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Richard E Baker PhD

TitleAssociate Professor
InstitutionUniversity of Massachusetts Medical School
DepartmentMicrobiology and Physiological Systems
AddressUniversity of Massachusetts Medical School
55 Lake Avenue North
Worcester MA 01655
Phone508-856-6046
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    Other Positions
    InstitutionUMMS - School of Medicine
    DepartmentMicrobiology and Physiological Systems

    InstitutionUMMS - Graduate School of Biomedical Sciences
    DepartmentMolecular Genetics and Microbiology


    Collapse Biography 
    Collapse education and training
    College of William and Mary, Charlottesville, VA, United StatesBSChemistry
    Penn State College of Medicine, Hershey, PA, United StatesPHDBiological Chemistry

    Collapse Overview 
    Collapse overview


    Academic Background



    Ph. D. (1980) Pennsylvania State University



    Molecular Mechanisms of Chromosome Segregation



    For over 20 years, my lab studied centromere function and chromosome segregation using the model organism S. cerevisiae. In collaboration with Dr. Molly Fitzgerald-Hayes (UMass Amherst), we carried out groundbreaking work on the structure and function of the yeast centromeric H3 variant Cse4 and discovered the key CenH3 chaperone Scm3/HJURP. The research took full advantage of the combined genetic and biochemical methods available with this model organism and its sequenced genome, and the research increasingly included genomic and computational components. Currently I devote most of my time to bioinformatics and computational biology while pursuing my interest in yeast centromeres via ongoing collaborations. Presently, I serve as the de facto departmental bioinformatician, assisting our "wet lab" scientists to assemble and analyze data, and navigate the numerous assets of the Institution's Bioinformatics Core. I am actively engaged in several collaborative projects, including genome-wide analysis of double-strand breaks in activated B cells, high density transposon mutagenesis studies in both Yersinia and M. tuberculosis, ribosome profiling in yeast, and combined RNA-seq/ChIP-seq analysis of developmental gene regulation in the mouse cerebellum.



     




    Collapse Bibliographic 
    Collapse selected publications
    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.
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    1. Mishra PK, Olafsson G, Boeckmann L, Westlake TJ, Jowhar ZM, Dittman LE, Baker RE, D'Amours D, Thorpe PH, Basrai MA. Cell cycle dependent association of polo kinase Cdc5 with CENP-A contributes to faithful chromosome segregation in budding yeast. Mol Biol Cell. 2019 Feb 06; mbcE18090584. PMID: 30726152.
      View in: PubMed
    2. Rittershaus ESC, Baek SH, Krieger IV, Nelson SJ, Cheng YS, Nambi S, Baker RE, Leszyk JD, Shaffer SA, Sacchettini JC, Sassetti CM. A Lysine Acetyltransferase Contributes to the Metabolic Adaptation to Hypoxia in Mycobacterium tuberculosis. Cell Chem Biol. 2018 Oct 04. PMID: 30318462.
      View in: PubMed
    3. Ohkuni K, Pasupala N, Peek J, Holloway GL, Sclar GD, Levy-Myers R, Baker RE, Basrai MA, Kerscher O. SUMO-Targeted Ubiquitin Ligases (STUbLs) Reduce the Toxicity and Abnormal Transcriptional Activity Associated With a Mutant, Aggregation-Prone Fragment of Huntingtin. Front Genet. 2018; 9:379. PMID: 30279700.
      View in: PubMed
    4. Ciftci-Yilmaz S, Au WC, Mishra PK, Eisenstatt JR, Chang J, Dawson AR, Zhu I, Rahman M, Bilke S, Costanzo M, Baryshnikova A, Myers CL, Meltzer PS, Landsman D, Baker RE, Boone C, Basrai MA. A Genome-Wide Screen Reveals a Role for the HIR Histone Chaperone Complex in Preventing Mislocalization of Budding Yeast CENP-A. Genetics. 2018 Jul 16. PMID: 30012561.
      View in: PubMed
    5. Ohkuni K, Levy-Myers R, Warren J, Au WC, Takahashi Y, Baker RE, Basrai MA. N-terminal Sumoylation of Centromeric Histone H3 Variant Cse4 Regulates Its Proteolysis To Prevent Mislocalization to Non-centromeric Chromatin. G3 (Bethesda). 2018 Mar 28; 8(4):1215-1223. PMID: 29432128.
      View in: PubMed
    6. Mishra BB, Lovewell RR, Olive AJ, Zhang G, Wang W, Eugenin E, Smith CM, Phuah JY, Long JE, Dubuke ML, Palace SG, Goguen JD, Baker RE, Nambi S, Mishra R, Booty MG, Baer CE, Shaffer SA, Dartois V, McCormick BA, Chen X, Sassetti CM. Nitric oxide prevents a pathogen-permissive granulocytic inflammation during tuberculosis. Nat Microbiol. 2017 May 15; 2:17072. PMID: 28504669.
      View in: PubMed
    7. DeJesus MA, Nambi S, Smith CM, Baker RE, Sassetti CM, Ioerger TR. Statistical analysis of genetic interactions in Tn-Seq data. Nucleic Acids Res. 2017 Feb 22. PMID: 28334803.
      View in: PubMed
    8. Smith CM, Proulx MK, Olive AJ, Laddy D, Mishra BB, Moss C, Gutierrez NM, Bellerose MM, Barreira-Silva P, Phuah JY, Baker RE, Behar SM, Kornfeld H, Evans TG, Beamer G, Sassetti CM. Tuberculosis Susceptibility and Vaccine Protection Are Independently Controlled by Host Genotype. MBio. 2016 Sep 20; 7(5). PMID: 27651361.
      View in: PubMed
    9. Mishra PK, Ciftci-Yilmaz S, Reynolds D, Au WC, Boeckmann L, Dittman LE, Jowhar Z, Pachpor T, Yeh E, Baker RE, Hoyt MA, D'Amours D, Bloom K, Basrai MA. Polo kinase Cdc5 associates with centromeres to facilitate the removal of centromeric cohesin during mitosis. Mol Biol Cell. 2016 Jul 15; 27(14):2286-300. PMID: 27226485.
      View in: PubMed
    10. Ohkuni K, Takahashi Y, Fulp A, Lawrimore J, Au WC, Pasupala N, Levy-Myers R, Warren J, Strunnikov A, Baker RE, Kerscher O, Bloom K, Basrai MA. SUMO-Targeted Ubiquitin Ligase (STUbL) Slx5 regulates proteolysis of centromeric histone H3 variant Cse4 and prevents its mislocalization to euchromatin. Mol Biol Cell. 2016 Mar 9. PMID: 26960795.
      View in: PubMed
    11. Khair L, Baker RE, Linehan EK, Schrader CE, Stavnezer J. Nbs1 ChIP-Seq Identifies Off-Target DNA Double-Strand Breaks Induced by AID in Activated Splenic B Cells. PLoS Genet. 2015 Aug; 11(8):e1005438. PMID: 26263206.
      View in: PubMed
    12. Perreira JM, Aker AM, Savidis G, Chin CR, McDougall WM, Portmann JM, Meraner P, Smith MC, Rahman M, Baker RE, Gauthier A, Franti M, Brass AL. RNASEK Is a V-ATPase-Associated Factor Required for Endocytosis and the Replication of Rhinovirus, Influenza A Virus, and Dengue Virus. Cell Rep. 2015 Aug 4; 12(5):850-63. PMID: 26212330.
      View in: PubMed
    13. Long JE, DeJesus M, Ward D, Baker RE, Ioerger T, Sassetti CM. Identifying essential genes in Mycobacterium tuberculosis by global phenotypic profiling. Methods Mol Biol. 2015; 1279:79-95. PMID: 25636614.
      View in: PubMed
    14. Zhu J, Davoli T, Perriera JM, Chin CR, Gaiha GD, John SP, Sigiollot FD, Gao G, Xu Q, Qu H, Pertel T, Sims JS, Smith JA, Baker RE, Maranda L, Ng A, Elledge SJ, Brass AL. Comprehensive identification of host modulators of HIV-1 replication using multiple orthologous RNAi reagents. Cell Rep. 2014 Oct 23; 9(2):752-66. PMID: 25373910.
      View in: PubMed
    15. Palace SG, Proulx MK, Lu S, Baker RE, Goguen JD. Genome-wide mutant fitness profiling identifies nutritional requirements for optimal growth of Yersinia pestis in deep tissue. MBio. 2014 Aug 19; 5(4). PMID: 25139902.
      View in: PubMed
    16. Boeckmann L, Takahashi Y, Au WC, Mishra PK, Choy JS, Dawson AR, Szeto MY, Waybright TJ, Heger C, McAndrew C, Goldsmith PK, Veenstra TD, Baker RE, Basrai MA. Phosphorylation of centromeric histone H3 variant regulates chromosome segregation in Saccharomyces cerevisiae. Mol Biol Cell. 2013 Jun; 24(12):2034-44. PMID: 23637466.
      View in: PubMed
    17. Au WC, Dawson AR, Rawson DW, Taylor SB, Baker RE, Basrai MA. A novel role of the N terminus of budding yeast histone H3 variant Cse4 in ubiquitin-mediated proteolysis. Genetics. 2013 Jun; 194(2):513-8. PMID: 23525333.
      View in: PubMed
    18. Mishra PK, Au WC, Choy JS, Kuich PH, Baker RE, Foltz DR, Basrai MA. Misregulation of Scm3p/HJURP causes chromosome instability in Saccharomyces cerevisiae and human cells. PLoS Genet. 2011 Sep; 7(9):e1002303. PMID: 21980305.
      View in: PubMed
    19. Staszewski O, Baker RE, Ucher AJ, Martier R, Stavnezer J, Guikema JE. Activation-induced cytidine deaminase induces reproducible DNA breaks at many non-Ig Loci in activated B cells. Mol Cell. 2011 Jan 21; 41(2):232-42. PMID: 21255732.
      View in: PubMed
    20. Baker RE. CENP-A targeting moves a step back. Mol Cell. 2009 Feb 27; 33(4):411-3. PMID: 19250900.
      View in: PubMed
    21. Stoler S, Rogers K, Weitze S, Morey L, Fitzgerald-Hayes M, Baker RE. Scm3, an essential Saccharomyces cerevisiae centromere protein required for G2/M progression and Cse4 localization. Proc Natl Acad Sci U S A. 2007 Jun 19; 104(25):10571-6. PMID: 17548816.
      View in: PubMed
    22. Baker RE, Rogers K. Phylogenetic analysis of fungal centromere H3 proteins. Genetics. 2006 Nov; 174(3):1481-92. PMID: 17028330.
      View in: PubMed
    23. Baker RE, Rogers K. Genetic and genomic analysis of the AT-rich centromere DNA element II of Saccharomyces cerevisiae. Genetics. 2005 Dec; 171(4):1463-75. PMID: 16079225.
      View in: PubMed
    24. Morey L, Barnes K, Chen Y, Fitzgerald-Hayes M, Baker RE. The histone fold domain of Cse4 is sufficient for CEN targeting and propagation of active centromeres in budding yeast. Eukaryot Cell. 2004 Dec; 3(6):1533-43. PMID: 15590827.
      View in: PubMed
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