David Gifford

About

David Gifford, PhD, is a Professor of Electrical Engineering and Computer Science, as well as a Professor of Biological Engineering at MIT. He received his BS from MIT in 1976 and his PhD from Stanford University in 1981. Since joining the MIT faculty in 1982, he has developed new machine learning techniques and algorithms to model transcriptional regulatory networks that control gene expression programs in living cells. His research group focuses on creating combined computational and experimental approaches to discover novel biology and human therapeutics, utilizing interpretable computational models trained and validated with experimental evidence. Gifford's work involves applying these models to problems in experiment design, developmental biology, gene regulation, immunology, genomics, and human therapeutics. His group evaluates models and uncovers new biology through multiplexed high-throughput experimental studies involving populations of cells and single cells. A key challenge addressed by his research is the incomplete knowledge of biological systems, leading to model uncertainty. His team actively develops uncertainty metrics for models to guide experiment design and improve model accuracy. His computational approaches incorporate large-scale linear and non-linear models, Bayesian methods, and deep learning. His current biological focus areas include motor neuron development, single-cell perturbation studies, chromatin accessibility regulation, the regulatory…

Research topics

• Computational biology
• Genetics
• Biology
• Computer Science
• Artificial Intelligence
• Evolutionary biology
• Medicine
• Virology

Selected publications

• Expanded encyclopaedias of DNA elements in the human and mouse genomes

  Nature · 2020 · 2538 citations

  data. We have developed a registry of 926,535 human and 339,815 mouse candidate cis-regulatory elements, covering 7.9 and 3.4% of their respective genomes, by integrating selected datatypes associated with gene regulation, and constructed a web-based server (SCREEN; http://screen.encodeproject.org) to provide flexible, user-defined access to this resource. Collectively, the ENCODE data and registry provide an expansive resource for the scientific community to build a better understanding of the…

  DOI

• Perspectives on ENCODE

  Nature · 2020 · 222 citations

  . The project has been extended to model organisms, particularly the mouse. In the third phase of ENCODE, nearly a million and more than 300,000 cCRE annotations have been generated for human and mouse, respectively, and these have provided a valuable resource for the scientific community.

  DOI

• Computationally Optimized SARS-CoV-2 MHC Class I and II Vaccine Formulations Predicted to Target Human Haplotype Distributions

  Cell Systems · 2020 · 78 citations

  Senior authorCorresponding
  DOI

• Predicted Cellular Immunity Population Coverage Gaps for SARS-CoV-2 Subunit Vaccines and Their Augmentation by Compact Peptide Sets

  Cell Systems · 2020-11-26 · 52 citations

  articleOpen accessSenior author
  PublisherOA PDFDOI

• An expansion of the non-coding genome and its regulatory potential underlies vertebrate neuronal diversity

  Neuron · 2021-11-01 · 41 citations

  articleOpen accessCorresponding
  PublisherOA PDFDOI

Recent grants

• NIH Grant P01NS055923

  NIH · $13.2M · 2013

• NIH Grant R01GM069676

  NIH · $3.0M · 2008

• Deep learning based antibody design using high-throughput affinity testing of synthetic sequences

  NIH · $2.9M · 2018–2026

Frequent coauthors

• Richard I. Sherwood

  Brigham and Women's Hospital

  71 shared

• Richard A. Young

  55 shared

• Tommi Jaakkola

  52 shared

• Shaun Mahony

  43 shared

• Yuchun Guo

  Fujian Agriculture and Forestry University

  29 shared

• Georg K. Gerber

  Brigham and Women's Hospital

  29 shared

• Gerald R. Fink

  Whitehead Institute for Biomedical Research

  28 shared

• Douglas A. Melton

  University of Missouri

  23 shared

Education

• Ph.D., Biomolecular Engineering

  Massachusetts Institute of Technology

  1995

• B.S., Chemical Engineering

  University of California, Berkeley

  1990

Awards & honors

• Wishnok Prize

Similar researchers at Massachusetts Institute of Technology

• James J. Collinsh-232
• Roger D. Kammh-129
• James G. Foxh-114