Thomas MacCarthy

Summary

Affiliation: Albert Einstein College of Medicine
Country: USA

Publications

  1. pmc The limits of subfunctionalization
    Thomas MacCarthy
    Department of Pathology, Albert Einstein College of Medicine, Bronx, NY 10461, USA
    BMC Evol Biol 7:213. 2007
  2. pmc SHMTool: a webserver for comparative analysis of somatic hypermutation datasets
    Thomas MacCarthy
    Dept of Systems and Computational Biology, Albert Einstein College of Medicine, 1300 Morris Park Ave, Bronx, NY 10461, USA
    DNA Repair (Amst) 8:137-41. 2009
  3. pmc Overlapping hotspots in CDRs are critical sites for V region diversification
    Lirong Wei
    Department of Cell Biology, Albert Einstein College of Medicine, Bronx, NY 10461
    Proc Natl Acad Sci U S A 112:E728-37. 2015
  4. pmc Disease-enhancing antibodies improve the efficacy of bacterial toxin-neutralizing antibodies
    Siu Kei Chow
    Department of Microbiology and Immunology, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, NY 10461, USA
    Cell Host Microbe 13:417-28. 2013
  5. pmc A core erythroid transcriptional network is repressed by a master regulator of myelo-lymphoid differentiation
    Sandeep N Wontakal
    Department of Cell Biology, Albert Einstein College of Medicine, Bronx, NY 10461, USA
    Proc Natl Acad Sci U S A 109:3832-7. 2012
  6. pmc V-region mutation in vitro, in vivo, and in silico reveal the importance of the enzymatic properties of AID and the sequence environment
    Thomas MacCarthy
    Department of Systems and Computational Biology, Albert Einstein College of Medicine, Bronx NY 10461, USA
    Proc Natl Acad Sci U S A 106:8629-34. 2009
  7. doi request reprint Cancer as the Disintegration of Robustness: Population-Level Variance in Gene Expression Identifies Key Differences Between Tobacco- and HPV-Associated Oropharyngeal Carcinogenesis
    Miriam M Ben-Dayan
    From the Departments of Pathology Ms Ben Dayan and Drs Belbin, Childs, and Prystowsky, Epidemiology and Population Health Dr Schlecht, and Computational and Systems Biology Dr Bergman, Albert Einstein College of Medicine, Bronx, New York the Department of Applied Mathematics and Statistics, SUNY Stony Brook, Stony Brook, New York Dr MacCarthy and the Department of Otorhinolaryngology, Montefiore Medical Center, Bronx, New York Dr Smith
    Arch Pathol Lab Med 139:1362-72. 2015
  8. pmc Epigenetics decouples mutational from environmental robustness. Did it also facilitate multicellularity?
    Saurabh Gombar
    Department of Systems and Computational Biology, Albert Einstein College of Medicine, Bronx, New York, New York, United States of America
    PLoS Comput Biol 10:e1003450. 2014
  9. pmc The underlying molecular and network level mechanisms in the evolution of robustness in gene regulatory networks
    Mario Pujato
    Department of Systems and Computational Biology, Albert Einstein College of Medicine, Bronx, New York, United States of America
    PLoS Comput Biol 9:e1002865. 2013
  10. pmc Ubiquitylated PCNA plays a role in somatic hypermutation and class-switch recombination and is required for meiotic progression
    Sergio Roa
    Departments of Cell Biology and Systems and Computational Biology, Albert Einstein College of Medicine, Bronx, NY 10461, USA
    Proc Natl Acad Sci U S A 105:16248-53. 2008

Collaborators

Detail Information

Publications13

  1. pmc The limits of subfunctionalization
    Thomas MacCarthy
    Department of Pathology, Albert Einstein College of Medicine, Bronx, NY 10461, USA
    BMC Evol Biol 7:213. 2007
    ..We distinguish between subfunctionalization at the regulatory level and at the product level (e.g within temporal or spatial expression domains)...
  2. pmc SHMTool: a webserver for comparative analysis of somatic hypermutation datasets
    Thomas MacCarthy
    Dept of Systems and Computational Biology, Albert Einstein College of Medicine, 1300 Morris Park Ave, Bronx, NY 10461, USA
    DNA Repair (Amst) 8:137-41. 2009
    ..To overcome these problems and facilitate a standardized analysis and display of similar data, we present a webserver (SHMTool) for comparing SHM datasets, available at http://scb.aecom.yu.edu/shmtool...
  3. pmc Overlapping hotspots in CDRs are critical sites for V region diversification
    Lirong Wei
    Department of Cell Biology, Albert Einstein College of Medicine, Bronx, NY 10461
    Proc Natl Acad Sci U S A 112:E728-37. 2015
    ..Our analysis suggests that the local sequence environment of the V region, and especially of the CDR1 and CDR2, is highly evolved to recruit mutations to key residues in the CDRs of the IgV region. ..
  4. pmc Disease-enhancing antibodies improve the efficacy of bacterial toxin-neutralizing antibodies
    Siu Kei Chow
    Department of Microbiology and Immunology, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, NY 10461, USA
    Cell Host Microbe 13:417-28. 2013
    ..These data suggest that functional assessments of single Abs may inaccurately predict how the same Abs will operate in polyclonal preparations and imply that potentially therapeutic mAbs may be overlooked in single Ab screens...
  5. pmc A core erythroid transcriptional network is repressed by a master regulator of myelo-lymphoid differentiation
    Sandeep N Wontakal
    Department of Cell Biology, Albert Einstein College of Medicine, Bronx, NY 10461, USA
    Proc Natl Acad Sci U S A 109:3832-7. 2012
    ....
  6. pmc V-region mutation in vitro, in vivo, and in silico reveal the importance of the enzymatic properties of AID and the sequence environment
    Thomas MacCarthy
    Department of Systems and Computational Biology, Albert Einstein College of Medicine, Bronx NY 10461, USA
    Proc Natl Acad Sci U S A 106:8629-34. 2009
    ..While we have confirmed that AID targeting of hot and cold spots is a key part of the mutation process, our results suggest that the sequence environment plays an equally important role...
  7. doi request reprint Cancer as the Disintegration of Robustness: Population-Level Variance in Gene Expression Identifies Key Differences Between Tobacco- and HPV-Associated Oropharyngeal Carcinogenesis
    Miriam M Ben-Dayan
    From the Departments of Pathology Ms Ben Dayan and Drs Belbin, Childs, and Prystowsky, Epidemiology and Population Health Dr Schlecht, and Computational and Systems Biology Dr Bergman, Albert Einstein College of Medicine, Bronx, New York the Department of Applied Mathematics and Statistics, SUNY Stony Brook, Stony Brook, New York Dr MacCarthy and the Department of Otorhinolaryngology, Montefiore Medical Center, Bronx, New York Dr Smith
    Arch Pathol Lab Med 139:1362-72. 2015
    ....
  8. pmc Epigenetics decouples mutational from environmental robustness. Did it also facilitate multicellularity?
    Saurabh Gombar
    Department of Systems and Computational Biology, Albert Einstein College of Medicine, Bronx, New York, New York, United States of America
    PLoS Comput Biol 10:e1003450. 2014
    ....
  9. pmc The underlying molecular and network level mechanisms in the evolution of robustness in gene regulatory networks
    Mario Pujato
    Department of Systems and Computational Biology, Albert Einstein College of Medicine, Bronx, New York, United States of America
    PLoS Comput Biol 9:e1002865. 2013
    ..Meanwhile, in highly interconnected architectures (represented by long promoters), robustness evolves almost entirely via network level changes, deleting and creating binding sites that modify the network architecture...
  10. pmc Ubiquitylated PCNA plays a role in somatic hypermutation and class-switch recombination and is required for meiotic progression
    Sergio Roa
    Departments of Cell Biology and Systems and Computational Biology, Albert Einstein College of Medicine, Bronx, NY 10461, USA
    Proc Natl Acad Sci U S A 105:16248-53. 2008
    ....
  11. pmc Buffering mechanisms in aging: a systems approach toward uncovering the genetic component of aging
    Aviv Bergman
    Department of Pathology, Albert Einstein College of Medicine, New York, New York, United States of America
    PLoS Comput Biol 3:e170. 2007
    ..It also provides a framework for developing strategies to prevent some age-related diseases by intervention at the appropriate level...
  12. pmc Using large-scale perturbations in gene network reconstruction
    Thomas MacCarthy
    CoMPLEX, University College London, 4 Stephenson Way, London NW1 2HE, UK
    BMC Bioinformatics 6:11. 2005
    ..The method is tested on artificial gene networks with biologically realistic in/out degree characteristics...
  13. ncbi request reprint The evolutionary potential of the Drosophila sex determination gene network
    Thomas MacCarthy
    CoMPLEX, University College London, 4 Stephenson Way, NW1 2HE London, UK
    J Theor Biol 225:461-8. 2003
    ....