Adam M. Phillippy

Adam M. Phillippy

Genome Informatics Section at the National Human Genome Research Institute
Dr. Adam Phillippy is a Senior Investigator and head of the Genome Informatics Section at the National Human Genome Research Institute. His lab develops and applies computational methods for the analysis of massive genomics datasets, focusing on the challenges of genome sequencing and comparative genomics. He is a pioneer of single-molecule sequencing for the reconstruction of complete genomes and is best known for his work on completing the human genome from “telomere to telomere”.

Interests

  • Development and application of computational methods for the analysis of massive genomics datasets
  • Genome sequencing and comparative genomics

Education

  • Ph.D.
    University of Maryland, College Park
  • M.S.
    University of Maryland, College Park

Publications

G Formenti, DE Absolon, LAL Abueg, F Ackerman, FO Al-Ajli, A Aleixo, A Antunes, D Arcila, J-N Audet, JR Balacco, AJS Beavan, K Belov, R Betancur-R, SL Bidwell, MT Biegler, I Bista, M Blaxter, K Boyer, I Braasch, IR Bradbury, N Brajuka, AM Bronikowski, T Brown, G Butler, S Cao, E Charvel, Y Chen, C Ciofi, HM Clawson, JC Collins, S Correard, S Corrigan, M Couture, AJ Crawford, ND D’Alessandre, HB da Conceicao, RR da Fonseca, M Daigavane, J Dalapicolla, M de Bruyn, E de Jong, DN De Panis, HW Detrich III, C DeWeese Scott, M Diekhans, E Duarte, R Durbin, M Escalona, M Eschenbrenner, O Fedrigo, J Fenn, P Flannery, N Forde, SM Gable, PA Galante, R Ganesan, A Gardiner, E Garrison, NJ Gemmell, MTP Gilbert, F Giudicelli, TM Gonçalves, GDA Guardia, A Guarracino, A Gupta, B Haase, D Hays, G Hickey, M Hiller, PM Hime, CJ Hogg, KM Horan, K Howe, D Jackson, N Jain, L Kang, S Kliver, Byung June Ko, K-P Koepfli, A Komissarov, LM Komoroske, B Koo, S Koren, J Korlach, I Kovacic, K Krasheninnikova, LF Kuderna, RA Langlois, D Lariviere, DM Larkin, C Lee, YH Lee, HA Lewin, D Lim, RN Lou, SS Mak, Kateryna Makova, Ph.D., L Marín-Gual, T Marques-Bonet, FJ Martin, TC Mathers, CJ Mazzoni, K McCaffrey, SA McCarthy, JA Medico, RLV Mercuri, A Meyer, P Michalak, S Mirarab, PA Morin, J Mountcastle, RW Murphy, TD Murphy, EW Myers, GJ Naylor, T Near, Anton Nekrutenko, Z Ning, BJ Novak, MF O’Brien, MJ O’Connell, BP O’Toole, S Paez, B Paten, M Paulini, SE Pelan, M Pennell, AR Pfenning, Adam M. Phillippy, B Pinto, M Pippel, M Popova, M Prylutskyi, A Rhie, H Roest Crollius, A Ruiz-Herrera, O Ryder, Y Safonova, CA Santos, MC Schatz, S Secomandi, HB Shaffer, L Shalmiyev, B Shapiro, JJ Smith, M Sollitto, CG Sotero-Caio, CC Steiner, PH Sudmant, DJ Sweeney, SC Talbot, CH Taylor, EC Teeling, F Thibaud-Nissen, T Tilley, N Timoshevskaya, P Traore, Y Turakhia, M Uliano-Silva, C Venditti, B Venkatesh, SC Vernes, WC Warren, CV Whelan, Melissa A. Wilson Sayres, S Winkler, JM Wood, G Zhang, G Zhao, ED Jarvis, the Vertebrate Genomes Project Consortium Phase I (2026). The Vertebrate Genomes Project Phase I: A global reference genome resource. BIORXIV.
Paper Link Sex chromosome
P Hallast, A Rhie, M Loftus, M Mazzetto, P Ebert, S Gao, GV Martino, PA Audano, H Ashraf, Karol Pal, R Siford, J Ebler, S Koren, D Yoo, K Kim, Y Jiang, NF Hansen, P Hebbar, T Kanno, O Purnoch, C Montano, J Lin, KK Oshima, L Ren, A Guarracino, M Jensen, BJ Pinto, D Porubsky, S Kuziel, L Ni, J Li, P Balachandran, F Yilmaz, Human Genome Structural Variation Consortium (HGSVC), Human Pangenome Reference Consortium (HPRC), JO Korbel, B Paten, M Gerstein, Kateryna Makova, Ph.D., X Shi, Evan E. Eichler, CR Beck, MR Wilson, MK Konkel, T Marschall, Monika Cechova (Michalovova), G Logsdon, Adam M. Phillippy, C Lee (2026). Population-scale Y chromosome assemblies reveal recurrent remodeling within constrained architectures. BIORXIV.
Paper Link Sex chromosome
G Formenti, N Jain, JA Medico, M Sollitto, D Antipov, S Barcellos, M Biegler, I Borges, JK Chang, Y Chen, H Cheng, H Conceição, M Davenport, L De Oliveira, E Duarte, G Durham, J Fenn, N Forde, PA Galante, K Gerhardt, AM Giani, S Giunta, J Kim, A Komissarov, B Koo, S Koren, D Larkin, C Lee, H Li, K Makova, P Masterson, T Murphy, K McCaffrey, RLV Mercuri, Y Na, MJ O’Connell, S Ou, A Phillippy, M Popova, A Rhie, FJ Ruiz-Ruano, S Secomandi, Linnéa Smeds, A Suh, T Tilley, N Vontzou, PD Waters, J Balacco, ED Jarvis (2026). The complete genome of a songbird. CELL, ACCEPTED.
Paper Link Non-B DNA & Microsatellite
D Yoo, A Rhie, P Hebbar, F Antonacci, GA Logsdon, SJ Solar, D Antipov, BD Pickett, Y Safonova, F Montinaro, Y Luo, J Malukiewicz, JM Storer, J Lin, AN Sequeira, RJ Mangan, G Hickey, GM Anez, P Balachandran, A Bankevich, CR Beck, A Biddanda, M Borchers, GG Bouffard, E Brannan, SY Brooks, L Carbone, Laura Carrel, AP Chan, J Crawford, M Diekhans, E Engelbrecht, C Feschotte, G Formenti, GH Garcia, L de Gennaro, D Gilbert, RE Green, A Guarracino, I Gupta, D Haddad, J Han, Robert Harris, GA Hartley, WT Harvey, M Hiller, K Hoekzema, ML Houck, H Jeong, Kaivan Kamali, M Kellis, B Kille, C Lee, Y Lee, W Lees, AP Lewis, Q Li, M Loftus, YHE Loh, H Loucks, J Ma, Y Mao, JFI Martinez, P Masterson, RC McCoy, Barb McGrath, S McKinney, BS Meyer, KH Miga, Saswat Kumar Mohanty, KM Munson, Karol Pal, M Pennell, PA Pevzner, D Porubsky, T Potapova, FR Ringeling, JL Rocha, Oliver Ryder, S Sacco, S Saha, T Sasaki, MC Schatz, NJ Schork, C Shanks, Linnéa Smeds, DR Son, C Steiner, AP Sweeten, MG Tassia, F Thibaud-Nissen, Edmundo Torres-González, M Trivedi, W Wei, J Wertz, M Yang, P Zhang, S Zhang, Y Zhang, Z Zhang, SA Zhao, Y Zhu, ED Jarvis, JL Gerton, I Rivas-González, B Paten, ZA Szpiech, CD Huber, TL Lenz, MK Konkel, SV Yi, S Canzar, CT Watson, PH Sudmant, E Molloy, E Garrison, CB Lowe, M Ventura, RJ O’Neill, S Koren, Kateryna Makova, Ph.D., Adam M. Phillippy, EE Eichler (2025). Complete sequencing of ape genomes. NATURE.
Paper Link Sex chromosome
Kateryna Makova, Ph.D., BD Pickett, Robert Harris, GA Hartley, Monika Cechova (Michalovova), Karol Pal, S Nurk, D Yoo, Q Li, P Hebbar, BC McGrath, F Antonacci, M Aubel, A Biddanda, M Borchers, E Bomberg, GG Bouffard, SY Brooks, L Carbone, Laura Carrel, A Carroll, PC Chang, CS Chin, DE Cook, Sarah J. Carnahan Craig, L de Gennaro, M Diekhans, A Dutra, GH Garcia, PGS Grady, RE Green, D Haddad, P Hallast, WT Harvey, G Hickey, DA Hillis, SJ Hoyt, H Jeong, Kaivan Kamali, SL Kosakovsky Pond, TM LaPolice, C Lee, AP Lewis, YE Loh, P Masterson, RC McCoy, Paul Medvedev, KH Miga, KM Munson, E Pak, B Paten, BJ Pinto, T Potapova, A Rhie, JL Rocha, F Ryabov, Oliver Ryder, S Sacco, K Shafin, VA Shepelev, V Slon, SJ Solar, JM Storer, PH Sudmant, Sweetalana, A Sweeten, MG Tassia, F Thibaud-Nissen, M Ventura, Melissa A. Wilson Sayres, AC Young, Huiqing Zeng, Xinru Zhang, ZA Szpiech, CD Huber, JL Gerton, SV Yi, MC Schatz, IA Alexandrov, S Koren, RJ O’Neill, Evan E. Eichler, Adam M. Phillippy (2024). The Complete Sequence and Comparative Analysis of Ape Sex Chromosomes. NATURE.
Video Press release Paper Link Sex chromosome
A Rhie, S Nurk, Monika Cechova (Michalovova), SJ Hoyt, DJ Taylor, N Altemose, PW Hook, S Koren, M Rautiainen, IA Alexandrov, J Allen, M Asri, AV Bzikadze, N-C Chen, C-S Chin, M Diekhans, P Flicek, G Formenti, Arkarachai Fungtammasan, CG Giron, E Garrison, A Gershman, JL Gerton, PGS Grady, A Guarracino, L Haggerty, R Halabian, NF Hansen, R Harris, GA Hartley, WT Harvey, M Haukness, J Heinz, T Hourlier, RM Hubley, SE Hunt, S Hwang, M Jain, RK Kesharwani, AP Lewis, H Li, GA Logsdon, JK Lucas, W Makalowski, C Markovic, FJ Martin, AM McCartney, RC McCoy, J McDaniel, BM McNulty, Paul Medvedev, A Mikheenko, KM Munson, TD Murphy, HE Olsen, ND Olson, LF Paulin, D Porubsky, T Potapova, F Ryabov, SL Salzberg, MEG Sauria, FJ Sedlazeck, K Shafin, VA Shepelev, A Shumate, JM Storer, L Surapaneni, AM Taravella Oill, F Thibaud-Nissen, W Timp, Marta Tomaszkiewicz, MR Vollger, BP Walenz, AC Watwood, MH Weissensteiner, AM Wenger, Melissa A. Wilson Sayres, S Zarate, Y Zhu, JM Zook, EE Eichler, RJ O’Neill, MC Schatz, KH Miga, Kateryna Makova, Ph.D., Adam M. Phillippy (2023). The complete sequence of a human Y chromosome. NATURE.
Paper Link Sex chromosome
A Rhie, SA McCarthy, O Fedrigo, J Damas, G Formenti, S Koren, M Uliano-Silva, W Chow, Arkarachai Fungtammasan, GL Gedman, LJ Cantin, F Thibaud-Nissen, L Haggerty, C Lee, Byung June Ko, J Kim, I Bista, M Smith, B Haase, J Mountcastle, S Winkler, S Paez, J Howard, SC Vernes, TM Lama, F Grutzner, WC Warren, C Balakrishnan, D Burt, JM George, M Biegler, D Iorns, A Digby, D Eason, T Edwards, M Wilkinson, G Turner, A Meyer, AF Kautt, P Franchini, HW Detrich III, H Svardal, M Wagner, GJP Naylor, M Pippel, M Malinsky, M Mooney, M Simbirsky, BT Hannigan, T Pesout, M Houck, A Misuraca, SB Kingan, R Hall, Z Kronenberg, J Korlach, I Sović, C Dunn, Z Ning, A Hastie, J Lee, S Selvaraj, RE Green, NH Putnam, J Ghurye, E Garrison, Y Sims, J Collins, S Pelan, J Torrance, A Tracey, J Wood, D Guan, SE London, DF Clayton, CV Mello, SR Friedrich, PV Lovell, E Osipova, FO Al-Ajli, S Secomandi, H Kim, C Theofanopoulou, Y Zhou, Robert Harris, Kateryna Makova, Ph.D., Paul Medvedev, J Hoffman, P Masterson, K Clark, F Martin, K Howe, P Flicek, BP Walenz, W Kwak, H Clawson, M Diekhans, L Nassar, B Paten, RHS Kraus, H Lewin, AJ Crawford, MTP Gilbert, G Zhang, B Venkatesh, RW Murphy, KP Koepfli, B Shapiro, WE Johnson, F Di Palma, T Margues-Bonet, EC Teeling, T Warnow, JM Graves, Oliver Ryder, D Hausler, SJ O’Brien, K Howe, EW Myers, R Durbin, Adam M. Phillippy, ED Jarvis (2021). Towards complete and error-free genome assemblies of all vertebrate species. NATURE.
Paper Link Sex chromosome