Tom Tullius

About

Tom Tullius is a professor conducting research in genomics, structural biology, and biophysical chemistry. He holds a faculty appointment in Chemistry and is also a Professor of Pharmacology and Experimental Therapeutics at the Boston University School of Medicine. His research group introduced hydroxyl radical footprinting, a widely used technique for studying the structure of DNA, DNA-protein complexes, and RNA. His work investigates the connection between the structural properties of DNA and genomics, including studies on DNA shape and its role in evolutionary selection, as well as mapping DNA and RNA structures at high resolution. Professor Tullius is an elected Fellow of the American Association for the Advancement of Science and serves on the Editorial Board of the open access journal PeerJ. He is the Director of the Boston University Bioinformatics Program. His research projects include developing methods to map DNA shape at single nucleotide resolution and exploring RNA tertiary structure transcriptome-wide. His work has contributed to understanding how DNA shape influences transcription factor binding and gene regulation, and his lab collaborates with NIH and other institutions to advance genomic and structural biology research.

Research topics

• Chemistry
• Biology
• Computational biology
• Genetics
• Stereochemistry

Selected publications

• Comparative analysis of metazoan chromatin organization

  Nature · 2014-08-26 · 448 citations

  articleOpen access
  PublisherOA PDFDOI

• A Map of Minor Groove Shape and Electrostatic Potential from Hydroxyl Radical Cleavage Patterns of DNA

  ACS Chemical Biology · 2011-10-03 · 88 citations

  letterSenior author

  DNA shape variation and the associated variation in minor groove electrostatic potential are widely exploited by proteins for DNA recognition. Here we show that the hydroxyl radical cleavage pattern is a quantitative measure of DNA backbone solvent accessibility, minor groove width, and minor groove electrostatic potential, at single nucleotide resolution. We introduce maps of DNA shape and electrostatic potential as tools for understanding how proteins recognize binding sites in a genome. These…

  PublisherDOI

• GBshape: a genome browser database for DNA shape annotations

  Nucleic Acids Research · 2014-10-17 · 65 citations

  articleOpen access

  Many regulatory mechanisms require a high degree of specificity in protein-DNA binding. Nucleotide sequence does not provide an answer to the question of why a protein binds only to a small subset of the many putative binding sites in the genome that share the same core motif. Whereas higher-order effects, such as chromatin accessibility, cooperativity and cofactors, have been described, DNA shape recently gained attention as another feature that fine-tunes the DNA binding specificities of some…

  PublisherOA PDFDOI

• DNA shape, genetic codes, and evolution

  Current Opinion in Structural Biology · 2011-04-14 · 43 citations

  reviewSenior authorCorresponding
  PublisherDOI

• Experimental maps of DNA structure at nucleotide resolution distinguish intrinsic from protein-induced DNA deformations

  Nucleic Acids Research · 2018-01-15 · 29 citations

  articleOpen accessSenior authorCorresponding

  Recognition of DNA by proteins depends on DNA sequence and structure. Often unanswered is whether the structure of naked DNA persists in a protein-DNA complex, or whether protein binding changes DNA shape. While X-ray structures of protein-DNA complexes are numerous, the structure of naked cognate DNA is seldom available experimentally. We present here an experimental and computational analysis pipeline that uses hydroxyl radical cleavage to map, at single-nucleotide resolution, DNA minor groove…

  PublisherOA PDFDOI

Recent grants

• NIH Grant R01CA037444

  NIH · $252k · 1988

• NIH Grant R01GM041930

  NIH · $2.5M · 2005

• NIH Grant R01GM040894

  NIH · $2.4M · 2003

Frequent coauthors

• Mair E. A. Churchill

  Takeda (United States)

  50 shared

• Stephen C. J. Parker

  45 shared

• Neville R. Kallenbach

  35 shared

• Hsilin Ch'ng

  Columbia University

  25 shared

• Goran Bačić

  25 shared

• Richard L. Rubin

  George Washington University

  25 shared

• Jack D. Griffith

  University of North Carolina at Chapel Hill

  25 shared

• Jurek Dobrucki

  Jagiellonian University

  25 shared

Labs

• Tullius GroupPI

Education

• Ph.D., Chemistry

  Stanford University

  1979

• B.S., Chemistry

  UCLA

  1973

Awards & honors

• Fellow of the American Association for the Advancement of Sc…

Similar researchers at Boston University

• John E. Straubh-69
• James Panekh-58
• Karen Allenh-56