| The Makova Lab at Penn State

Adam M. Phillippy

Senior Investigator, Genome Informatics Section at the National Human Genome Research Institute

Personal website

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

Biography

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”.

Publications

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, L 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, RS Harris, GA Hartley, WT Harvey, M Hiller, K Hoekzema, ML Houck, H Jeong, K 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, B McGrath, S McKinney, BS Meyer, KH Miga, SK Mohanty, KM Munson, K Pal, M Pennell, PA Pevzner, D Porubsky, T Potapova, FR Ringeling, JL Rocha, OA Ryder, S Sacco, S Saha, T Sasaki, MC Schatz, NJ Schork, C Shanks, L Smeds, DR Son, C Steiner, AP Sweeten, MG Tassia, F Thibaud-Nissen, E 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, KD Makova, AM Phillippy, EE Eichler. Complete sequencing of ape genomes. BIORXIV, 2024.

Paper Link

KD Makova, BD Pickett, RS Harris, GA Hartley, M Cechova, K 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, L Carrel, A Carroll, PC Chang, CS Chin, DE Cook, SJC 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, K Kamali, SL Kosakovsky Pond, TM LaPolice, C Lee, AP Lewis, YE Loh, P Masterson, RC McCoy, P Medvedev, KH Miga, KM Munson, E Pak, B Paten, BJ Pinto, T Potapova, A Rhie, JL Rocha, F Ryabov, OA 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, MA Wilson, AC Young, H Zeng, X Zhang, ZA Szpiech, CD Huber, JL Gerton, SV Yi, MC Schatz, IA Alexandrov, S Koren, RJ O’Neill, E Eichler, AM Phillippy. The Complete Sequence and Comparative Analysis of Ape Sex Chromosomes. NATURE, 2024.

Sex chromosome Video Paper Link Press release

A Rhie, S Nurk, M Cechova, 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, A 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, P 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, M Tomaszkiewicz, MR Vollger, BP Walenz, AC Watwood, MH Weissensteiner, AM Wenger, MA Wilson, S Zarate, Y Zhu, JM Zook, EE Eichler, RJ O’Neill, MC Schatz, KH Miga, KD Makova, AM Phillippy. The complete sequence of a human Y chromosome. NATURE, 2023.

Sex chromosome Paper Link

A Rhie, SA McCarthy, O Fedrigo, J Damas, G Formenti, S Koren, M Uliano-Silva, W Chow, A Fungtammasan, GL Gedman, LJ Cantin, F Thibaud-Nissen, L Haggerty, C Lee, BJ 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, RS Harris, KD Makova, P 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, OA Ryder, D Hausler, SJ O’Brien, K Howe, EW Myers, R Durbin, AM Phillippy, ED Jarvis. Towards complete and error-free genome assemblies of all vertebrate species. NATURE, 2021.

Sex chromosome Paper Link