Thomas D. Tullius, PhD
Professor
Boston University College of Arts and Sciences
Dept of Chemistry

PhD, Stanford University



Tom Tullius conducts research in genomics, structural biology, and biophysical chemistry. In addition to Chemistry, he is Professor of Pharmacology and Professor of Experimental Therapeutics in the Boston University School of Medicine. He is an elected Fellow of the American Association for the Advancement of Science and he is on the Editorial Advisory Board of the Chemistry Central Journal. Professor Tullius is a faculty affiliate and Director of the Boston University Bioinformatics Program.

The Tullius Group introduced hydroxyl radical footprinting, which is widely used for the structural study of DNA, DNA-protein complexes, and RNA. They investigate the connection between structural properties of DNA and genomics, including evolutionary selection for DNA structure in the human genome. Their human genome studies were initiated with funding from the ENCODE (Encyclopedia of DNA Elements) Pilot Project, which was organized by the National Human Genome Research Institute of the NIH to discover functional elements in the human genome.

Measurement of the Deuterium Kinetic Isotope Effect on Hydroxyl Radical Cleavage of RNA aims to synthesize a complete set of nucleoside and deoxynucleoside triphosphates specifically deuterated at each sugar carbon atom. The deuterated nucleoside triphosphates are used in kinetic isotope effect experiments on hydroxyl radical cleavage of RNA, to provide more detailed information on the structural features of RNA to which the hydroxyl radical is sensitive. The goal of this work is the development of a chemical probe of RNA structure of unprecedented resolution.

Genome damage and aging: whole-genome maps of oxidative DNA lesions at single-nucleotide resolution investigates a new way to map, at single nucleotide resolution for an entire genome, the sites of oxidative damage that are induced in the DNA backbone by the hydroxyl radical. The study uses an advanced sequencing platform to comprehensively identify sites of DNA strand breaks. With these experiments it is possible to visualize, at single-nucleotide resolution, what parts of a genome are sensitive to attack by the hydroxyl radical and what parts are resistant. This work will provide unique new information on how oxidative damage affects the genome and so contributes to aging.

Techniques & Resources:

ORChID (OH Radical Cleavage Intensity Database) – Database of experimentally determined hydroxyl radical cleavage patterns of naked DNA molecules. Algorithm to predict the cleavage pattern of any DNA sequence.

ORChID in the UCSC Genome Browser – ORChID values predicted for the human genome. The data is viewable and available for download from the UCSC genome browser.

Chai regions in the UCSC Genome Browser – Chai is a structure-informed evolutionary sequence constraint detection algorithm. Chai-identified regions are available from the UCSC genome browser.

Professor
Boston University School of Medicine
Department of Pharmacology & Experimental Therapeutics


Director
Boston University
Department of Bioinformatics Graduate Program




Chemical probing of RNA tertiary structure in a whole transcriptome at single-atom resolution
07/01/2016 - 06/30/2019 (PI)
National Science Foundation
MCB-1616388

Genome Analysis Based on the Integration of DNA Sequence and Shape
02/01/2014 - 01/31/2018 (PI)
University of Southern California NIH NIGMS
5R01GM106056-04

Predoctoral Training in Bioinformatics and Computational Biology
07/01/2016 - 06/30/2017 (PI)
NIH/National Institute of General Medical Sciences
4T32GM100842-05

Predoctoral Training in Bioinformatics and Computational Biology
07/01/2012 - 06/30/2016 (PI)
NIH/National Institute of General Medical Sciences
5T32GM100842-04

GENOME DAMAGE AND AGING: WHOLE-GENOME MAPS OF OXIDATIVE DNA LESIONS AT SINGLE-NUCLEOTIDE RESOLUTION
11/01/2009 - 10/31/2014 (PI)
Ellison Medical Foundation

NATIONAL CENTER: MULTI-SCALE STUDY OF CELLULAR NETWORKS
09/01/2010 - 07/31/2013 (PI)
Trustees Of Columbia University In The City Of New York NIH NCI
5U54CA121852

Billing Agreement: Off Campus funding for Eric Bishop.
07/01/2011 - 06/30/2012 (PI)
President and Fellows of Harvard College




Yr Title Project-Sub Proj Pubs
2016 Predoctoral Training in Bioinformatics and Computational Biology 4T32GM100842-05
2014 Predoctoral Training in Bioinformatics and Computational Biology 5T32GM100842-03
2013 Predoctoral Training in Bioinformatics and Computational Biology 5T32GM100842-02
2012 Predoctoral Training in Bioinformatics and Computational Biology 1T32GM100842-01
2010 Structure of genomic DNA at single-nucleotide resolution 5R01HG003541-05 9
2009 Structure of genomic DNA at single-nucleotide resolution 2R01HG003541-04A1 9
2006 Structure of genomic DNA at single-nucleotide resolution 5R01HG003541-03 9
2005 Structure of genomic DNA at single-nucleotide resolution 5R01HG003541-02 9
2004 Structure of genomic DNA at single-nucleotide resolution 1R01HG003541-01 9
2003 FOOTPRINTING WITH IRON (II)-GENERATED HYDROXYL RADICAL 5R01GM041930-14 15
Showing 10 of 28 results. Show All Results
Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Faculty can login to make corrections and additions.

  1. Chiu TP, Yang L, Zhou T, Main BJ, Parker SC, Nuzhdin SV, Tullius TD, Rohs R. 28 GBshape: a genome browser database for DNA shape annotations. J Biomol Struct Dyn. 2015; 33 Suppl 1:16. PMID: 26103240; DOI: 10.1080/07391102.2015.1032568;.
  2. Chiu TP, Yang L, Zhou T, Main BJ, Parker SC, Nuzhdin SV, Tullius TD, Rohs R. GBshape: a genome browser database for DNA shape annotations. Nucleic Acids Res. 2015 Jan; 43(Database issue):D103-9. PMID: 25326329; PMCID: PMC4384032; DOI: 10.1093/nar/gku977;.
  3. Ingle S, Azad RN, Jain SS, Tullius TD. Chemical probing of RNA with the hydroxyl radical at single-atom resolution. Nucleic Acids Res. 2014 Nov 10; 42(20):12758-67. PMID: 25313156; PMCID: PMC4227780; DOI: 10.1093/nar/gku934;.
  4. Ho JW, Jung YL, Liu T, Alver BH, Lee S, Ikegami K, Sohn KA, Minoda A, Tolstorukov MY, Appert A, Parker SC, Gu T, Kundaje A, Riddle NC, Bishop E, Egelhofer TA, Hu SS, Alekseyenko AA, Rechtsteiner A, Asker D, Belsky JA, Bowman SK, Chen QB, Chen RA, Day DS, Dong Y, Dose AC, Duan X, Epstein CB, Ercan S, Feingold EA, Ferrari F, Garrigues JM, Gehlenborg N, Good PJ, Haseley P, He D, Herrmann M, Hoffman MM, Jeffers TE, Kharchenko PV, Kolasinska-Zwierz P, Kotwaliwale CV, Kumar N, Langley SA, Larschan EN, Latorre I, Libbrecht MW, Lin X, Park R, Pazin MJ, Pham HN, Plachetka A, Qin B, Schwartz YB, Shoresh N, Stempor P, Vielle A, Wang C, Whittle CM, Xue H, Kingston RE, Kim JH, Bernstein BE, Dernburg AF, Pirrotta V, Kuroda MI, Noble WS, Tullius TD, Kellis M, MacAlpine DM, Strome S, Elgin SC, Liu XS, Lieb JD, Ahringer J, Karpen GH, Park PJ. Comparative analysis of metazoan chromatin organization. Nature. 2014 Aug 28; 512(7515):449-52. PMID: 25164756; PMCID: PMC4227084; DOI: 10.1038/nature13415;.
  5. Bishop EP, Rohs R, Parker SC, West SM, Liu P, Mann RS, Honig B, Tullius TD. A map of minor groove shape and electrostatic potential from hydroxyl radical cleavage patterns of DNA. ACS Chem Biol. 2011 Dec 16; 6(12):1314-20. PMID: 21967305; PMCID: PMC3241897; DOI: 10.1021/cb200155t;.
  6. Parker SC, Tullius TD. DNA shape, genetic codes, and evolution. Curr Opin Struct Biol. 2011 Jun; 21(3):342-7. PMID: 21439813; PMCID: PMC3112471; DOI: 10.1016/j.sbi.2011.03.002;.
  7. Parker SC, Harlap A, Tullius TD. A computational method to search for DNA structural motifs in functional genomic elements. Methods Mol Biol. 2011; 759:367-79. PMID: 21863498; DOI: 10.1007/978-1-61779-173-4_21;.
  8. Parker SC, Hansen L, Abaan HO, Tullius TD, Margulies EH. Local DNA topography correlates with functional noncoding regions of the human genome. Science. 2009 Apr 17; 324(5925):389-92. PMID: 19286520; PMCID: PMC2749491; DOI: 10.1126/science.1169050;.
  9. Parker SC, Margulies EH, Tullius TD. The relationship between fine scale DNA structure, GC content, and functional elements in 1% of the human genome. Genome Inform. 2008; 20:199-211. PMID: 19425134.
  10. Jain SS, Tullius TD. Footprinting protein-DNA complexes using the hydroxyl radical. Nat Protoc. 2008; 3(6):1092-1100. PMID: 18546600.
Showing 10 of 71 results. Show More

This graph shows the total number of publications by year, by first, middle/unknown, or last author.

Bar chart showing 70 publications over 28 distinct years, with a maximum of 8 publications in 1990

YearPublications
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20151
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