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Thomas MacCarthy - Publications

Affiliations: 
Albert Einstein College of Medicine, New York, New York, United States 
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42 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2024 Song JH, Zeng Y, Dávalos LM, MacCarthy T, Larijani M, Damaghi M. Human and bats genome robustness under COSMIC mutational signatures. Biorxiv : the Preprint Server For Biology. PMID 39314309 DOI: 10.1101/2024.09.05.611453  0.345
2024 Tambe A, MacCarthy T, Pavri R. Interpretable deep learning reveals the role of an E-box motif in suppressing somatic hypermutation of AGCT motifs within human immunoglobulin variable regions. Frontiers in Immunology. 15: 1407470. PMID 38863710 DOI: 10.3389/fimmu.2024.1407470  0.314
2023 Delamonica B, Davalos L, Larijani M, Anthony SJ, Liu J, MacCarthy T. Evolutionary potential of the monkeypox genome arising from interactions with human APOBEC3 enzymes. Virus Evolution. 9: vead047. PMID 37577211 DOI: 10.1093/ve/vead047  0.317
2021 Tang C, Krantsevich A, MacCarthy T. Deep learning model of somatic hypermutation reveals importance of sequence context beyond hotspot targeting. Iscience. 25: 103668. PMID 35036866 DOI: 10.1016/j.isci.2021.103668  0.328
2021 Yu G, Wu Y, Duan Z, Tang C, Xing H, Scharff MD, MacCarthy T. A Bayesian model based computational analysis of the relationship between bisulfite accessible single-stranded DNA in chromatin and somatic hypermutation of immunoglobulin genes. Plos Computational Biology. 17: e1009323. PMID 34491985 DOI: 10.1371/journal.pcbi.1009323  0.341
2021 Duan Z, Baughn LB, Wang X, Zhang Y, Gupta V, MacCarthy T, Scharff MD, Yu G. Role of Dot1L and H3K79 methylation in regulating somatic hypermutation of immunoglobulin genes. Proceedings of the National Academy of Sciences of the United States of America. 118. PMID 34253616 DOI: 10.1073/pnas.2104013118  0.338
2021 Bagnara D, Tang C, Brown JR, Kasar S, Fernandes S, Colombo M, Vergani S, Mazzarello AN, Ghiotto F, Bruno S, Morabito F, Rai KR, Kolitz JE, Barrientos JC, Allen SL, ... ... MacCarthy T, et al. Post-Transformation IGHV-IGHD-IGHJ Mutations in Chronic Lymphocytic Leukemia B Cells: Implications for Mutational Mechanisms and Impact on Clinical Course. Frontiers in Oncology. 11: 640731. PMID 34113563 DOI: 10.3389/fonc.2021.640731  0.36
2020 Krantsevich A, Tang C, MacCarthy T. Correlations in Somatic Hypermutation Between Sites in IGHV Genes Can Be Explained by Interactions Between AID and/or Polη Hotspots. Frontiers in Immunology. 11: 618409. PMID 33603748 DOI: 10.3389/fimmu.2020.618409  0.368
2020 Tang C, Bagnara D, Chiorazzi N, Scharff MD, MacCarthy T. AID Overlapping and Polη Hotspots Are Key Features of Evolutionary Variation Within the Human Antibody Heavy Chain (IGHV) Genes. Frontiers in Immunology. 11: 788. PMID 32425948 DOI: 10.3389/Fimmu.2020.00788  0.413
2019 Martinez T, Shapiro M, Bhaduri-McIntosh S, MacCarthy T. Evolutionary effects of the AID/APOBEC family of mutagenic enzymes on human gamma-herpesviruses. Virus Evolution. 5: vey040. PMID 30792902 DOI: 10.1093/Ve/Vey040  0.393
2018 Dong Q, Smith KR, Oldenburg DG, Shapiro M, Schutt WR, Malik L, Plummer JB, Mu Y, MacCarthy T, White DW, McBride KM, Krug LT. Combinatorial Loss of the Enzymatic Activities of Viral Uracil-DNA Glycosylase and Viral dUTPase Impairs Murine Gammaherpesvirus Pathogenesis and Leads to Increased Recombination-Based Deletion in the Viral Genome. Mbio. 9. PMID 30377280 DOI: 10.1128/Mbio.01831-18  0.314
2018 Shapiro M, Meier S, MacCarthy T. Correction to: The cytidine deaminase under-representation reporter (CDUR) as a tool to study evolution of sequences under deaminase mutational pressure. Bmc Bioinformatics. 19: 256. PMID 29973133 DOI: 10.1186/S12859-018-2259-2  0.306
2018 Shapiro M, Meier S, MacCarthy T. The cytidine deaminase under-representation reporter (CDUR) as a tool to study evolution of sequences under deaminase mutational pressure. Bmc Bioinformatics. 19: 163. PMID 29716522 DOI: 10.1186/s12859-018-2161-y  0.327
2017 Chen J, MacCarthy T. The preferred nucleotide contexts of the AID/APOBEC cytidine deaminases have differential effects when mutating retrotransposon and virus sequences compared to host genes. Plos Computational Biology. 13: e1005471. PMID 28362825 DOI: 10.1371/Journal.Pcbi.1005471  0.432
2017 Yuan C, Chu CC, Yan XJ, Bagnara D, Chiorazzi N, MacCarthy T. The Number of Overlapping AID Hotspots in Germline IGHV Genes Is Inversely Correlated with Mutation Frequency in Chronic Lymphocytic Leukemia. Plos One. 12: e0167602. PMID 28125682 DOI: 10.1371/Journal.Pone.0167602  0.453
2016 Shin J, MacCarthy T. Potential for evolution of complex defense strategies in a multi-scale model of virus-host coevolution. Bmc Evolutionary Biology. 16: 233. PMID 27784264 DOI: 10.1186/S12862-016-0804-Z  0.306
2016 Maul RW, MacCarthy T, Frank EG, Donigan KA, McLenigan MP, Yang W, Saribasak H, Huston DE, Lange SS, Woodgate R, Gearhart PJ. DNA polymerase ι functions in the generation of tandem mutations during somatic hypermutation of antibody genes. The Journal of Experimental Medicine. PMID 27455952 DOI: 10.1084/Jem.20151227  0.441
2016 Patten PE, Ferrer G, Chen SS, Simone R, Marsilio S, Yan XJ, Gitto Z, Yuan C, Kolitz JE, Barrientos J, Allen SL, Rai KR, MacCarthy T, Chu CC, Chiorazzi N. Chronic lymphocytic leukemia cells diversify and differentiate in vivo via a nonclassical Th1-dependent, Bcl-6-deficient process. Jci Insight. 1. PMID 27158669 DOI: 10.1172/Jci.Insight.86288  0.334
2015 Shin J, MacCarthy T. Antagonistic Coevolution Drives Whack-a-Mole Sensitivity in Gene Regulatory Networks. Plos Computational Biology. 11: e1004432. PMID 26451700 DOI: 10.1371/Journal.Pcbi.1004432  0.433
2015 Ben-Dayan MM, MacCarthy T, Schlecht NF, Belbin TJ, Childs G, Smith RV, Prystowsky MB, Bergman A. Cancer as the Disintegration of Robustness: Population-Level Variance in Gene Expression Identifies Key Differences Between Tobacco- and HPV-Associated Oropharyngeal Carcinogenesis. Archives of Pathology & Laboratory Medicine. PMID 26132601 DOI: 10.5858/Arpa.2014-0624-Oa  0.576
2015 Kim M, McKinnon D, MacCarthy T, Rosati B, McKinnon D. Regulatory evolution and voltage-gated ion channel expression in squid axon: selection-mutation balance and fitness cliffs. Plos One. 10: e0120785. PMID 25875483 DOI: 10.1371/Journal.Pone.0120785  0.32
2015 Wei L, Chahwan R, Wang S, Wang X, Pham PT, Goodman MF, Bergman A, Scharff MD, MacCarthy T. Overlapping hotspots in CDRs are critical sites for V region diversification. Proceedings of the National Academy of Sciences of the United States of America. 112: E728-37. PMID 25646473 DOI: 10.1073/Pnas.1500788112  0.663
2015 Chu CC, Yan X, Dhayalan A, Patten PE, MacCarthy T, Yuan C, Barrientos JC, Kolitz JE, Allen SL, Rai KR, Chiorazzi N. The Correlation of APOBEC Gene Family Member Expression with Worse CLL Patient Outcome Suggests a Role in CLL Mutational Evolution Blood. 126: 363-363. DOI: 10.1182/Blood.V126.23.363.363  0.409
2014 Minkah N, Chavez K, Shah P, Maccarthy T, Chen H, Landau N, Krug LT. Host restriction of murine gammaherpesvirus 68 replication by human APOBEC3 cytidine deaminases but not murine APOBEC3. Virology. 454: 215-26. PMID 24725948 DOI: 10.1016/J.Virol.2014.02.022  0.317
2014 Gombar S, MacCarthy T, Bergman A. Epigenetics decouples mutational from environmental robustness. Did it also facilitate multicellularity? Plos Computational Biology. 10: e1003450. PMID 24604070 DOI: 10.1371/Journal.Pcbi.1003450  0.737
2014 Chu CC, Patten PE, MacCarthy T, Yuan C, Yan X, Barrientos JC, Kolitz JE, Allen SL, Rai KR, Chiorazzi N. IGHV-D-J Ultra-Deep Sequencing Reveals APOBEC and AID Targeted Mutations during Clonal Evolution of CLL in a Xenograft Mouse Model Blood. 124: 300-300. DOI: 10.1182/Blood.V124.21.300.300  0.439
2013 Chow SK, Smith C, MacCarthy T, Pohl MA, Bergman A, Casadevall A. Disease-enhancing antibodies improve the efficacy of bacterial toxin-neutralizing antibodies. Cell Host & Microbe. 13: 417-28. PMID 23601104 DOI: 10.1016/J.Chom.2013.03.001  0.65
2013 Pujato M, MacCarthy T, Fiser A, Bergman A. The underlying molecular and network level mechanisms in the evolution of robustness in gene regulatory networks. Plos Computational Biology. 9: e1002865. PMID 23300434 DOI: 10.1371/Journal.Pcbi.1002865  0.721
2013 Chu CC, Patten PE, MacCarthy T, Yan X, Barrientos JC, Kolitz JE, Allen SL, Rai KR, Chiorazzi N. Evaluation of IGHV Ultra-Deep Sequences for Activation-Induced Deaminase Characteristics in CLL Cells after T Cell Stimulation Blood. 122: 2583-2583. DOI: 10.1182/Blood.V122.21.2583.2583  0.44
2012 Patten PE, Chu CC, Albesiano E, Damle RN, Yan XJ, Kim D, Zhang L, Magli AR, Barrientos J, Kolitz JE, Allen SL, Rai KR, Roa S, Mongini PK, MacCarthy T, et al. IGHV-unmutated and IGHV-mutated chronic lymphocytic leukemia cells produce activation-induced deaminase protein with a full range of biologic functions. Blood. 120: 4802-11. PMID 23071276 DOI: 10.1182/Blood-2012-08-449744  0.343
2012 Wontakal SN, Guo X, Smith C, MacCarthy T, Bresnick EH, Bergman A, Snyder MP, Weissman SM, Zheng D, Skoultchi AI. A core erythroid transcriptional network is repressed by a master regulator of myelo-lymphoid differentiation. Proceedings of the National Academy of Sciences of the United States of America. 109: 3832-7. PMID 22357756 DOI: 10.1073/Pnas.1121019109  0.689
2012 Patten PE, MacCarthy T, Yan X, Kolitz JE, Allen SL, Barrientos JC, Rai KR, Chiorazzi N, Chu CC. Ultra-Deep Sequencing of De Novo IGHV Mutations in Activated CLL Cells: Evidence for Activation-Induced Deaminase Function. Blood. 120: 2545-2545. DOI: 10.1182/Blood.V120.21.2545.2545  0.42
2011 Baughn LB, Kalis SL, MacCarthy T, Wei L, Fan M, Bergman A, Scharff MD. Recombinase-mediated cassette exchange as a novel method to study somatic hypermutation in Ramos cells. Mbio. 2. PMID 21990614 DOI: 10.1128/Mbio.00186-11  0.655
2010 MacCarthy T, Seymour RM, Pomiankowski A. Differential regulation drives plasticity in sex determination gene networks Bmc Evolutionary Biology. 10. PMID 21162741 DOI: 10.1186/1471-2148-10-388  0.38
2009 MacCarthy T, Kalis SL, Roa S, Pham P, Goodman MF, Scharff MD, Bergman A. V-region mutation in vitro, in vivo, and in silico reveal the importance of the enzymatic properties of AID and the sequence environment. Proceedings of the National Academy of Sciences of the United States of America. 106: 8629-34. PMID 19443686 DOI: 10.1073/Pnas.0903803106  0.661
2009 Maccarthy T, Roa S, Scharff MD, Bergman A. SHMTool: a webserver for comparative analysis of somatic hypermutation datasets. Dna Repair. 8: 137-41. PMID 18952008 DOI: 10.1016/J.Dnarep.2008.09.006  0.65
2008 Roa S, Avdievich E, Peled JU, Maccarthy T, Werling U, Kuang FL, Kan R, Zhao C, Bergman A, Cohen PE, Edelmann W, Scharff MD. Ubiquitylated PCNA plays a role in somatic hypermutation and class-switch recombination and is required for meiotic progression. Proceedings of the National Academy of Sciences of the United States of America. 105: 16248-53. PMID 18854411 DOI: 10.1073/Pnas.0808182105  0.658
2007 MacCarthy T, Bergman A. The limits of subfunctionalization. Bmc Evolutionary Biology. 7: 213. PMID 17988397 DOI: 10.1186/1471-2148-7-213  0.605
2007 Bergman A, Atzmon G, Ye K, MacCarthy T, Barzilai N. Buffering mechanisms in aging: a systems approach toward uncovering the genetic component of aging. Plos Computational Biology. 3: e170. PMID 17784782 DOI: 10.1371/Journal.Pcbi.0030170  0.609
2007 MacCarthy T, Bergman A. Coevolution of robustness, epistasis, and recombination favors asexual reproduction. Proceedings of the National Academy of Sciences of the United States of America. 104: 12801-6. PMID 17646644 DOI: 10.1073/Pnas.0705455104  0.613
2005 MacCarthy T, Pomiankowski A, Seymour R. Using large-scale perturbations in gene network reconstruction Bmc Bioinformatics. 6. PMID 15659246 DOI: 10.1186/1471-2105-6-11  0.364
2003 MacCarthy T, Seymour R, Pomiankowski A. The evolutionary potential of the Drosophila sex determination gene network Journal of Theoretical Biology. 225: 461-468. PMID 14615204 DOI: 10.1016/S0022-5193(03)00282-0  0.407
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