Header Logo

Richard E Baker PhD

TitleAssociate Professor
InstitutionUMass Chan Medical School
DepartmentMicrobiology and Physiological Systems
AddressUMass Chan Medical School
55 Lake Avenue North
Worcester MA 01655
Phone508-856-6046
vCardDownload vCard
    Other Positions
    InstitutionT.H. Chan School of Medicine
    DepartmentMicrobiology and Physiological Systems


    Collapse Biography 
    Collapse education and training
    College of William and Mary, Williamsburg, VA, United StatesBSChemistry
    Pennsylvania 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.
    Newest   |   Oldest   |   Most Cited   |   Most Discussed   |   Timeline   |   Field Summary   |   Plain Text
    PMC Citations indicate the number of times the publication was cited by articles in PubMed Central, and the Altmetric score represents citations in news articles and social media. (Note that publications are often cited in additional ways that are not shown here.) Fields are based on how the National Library of Medicine (NLM) classifies the publication's journal and might not represent the specific topic of the publication. Translation tags are based on the publication type and the MeSH terms NLM assigns to the publication. Some publications (especially newer ones and publications not in PubMed) might not yet be assigned Field or Translation tags.) Click a Field or Translation tag to filter the publications.
    1. Koh EI, Oluoch PO, Ruecker N, Proulx MK, Soni V, Murphy KC, Papavinasasundaram K, Reames CJ, Trujillo C, Zaveri A, Zimmerman MD, Aslebagh R, Baker RE, Shaffer SA, Guinn KM, Fitzgerald M, Dartois V, Ehrt S, Hung DT, Ioerger TR, Rubin EJ, Rhee KY, Schnappinger D, Sassetti CM. Chemical-genetic interaction mapping links carbon metabolism and cell wall structure to tuberculosis drug efficacy. Proc Natl Acad Sci U S A. 2022 04 12; 119(15):e2201632119. PMID: 35380903.
      Citations:    Fields:    Translation:HumansCells
    2. Smith CM, Baker RE, Proulx MK, Mishra BB, Long JE, Park SW, Lee HN, Kiritsy MC, Bellerose MM, Olive AJ, Murphy KC, Papavinasasundaram K, Boehm FJ, Reames CJ, Meade RK, Hampton BK, Linnertz CL, Shaw GD, Hock P, Bell TA, Ehrt S, Schnappinger D, Pardo-Manuel de Villena F, Ferris MT, Ioerger TR, Sassetti CM. Host-pathogen genetic interactions underlie tuberculosis susceptibility in genetically diverse mice. Elife. 2022 02 03; 11. PMID: 35112666.
      Citations: 6     Fields:    Translation:AnimalsCells
    3. Sterrett MC, Enyenihi L, Leung SW, Hess L, Strassler SE, Farchi D, Lee RS, Withers ES, Kremsky I, Baker RE, Basrai MA, van Hoof A, Fasken MB, Corbett AH. A budding yeast model for human disease mutations in the EXOSC2 cap subunit of the RNA exosome complex. RNA. 2021 09; 27(9):1046-1067. PMID: 34162742.
      Citations:    Fields:    Translation:HumansAnimalsCells
    4. Bellerose MM, Proulx MK, Smith CM, Baker RE, Ioerger TR, Sassetti CM. Distinct Bacterial Pathways Influence the Efficacy of Antibiotics against Mycobacterium tuberculosis. mSystems. 2020 Aug 04; 5(4). PMID: 32753506.
      Citations:    
    5. Ohkuni K, Suva E, Au WC, Walker RL, Levy-Myers R, Meltzer PS, Baker RE, Basrai MA. Deposition of Centromeric Histone H3 Variant CENP-A/Cse4 into Chromatin Is Facilitated by Its C-Terminal Sumoylation. Genetics. 2020 04; 214(4):839-854. PMID: 32111629.
      Citations: 10     Fields:    Translation:AnimalsCells
    6. Au WC, Zhang T, Mishra PK, Eisenstatt JR, Walker RL, Ocampo J, Dawson A, Warren J, Costanzo M, Baryshnikova A, Flick K, Clark DJ, Meltzer PS, Baker RE, Myers C, Boone C, Kaiser P, Basrai MA. Skp, Cullin, F-box (SCF)-Met30 and SCF-Cdc4-Mediated Proteolysis of CENP-A Prevents Mislocalization of CENP-A for Chromosomal Stability in Budding Yeast. PLoS Genet. 2020 02; 16(2):e1008597. PMID: 32032354.
      Citations: 13     Fields:    Translation:AnimalsCells
    7. Smith CM, Proulx MK, Lai R, Kiritsy MC, Bell TA, Hock P, Pardo-Manuel de Villena F, Ferris MT, Baker RE, Behar SM, Sassetti CM. Functionally Overlapping Variants Control Tuberculosis Susceptibility in Collaborative Cross Mice. mBio. 2019 11 26; 10(6). PMID: 31772048.
      Citations: 7     Fields:    Translation:HumansAnimalsCells
    8. Subramaniyam S, DeJesus MA, Zaveri A, Smith CM, Baker RE, Ehrt S, Schnappinger D, Sassetti CM, Ioerger TR. Statistical analysis of variability in TnSeq data across conditions using zero-inflated negative binomial regression. BMC Bioinformatics. 2019 Nov 21; 20(1):603. PMID: 31752678.
      Citations: 8     Fields:    Translation:AnimalsCells
    9. Bellerose MM, Baek SH, Huang CC, Moss CE, Koh EI, Proulx MK, Smith CM, Baker RE, Lee JS, Eum S, Shin SJ, Cho SN, Murray M, Sassetti CM. Common Variants in the Glycerol Kinase Gene Reduce Tuberculosis Drug Efficacy. mBio. 2019 07 30; 10(4). PMID: 31363023.
      Citations: 32     Fields:    Translation:Cells
    10. 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 04 01; 30(8):1020-1036. PMID: 30726152.
      Citations: 8     Fields:    Translation:AnimalsCells
    11. 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 12 20; 25(12):1495-1505.e3. PMID: 30318462.
      Citations: 8     Fields:    Translation:HumansAnimalsCells
    12. 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.
      Citations:    
    13. 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 09; 210(1):203-218. PMID: 30012561.
      Citations: 14     Fields:    Translation:AnimalsCells
    14. 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 03 28; 8(4):1215-1223. PMID: 29432128.
      Citations: 21     Fields:    Translation:AnimalsCells
    15. 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 Jun 20; 45(11):e93. PMID: 28334803.
      Citations: 16     Fields:    Translation:Cells
    16. 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.
      Citations: 106     Fields:    Translation:HumansAnimalsCells
    17. 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 09 20; 7(5). PMID: 27651361.
      Citations: 55     Fields:    Translation:HumansAnimalsCells
    18. 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 07 15; 27(14):2286-300. PMID: 27226485.
      Citations: 14     Fields:    Translation:AnimalsCells
    19. 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 09. PMID: 26960795.
      Citations: 41     Fields:    
    20. 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.
      Citations: 8     Fields:    Translation:AnimalsCells
    21. 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 04; 12(5):850-63. PMID: 26212330.
      Citations: 29     Fields:    Translation:HumansCells
    22. 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.
      Citations: 37     Fields:    Translation:Cells
    23. 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.
      Citations: 32     Fields:    Translation:HumansCells
    24. 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.
      Citations: 41     Fields:    Translation:AnimalsCells
    25. 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.
      Citations: 28     Fields:    Translation:AnimalsCells
    26. 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.
      Citations: 42     Fields:    Translation:AnimalsCells
    27. 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.
      Citations: 40     Fields:    Translation:HumansAnimalsCells
    28. 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.
      Citations: 57     Fields:    Translation:AnimalsCells
    29. Baker RE. CENP-A targeting moves a step back. Mol Cell. 2009 Feb 27; 33(4):411-3. PMID: 19250900.
      Citations: 1     Fields:    Translation:AnimalsCells
    30. 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.
      Citations: 109     Fields:    Translation:AnimalsCells
    31. Baker RE, Rogers K. Phylogenetic analysis of fungal centromere H3 proteins. Genetics. 2006 Nov; 174(3):1481-92. PMID: 17028330.
      Citations: 23     Fields:    Translation:AnimalsCells
    32. 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.
      Citations: 19     Fields:    Translation:AnimalsCells
    33. 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.
      Citations: 19     Fields:    Translation:AnimalsCells
    Baker's Networks
    Click the
    Explore
    buttons for more information and interactive visualizations!
    Concepts (201)
    Explore
    _
    Co-Authors (13)
    Explore
    _
    Similar People (60)
    Explore
    _
    Same Department Expand Description
    Explore
    _
    Physical Neighbors
    _