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1.

Chromosome-length genome assemblies and cytogenomic analyses of pangolins reveal remarkable chromosome counts and plasticity.

Houck, Marlys L; Koepfli, Klaus-Peter; Hains, Taylor; Khan, Ruqayya; Charter, Suellen J; Fronczek, Julie A; Misuraca, Ann C; Kliver, Sergei; Perelman, Polina L; Beklemisheva, Violetta; Graphodatsky, Alexander; Luo, Shu-Jin; O'Brien, Stephen J; Lim, Norman T-L; Chin, Jason S C; Guerra, Vanessa; Tamazian, Gaik; Omer, Arina; Weisz, David; Kaemmerer, Kenneth; Sturgeon, Ginger; Gaspard, Joseph; Hahn, Alicia; McDonough, Mark; Garcia-Treviño, Isabel; Gentry, Jordan; Coke, Rob L; Janecka, Jan E; Harrigan, Ryan J; Tinsman, Jen; Smith, Thomas B; Aiden, Erez Lieberman; Dudchenko, Olga.

Chromosome Res ; 31(2): 13, 2023 04 12.

Article in English | MEDLINE | ID: mdl-37043058

2.

Genome-wide association study reveals genetic variants associated with HIV-1C infection in a Botswana study population.

Shevchenko, Andrey K; Zhernakova, Daria V; Malov, Sergey V; Komissarov, Alexey; Kolchanova, Sofia M; Tamazian, Gaik; Antonik, Alexey; Cherkasov, Nikolay; Kliver, Sergey; Turenko, Anastasiia; Rotkevich, Mikhail; Evsyukov, Igor; Vlahov, David; Thami, Prisca K; Gaseitsiwe, Simani; Novitsky, Vladimir; Essex, Myron; O'Brien, Stephen J.

Proc Natl Acad Sci U S A ; 118(47)2021 11 23.

Article in English | MEDLINE | ID: mdl-34782459

3.

The platypus genome unraveled.

O'Brien, Stephen J.

Cell ; 133(6): 953-5, 2008 Jun 13.

Article in English | MEDLINE | ID: mdl-18555772

4.

The evolutionary history of extinct and living lions.

de Manuel, Marc; Barnett, Ross; Sandoval-Velasco, Marcela; Yamaguchi, Nobuyuki; Garrett Vieira, Filipe; Zepeda Mendoza, M Lisandra; Liu, Shiping; Martin, Michael D; Sinding, Mikkel-Holger S; Mak, Sarah S T; Carøe, Christian; Liu, Shanlin; Guo, Chunxue; Zheng, Jiao; Zazula, Grant; Baryshnikov, Gennady; Eizirik, Eduardo; Koepfli, Klaus-Peter; Johnson, Warren E; Antunes, Agostinho; Sicheritz-Ponten, Thomas; Gopalakrishnan, Shyam; Larson, Greger; Yang, Huanming; O'Brien, Stephen J; Hansen, Anders J; Zhang, Guojie; Marques-Bonet, Tomas; Gilbert, M Thomas P.

Proc Natl Acad Sci U S A ; 117(20): 10927-10934, 2020 05 19.

Article in English | MEDLINE | ID: mdl-32366643

5.

Evolution of gene regulation in ruminants differs between evolutionary breakpoint regions and homologous synteny blocks.

Farré, Marta; Kim, Jaebum; Proskuryakova, Anastasia A; Zhang, Yang; Kulemzina, Anastasia I; Li, Qiye; Zhou, Yang; Xiong, Yingqi; Johnson, Jennifer L; Perelman, Polina L; Johnson, Warren E; Warren, Wesley C; Kukekova, Anna V; Zhang, Guojie; O'Brien, Stephen J; Ryder, Oliver A; Graphodatsky, Alexander S; Ma, Jian; Lewin, Harris A; Larkin, Denis M.

Genome Res ; 29(4): 576-589, 2019 04.

Article in English | MEDLINE | ID: mdl-30760546

6.

Increased Expression of Long Non-coding RNA H19 is Associated With Colon Cancer Recurrence.

O'Brien, Stephen J; Scheurlen, Katharina; Rochet, Andre; Fiechter, Casey; Paas, Mason; Pan, Jianmin; Rai, Shesh N; Galandiuk, Susan.

J Surg Res ; 269: 59-68, 2022 01.

Article in English | MEDLINE | ID: mdl-34520983

7.

White shark genome reveals ancient elasmobranch adaptations associated with wound healing and the maintenance of genome stability.

Marra, Nicholas J; Stanhope, Michael J; Jue, Nathaniel K; Wang, Minghui; Sun, Qi; Pavinski Bitar, Paulina; Richards, Vincent P; Komissarov, Aleksey; Rayko, Mike; Kliver, Sergey; Stanhope, Bryce J; Winkler, Chuck; O'Brien, Stephen J; Antunes, Agostinho; Jorgensen, Salvador; Shivji, Mahmood S.

Proc Natl Acad Sci U S A ; 116(10): 4446-4455, 2019 03 05.

Article in English | MEDLINE | ID: mdl-30782839

8.

Decreased Tumoral Expression of Colon-Specific Water Channel Aquaporin 8 Is Associated With Reduced Overall Survival in Colon Adenocarcinoma.

O'Brien, Stephen J; Kalbfleisch, Theodore; Srivastava, Sudhir; Pan, Jianmin; Rai, Shesh; Petras, Robert E; Ronquillo, Nemencio; Polk, Hiram C; Galandiuk, Susan.

Dis Colon Rectum ; 64(9): 1083-1095, 2021 09 01.

Article in English | MEDLINE | ID: mdl-33990498

9.

Ultracontinuous Single Haplotype Genome Assemblies for the Domestic Cat (Felis catus) and Asian Leopard Cat (Prionailurus bengalensis).

Bredemeyer, Kevin R; Harris, Andrew J; Li, Gang; Zhao, Le; Foley, Nicole M; Roelke-Parker, Melody; O'Brien, Stephen J; Lyons, Leslie A; Warren, Wesley C; Murphy, William J.

J Hered ; 112(2): 165-173, 2021 03 29.

Article in English | MEDLINE | ID: mdl-33305796

10.

Draft de novo Genome Assembly of the Elusive Jaguarundi, Puma yagouaroundi.

Tamazian, Gaik; Dobrynin, Pavel; Zhuk, Anna; Zhernakova, Daria V; Perelman, Polina L; Serdyukova, Natalia A; Graphodatsky, Alexander S; Komissarov, Aleksey; Kliver, Sergei; Cherkasov, Nikolay; Scott, Alan F; Mohr, David W; Koepfli, Klaus-Peter; O'Brien, Stephen J; Krasheninnikova, Ksenia.

J Hered ; 112(6): 540-548, 2021 11 01.

Article in English | MEDLINE | ID: mdl-34146095

11.

Genome-wide sequence analyses of ethnic populations across Russia.

Zhernakova, Daria V; Brukhin, Vladimir; Malov, Sergey; Oleksyk, Taras K; Koepfli, Klaus Peter; Zhuk, Anna; Dobrynin, Pavel; Kliver, Sergei; Cherkasov, Nikolay; Tamazian, Gaik; Rotkevich, Mikhail; Krasheninnikova, Ksenia; Evsyukov, Igor; Sidorov, Sviatoslav; Gorbunova, Anna; Chernyaeva, Ekaterina; Shevchenko, Andrey; Kolchanova, Sofia; Komissarov, Alexei; Simonov, Serguei; Antonik, Alexey; Logachev, Anton; Polev, Dmitrii E; Pavlova, Olga A; Glotov, Andrey S; Ulantsev, Vladimir; Noskova, Ekaterina; Davydova, Tatyana K; Sivtseva, Tatyana M; Limborska, Svetlana; Balanovsky, Oleg; Osakovsky, Vladimir; Novozhilov, Alexey; Puzyrev, Valery; O'Brien, Stephen J.

Genomics ; 112(1): 442-458, 2020 01.

Article in English | MEDLINE | ID: mdl-30902755

12.

Preoperative Opioid Prescription Is Associated With Major Complications in Patients With Crohn's Disease Undergoing Elective Ileocolic Resection.

O'Brien, Stephen J; Chen, Ryan C; Stephen, Vincent T; Jorden, Jeffrey; Farmer, Russell; Manek, Stephen; Schmidt, Miranda; Pan, Jianmin; Rai, Shesh N; Galandiuk, Susan.

Dis Colon Rectum ; 63(8): 1090-1101, 2020 08.

Article in English | MEDLINE | ID: mdl-32015287

13.

Correlating serum alpha-fetoprotein in hepatocellular carcinoma with response to Yttrium-90 transarterial radioembolization with glass microspheres (TheraSphere™).

Bhutiani, Neal; O'Brien, Stephen J; Priddy, Erin E; Egger, Michael E; Hong, Young K; Mercer, Megan K; McMasters, Kelly M; Martin, Robert C G; Potts, Melissa H; Scoggins, Charles R.

HPB (Oxford) ; 22(9): 1330-1338, 2020 09.

Article in English | MEDLINE | ID: mdl-31917103

14.

New high copy tandem repeat in the content of the chicken W chromosome.

Komissarov, Aleksey S; Galkina, Svetlana A; Koshel, Elena I; Kulak, Maria M; Dyomin, Aleksander G; O'Brien, Stephen J; Gaginskaya, Elena R; Saifitdinova, Alsu F.

Chromosoma ; 127(1): 73-83, 2018 03.

Article in English | MEDLINE | ID: mdl-28951974

15.

Pangolin genomes and the evolution of mammalian scales and immunity.

Choo, Siew Woh; Rayko, Mike; Tan, Tze King; Hari, Ranjeev; Komissarov, Aleksey; Wee, Wei Yee; Yurchenko, Andrey A; Kliver, Sergey; Tamazian, Gaik; Antunes, Agostinho; Wilson, Richard K; Warren, Wesley C; Koepfli, Klaus-Peter; Minx, Patrick; Krasheninnikova, Ksenia; Kotze, Antoinette; Dalton, Desire L; Vermaak, Elaine; Paterson, Ian C; Dobrynin, Pavel; Sitam, Frankie Thomas; Rovie-Ryan, Jeffrine J; Johnson, Warren E; Yusoff, Aini Mohamed; Luo, Shu-Jin; Karuppannan, Kayal Vizi; Fang, Gang; Zheng, Deyou; Gerstein, Mark B; Lipovich, Leonard; O'Brien, Stephen J; Wong, Guat Jah.

Genome Res ; 26(10): 1312-1322, 2016 10.

Article in English | MEDLINE | ID: mdl-27510566

16.

Chromosomal-Level Assembly of the Asian Seabass Genome Using Long Sequence Reads and Multi-layered Scaffolding.

Vij, Shubha; Kuhl, Heiner; Kuznetsova, Inna S; Komissarov, Aleksey; Yurchenko, Andrey A; Van Heusden, Peter; Singh, Siddharth; Thevasagayam, Natascha M; Prakki, Sai Rama Sridatta; Purushothaman, Kathiresan; Saju, Jolly M; Jiang, Junhui; Mbandi, Stanley Kimbung; Jonas, Mario; Hin Yan Tong, Amy; Mwangi, Sarah; Lau, Doreen; Ngoh, Si Yan; Liew, Woei Chang; Shen, Xueyan; Hon, Lawrence S; Drake, James P; Boitano, Matthew; Hall, Richard; Chin, Chen-Shan; Lachumanan, Ramkumar; Korlach, Jonas; Trifonov, Vladimir; Kabilov, Marsel; Tupikin, Alexey; Green, Darrell; Moxon, Simon; Garvin, Tyler; Sedlazeck, Fritz J; Vurture, Gregory W; Gopalapillai, Gopikrishna; Kumar Katneni, Vinaya; Noble, Tansyn H; Scaria, Vinod; Sivasubbu, Sridhar; Jerry, Dean R; O'Brien, Stephen J; Schatz, Michael C; Dalmay, Tamás; Turner, Stephen W; Lok, Si; Christoffels, Alan; Orbán, László.

PLoS Genet ; 12(4): e1005954, 2016 Apr.

Article in English | MEDLINE | ID: mdl-27082250

17.

Correction: Chromosomal-Level Assembly of the Asian Seabass Genome Using Long Sequence Reads and Multi-layered Scaffolding.

Vij, Shubha; Kuhl, Heiner; Kuznetsova, Inna S; Komissarov, Aleksey; Yurchenko, Andrey A; Van Heusden, Peter; Singh, Siddharth; Thevasagayam, Natascha M; Prakki, Sai Rama Sridatta; Purushothaman, Kathiresan; Saju, Jolly M; Jiang, Junhui; Mbandi, Stanley Kimbung; Jonas, Mario; Hin Yan Tong, Amy; Mwangi, Sarah; Lau, Doreen; Ngoh, Si Yan; Liew, Woei Chang; Shen, Xueyan; Hon, Lawrence S; Drake, James P; Boitano, Matthew; Hall, Richard; Chin, Chen-Shan; Lachumanan, Ramkumar; Korlach, Jonas; Trifonov, Vladimir; Kabilov, Marsel; Tupikin, Alexey; Green, Darrell; Moxon, Simon; Garvin, Tyler; Sedlazeck, Fritz J; Vurture, Gregory W; Gopalapillai, Gopikrishna; Katneni, Vinaya Kumar; Noble, Tansyn H; Scaria, Vinod; Sivasubbu, Sridhar; Jerry, Dean R; O'Brien, Stephen J; Schatz, Michael C; Dalmay, Tamás; Turner, Stephen W; Lok, Si; Christoffels, Alan; Orbán, László.

PLoS Genet ; 12(12): e1006500, 2016 Dec.

Article in English | MEDLINE | ID: mdl-27935956

18.

Adaptive genomic evolution of opsins reveals that early mammals flourished in nocturnal environments.

Borges, Rui; Johnson, Warren E; O'Brien, Stephen J; Gomes, Cidália; Heesy, Christopher P; Antunes, Agostinho.

BMC Genomics ; 19(1): 121, 2018 02 05.

Article in English | MEDLINE | ID: mdl-29402215

19.

Whole-Genome Analysis of Mycobacterium tuberculosis from Patients with Tuberculous Spondylitis, Russia.

Chernyaeva, Ekaterina; Rotkevich, Mikhail; Krasheninnikova, Ksenia; Yurchenko, Andrey; Vyazovaya, Anna; Mokrousov, Igor; Solovieva, Natalia; Zhuravlev, Viacheslav; Yablonsky, Piotr; O'Brien, Stephen J.

Emerg Infect Dis ; 24(3): 579-583, 2018 03.

Article in English | MEDLINE | ID: mdl-29460750

20.

The role of the miR-200 family in epithelial-mesenchymal transition in colorectal cancer: a systematic review.

O'Brien, Stephen J; Carter, Jane V; Burton, James F; Oxford, Brent G; Schmidt, Miranda N; Hallion, Jacob C; Galandiuk, Susan.

Int J Cancer ; 142(12): 2501-2511, 2018 06 15.

Article in English | MEDLINE | ID: mdl-29388209

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