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  1. 1.   How to recover from a bad start: adaptation of HIV-1 transcription start site mutants during serial passaging in culture
  2. Nikolaitchik,Olga; Chameettachal,Akhil; Islam,Mohammad Saiful; Keele,Brandon; Delviks-Frankenberry, Krista; Pathak,Vinay; Hu,Wei-Shau; Cheng,Zetao
  3. Journal of Virology. 2025, May 07; e0015925.
  1. 2.   Genomes and epigenomes of matched normal and tumor breast tissue reveal diverse evolutionary trajectories and tumor-host interactions
  2. Zhu, Bin; Tapinos, Avraam; Koka, Hela; Yi Lee, Priscilla Ming; Zhang, Tongwu; Zhu, Wei; Wang, Xiaoyu; Klein, Alyssa; Lee, DongHyuk; Tse, Gary M; Tsang, Koon-Ho; Wu, Cherry; Hua, Min; Highfill,Chad; Lenz,Petra; Zhou,Weiyin; Wang,Difei; Luo,Wen; Jones,Kristine; Hutchinson,Amy; Hicks,Belynda; Garcia-Closas, Montserrat; Chanock, Stephen; Tse, Lap Ah; Wedge, David C; Yang, Xiaohong R
  3. American Journal of Human Genetics. 2024, Oct 29;
  1. 3.   Evaluation of somatic copy number variation detection by NGS technologies and bioinformatics tools on a hyper-diploid cancer genome
  2. Masood, Daniall; Ren, Luyao; Nguyen, Cu; Brundu, Francesco G; Zheng, Lily; Zhao,Yongmei; Jaeger, Erich; Li, Yong; Cha, Seong Won; Halpern, Aaron; Truong, Sean; Virata, Michael; Yan, Chunhua; Chen, Qingrong; Pang, Andy; Alberto, Reyes; Xiao, Chunlin; Yang, Zhaowei; Chen, Wanqiu; Wang, Charles; Cross, Frank; Catreux, Severine; Shi, Leming; Beaver, Julia A; Xiao, Wenming; Meerzaman, Daoud M
  3. Genome Biology. 2024, Jun 20; 25(1): 163.
  1. 4.   Comprehensive proteogenomic characterization of rare kidney tumors
  2. Li, Ginny Xiaohe; Chen, Lijun; Hsiao, Yi; Mannan, Rahul; Zhang, Yuping; Luo, Jie; Petralia, Francesca; Cho, Hanbyul; Hosseini, Noshad; Leprevost, Felipe da Veiga; Calinawan, Anna; Li, Yize; Anand, Shankara; Dagar, Aniket; Geffen, Yifat; Kumar-Sinha, Chandan; Chugh, Seema; Le, Anne; Ponce, Sean; Guo, Shenghao; Zhang, Cissy; Schnaubelt, Michael; Al Deen, Nataly Naser; Chen, Feng; Caravan, Wagma; Houston, Andrew; Hopkins, Alex; Newton, Chelsea J; Wang, Xiaoming; Polasky, Daniel A; Haynes, Sarah; Yu, Fengchao; Jing, Xiaojun; Chen, Siqi; Robles, Ana I; Mesri, Mehdi; Thiagarajan,Mathangi; An, Eunkyung; Getz, Gad A; Linehan, W Marston; Hostetter, Galen; Jewell, Scott D; Chan, Daniel W; Wang, Pei; Omenn, Gilbert S; Mehra, Rohit; Ricketts, Christopher J; Ding, Li; Chinnaiyan, Arul M; Cieslik, Marcin P; Dhanasekaran, Saravana M; Zhang, Hui; Nesvizhskii, Alexey I
  3. Cell Reports. Medicine. 2024, May 21; 5(5): 101547.
  1. 5.   Natural history of Ebola virus disease in rhesus monkeys shows viral variant emergence dynamics and tissue-specific host responses
  2. Normandin, Erica; Triana, Sergio; Raju, Siddharth S; Lan, Tammy C T; Lagerborg, Kim; Rudy, Melissa; Adams, Gordon C; DeRuff, Katherine C; Logue, James; Liu, David; Strebinger, Daniel; Rao, Arya; Messer, Katelyn S; Sacks, Molly; Adams, Ricky D; Janosko, Krisztina; Kotliar, Dylan; Shah, Rickey; Crozier,Ian; Rinn, John L; Melé, Marta; Honko, Anna N; Zhang, Feng; Babadi, Mehrtash; Luban, Jeremy; Bennett, Richard S; Shalek, Alex K; Barkas, Nikolaos; Lin, Aaron E; Hensley, Lisa E; Sabeti, Pardis C; Siddle, Katherine J
  3. Cell Genomics. 2023, Dec 13; 3(12): 100440.
  1. 6.   Genome-wide Association Study of Bladder Cancer Reveals New Biological and Translational Insights
  2. Koutros, Stella; Kiemeney, Lambertus A; Pal Choudhury, Parichoy; Milne, Roger L; Lopez de Maturana, Evangelina; Ye, Yuanqing; Joseph, Vijai; Florez-Vargas, Oscar; Dyrskjøt, Lars; Figueroa, Jonine; Dutta, Diptavo; Giles, Graham G; Hildebrandt, Michelle A T; Offit, Kenneth; Kogevinas, Manolis; Weiderpass, Elisabete; McCullough, Marjorie L; Freedman, Neal D; Albanes, Demetrius; Kooperberg, Charles; Cortessis, Victoria K; Karagas, Margaret R; Johnson, Alison; Schwenn, Molly R; Baris, Dalsu; Furberg, Helena; Bajorin, Dean F; Cussenot, Olivier; Cancel-Tassin, Geraldine; Benhamou, Simone; Kraft, Peter; Porru, Stefano; Carta, Angela; Bishop, Timothy; Southey, Melissa C; Matullo, Giuseppe; Fletcher, Tony; Kumar, Rajiv; Taylor, Jack A; Lamy, Philippe; Prip, Frederik; Kalisz, Mark; Weinstein, Stephanie J; Hengstler, Jan G; Selinski, Silvia; Harland, Mark; Teo, Mark; Kiltie, Anne E; Tardón, Adonina; Serra, Consol; Carrato, Alfredo; García-Closas, Reina; Lloreta, Josep; Schned, Alan; Lenz,Petra; Riboli, Elio; Brennan, Paul; Tjønneland, Anne; Otto, Thomas; Ovsiannikov, Daniel; Volkert, Frank; Vermeulen, Sita H; Aben, Katja K; Galesloot, Tessel E; Turman, Constance; De Vivo, Immaculata; Giovannucci, Edward; Hunter, David J; Hohensee, Chancellor; Hunt, Rebecca; Patel, Alpa V; Huang, Wen-Yi; Thorleifsson, Gudmar; Gago-Dominguez, Manuela; Amiano, Pilar; Golka, Klaus; Stern, Mariana C; Yan, Wusheng; Liu,Jia; Li,Shengchao; Katta,Shilpa; Hutchinson,Amy; Hicks,Belynda; Wheeler, William A; Purdue, Mark P; McGlynn, Katherine A; Kitahara, Cari M; Haiman, Christopher A; Greene, Mark H; Rafnar, Thorunn; Chatterjee, Nilanjan; Chanock, Stephen J; Wu, Xifeng; Real, Francisco X; Silverman, Debra T; Garcia-Closas, Montserrat; Stefansson, Kari; Prokunina-Olsson, Ludmila; Malats, Núria; Rothman, Nathaniel
  3. European Urology. 2023, Jul; 48(1): 127-137.
  1. 7.   HIV-1 usurps transcription start site heterogeneity of host RNA polymerase II to maximize replication fitness
  2. Nikolaitchik,Olga; Islam,Mohammad Saiful; Kitzrow,Jonathan; Duchon,Alice; Cheng,Zetao; Liu, Yang; Rawson, Jonathan M O; Shao,Wei; Nikolaitchik, Maria; Kearney,Mary; Maldarelli,Frank; Musier-Forsyth, Karin; Pathak,Vinay; Hu,Wei-Shau
  3. Proceedings of the National Academy of Sciences of the United States of America. 2023, Jun 06; 120(23): e2305103120.
  1. 8.   Revisiting and corrections to the annotated SRSF3 (SRp20) gene structure and RefSeq sequences from the human and mouse genomes
  2. Yu,Lulu; Majerciak,Vladimir; Jia, Rong; Zheng,Zhi-Ming
  3. Cell Insight. 2023, Apr ; 2(2): 100089.
  1. 9.   Oral microbiome and risk of incident head and neck cancer: A nested case-control study
  2. Wu, Zeni; Han, Yongli; Wan, Yunhu; Hua, Xing; Chill, Samantha S; Teshome, Kedest; Zhou, Weiyin; Liu, Jia; Wu, Dongjing; Hutchinson,Amy; Jones,Kristine; Dagnall,Casey; Hicks,Belynda; Liao, Linda; Hallen-Adams, Heather; Shi, Jianxin; Abnet, Christian C; Sinha, Rashmi; Chaturvedi, Anil; Vogtmann, Emily
  3. Oral Oncology. 2023, Jan 05; 137: 106305.
  1. 10.   Transcription Start Site Heterogeneity and Preferential Packaging of Specific Full-Length RNA Species Are Conserved Features of Primate Lentiviruses
  2. Rawson, Jonathan M O; Nikolaitchik,Olga; Shakya,Saurabh; Keele,Brandon; Pathak,Vinay; Hu,Wei-Shau
  3. Microbiology Spectrum. 2022, Jun 23; e0105322.
  1. 11.   Deep Sequencing Analysis of Individual HIV-1 Proviruses Reveals Frequent Asymmetric Long Terminal Repeats
  2. Joseph, Kevin W; Halvas, Elias K; Brandt, Leah D; Patro,Sean; Rausch,Jason; Chopra, Abha; Mallal, Simon; Kearney,Mary; Coffin, John M; Mellors, John W
  3. Journal of Virology. 2022, Jun 08; e0012222.
  1. 12.   Systematic Analysis of Kaposi's Sarcoma-associated Herpesvirus Genomes from a Kaposi's Sarcoma (KS) Case-Control Study in Cameroon: Evidence of Dual Infections but No Association Between Viral Sequence Variation and KS Risk
  2. Marshall,Vickie; Fisher, Nicholas C; Goodman,Charles; Cornejo Castro,Elena; Liu, Isabella; Khanal, Sirish; Holdridge,Benjamin; Thorpe, Abigail L; Labo,Nazzarena; Stolka, Kristen B; Hemingway-Foday, Jennifer J; Abassora, Mahamat; N'Dom, Paul; Smith, Jennifer S; Sallah, Neneh; Palser, Anne L; Kellam, Paul; Keele,Brandon; Whitby,Denise
  3. International Journal of Cancer. 2022, May 24;
  1. 13.   Genetic variation within the human papillomavirus type 16 genome is associated with oropharyngeal cancer prognosis
  2. Lang Kuhs, K A; Faden, D L; Chen, L; Smith, D K; Pinheiro, M; Wood, C B; Davis, S; Yeager,Meredith; Boland, J F; Cullen, M; Steinberg, M; Bass, S; Wang, X; Liu, P; Mehrad, M; Tucker, T; Lewis, J S; Ferris, R L; Mirabello, L
  3. Annals of Oncology : official journal of the European Society for Medical Oncology. 2022, Mar 16; 33(6): 638-648.
  1. 14.   Complete Genome Sequence of Herpes Simplex Virus 2 Strain G
  2. Chang,Weizhong; Jiao, Xiaoli; Sui,Hongyan; Goswami, Suranjana; Sherman,Brad; Fromont,Caroline; Caravaca-Guasch,Juan Manuel; Tran,Bao; Imamichi,Tomozumi
  3. Viruses. 2022, Mar 05; 14(3):
  1. 15.   WRN helicase safeguards deprotected replication forks in BRCA2-mutated cancer cells
  2. Datta, Arindam; Biswas, Kajal; Sommers, Joshua A.; Thompson, Haley; Awate, Sanket; Nicolae, Claudia M.; Thakar, Tanay; Moldovan, George-Lucian; Shoemaker, Robert H.; Sharan, Shyam K.; Brosh, Robert M.
  3. Nature Communications. 2021, Nov 12; 12(1):
  1. 16.   A 584 bp deletion in CTRB2 inhibits chymotrypsin B2 activity and secretion and confers risk of pancreatic cancer
  2. Jermusyk, Ashley; Zhong, Jun; Connelly, Katelyn E.; Gordon, Naomi; Perera, Sumeth; Abdolalizadeh, Ehssan; Zhang, Tongwu; O'Brien, Aidan; Hoskins, Jason W.; Collins, Irene; Eiser, Daina; Yuan, Chen; Risch, Harvey A.; Jacobs, Eric J.; Li, Donghui; Du, Mengmeng; Stolzenberg-Solomon, Rachael Z.; Klein, Alison P.; Smith, Jill P.; Wolpin, Brian M.; Chanock, Stephen J.; Shi, Jianxin; Petersen, Gloria M.; Westlake,Christopher; Amundadottir, Laufey T.
  3. American Journal of Human Genetics. 2021, Oct 7; 108(10): 1852-1865.
  1. 17.   NanoHIV: A Bioinformatics Pipeline for Producing Accurate, Near Full-Length HIV Proviral Genomes Sequenced Using the Oxford Nanopore Technology
  2. Wright, Imogen A.; Delaney, Kayla E.; Katusiime, Mary Grace K.; Botha, Johannes C.; Engelbrecht, Susan; Kearney,Mary; van Zyl, Gert U.
  3. Cells. 2021, Sep 28; 10(10):
  1. 18.   Proteogenomic characterization of pancreatic ductal adenocarcinoma
  2. Cao, Liwei; Huang, Chen; Zhou, Daniel Cui; Hu, Yingwei; Lih, T. Mamie; Savage, Sara R.; Krug, Karsten; Clark, David J.; Schnaubelt, Michael; Chen, Lijun; Leprevost, Felipe da Veiga; Eguez, Rodrigo Vargas; Yang, Weiming; Pan, Jianbo; Wen, Bo; Dou, Yongchao; Jiang, Wen; Liao, Yuxing; Shi, Zhiao; Terekhanova, Nadezhda; Cao, Song; Lu, Rita Jui-Hsien; Li, Yize; Liu, Ruiyang; Zhu, Houxiang; Ronning, Peter; Wu, Yige; Wyczalkowski, Matthew A.; Easwaran, Hariharan; Danilova, Ludmila; Mer, Arvind Singh; Yoo, Seungyeul; Wang, Joshua M.; Liu, Wenke; Haibe-Kains, Benjamin; Thiagarajan,Mathangi; Jewell, Scott D.; Hostetter, Galen; Newton, Chelsea J.; Li, Qing Kay; Roehr, Michael H.; Fenyo, David; Wang, Pei; Nesvizhskii, Alexey; Mani, D. R.; Omenn, Gilbert S.; Boja, Emily S.; Mesri, Mehdi; Robles, Ana; Rodriguez, Henry; Bathe, Oliver F.; Chan, Daniel W.; Hruban, Ralph H.; Ding, Li; Zhang, Bing; Zhang, Hui
  3. Cell. 2021, Sep 16; 184(19): 5031-5052.e26.
  1. 19.   A UVB-responsive common variant at chromosome band 7p21.1 confers tanning response and melanoma risk via regulation of the aryl hydrocarbon receptor, AHR
  2. Xu, Mai; Mehl, Lindsey; Zhang, Tongwu; Thakur, Rohit; Sowards, Hayley; Myers, Timothy; Jessop, Lea; Chesi, Alessandra; Johnson, Matthew E; Wells, Andrew D; Michael, Helen T; Bunda, Patricia; Jones, Kristine; Higson, Herbert; Hennessey, Rebecca C; Jermusyk, Ashley; Kovacs, Michael A; Landi, Maria Teresa; Iles, Mark M; Goldstein, Alisa M; Choi, Jiyeon; Chanock, Stephen J; Grant, Struan F A; Chari,Raj; Merlino, Glenn; Law, Matthew H; Brown, Kevin M
  3. American journal of human genetics. 2021, Sep 2; 108(9): 1611-1630.
  1. 20.   Disseminated Mycobacterium marinum in HIV unmasked by Immune Reconstitution Inflammatory Syndrome
  2. Manion, Maura; Dulanto Chiang, Augusto; Pei, Luxin; Wong, Chun-Shu; Khil, Pavel; Hammoud, Dima A; Anderson, Megan; Laidlaw, Elizabeth; Kuriakose,Safia; Lisco, Andrea; Zelazny, Adrian M; Dekker, John P; Sereti, Irini
  3. The Journal of infectious diseases. 2021, Aug 1; 224(3): 453-457.
  1. 21.   Targeted Deep Sequencing of Bladder Tumors Reveals Novel Associations between Cancer Gene Mutations and Mutational Signatures with Major Risk Factors
  2. Koutros, Stella; Rao, Nina; Moore, Lee E.; Nickerson, Michael L.; Lee, Donghyuk; Zhu, Bin; Pardo, Larissa A.; Baris, Dalsu; Schwenn, Molly; Johnson, Alison; Jones,Kristine; Garcia-Closas, Montserrat; Prokunina-Olsson, Ludmila; Silverman, Debra T.; Rothman, Nathaniel; Dean,Michael
  3. CLINICAL CANCER RESEARCH. 2021, Jul; 27(13): 3725-3733.
  1. 22.   Dynamic imaging of nascent RNA reveals general principles of transcription dynamics and stochastic splice site selection
  2. Wan, Yihan; Anastasakis, Dimitrios G.; Rodriguez, Joseph; Palangat, Murali; Gudla, Prabhakar; Zaki,George; Tandon,Mayank; Pegoraro, Gianluca; Chow, Carson C.; Hafner, Markus; Larson, Daniel R.
  3. CELL. 2021, May 27; 184(11): 2878-2895.e20.
  1. 23.   CpG Methylation Profiles of HIV-1 Proviral DNA in Individuals on ART
  2. Boltz,Valerie; Ceriani, Cristina; Rausch,Jason; Shao,Wei; Bale, Michael J.; Keele,Brandon; Hoh, Rebecca; Milush, Jeffrey M.; Deeks, Steve G.; Maldarelli,Frank; Kearney,Mary; Coffin, John M.
  3. VIRUSES-BASEL. 2021, May; 13(5):
  1. 24.   Proteogenomic and metabolomic characterization of human glioblastoma
  2. Wang, Liang-Bo; Karpova, Alla; Gritsenko, Marina A.; Kyle, Jennifer E.; Cao, Song; Li, Yize; Rykunov, Dmitry; Colaprico, Antonio; Rothstein, Joseph H.; Hong, Runyu; Stathias, Vasileios; Cornwell, MacIntosh; Petralia, Francesca; Wu, Yige; Reva, Boris; Krug, Karsten; Pugliese, Pietro; Kawaler, Emily; Olsen, Lindsey K.; Liang, Wen-Wei; Song, Xiaoyu; Dou, Yongchao; Wendl, Michael C.; Caravan, Wagma; Liu, Wenke; Zhou, Daniel Cui; Ji, Jiayi; Tsai, Chia-Feng; Petyuk, Vladislav A.; Moon, Jamie; Ma, Weiping; Chu, Rosalie K.; Weitz, Karl K.; Moore, Ronald J.; Monroe, Matthew E.; Zhao, Rui; Yang, Xiaolu; Yoo, Seungyeul; Krek, Azra; Demopoulos, Alexis; Zhu, Houxiang; Wyczalkowski, Matthew A.; McMichael, Joshua F.; Henderson, Brittany L.; Lindgren, Caleb M.; Boekweg, Hannah; Lu, Shuangjia; Baral, Jessika; Yao, Lijun; Stratton, Kelly G.; Bramer, Lisa M.; Zink, Erika; Couvillion, Sneha P.; Bloodsworth, Kent J.; Satpathy, Shankha; Sieh, Weiva; Boca, Simina M.; Schurer, Stephan; Chen, Feng; Wiznerowicz, Maciej; Ketchum, Karen A.; Boja, Emily S.; Kinsinger, Christopher R.; Robles, Ana; Hiltke, Tara; Thiagarajan,Mathangi; Nesvizhskii, Alexey; Zhang, Bing; Mani, D. R.; Ceccarelli, Michele; Chen, Xi S.; Cottingham, Sandra L.; Li, Qing Kay; Kim, Albert H.; Fenyo, David; Ruggles, Kelly; Rodriguez, Henry; Mesri, Mehdi; Payne, Samuel H.; Resnick, Adam C.; Wang, Pei; Smith, Richard D.; Iavarone, Antonio; Chheda, Milan G.; Barnholtz-Sloan, Jill S.; Rodland, Karin D.; Liu, Tao; Ding, Li
  3. Cancer Cell. 2021, Apr 12; 39(4): 509-528.e20.
  1. 25.   Ultracontinuous single haplotype genome assemblies for the domestic cat (Felis catus) and Asian leopard cat (Prionailurus bengalensis)
  2. 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
  3. The Journal of heredity. 2021, Mar; 112(2): 165-173.
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