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Bioinformatics and Computational Biology Program

Ph.D. and MD/Ph.D. students in the Bioinformatics and Computational Biology Program (BCB) work with leading researchers in the field to develop and apply computational and mathematical models to solve biological problems, with an emphasis on large-scale genomic, proteomic, cellular and epidemiological data. We welcome students with undergraduate training in biological sciences, physical sciences, mathematics and computer sciences. Our Advanced Topic courses, taught by professors in the Program in Bioinformatics and Integrative Biology (BIB), complement BCB’s overriding goal: to educate talented and highly motivated individuals for research in the post-genomic era. Graduates of our program are in high demand in both academia and in the biotech industry. 

BCB research topics  include functional and evolutionary biology; machine learning of gene regulatory networks; structure and organization of genomes and comparative genomics; population genetics and molecular evolution; RNA biology and regulation; modeling and visualization of large-scale biological systems; genetics of human diseases and pet dog behavior; cell signaling of autoimmune diseases. Students receive rigorous training in modern bioinformatics and computational biology that integrates guided research, coursework, and participation in seminar programs. The program aims to train a new generation of scientists with the multidisciplinary skill set for careers in cutting-edge, highly quantitative biomedical research.

OUR STUDENTS

Gregory Andrews, PhD candidate

Gregory Andrews studies transcription factor binding with his mentor, Zhiping Weng, PhD, Li Weibo Chair in Biomedical Research, professor of biochemistry & molecular biotechnology and director of the Program in Bioinformatics & Integrative Biology, using deep learning, a state-of-the-art machine learning technology.

Learn more about Gregory Andrews

Kaili Fan, MSc, PhD candidate

Kaili Fan selected UMass Chan’s Program in Bioinformatics and Computational Biology specifically for the opportunity to be mentored by Zhiping Weng, PhD, Li Weibo Chair in Biomedical Research, professor of biochemistry & molecular biotechnology and director of the Program in Bioinformatics & Integrative Biology.

Learn more about Kaili Fan

Kathleen Morrill, PhD candidate

Kathleen Morrill is doing her dissertation on the behavioral genomics of domestic dogs. Her mentor is Elinor Karlsson, PhD, associate professor of molecular medicine. Rotating through different labs in her first year at UMass Chan allowed Morrill to find a new enthusiasm for computational biology.

Learn more about Kathleen Morrill

REQUIREMENTS FOR SPECIALIZATION

All Basic Biomedical Science students must complete the core curriculum as well as electives required by their program. Students in the Bioinformatics and Computational Biology program must take 3 graded elective courses of 2-4 credits each, two of which must be in Bioinformatics. Students choose elective courses from among those offered by the program, or relevant courses offered by other GSBS programs. The plan of coursework is designed to be flexible in order to accommodate each student’s needs and areas of interest.

View PhD Program Schedule  |  View Courses

OUR LEADERSHIP & FACULY

PROGRAM DIRECTOR

Zhiping Weng, PhD
Professor and Director, Program in Bioinformatics and Integrative Biology
Li Weibo Chair in Biomedical Research
email Dr. Weng

FACULTY

View the affiliated faculty listing for the Bioinformatics & Computational Biology Program or learn more about a few of our prominent labs: Weng Lab, Colubri Lab, Garber Lab, Karlsson Lab, Lim Lab, Moore Lab, and Abdennur Lab

PUBLICATIONS

A number of students in the BCB program have been involved in the research and subsequent publications of the ENCODE Consortium. ENCODE is a public research consortium aimed at identifying all functional elements in the human and mouse genomes. Articles about this research have appeared in leading journals such as:

  • An Integrated Encyclopedia of DNA Elements in the Human Genome. Nature. 2012 Sep 6; 489(7414):57-74. doi: 10.1038/nature11247.  BCB students including Jiali Zhuang in the Weng Lab, Bryan Lajoie in the Dekker Lab and faculty members Zhiping Weng and Job Dekker co-authored this article.
  • Expanded Encyclopedias of DNA Elements in the Human and Mouse Genomes. Nature. 2020 July 29. BCB students Jill Moore, Michael Purcaro, and Henry Pratt from the Weng lab were co-first authors as they made major contributions to data analysis, and Prof. Zhiping Weng was a co-corresponding author, leading the data analysis effort for this paper.

BCB students have also been involved in the research of the PsychENCODE Consortium. The PsychENCODE Consortium aims to produce a public resource of multidimensional genomic data using tissue- and cell type-specific samples from phenotypically well-characterized, high-quality, healthy and disease-affected human post-mortem brains, and to functionally characterize disease-associated regulatory elements and variants in model systems. Articles describing PsychENCODE research include:

  • Neuron-specific signatures in the chromosomal connectome associated with schizophrenia risk.
    Science. 2018 Dec 14; 362(6420):eaat4311. doi: 10.1126/science.aat4311.  PMID: 30545851 PMCID: PMC6408958. BCB student Tyler Borrman was a co-first author and his mentor Prof. Zhiping Weng was a co-corresponding author of this article.
  • Comprehensive Functional Genomic Resource and Integrative Model for the Human Brain. Science. 2018 Dec 14; 362(6420):eaat8464. doi: 10.1126/science.aat8464. BCB student Jill Moore and her mentor Prof. Zhiping Weng co-authored this article.

BCB students co-authored a number of papers in leading journals:

  • Henry Pratt, Weng Lab
    Nucleic Acid Research. 2022 Jan 7;50(D1):D141-D149. doi: 10.1093/nar/gkab1039. Factorbook: an updated catalog of transcription factor motifs and candidate regulatory motif sites.
  • Kathleen Morrill, Karlsson Lab
    Science. 2022 Apr 29;376(6592):eabk0639. doi: 10.1126/science.abk0639. Epub 2022 Apr 29. Ancestry-inclusive dog genomics challenges popular breed stereotypes.
  • Kaili Fan, Weng Lab
    Nucleic Acids Research. 2021 Jun 4;49(10):5705-5725. doi: 10.1093/nar/gkab345. Genetic and epigenetic features of promoters with ubiquitous chromatin accessibility support ubiquitous transcription of cell-essential genes.
  • Yuming Cao, Garber Lab
    Cell. 2020 May 28;181(5):1016-1035.e19. doi: 10.1016/j.cell.2020.04.035. Epub 2020 Apr 27. SARS-CoV-2 Receptor ACE2 Is an Interferon-Stimulated Gene in Human Airway Epithelial Cells and Is Detected in Specific Cell Subsets Across Tissues.
  • Kyle Gellatly, Garber Lab
    Nature Immunology. 2020 Mar;21(3):274-286. doi: 10.1038/s41590-020-0593-9. Epub 2020 Feb 17. HIV-1-induced Cytokines Deplete Homeostatic Innate Lymphoid Cells and Expand TCF7-dependent Memory NK Cells.
  • Jill Moore, Weng Lab
    Genome Biology. 2020 Jan 22;21(1):17. doi: 10.1186/s13059-019-1924-8. A Curated Benchmark of Enhancer-Gene Interactions for Evaluating Enhancer-Target Gene Prediction Methods.
  • Tyler Borrman, Weng Lab
    Proteins. 2019 Dec;87(12):1200-1221. doi: 10.1002/prot.25838. Epub 2019 Oct 25. Blind Prediction of Homo- And Hetero-Protein Complexes: The CASP13-CAPRI Experiment.
  • Serkin Sayin, Mitchell Lab
    PLoS Biology. 2019 Jun 26;17(6):e3000348. doi: 10.1371/journal.pbio.3000348. eCollection 2019 Jun. Harnessing Robotic Automation and Web-Based Technologies to Modernize Scientific Outreach
  • Xue Li, Karlsson Lab
    Genes. 2019 Jun 7;10(6):433. doi: 10.3390/genes10060433. BarkBase: Epigenomic Annotation of Canine Genomes.
  • Jiali Zhuang, Weng Lab
    Nucleic Acids Research. 2015 Sep 30;43(17):8146-56. doi: 10.1093/nar/gkv831. Epub 2015 Aug 17. Local Sequence Assembly Reveals a High-Resolution Profile of Somatic Structural Variations in 97 Cancer Genomes.

POST-DEGREE CAREERS

The BCB program has prepared students for careers at leading companies and academic institutions in the field of Bioinformatics.

KAILI FAN

Weng Lab, October 2022

POSTDOCTORAL ASSOCIATE, JASON BUENROSTRO LAB
Harvard University, Boston, MA

KYLE GELLATLY

Garber Lab, November 2021

MACHINE LEARNING ENGINEER
FoxyAI, Huntington, NY

Dissertation: Network analysis of human vitiligo scRNA-seq data reveals complex mechanisms of immune activation

TYLER BORRMAN

Weng Lab, November 2020

SCIENTIST
PACT Pharma, San Francisco, CA

Dissertation: Measuring Stability of 3D Chromatin Conformations and Identifying Neuron Specific Chromatin Loops Associated with Schizophrenia Risk

YASIN KAYMAZ

Bailey Lab, July 2017

BIOINFORMATICS SCIENTIST
Harvard University, Cambridge, MA

Dissertation: Genomic and Transcriptomic Investigation of Endemic Burkitt Lymphoma and Epstein Barr Virus.

BRYAN LAJOIE

Dekker Lab, February 2016

INFORMATICS SOLUTION ARCHITECT
Illumina, San Diego, CA

Dissertation: Computational Approaches for the Analysis of Chromosome Conformation Capture Data and Their Application to Study Long-Range Gene Regulation.

JILL MOORE

Weng Lab, October 2017

ASSISTANT PROFESSOR
UMass Chan Medical School, Worcester, MA

Dissertation: Defining a Registry of Candidate Regulatory Elements to Interpret Disease-Associated Genetic Variation.

MERCEDEH JAVANBAKHT MOVASSAGH

Bailey Lab, April 2019

POSTDOCTORAL RESEARCH FELLOW
Harvard T.H. Chan School of Public Health in Biostatistics
Cambridge, MA

Dissertation: Comprehensive Computational Assessment And Evaluation of Epstein Barr virus (EBV) Variations, miRNAs, And EBERs in eBL, AML And Across Cancers.

WEI WANG

Weng Lab, October 2015

SENIOR BIOINFORMATICS SCIENTIST
Voyager Therapeutics, Cambridge, MA

Dissertation: Unveiling Molecular Mechanisms of piRNA Pathway from Small Signals in Big Data.

JIALI ZHUANG

Weng Lab, September 2015

BIOINFORMATICS SCIENTIST
Molecular Stethoscope, San Diego, CA

Dissertation: Structural Variation Discovery and Genotyping from Whole Genome Sequencing: Methodology and Applications.