actively participate, and help the CBI reduce the activation barriers that would prevent Tufts researchers from using the power of genomics and bioinformatics in their research. Minimally this means that you’re willing to spend a bit of time helping other local researchers learn about techniques you have expertise in, or that you’re willing to compare notes with others who are trying to learn the same new techniques you are. If you also want to help us choose speakers, design symposia, develop new classes, manage genomics resources or contribute to the web site, that’s great, but by no means required. See below to learn about current CBI members and their research, or click on the Contact Us tab if you’d like to become a member.

Partners

Our strength and success is based on the partnerships that we continue to establish across Tufts and TMC. Some of our partners are:

  • Center for Neuroscience Research, Tufts University
  • Molecular Cardiology Research Institute, TMC
  • Mother and Infant Research Institute, TMC
  • Translational Immunology Science Center, TMC
  • Research & Geospatial Technology Services (RGTS)
  • Tufts Technology Services (TTS) at Tufts University
  • Office of Information Technology, TUSM
  • Tufts Libraries
  • Tufts Clinical and Translational Sciences Institute (CTSI)

Projects

Along with our partners we are involved in a number of projects developing “genomic education” programs, computational infrastructure and protocols and procedures for high throughput genomics studies.



 

Profiles of CBI members and their research

 
Andrew Camilli, PhD, Professor, Tufts University School of Medicine, Department of Molecular Biology & Microbiology and Howard Hughes Medical Institute, Experience in: Next generation sequencing; genome sequencing and resequencing, Tn-seq.

Brent Cochran, PhD, Professor of Developmental, Molecular & Chemical Biology, Tufts U. Medical School. Experience in: ChIP-seq from a small number of cells, pooled analysis of NGS data, boolean models of signaling pathways & literature text mining. Exploring: RNA-seq. More…

Trent Fowler, PhD, Postdoctoral Fellow in Dr. Ananda Roy’s laboratory, Dept. of Molecular & Chemical Biology, Tufts U. Medical School. Experience in: RNA-seq for differential expression, gene ontology/pathway analysis, ChIP-seq, using bedtools, bowtie and Biocondutor R programs. Exploring: miRNA-seq, HOMER analysis suite. More…

Linden Hu, MD, Professor of Medicine, Tufts University School of Medicine, Attending Physician & Vice-Chairman for Faculty Development, Dept. of Medicine, Tufts Medical Center, Boston, MA. Experienced in: Tn-seq. Exploring: whole genome sequencing of bacteria, RNA-seq.

Gordon Huggins, MD, Associate Professor of Medicine, Tufts University School of Medicine; Physician Investigator, Cardiology Division, Tufts Medical Center; Faculty Member, Genetics Program, Cell, Molecular and Developmental Biology Program, Sackler Graduate School of Biomedical Sciences, Tufts University. My laboratory seeks to apply genetic approaches to identify genes that contribute to cardiovascular disease, that can later become the focus of hypothesis-driven research using animal and cellular models. Experience in: genetic association studies, mutation and polymorphism detection and measurement, and gene expression studies using array and sequencing-based approaches.

Lakshmanan K. Iyer, PhD, Research Assistant Professor of Neuroscience, Neuroscience Department, Tufts University School of Medicine; Senior Manager, Genomics core, Center for Neuroscience Research; Assistant Professor, Molecular Cardiology Research Center, Molecular Cardiology Research Institute, Tufts Medical Center. Experience in: development and application of computational methodologies, tools and resources to address biological research problems, in collaboration with basic scientists and clinician scientists on a wide range of biological research projects.

Rob Jackson, PhD, Professor of Neuroscience, Tufts University School of Medicine, Boston, MA. Experience in: Translational profiling techniques (translating ribosome affinity purification, TRAP) and RNA-seq to perform cell type-specific gene expression profiling studies.

Iris Jaffe, MD, PhD, Associate Professor, Molecular Cardiology Research Institute, Tufts Medical Center, Boston MA. Experience in: Basic analysis of expression microarray data.

Carol Kumamoto, PhD, Professor of Molecular Biology and Microbiology, Tufts University School of Medicine, Boston, MA

David Lapointe PhD (link opens e-mail message), Sr. Bioinformatics Specialist, Research and Geospatial Technology Services, Tufts Technology Services (TTS), Tufts University. Phone: 617-627-5319, Fax: 617-627-3667. Can provide assistance in adapting & using the Unix cluster & other UIT resources for your research.

Jose Ordovas, PhD, Senior Scientist and Director, Nutrition and Genomics Laboratory & Chair, Functional Genomics Core Scientific Advisory Committee, JM-USDA Human Nutrition Research Center on Aging at Tufts University Boston, MA

Larry Parnell, PhD, Computational Biologist, Nutritional Genomics Laboratory. JM-USDA Human Nutrition Research Center on Aging at Tufts University Boston, MA

Sasha Poltorak, PhD, Associate Professor of Integrative Physiology & Pathobiology, Tufts University School of Medicine, Boston, MA. Experience in: [Mouse genetics, RNA-seq, more details soon].

Kris Richardson, PhD, Scientist III, Nutritional Genomics Laboratory. JM-USDA Human Nutrition Research Center on Aging at Tufts University Boston, MA

Ananda Roy, PhD, Associate Professor of Developmental, Molecular & Chemical Biology, Tufts U. Medical School, Boston MA.

Gavin R Schnitzler PhD, Investigator, Molecular Cardiology Research Institute, Tufts Medical Center; Assistant Professor of Medicine, Tufts University School of Medicine; Faculty Member in the Genetics and Biochemistry Programs, Sackler Graduate School of Biomedical Sciences, Tufts University.      Experience in: Microarray, RNA-seq, ChIP-seq analysis using programs on the cluster, in R & on the web, transcription factor consensus sequence enrichment analysis, some PERL coding.

Samuel Stampfer, MD-PhD Student (M’ 2015), Heldwein Lab, Biochemistry Program, Tufts U. School of Medicine. Experience in: Protein sequence analysis to detect functional regions using evolutionary conservation. Contact Sam…

Albert Tai, PhD Manager, Tufts University Genomics Core, Tufts University School of Medicine, 136 Harrison Avenue, Stearns 815D, Boston, MA

Philip Tsichlis, MD, Executive Director, Molecular Oncology Research Institute; Professor and Jane F. Desforges Chair in Hematology and Oncology, Tufts University School of Medicine.

Giovanni Widmer, PhD, Tufts Cummings School of Veterinary Medicine, Department of Infectious Disease & Global Health Experience in: 16S amplicon sequencing, 18S amplicon sequencing; analysis of microbial populations (gut microbiome, water microbiome) based on amplicon sequencing. Exploring: data analysis in R.

Lionel Zupan PhD, Director, Research and Geospatial Technology Services, Tufts Technology Services, Tufts University.

Junior CBI members

Sean Harrington, Undergraduate in Tufts Computer Science Department and Biotechnology Program. Sean writes code and, working with Larry Parnell, has parsed metabolite, gene and disease relationships from the human metabolome database. Those data are available under the How-To and Courses section.

 

 
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