Several lines of our recent research have had mammalian sex chromosome evolution as a common theme. We have been studying the genomic determinants of X chromosome inactivation (XCI; Carrel et al. 2006). By contrasting the evolution of genes on sex chromosomes in eutherians with that of their autosomal homologs in marsupials and monotremes, we were able to shed light on the earliest stages of eutherian sex chromosome evolution (Wilson and Makova 2009). We also recently generated a comprehensive list of pseudogenes on the human Y and studied what determines whether a gene will survive or die on this chromosome (Wilson Sayres and Makova 2013). To test whether selection or drift leads to loss of genes on chromosome Y, we sequenced and analyzed all X-degenerate Y chromosome genes in gorilla (Goto et al. 2009) and are currently characterizing such genes in other primates. (Figure : Wilson Sayres & Makova 2013). Collaborators: Laura Carrel, Paul Medvedev.
Researchers have reconstructed the ancestral sequence of the great ape Y chromosome by comparing three existing (gorilla, human, and …
Sam Sholtis
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.
NATURE,
2025.
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.
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.
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.
RA Gibbs, J Rogers, MG Katze, R Bumgarner, GM Weinstock, ER Mardis, KA Remington, RL Strausberg, JC Venter, RK Wilson, MA Batzer, CD Bustamante, EE Eichler, MW Hahn, RC Hardison, KD Makova, W Miller, A Milosavljevic, RE Palermo, A Siepel, JM Sikela, T Attaway, S Bell, KE Bernard, CJ Buhay, MN Chandrabose, M Dao, C Davis, KD Delehaunty, Y Ding, HH Dinh, S Dugan-Rocha, LA Fulton, RA Gabisi, TT Garner, J Godfrey, AC Hawes, J Hernandez, S Hines, M Holder, J Hume, SN Jhangiani, V Joshi, ZM Khan, EF Kirkness, A Cree, RG Fowler, S Lee, LR Lewis, Z Li, Y-S Liu, SM Moore, DM Muzny, LV Nazareth, DN Ngo, GO Okwuonu, G Pai, D Parker, HA Paul, CM Pfannkoch, CS Pohl, Y-H Rogers, SJ Ruiz, A Sabo, J Santibanez, BW Schneider, SM Smith, EJ Sodergren, AF Svatek, TR Utterback, S Vattathil, W Warren, CS White, AT Chinwalla, Y Feng, AL Halpern, LW Hillier, X Huang, P Minx, JO Nelson, KH Pepin, X Qin, GG Sutton, E Venter, BP Walenz, JW Wallis, KC Worley, S-P Yang, SM Jones, MA Marra, M Rocchi, JE Schein, R Baertsch, L Clarke, M Csürös, J Glasscock, RA Harris, PH Havlak, AR Jackson, H Jiang, Y Liu, DN Messina, Y Shen, HX-Z Song, T Wylie, L Zhang, E Birney, K Han, MK Konkel, J Lee, AFA Smit, B Ullmer, H Wang, J Xing, RC Burhans, Z Cheng, JE Karro, J Ma, B Raney, X She, MJ Cox, JP Demuth, LJ Dumas, S-G Han, J Hopkins, A Karimpour-Fard, YH Kim, JR Pollack, T Vinar, C Addo-Quaye, J Degenhardt, A Denby, MJ Hubisz, A Indap, C Kosiol, BT Lahn, HA Lawson, A Marklein, R Nielsen, EJ Vallender, AG Clark, B Ferguson, RD Hernandez, K Hirani, H Kehrer-Sawatzki, J Kolb, S Patil, L-L Pu, Y Ren, DG Smith, DA Wheeler, I Schenck, EV Ball, R Chen, DN Cooper, B Giardine, F Hsu, WJ Kent, A Lesk, DL Nelson, WE O’Brien, K Prüfer, PD Stenson, JC Wallace, H Ke, X-M Liu, P Wang, AP Xiang, F Yang, GP Barber, D Haussler, D Karolchik, AD Kern, RM Kuhn, KE Smith, AS Zwieg.
Evolutionary and Biomedical Insights from the Rhesus Macaque Genome.
SCIENCE,
2007.
International Chicken Genome Sequencing Consortium, LW Hillier, W Miller, E Birney, W Warren, RC Hardison, CP Ponting, P Bork, DW Burt, MAM Groenen, ME Delany, JB Dodgson, AT Chinwalla, PF Cliften, SW Clifton, KD Delehaunty, C Fronick, RS Fulton, TA Graves, C Kremitzki, D Layman, V Magrini, JD McPherson, TL Miner, P Minx, WE Nash, MN Nhan, JO Nelson, LG Oddy, CS Pohl, J Randall-Maher, SM Smith, JW Wallis, S-P Yang, MN Romanov, CM Rondelli, B Paton, J Smith, D Morrice, L Daniels, HG Tempest, L Robertson, JS Masabanda, DK Griffin, A Vignal, V Fillon, L Jacobbson, S Kerje, L Andersson, RPM Crooijmans, J Aerts, JJ van der Poel, H Ellegren, RB Caldwell, SJ Hubbard, DV Grafham, AM Kierzek, SR McLaren, IM Overton, H Arakawa, KJ Beattie, Y Bezzubov, PE Boardman, JK Bonfield, MDR Croning, RM Davies, MD Francis, SJ Humphray, CE Scott, RG Taylor, C Tickle, WRA Brown, J Rogers, J-M Buerstedde, SA Wilson, L Stubbs, I Ovcharenko, L Gordon, S Lucas, MM Miller, H Inoko, T Shiina, J Kaufman, J Salomonsen, K Skjoedt, GK-S Wong, J Wang, B Liu, J Wang, J Yu, H Yang, M Nefedov, M Koriabine, PJ deJong, L Goodstadt, C Webber, NJ Dickens, I Letunic, M Suyama, D Torrents, C von Mering, EM Zdobnov, KD Makova, A Nekrutenko, L Elnitski, P Eswara, DC King, S Yang, S Tyekucheva, A Radakrishnan, RS Harris, F Chiaromonte, J Taylor, J He, M Rijnkels, S Griffiths-Jones, A Ureta-Vidal, MM Hoffman, J Severin, SMJ Searle, AS Law, D Speed, D Waddington, Z Cheng, E Tuzun, EE Eichler, Z Bao, P Flicek, DD Shteynberg, MR Brent, JM Bye, EJ Huckle, S Chatterji, C Dewey, L Pachter, A Kouranov, Z Mourelatos, AG Hatzigeorgiou, AH Paterson, R Ivarie, M Brandstrom, E Axelsson, N Backstrom, S Berlin, MT Webster, O Pourquie, A Reymond, C Ucla, SE Antonarakis, M Long, JJ Emerson, E Betrán, I Dupanloup, H Kaessmann, AS Hinrichs, G Bejerano, TS Furey, RA Harte, B Raney, A Siepel, WJ Kent, D Haussler, E Eyras, R Castelo, JF Abril, S Castellano, F Camara, G Parra, R Guigo, G Bourque, G Tesler, PA Pevzner, AFA Smit, LA Fulton, ER Mardis, RK Wilson.
Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution.
NATURE,
2004.
Rat Genome Sequencing Project Consortium, RA Gibbs, GM Weinstock, ML Metzker, DM Muzny, EJ Sodergren, S Scherer, G Scott, D Steffen, KC Worley, PE Burch, GO Okwuonu, S Hines, LR Lewis, C DeRamo, O Delgado, S Dugan-Rocha, G Miner, M Morgan, AC Hawes, R Gill, CRA Holt, MD Adams, PG Amanatides, H Baden-Tillson, M Barnstead, S Chin, CA Evans, S Ferriera, C Fosler, A Glodek, Z Gu, D Jennings, CL Kraft, T Nguyen, CM Pfannkoch, C Sitter, GG Sutton, JC Venter, T Woodage, D Smith, H-M Lee, E Gustafson, P Cahill, A Kana, L Doucette-Stamm, K Weinstock, K Fechtel, RB Weiss, DM Dunn, ED Green, RW Blakesley, GG Bouffard, PJ de Jong, K Osoegawa, B Zhu, MA Marra, JE Schein, I Bosdet, C Fjell, SM Jones, M Krzywinski, C Mathewson, A Siddiqui, N Wye, JD McPherson, S Zhao, CM Fraser, J Shetty, S Shatsman, K Geer, Y Chen, S Abramzon, WC Nierman, RA Gibbs, GM Weinstock, PH Havlak, R Chen, K James Durbin, A Egan, Y Ren, HX-Z Song, B Li, Y Liu, X Qin, S Cawley, GM Weinstock, KC Worley, AJ Cooney, RA Gibbs, LM D’Souza, K Martin, J Qian Wu, ML Gonzalez-Garay, AR Jackson, KJ Kalafus, MP McLeod, A Milosavljevic, D Virk, A Volkov, DA Wheeler, Z Zhang, JA Bailey, EE Eichler, E Tuzun, E Birney, E Mongin, A Ureta-Vidal, C Woodwark, EM Zdobnov, P Bork, M Suyama, D Torrents, M Alexandersson, BJ Trask, JM Young, D Smith, H Huang, K Fechtel, H Wang, H Xing, K Weinstock, S Daniels, D Gietzen, J Schmidt, K Stevens, U Vitt, J Wingrove, F Camara, M Mar Albà, JF Abril, R Guigo, AFA Smit, I Dubchak, EM Rubin, O Couronne, A Poliakov, N Hübner, D Ganten, C Goesele, O Hummel, T Kreitler, Y-A Lee, J Monti, H Schulz, H Zimdahl, H Himmelbauer, H Lehrach, HJ Jacob, S Bromberg, J Gullings-Handley, MI Jensen-Seaman, AE Kwitek, J Lazar, D Pasko, PJ Tonellato, S Twigger, CP Ponting, JM Duarte, S Rice, L Goodstadt, SA Beatson, RD Emes, EE Winter, C Webber, P Brandt, G Nyakatura, M Adetobi, F Chiaromonte, L Elnitski, P Eswara, RC Hardison, M Hou, D Kolbe, KD Makova, W Miller, A Nekrutenko, C Riemer, S Schwartz, J Taylor, S Yang, Y Zhang, K Lindpaintner, TD Andrews, M Caccamo, M Clamp, L Clarke, V Curwen, R Durbin, E Eyras, SMJ Searle, GM Cooper, S Batzoglou, M Brudno, A Sidow, EA Stone, J Craig Venter, BA Payseur, G Bourque, C López-Otín, XS Puente, K Chakrabarti, S Chatterji, C Dewey, L Pachter, N Bray, VB Yap, A Caspi, G Tesler, PA Pevzner, D Haussler, KM Roskin, R Baertsch, H Clawson, TS Furey, AS Hinrichs, D Karolchik, WJ Kent, KR Rosenbloom, H Trumbower, M Weirauch, DN Cooper, PD Stenson, B Ma, MR Brent, M Arumugam, DD Shteynberg, RR Copley, MS Taylor, H Riethman, U Mudunuri, J Peterson, M Guyer, A Felsenfeld, S Old, S Mockrin, F Collins.
Genome sequence of the Brown Norway rat yields insights into mammalian evolution.
NATURE,
2004.
