Bony De Kumar, PhD
Research Scientist; Director of Operations of the Yale Center for Genome Analysis
Research & Publications
Biography
Locations
Coauthors
Selected Publications
- Multiscale genetic architecture of donor-recipient differences reveals intronic LIMS1 mismatches associated with kidney transplant survivalSun Z, Zhang Z, Banu K, Gibson I, Colvin R, Yi Z, Zhang W, De Kumar B, Reghuvaran A, Pell J, Manes T, Djamali A, Gallon L, O'Connell P, He J, Pober J, Heeger P, Menon M. Multiscale genetic architecture of donor-recipient differences reveals intronic LIMS1 mismatches associated with kidney transplant survival. Journal Of Clinical Investigation 2023, 133: e170420. PMID: 37676733, PMCID: PMC10617779, DOI: 10.1172/jci170420.
- Shared retinoic acid responsive enhancers coordinately regulate nascent transcription of Hoxb coding and non-coding RNAs in the developing mouse neural tubeAfzal Z, Lange J, Nolte C, McKinney S, Wood C, Paulson A, De Kumar B, Unruh J, Slaughter B, Krumlauf R. Shared retinoic acid responsive enhancers coordinately regulate nascent transcription of Hoxb coding and non-coding RNAs in the developing mouse neural tube. Development 2023, 150: dev201259. PMID: 37102683, PMCID: PMC10233718, DOI: 10.1242/dev.201259.
- Enhanced inhibition of MHC-I expression by SARS-CoV-2 Omicron subvariantsMoriyama M, Lucas C, Monteiro V, Initiative Y, Iwasaki A, Chen N, Breban M, Hahn A, Pham K, Koch T, Chaguza C, Tikhonova I, Castaldi C, Mane S, De Kumar B, Ferguson D, Kerantzas N, Peaper D, Landry M, Schulz W, Vogels C, Grubaugh N. Enhanced inhibition of MHC-I expression by SARS-CoV-2 Omicron subvariants. Proceedings Of The National Academy Of Sciences Of The United States Of America 2023, 120: e2221652120. PMID: 37036977, PMCID: PMC10120007, DOI: 10.1073/pnas.2221652120.
- Utility of promoter hypermethylation in malignant risk stratification of intraductal papillary mucinous neoplasmsChhoda A, Sharma A, Sailo B, Tang H, Ruzgar N, Tan W, Ying L, Khatri R, Narayanan A, Mane S, De Kumar B, Wood L, Iacobuzio-Donahue C, Wolfgang C, Kunstman J, Salem R, Farrell J, Ahuja N. Utility of promoter hypermethylation in malignant risk stratification of intraductal papillary mucinous neoplasms. Clinical Epigenetics 2023, 15: 28. PMID: 36803844, PMCID: PMC9942382, DOI: 10.1186/s13148-023-01429-5.
- Age-dependent impairment in antibody responses elicited by a homologous CoronaVac booster doseFilardi B, Monteiro V, Schwartzmann P, do Prado Martins V, Zucca L, Baiocchi G, Malik A, Silva J, Hahn A, Chen N, Pham K, Pérez-Then E, Miric M, Brache V, Cochon L, Larocca R, Della Rosa Mendez R, Silveira D, Pinto A, Croda J, Yildirim I, Omer S, Ko A, Vermund S, Grubaugh N, Iwasaki A, Lucas C, Initiative Y, Vogels C, Breban M, Koch T, Chaguza C, Tikhonova I, Castaldi C, Mane S, De Kumar B, Ferguson D, Kerantzas N, Peaper D, Landry M, Schulz W. Age-dependent impairment in antibody responses elicited by a homologous CoronaVac booster dose. Science Translational Medicine 2023, 15: eade6023. PMID: 36791210, DOI: 10.1126/scitranslmed.ade6023.
- Accelerated SARS-CoV-2 intrahost evolution leading to distinct genotypes during chronic infectionChaguza C, Hahn A, Petrone M, Zhou S, Ferguson D, Breban M, Pham K, Peña-Hernández M, Castaldi C, Hill V, Initiative Y, Billig K, Earnest R, Fauver J, Kalinch C, Kerantzas N, Koch T, De Kumar B, Landry M, Ott I, Peaper D, Tikhonova I, Vogels C, Schulz W, Swanstrom R, Roberts S, Grubaugh N. Accelerated SARS-CoV-2 intrahost evolution leading to distinct genotypes during chronic infection. Cell Reports Medicine 2023, 4: 100943. PMID: 36791724, PMCID: PMC9906997, DOI: 10.1016/j.xcrm.2023.100943.
- DNA methylation of the promoter region at the CREB1 binding site is a mechanism for the epigenetic regulation of brain-specific PKMζPramio D, Vieceli F, Varella-Branco E, Goes C, Kobayashi G, da Silva Pelegrina D, de Moraes B, El Allam A, De Kumar B, Jara G, Farfel J, Bennett D, Kundu S, Viapiano M, Reis E, de Oliveira P, Dos Santos E Passos-Bueno M, Rothlin C, Ghosh S, Schechtman D. DNA methylation of the promoter region at the CREB1 binding site is a mechanism for the epigenetic regulation of brain-specific PKMζ. Biochimica Et Biophysica Acta (BBA) - Gene Regulatory Mechanisms 2023, 1866: 194909. PMID: 36682583, PMCID: PMC10037092, DOI: 10.1016/j.bbagrm.2023.194909.
- Cellular Heterogeneity and Molecular Reprogramming of the Host Response during Influenza Acute Lung InjuryGuo K, Yombo D, Schmit T, Wang Z, Navaeiseddighi Z, Sathish V, Mathur R, Wu M, De Kumar B, Hur J, Khan N. Cellular Heterogeneity and Molecular Reprogramming of the Host Response during Influenza Acute Lung Injury. Journal Of Virology 2022, 96: e01246-22. PMID: 36286482, PMCID: PMC9645213, DOI: 10.1128/jvi.01246-22.
- Rapid emergence of SARS-CoV-2 Omicron variant is associated with an infection advantage over Delta in vaccinated personsChaguza C, Coppi A, Earnest R, Ferguson D, Kerantzas N, Warner F, Young HP, Breban MI, Billig K, Koch RT, Pham K, Kalinich CC, Ott IM, Fauver JR, Hahn AM, Tikhonova IR, Castaldi C, De Kumar B, Pettker CM, Warren JL, Weinberger DM, Landry ML, Peaper DR, Schulz W, Vogels CBF, Grubaugh ND. Rapid emergence of SARS-CoV-2 Omicron variant is associated with an infection advantage over Delta in vaccinated persons. Med 2022, 3: 325-334.e4. PMID: 35399324, PMCID: PMC8983481, DOI: 10.1016/j.medj.2022.03.010.
- Comparative transmissibility of SARS-CoV-2 variants Delta and Alpha in New England, USAEarnest R, Uddin R, Matluk N, Renzette N, Turbett SE, Siddle KJ, Loreth C, Adams G, Tomkins-Tinch CH, Petrone ME, Rothman JE, Breban MI, Koch RT, Billig K, Fauver JR, Vogels CBF, Bilguvar K, De Kumar B, Landry ML, Peaper DR, Kelly K, Omerza G, Grieser H, Meak S, Martha J, Dewey HB, Kales S, Berenzy D, Carpenter-Azevedo K, King E, Huard RC, Novitsky V, Howison M, Darpolor J, Manne A, Kantor R, Smole SC, Brown CM, Fink T, Lang AS, Gallagher GR, Pitzer VE, Sabeti PC, Gabriel S, MacInnis BL, Team N, Altajar A, DeJesus A, Brito A, Watkins A, Muyombwe A, Blumenstiel B, Neal C, Kalinich C, Liu C, Loreth C, Castaldi C, Pearson C, Bernard C, Nolet C, Ferguson D, Buzby E, Laszlo E, Reagan F, Vicente G, Rooke H, Munger H, Johnson H, Tikhonova I, Ott I, Razeq J, Meldrim J, Brown J, Wang J, Vostok J, Beauchamp J, Grimsby J, Hall J, Messer K, Larkin K, Vernest K, Madoff L, Green L, Webber L, Gagne L, Ulcena M, Ray M, Fisher M, Barter M, Lee M, DeFelice M, Cipicchio M, Smith N, Lennon N, Fitzgerald N, Kerantzas N, Hui P, Harrington R, Downing R, Haye R, Lynch R, Anderson S, Hennigan S, English S, Cofsky S, Clancy S, Mane S, Ash S, Baez S, Fleming S, Murphy S, Chaluvadi S, Alpert T, Rivard T, Schulz W, Mandese Z, Tewhey R, Adams M, Park D, Lemieux J, Grubaugh N. Comparative transmissibility of SARS-CoV-2 variants Delta and Alpha in New England, USA. Cell Reports Medicine 2022, 3: 100583. PMID: 35480627, PMCID: PMC8913280, DOI: 10.1016/j.xcrm.2022.100583.
- Assessment of Clinical Effectiveness of BNT162b2 COVID-19 Vaccine in US AdolescentsOliveira CR, Niccolai LM, Sheikha H, Elmansy L, Kalinich CC, Grubaugh ND, Shapiro ED, Billig K, Breban M, Brito A, Earnest R, Fauver J, Koch T, Ott I, Petrone M, Vogels C, Pham K, Tikhonova I, Castaldi C, Mane S, Bilguvar K, De Kumar B, Ferguson D, Kerantzas N, Landry M, Peaper D, Schulz W. Assessment of Clinical Effectiveness of BNT162b2 COVID-19 Vaccine in US Adolescents. JAMA Network Open 2022, 5: e220935. PMID: 35238933, PMCID: PMC8895259, DOI: 10.1001/jamanetworkopen.2022.0935.
- Analysis of lamprey meis genes reveals that conserved inputs from Hox, Meis and Pbx proteins control their expression in the hindbrain and neural tubeParker H, De Kumar B, Pushel I, Bronner M, Krumlauf R. Analysis of lamprey meis genes reveals that conserved inputs from Hox, Meis and Pbx proteins control their expression in the hindbrain and neural tube. Developmental Biology 2021, 479: 61-76. PMID: 34310923, DOI: 10.1016/j.ydbio.2021.07.014.
- Autocrine GMCSF Signaling Contributes to Growth of HER2+ Breast Leptomeningeal CarcinomatosisGMCSF Contributes to Breast Leptomeningeal CarcinomatosisAnsari K, Bhan A, Saotome M, Tyagi A, De Kumar B, Chen C, Takaku M, Jandial R. Autocrine GMCSF Signaling Contributes to Growth of HER2+ Breast Leptomeningeal CarcinomatosisGMCSF Contributes to Breast Leptomeningeal Carcinomatosis. Cancer Research 2021, 81: 4723-4735. PMID: 34247146, PMCID: PMC8986153, DOI: 10.1158/0008-5472.can-21-0259.
- The Hox protein conundrum: The “specifics” of DNA binding for Hox proteins and their partnersDe Kumar B, Darland D. The Hox protein conundrum: The “specifics” of DNA binding for Hox proteins and their partners. Developmental Biology 2021, 477: 284-292. PMID: 34102167, PMCID: PMC8846413, DOI: 10.1016/j.ydbio.2021.06.002.
- Genome-Wide Binding Analyses of HOXB1 Revealed a Novel DNA Binding Motif Associated with Gene RepressionSingh N, De Kumar B, Paulson A, Parrish M, Scott C, Zhang Y, Florens L, Krumlauf R. Genome-Wide Binding Analyses of HOXB1 Revealed a Novel DNA Binding Motif Associated with Gene Repression. Journal Of Developmental Biology 2021, 9: 6. PMID: 33546292, PMCID: PMC7931043, DOI: 10.3390/jdb9010006.
- A six-amino-acid motif is a major determinant in functional evolution of HOX1 proteinsSingh N, De Kumar B, Paulson A, Parrish M, Zhang Y, Florens L, Conaway J, Si K, Krumlauf R. A six-amino-acid motif is a major determinant in functional evolution of HOX1 proteins. Genes & Development 2020, 34: 1680-1696. PMID: 33184220, PMCID: PMC7706710, DOI: 10.1101/gad.342329.120.
- Analysis of DNA Methylation Changes in Mice Mediated by Early‐life Exposure to the Antidepressant S‐citalopramRodriquez M, Shetty M, Black E, Kretschmar M, Perley D, De Kumar B, Henry L. Analysis of DNA Methylation Changes in Mice Mediated by Early‐life Exposure to the Antidepressant S‐citalopram. The FASEB Journal 2020, 34: 1-1. DOI: 10.1096/fasebj.2020.34.s1.06398.
- Cancer-specific mutation of GATA3 disrupts the transcriptional regulatory network governed by Estrogen Receptor alpha, FOXA1 and GATA3Takaku M, Grimm S, De Kumar B, Bennett B, Wade P. Cancer-specific mutation of GATA3 disrupts the transcriptional regulatory network governed by Estrogen Receptor alpha, FOXA1 and GATA3. Nucleic Acids Research 2020, 48: 4756-4768. PMID: 32232341, PMCID: PMC7229857, DOI: 10.1093/nar/gkaa179.
- Hox genes: Downstream “effectors” of retinoic acid signaling in vertebrate embryogenesisNolte C, De Kumar B, Krumlauf R. Hox genes: Downstream “effectors” of retinoic acid signaling in vertebrate embryogenesis. Genesis 2019, 57: e23306. PMID: 31111645, DOI: 10.1002/dvg.23306.
- A Hox-TALE regulatory circuit for neural crest patterning is conserved across vertebratesParker H, De Kumar B, Green S, Prummel K, Hess C, Kaufman C, Mosimann C, Wiedemann L, Bronner M, Krumlauf R. A Hox-TALE regulatory circuit for neural crest patterning is conserved across vertebrates. Nature Communications 2019, 10: 1189. PMID: 30867425, PMCID: PMC6416258, DOI: 10.1038/s41467-019-09197-8.
- Retinoid-Sensitive Epigenetic Regulation of the Hoxb Cluster Maintains Normal Hematopoiesis and Inhibits LeukemogenesisQian P, De Kumar B, He X, Nolte C, Gogol M, Ahn Y, Chen S, Li Z, Xu H, Perry J, Hu D, Tao F, Zhao M, Han Y, Hall K, Peak A, Paulson A, Zhao C, Venkatraman A, Box A, Perera A, Haug J, Parmely T, Li H, Krumlauf R, Li L. Retinoid-Sensitive Epigenetic Regulation of the Hoxb Cluster Maintains Normal Hematopoiesis and Inhibits Leukemogenesis. Cell Stem Cell 2018, 22: 740-754.e7. PMID: 29727682, DOI: 10.1016/j.stem.2018.04.012.
- Hoxa1 targets signaling pathways during neural differentiation of ES cells and mouse embryogenesisDe Kumar B, Parker H, Paulson A, Parrish M, Zeitlinger J, Krumlauf R. Hoxa1 targets signaling pathways during neural differentiation of ES cells and mouse embryogenesis. Developmental Biology 2017, 432: 151-164. PMID: 28982536, DOI: 10.1016/j.ydbio.2017.09.033.
- HOXA1 and TALE proteins display cross-regulatory interactions and form a combinatorial binding code on HOXA1 targetsDe Kumar B, Parker H, Paulson A, Parrish M, Pushel I, Singh N, Zhang Y, Slaughter B, Unruh J, Florens L, Zeitlinger J, Krumlauf R. HOXA1 and TALE proteins display cross-regulatory interactions and form a combinatorial binding code on HOXA1 targets. Genome Research 2017, 27: 1501-1512. PMID: 28784834, PMCID: PMC5580710, DOI: 10.1101/gr.219386.116.
- Dynamic regulation of Nanog and stem cell-signaling pathways by Hoxa1 during early neuro-ectodermal differentiation of ES cellsDe Kumar B, Parker H, Parrish M, Lange J, Slaughter B, Unruh J, Paulson A, Krumlauf R. Dynamic regulation of Nanog and stem cell-signaling pathways by Hoxa1 during early neuro-ectodermal differentiation of ES cells. Proceedings Of The National Academy Of Sciences Of The United States Of America 2017, 114: 5838-5845. PMID: 28584089, PMCID: PMC5468655, DOI: 10.1073/pnas.1610612114.
- The Methylation-Sensitive Enhancer Derare Maintains Hematopoietic Stem Cells through Regulation of Hoxb ClusterQian P, De Kumar B, Ahn Y, Nolte C, Paulson A, He X, Li Z, Perry J, Zhao M, Tao F, Krumlauf R, Li L. The Methylation-Sensitive Enhancer Derare Maintains Hematopoietic Stem Cells through Regulation of Hoxb Cluster. Blood 2016, 128: 725. DOI: 10.1182/blood.v128.22.725.725.
- HOXs and lincRNAs: Two sides of the same coinDe Kumar B, Krumlauf R. HOXs and lincRNAs: Two sides of the same coin. Science Advances 2016, 2: e1501402. PMID: 27034976, PMCID: PMC4805430, DOI: 10.1126/sciadv.1501402.
- A Conserved Cis-Regulatory Retinoic Acid Responsive Element Is Essential for Maintenance of Primitive Hematopoietic Stem Cells through Regulation of Hoxb ClusterQian P, Ahn Y, De Kumar B, Nolte C, He X, Paulson A, Perry J, Li Z, Krumlauf R, Li L. A Conserved Cis-Regulatory Retinoic Acid Responsive Element Is Essential for Maintenance of Primitive Hematopoietic Stem Cells through Regulation of Hoxb Cluster. Blood 2015, 126: 2377. DOI: 10.1182/blood.v126.23.2377.2377.
- Analysis of dynamic changes in retinoid-induced transcription and epigenetic profiles of murine Hox clusters in ES cellsDe Kumar B, Parrish M, Slaughter B, Unruh J, Gogol M, Seidel C, Paulson A, Li H, Gaudenz K, Peak A, McDowell W, Fleharty B, Ahn Y, Lin C, Smith E, Shilatifard A, Krumlauf R. Analysis of dynamic changes in retinoid-induced transcription and epigenetic profiles of murine Hox clusters in ES cells. Genome Research 2015, 25: 1229-1243. PMID: 26025802, PMCID: PMC4510006, DOI: 10.1101/gr.184978.114.
- Hox Complex Analysis Through BAC RecombineeringParrish M, Ahn Y, Nolte C, De Kumar B, Krumlauf R. Hox Complex Analysis Through BAC Recombineering. 2014, 1196: 59-87. PMID: 25151158, DOI: 10.1007/978-1-4939-1242-1_5.
- Insights from transcriptional profiling the mouse hindbrain: Novel feedback between retinoids and Hox genesYurieva M, De Kumar B, Krumlauf R. Insights from transcriptional profiling the mouse hindbrain: Novel feedback between retinoids and Hox genes. The FASEB Journal 2013, 27: 966.1-966.1. DOI: 10.1096/fasebj.27.1_supplement.966.1.
- Poised RNA Polymerase II Changes over Developmental Time and Prepares Genes for Future ExpressionGaertner B, Johnston J, Chen K, Wallaschek N, Paulson A, Garruss A, Gaudenz K, De Kumar B, Krumlauf R, Zeitlinger J. Poised RNA Polymerase II Changes over Developmental Time and Prepares Genes for Future Expression. Cell Reports 2012, 2: 1670-1683. PMID: 23260668, PMCID: PMC3572839, DOI: 10.1016/j.celrep.2012.11.024.
- Dynamic transcriptional events in embryonic stem cells mediated by the super elongation complex (SEC)Lin C, Garrett A, De Kumar B, Smith E, Gogol M, Seidel C, Krumlauf R, Shilatifard A. Dynamic transcriptional events in embryonic stem cells mediated by the super elongation complex (SEC). Genes & Development 2011, 25: 1486-1498. PMID: 21764852, PMCID: PMC3143939, DOI: 10.1101/gad.2059211.