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  1. 1.   Whole-genome sequencing of 1,083 HPV45 cases and controls identifies genetic variants associated with glandular cervical lesions
  2. Koestler, Aimee J; Nelson, Chase W; Yeager,Stella; Chen, Zigui; Mishra,Sambit; Burdett, Laurie; Dean, Michael; Suh-Burgmann, Elizabeth; Lorey, Thomas; Clifford, Gary M; Wentzensen, Nicolas; Castle, Philip E; Schiffman, Mark; Burk, Robert D; Mirabello, Lisa
  3. International Journal of Cancer. 2025, May 05;
  1. 2.   Contribution of intact viral genomes persisting in blood and tissues during ART to plasma viral rebound in SHIV-infected rhesus macaques
  2. Trifone, César; Richard, Corentin; Pagliuzza, Amélie; Dufour, Caroline; Lemieux, Audrée; Clark, Natasha M; Janaka, Sanath K; Fennessey,Christine; Keele,Brandon; Fromentin, Rémi; Estes, Jacob D; Kaufmann, Daniel E; Finzi, Andrés; Evans, David T; Chomont, Nicolas
  3. iScience. 2025, Mar 21; 28(3): 111998.
  1. 3.   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. 4.   Repeated horizontal acquisition of lagriamide-producing symbionts in Lagriinae beetles
  2. Uppal, Siddharth; Simonson,Sam Waterworth; Nick, Alina; Vogel, Heiko; Flórez, Laura V; Kaltenpoth, Martin; Kwan, Jason C
  3. The ISME Journal. 2024, Oct 23;
  1. 5.   Genome-scale exon perturbation screens uncover exons critical for cell fitness
  2. Xiao,Meisheng; Damodaran,Arun Prasath; Kumari,Bandana; Dickson, Ethan; Xing, Kun; On, Tyler A; Parab, Nikhil; King, Helen E; Perez, Alexendar R; Guiblet,Wilfried; Duncan,Gerard; Che,Anney; Chari,Raj; Andresson,Thorkell; Vidigal, Joana A; Weatheritt, Robert J; Aregger,Michael; Gonatopoulos Pournatzis,Thomas
  3. Molecular Cell. 2024, Jul 11; 84(13): 2553-2572.
  1. 6.   IRF4 requires ARID1A to establish plasma cell identity in multiple myeloma
  2. Bolomsky, Arnold; Ceribelli, Michele; Scheich, Sebastian; Rinaldi, Kristina; Huang, Da Wei; Chakraborty, Papiya; Pham, Lisette; Wright, George W; Hsiao, Tony; Morris, Vivian; Choi, Jaewoo; Phelan, James D; Holewinski,Ronald; Andresson,Thorkell; Wisniewski, Jan; Riley, Deanna; Pittaluga, Stefania; Hill, Elizabeth; Thomas, Craig J; Muppidi, Jagan; Young, Ryan M
  3. Cancer Cell. 2024, Jul 8; 42(7): 1185-1201.
  1. 7.   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. 8.   Protocol for the saturation and multiplexing of genetic variants using CRISPR-Cas9
  2. Sahu,Sounak; Sullivan,Teresa; Southon,Eileen; Caylor,Dylan; Geh, Josephine; Sharan,Shyam
  3. STAR Protocols. 2023, Nov 08; 4(4): 102702.
  1. 9.   Detection of the DNA binding of transcription factors in situ at the single-cell resolution in cultured cells by proximity ligation assay
  2. Ram,Babul; Dai,Chengkai
  3. STAR Protocols. 2023, Nov 01; 4(4): 102692.
  1. 10.   Proteogenomic insights suggest druggable pathways in endometrial carcinoma
  2. Dou, Yongchao; Katsnelson, Lizabeth; Gritsenko, Marina A; Hu, Yingwei; Reva, Boris; Hong, Runyu; Wang, Yi-Ting; Kolodziejczak, Iga; Lu, Rita Jui-Hsien; Tsai, Chia-Feng; Bu, Wen; Liu, Wenke; Guo, Xiaofang; An, Eunkyung; Arend, Rebecca C; Bavarva, Jasmin; Chen, Lijun; Chu, Rosalie K; Czekanski, Andrzej; Davoli, Teresa; Demicco, Elizabeth G; DeLair, Deborah; Devereaux, Kelly; Dhanasekaran, Saravana M; Dottino, Peter; Dover, Bailee; Fillmore, Thomas L; Foxall, McKenzie; Hermann, Catherine E; Hiltke, Tara; Hostetter, Galen; Jedryka, Marcin; Jewell, Scott D; Johnson, Isabelle; Kahn, Andrea G; Ku, Amy T; Kumar-Sinha, Chandan; Kurzawa, Pawel; Lazar, Alexander J; Lazcano, Rossana; Lei, Jonathan T; Li, Yi; Liao, Yuxing; Lih, Tung-Shing M; Lin, Tai-Tu; Martignetti, John A; Masand, Ramya P; Matkowski, Rafal; McKerrow, Wilson; Mesri, Mehdi; Monroe, Matthew E; Moon, Jamie; Moore, Ronald J; Nestor, Michael D; Newton, Chelsea; Omelchenko, Tatiana; Omenn, Gilbert S; Payne, Samuel H; Petyuk, Vladislav A; Robles, Ana I; Rodriguez, Henry; Ruggles, Kelly V; Rykunov, Dmitry; Savage, Sara R; Schepmoes, Athena A; Shi, Tujin; Shi, Zhiao; Tan, Jimin; Taylor, Mason; Thiagarajan,Mathangi; Wang, Joshua M; Weitz, Karl K; Wen, Bo; Williams, C M; Wu, Yige; Wyczalkowski, Matthew A; Yi, Xinpei; Zhang, Xu; Zhao, Rui; Mutch, David; Chinnaiyan, Arul M; Smith, Richard D; Nesvizhskii, Alexey I; Wang, Pei; Wiznerowicz, Maciej; Ding, Li; Mani, D R; Zhang, Hui; Anderson, Matthew L; Rodland, Karin D; Zhang, Bing; Liu, Tao; Fenyö, David
  3. Cancer Cell. 2023, Sep 11; 41(9): 1586-1605.e15.
  1. 11.   Proteogenomic data and resources for pan-cancer analysis
  2. Li, Yize; Dou, Yongchao; Da Veiga Leprevost, Felipe; Geffen, Yifat; Calinawan, Anna P; Aguet, François; Akiyama, Yo; Anand, Shankara; Birger, Chet; Cao, Song; Chaudhary, Rekha; Chilappagari, Padmini; Cieslik, Marcin; Colaprico, Antonio; Zhou, Daniel Cui; Day, Corbin; Domagalski, Marcin J; Esai Selvan, Myvizhi; Fenyö, David; Foltz, Steven M; Francis, Alicia; Gonzalez-Robles, Tania; Gümüs, Zeynep H; Heiman, David; Holck, Michael; Hong, Runyu; Hu, Yingwei; Jaehnig, Eric J; Ji, Jiayi; Jiang, Wen; Katsnelson, Lizabeth; Ketchum, Karen A; Klein, Robert J; Lei, Jonathan T; Liang, Wen-Wei; Liao, Yuxing; Lindgren, Caleb M; Ma, Weiping; Ma, Lei; MacCoss, Michael J; Martins Rodrigues, Fernanda; McKerrow, Wilson; Nguyen, Ngoc; Oldroyd, Robert; Pilozzi, Alexander; Pugliese, Pietro; Reva, Boris; Rudnick, Paul; Ruggles, Kelly V; Rykunov, Dmitry; Savage, Sara R; Schnaubelt, Michael; Schraink, Tobias; Shi, Zhiao; Singhal, Deepak; Song, Xiaoyu; Storrs, Erik; Terekhanova, Nadezhda V; Thangudu, Ratna R; Thiagarajan,Mathangi; Wang, Liang-Bo; Wang, Joshua M; Wang, Ying; Wen, Bo; Wu, Yige; Wyczalkowski, Matthew A; Xin, Yi; Yao, Lijun; Yi, Xinpei; Zhang, Hui; Zhang, Qing; Zuhl, Maya; Getz, Gad; Ding, Li; Nesvizhskii, Alexey I; Wang, Pei; Robles, Ana I; Zhang, Bing; Payne, Samuel H
  3. Cancer Cell. 2023, Aug 14; (8): 1397-1406.
  1. 12.   Pan-cancer analysis of post-translational modifications reveals shared patterns of protein regulation
  2. Geffen, Yifat; Anand, Shankara; Akiyama, Yo; Yaron, Tomer M; Song, Yizhe; Johnson, Jared L; Govindan, Akshay; Babur, Özgün; Li, Yize; Huntsman, Emily; Wang, Liang-Bo; Birger, Chet; Heiman, David I; Zhang, Qing; Miller, Mendy; Maruvka, Yosef E; Haradhvala, Nicholas J; Calinawan, Anna; Belkin, Saveliy; Kerelsky, Alexander; Clauser, Karl R; Krug, Karsten; Satpathy, Shankha; Payne, Samuel H; Mani, D R; Gillette, Michael A; Dhanasekaran, Saravana M; Thiagarajan,Mathangi; Mesri, Mehdi; Rodriguez, Henry; Robles, Ana I; Carr, Steven A; Lazar, Alexander J; Aguet, François; Cantley, Lewis C; Ding, Li; Getz, Gad
  3. Cell. 2023, Aug 09;
  1. 13.   The genetic and evolutionary basis of gene expression variation in East Africans
  2. Kelly, Derek E; Ramdas, Shweta; Ma, Rong; Rawlings-Goss, Renata A; Grant, Gregory R; Ranciaro, Alessia; Hirbo, Jibril B; Beggs, William; Yeager,Meredith; Chanock, Stephen; Nyambo, Thomas B; Omar, Sabah A; Woldemeskel, Dawit; Belay, Gurja; Li, Hongzhe; Brown, Christopher D; Tishkoff, Sarah A
  3. Genome Biology. 2023, Feb 24; 24(1): 35.
  1. 14.   Detecting genomic deletions from high-throughput sequence data with unsupervised learning
  2. Li,Xin; Wu, Yufeng
  3. BMC Bioinformatics. 2023, Jan 27; 23(Suppl 8): 568.
  1. 15.   Histopathologic and proteogenomic heterogeneity reveals features of clear cell renal cell carcinoma aggressiveness
  2. Li, Yize; Lih, Tung-Shing M; Dhanasekaran, Saravana M; Mannan, Rahul; Chen, Lijun; Cieslik, Marcin; Wu, Yige; Lu, Rita Jiu-Hsien; Clark, David J; Kolodziejczak, Iga; Hong, Runyu; Chen, Siqi; Zhao, Yanyan; Chugh, Seema; Caravan, Wagma; Naser Al Deen, Nataly; Hosseini, Noshad; Newton, Chelsea J; Krug, Karsten; Xu, Yuanwei; Cho, Kyung-Cho; Hu, Yingwei; Zhang, Yuping; Kumar-Sinha, Chandan; Ma, Weiping; Calinawan, Anna; Wyczalkowski, Matthew A; Wendl, Michael C; Wang, Yuefan; Guo, Shenghao; Zhang, Cissy; Le, Anne; Dagar, Aniket; Hopkins, Alex; Cho, Hanbyul; Leprevost, Felipe da Veiga; Jing, Xiaojun; Teo, Guo Ci; Liu, Wenke; Reimers, Melissa A; Pachynski, Russell; Lazar, Alexander J; Chinnaiyan, Arul M; Van Tine, Brian A; Zhang, Bing; Rodland, Karin D; Getz, Gad; Mani, D R; Wang, Pei; Chen, Feng; Hostetter, Galen; Thiagarajan,Mathangi; Linehan, W Marston; Fenyö, David; Jewell, Scott D; Omenn, Gilbert S; Mehra, Rohit; Wiznerowicz, Maciej; Robles, Ana I; Mesri, Mehdi; Hiltke, Tara; An, Eunkyung; Rodriguez, Henry; Chan, Daniel W; Ricketts, Christopher J; Nesvizhskii, Alexey I; Zhang, Hui; Ding, Li
  3. Cancer Cell. 2023, Jan 9; 41(1): 139-163.
  1. 16.   Comparison of somatic mutation landscapes in Chinese versus European breast cancer patients
  2. Zhu, Bin; Joo, Lijin; Zhang, Tongwu; Koka, Hela; Lee, DongHyuk; Shi, Jianxin; Lee, Priscilla; Wang, Difei; Wang, Feng; Chan, Wing-Cheong; Law, Sze Hong; Tsoi, Yee-Kei; Tse, Gary M; Lai, Shui Wun; Wu, Cherry; Yang, Shuyuan; Yang Chan, Emily Ying; Shan Wong, Samuel Yeung; Wang, Mingyi; Song, Lei; Jones, Kristine; Zhu, Bin; Hutchinson, Amy; Hicks, Belynda; Prokunina-Olsson, Ludmila; Garcia-Closas, Montserrat; Chanock, Stephen; Tse, Lap Ah; Yang, Xiaohong R
  3. HGG Advances. 2021, Dec 3; 3(1): 100076.
  1. 17.   Nascent Prostate Cancer Heterogeneity Drives Evolution and Resistance to Intense Hormonal Therapy
  2. Wilkinson, Scott; Ye, Huihui; Karzai, Fatima; Harmon,Stephanie; Terrigino, Nicholas T; VanderWeele, David J; Bright, John R; Atway, Rayann; Trostel, Shana Y; Carrabba, Nicole V; Whitlock, Nichelle C; Walker, Stephanie M; Lis, Rosina T; Abdul Sater, Houssein; Capaldo, Brian J; Madan, Ravi A; Gulley, James L; Chun, Guinevere; Merino, Maria J; Pinto, Peter A; Salles, Daniela C; Kaur, Harsimar B; Lotan, Tamara L; Venzon, David J; Choyke, Peter L; Turkbey, Baris; Dahut, William L; Sowalsky, Adam G
  3. European Urology. 2021, Dec; 80(6): 746-757.
  1. 18.   Immuno-transcriptomic profiling of extracranial pediatric solid malignancies
  2. Brohl, Andrew S; Sindiri, Sivasish; Wei, Jun S; Milewski, David; Chou, Hsien-Chao; Song, Young K; Wen, Xinyu; Kumar, Jeetendra; Reardon, Hue V; Mudunuri,Uma; Collins,Jack; Nagaraj, Sushma; Gangalapudi, Vineela; Tyagi, Manoj; Zhu, Yuelin J; Masih, Katherine E; Yohe, Marielle E; Shern, Jack F; Qi, Yue; Guha, Udayan; Catchpoole, Daniel; Orentas, Rimas J; Kuznetsov, Igor B; Llosa, Nicolas J; Ligon, John A; Turpin, Brian K; Leino, Daniel G; Iwata, Shintaro; Andrulis, Irene L; Wunder, Jay S; Toledo, Silvia R C; Meltzer, Paul S; Lau, Ching; Teicher, Beverly A; Magnan, Heather; Ladanyi, Marc; Khan, Javed
  3. Cell reports. 2021, Nov 23; 37(8): 110047.
  1. 19.   Application of CHyMErA Cas9-Cas12a combinatorial genome-editing platform for genetic interaction mapping and gene fragment deletion screening
  2. Aregger,Michael; Xing, Kun; Gonatopoulos Pournatzis,Thomas
  3. Nature Protocols . 2021, Sep 10; 16(10): 4722-4765.
  1. 20.   A proteogenomic portrait of lung squamous cell carcinoma
  2. Satpathy, Shankha; Krug, Karsten; Jean Beltran, Pierre M; Savage, Sara R; Petralia, Francesca; Kumar-Sinha, Chandan; Dou, Yongchao; Reva, Boris; Kane, M Harry; Avanessian, Shayan C; Vasaikar, Suhas V; Krek, Azra; Lei, Jonathan T; Jaehnig, Eric J; Omelchenko, Tatiana; Geffen, Yifat; Bergstrom, Erik J; Stathias, Vasileios; Christianson, Karen E; Heiman, David I; Cieslik, Marcin P; Cao, Song; Song, Xiaoyu; Ji, Jiayi; Liu, Wenke; Li, Kai; Wen, Bo; Li, Yize; Gümüs, Zeynep H; Selvan, Myvizhi Esai; Soundararajan, Rama; Visal, Tanvi H; Raso, Maria G; Parra, Edwin Roger; Babur, Özgün; Vats, Pankaj; Anand, Shankara; Schraink, Tobias; Cornwell, MacIntosh; Rodrigues, Fernanda Martins; Zhu, Houxiang; Mo, Chia-Kuei; Zhang, Yuping; da Veiga Leprevost, Felipe; Huang, Chen; Chinnaiyan, Arul M; Wyczalkowski, Matthew A; Omenn, Gilbert S; Newton, Chelsea J; Schurer, Stephan; Ruggles, Kelly V; Fenyö, David; Jewell, Scott D; Thiagarajan,Mathangi; Mesri, Mehdi; Rodriguez, Henry; Mani, Sendurai A; Udeshi, Namrata D; Getz, Gad; Suh,James; Li, Qing Kay; Hostetter, Galen; Paik, Paul K; Dhanasekaran, Saravana M; Govindan, Ramaswamy; Ding, Li; Robles, Ana I; Clauser, Karl R; Nesvizhskii, Alexey I; Wang, Pei; Carr, Steven A; Zhang, Bing; Mani, D R; Gillette, Michael A
  3. Cell. 2021, Aug 05; 184(16): 4348-4371.e40.
  1. 21.   A GPC2 antibody-drug conjugate is efficacious against neuroblastoma and small-cell lung cancer via binding a conformational epitope
  2. Raman, Swetha; Buongervino, Samantha N.; Lane, Maria; Zhelev, Doncho; Zhu, Zhongyu; Cui, Hong; Martinez, Benjamin; Martinez, Daniel; Wang, Yanping; Upton, Kristen; Patel, Khushbu; Rathi, Komal S.; Navia, Carmen T.; Harmon, Daniel B.; Li, Yimei; Pawel, Bruce; Dimitrov, Dimiter S.; Maris, John M.; Julien, Jean-Philippe; Bosse, Kristopher R.
  3. Cell reports. Medicine. 2021, Jul 20; 2(7):
  1. 22.   Phase I Study of Zotiraciclib in Combination with Temozolomide for Patients with Recurrent High-grade Astrocytomas
  2. Wu, Jing; Yuan, Ying; Long-Priel,Debra; Fink,Dani; Peer, Cody J.; Sissung, Tristan M.; Su, Yu-Ting; Pang, Ying; Yu, Guangyang; Butler, Madison K.; Mendoza, Tito R.; Vera, Elizabeth; Ahmad, Salman; Bryla, Christine; Lindsley, Matthew; Grajkowska, Ewa; Mentges, Kelly; Boris, Lisa; Antony, Ramya; Garren, Nancy; Siegel, Christine; Lollo, Nicole; Cordova, Christine; Aboud, Orwa; Theeler, Brett J.; Burton, Eric M.; Penas-Prado, Marta; Leeper, Heather; Gonzales, Javier; Armstrong, Terri S.; Calvo, Katherine R.; Figg, William D.; Kuhns,Doug; Gallin, John; Gilbert, Mark R.
  3. Clinical Cancer Research : an Official Journal of the American Association for Cancer Research. 2021, Jun 15; 27(12): 3298-3306.
  1. 23.   TnIK Is a Therapeutic Target in Lung Squamous Cell Carcinoma and Regulates FAK Activation through Merlin
  2. Torres-Ayuso,Pedro; An, Elvira; Nyswaner,Katherine; Bensen,Ryan; Ritt,Daniel; Specht,Suzanne; Das,Sudipto; Andresson,Thorkell; Cachau,Raul; Liang, Roger J.; Ries,Amy; Robinson,Christina; Difilippantonio,Simone; Gouker,Brad; Gouker,Brad; Karim,Baktiar; Miller, Chad J.; Turk, Benjamin E.; Morrison,Deborah; Brognard,John
  3. Cancer Discovery. 2021, Jun; 11(6): 1411-1423.
  1. 24.   Proteogenomic Landscape of Breast Cancer Tumorigenesis and Targeted Therapy
  2. Krug, Karsten; Jaehnig, Eric J; Satpathy, Shankha; Blumenberg, Lili; Karpova, Alla; Anurag, Meenakshi; Miles, George; Mertins, Philipp; Geffen, Yifat; Tang, Lauren C; Heiman, David I; Cao, Song; Maruvka, Yosef E; Lei, Jonathan T; Huang, Chen; Kothadia, Ramani B; Colaprico, Antonio; Birger, Chet; Wang, Jarey; Dou, Yongchao; Wen, Bo; Shi, Zhiao; Liao, Yuxing; Wiznerowicz, Maciej; Wyczalkowski, Matthew A; Chen, Xi Steven; Kennedy, Jacob J; Paulovich, Amanda G; Thiagarajan,Mathangi; Kinsinger, Christopher R; Hiltke, Tara; Boja, Emily S; Mesri, Mehdi; Robles, Ana I; Rodriguez, Henry; Westbrook, Thomas F; Ding, Li; Getz, Gad; Clauser, Karl R; Fenyö, David; Ruggles, Kelly V; Zhang, Bing; Mani, D R; Carr, Steven A; Ellis, Matthew J; Gillette, Michael A
  3. Cell. 2020, NOV 25; 183(5): 1436-+.
  1. 25.   Identifying Candidate Genetic Markers of CDV Cross-Species Pathogenicity in African Lions
  2. Weckworth, Julie K; Davis, Brian W; Roelke-Parker,Melody; Wilkes, Rebecca P; Packer, Craig; Eblate, Ernest; Schwartz, Michael K; Mills, L Scott
  3. Pathogens (Basel, Switzerland). 2020, NOV; 9(11): E872.
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