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  1. 1.   The human oral microbiome and risk of colorectal cancer within three prospective cohort studies in the United States
  2. Vogtmann, Emily; Yano, Yukiko; Zouiouich, Semi; Hua,Xing; Wan, Yunhu; Purandare, Vaishnavi; Li, Shilan; Dagnall,Casey; Jones, Kristine; Hicks,Belynda; Hutchinson,Amy; Caporaso, J Gregory; Wheeler, William; Huang, Wen-Yi; Freedman, Neal D; Sandler, Dale P; Beane Freeman, Laura E; Liao, Linda M; Gail, Mitchell H; Shi, Jianxin; Abnet, Christian C; Sinha, Rashmi
  3. Cancer. 2025, Mar 15; 131(6): e35802.
  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.   Hemophagocytic Lymphohistiocytosis Gene Variants in Severe Aplastic Anemia and Their Impact on Hematopoietic Cell Transplantation Outcomes
  2. Rafati, Maryam; McReynolds, Lisa J; Wang, Youjin; Hicks,Belynda; Jones,Kristine; Spellman, Stephen R; He, Meilun; Bolon, Yung-Tsi; Arrieta-Bolaños, Esteban; Saultz, Jennifer N; Lee, Stephanie J; Savage, Sharon A; Gadalla, Shahinaz M
  3. Transplantation and Cellular Therapy. 2024, Aug ; 30(8): 770e1-770e10.
  1. 4.   Single-nucleus RNA sequencing reveals loss of DCT1 renal tubules in HIV Vpr transgenic mice
  2. Latt, Khun Zaw; Yoshida, Teruhiko; Shrivastav, Shashi; Abedini, Amin; Reece, Jeff M; Sun, Zeguo; Lee, Hewang; Okamoto, Koji; Dagur, Pradeep; Ishimoto, Yu; Heymann, Jurgen; Zhao,Yongmei; Chung, Joon-Yong; Hewitt, Stephen; Jose, Pedro A; Lee, Kyung; He, John Cijiang; Winkler,Cheryl; Knepper, Mark A; Kino, Tomoshige; Rosenberg, Avi Z; Susztak, Katalin; Kopp, Jeffrey B
  3. The American Journal of Pathology. 2024, Jul 18;
  1. 5.   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. 6.   The Janus kinase 1 is critical for pancreatic cancer initiation and progression
  2. Shrestha, Hridaya; Rädler, Patrick D; Dennaoui, Rayane; Wicker, Madison N; Rajbhandari, Nirakar; Sun, Yunguang; Peck, Amy R; Vistisen, Kerry; Triplett, Aleata A; Beydoun, Rafic; Sterneck,Esta; Saur, Dieter; Rui, Hallgeir; Wagner, Kay-Uwe
  3. Cell Reports. 2024, May 10; 43(5): 114202.
  1. 7.   Insights into the mechanisms and structure of breakage-fusion-bridge cycles in cervical cancer using long-read sequencing
  2. Rodriguez, Isabel; Rossi, Nicole M; Keskus, Ayse G; Xie, Yi; Ahmad, Tanveer; Bryant, Asher; Lou,Hong; Paredes, Jesica Godinez; Milano, Rose; Rao, Nina; Tulsyan, Sonam; Boland, Joseph F; Luo,Wen; Liu,Jia; O'Hanlon, Tim; Bess, Jazmyn; Mukhina, Vera; Gaykalova, Daria; Yuki, Yuko; Malik, Laksh; Billingsley, Kimberley J; Blauwendraat, Cornelis; Carrington, Mary; Yeager,Meredith; Mirabello, Lisa; Kolmogorov, Mikhail; Dean, Michael
  3. American Journal of Human Genetics. 2024, Jan 25;
  1. 8.   Transfer learning in a biomaterial fibrosis model identifies in vivo senescence heterogeneity and contributions to vascularization and matrix production across species and diverse pathologies
  2. Cherry, Christopher; Andorko, James I; Krishnan, Kavita; Mejías, Joscelyn C; Nguyen, Helen Hieu; Stivers, Katlin B; Gray-Gaillard, Elise F; Ruta, Anna; Han, Jin; Hamada, Naomi; Hamada, Masakazu; Sturmlechner, Ines; Trewartha, Shawn; Michel, John H; Davenport Huyer, Locke; Wolf,Matthew; Tam, Ada J; Peña, Alexis N; Keerthivasan, Shilpa; Le Saux, Claude Jordan; Fertig, Elana J; Baker, Darren J; Housseau, Franck; van Deursen, Jan M; Pardoll, Drew M; Elisseeff, Jennifer H
  3. GeroScience. 2023, Apr 20;
  1. 9.   Targeted long-read sequencing of the Ewing sarcoma 6p25.1 susceptibility locus identifies germline-somatic interactions with EWSR1-FLI1 binding
  2. Lee, Olivia W; Rodrigues, Calvin; Lin, Shu-Hong; Luo,Wen; Jones,Kristine; Brown, Derek W; Zhou,Weiyin; Karlins, Eric; Khan, Sairah M; Baulande, Sylvain; Raynal, Virginie; Surdez, Didier; Reynaud, Stephanie; Rubio, Rebeca Alba; Zaidi, Sakina; Grossetête, Sandrine; Ballet, Stelly; Lapouble, Eve; Laurence, Valérie; Pierron, Gaelle; Gaspar, Nathalie; Corradini, Nadège; Marec-Bérard, Perrine; Rothman, Nathaniel; Dagnall, Casey L; Burdett, Laurie; Manning, Michelle; Wyatt, Kathleen; Yeager, Meredith; Chari,Raj; Leisenring, Wendy M; Kulozik, Andreas E; Kriebel, Jennifer; Meitinger, Thomas; Strauch, Konstantin; Kirchner, Thomas; Dirksen, Uta; Mirabello, Lisa; Tucker, Margaret A; Tirode, Franck; Armstrong, Gregory T; Bhatia, Smita; Robison, Leslie L; Yasui, Yutaka; Romero-Pérez, Laura; Hartmann, Wolfgang; Metzler, Markus; Diver, W Ryan; Lori, Adriana; Freedman, Neal D; Hoover, Robert N; Morton, Lindsay M; Chanock, Stephen J; Grünewald, Thomas G P; Delattre, Olivier; Machiela, Mitchell J
  3. American Journal of Human Genetics. 2023, Mar 2; 110(3): 427-441.
  1. 10.   LINE1-Mediated Reverse Transcription and Genomic Integration of SARS-CoV-2 mRNA Detected in Virus-Infected but Not in Viral mRNA-Transfected Cells
  2. Zhang, Liguo; Bisht, Punam; Flamier, Anthony; Barrasa, M Inmaculada; Friesen, Max; Richards, Alexsia; Hughes,Stephen; Jaenisch, Rudolf
  3. Viruses. 2023, Feb 25; 15(3):
  1. 11.   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. 12.   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. 13.   Structural variant analysis of a cancer reference cell line sample using multiple sequencing technologies
  2. Talsania,Keyur; Shen,Tsai-Wei; Chen, Xiongfong; Jaeger, Erich; Li, Zhipan; Chen, Zhong; Chen, Wanqiu; Tran,Bao; Kusko, Rebecca; Wang, Limin; Pang, Andy Wing Chun; Yang, Zhaowei; Choudhari, Sulbha; Colgan, Michael; Fang, Li Tai; Carroll, Andrew; Shetty,Jyoti; Kriga,Yuliya; German,Oksana; Smirnova,Tatyana; Liu, Tiantain; Li, Jing; Kellman, Ben; Hong, Karl; Hastie, Alex R; Natarajan, Aparna; Moshrefi, Ali; Granat, Anastasiya; Truong, Tiffany; Bombardi, Robin; Mankinen, Veronnica; Meerzaman, Daoud; Mason, Christopher E; Collins, Jack; Stahlberg, Eric; Xiao, Chunlin; Wang, Charles; Xiao, Wenming; Zhao,Yongmei
  3. Genome Biology. 2022, Dec 13; 23(1): 255.
  1. 14.   Single-cell sequencing reveals activation of core transcription factors in PRC2-deficient malignant peripheral nerve sheath tumor
  2. Zhang, Xiyuan; Lou, Hannah E; Gopalan, Vishaka; Liu, Zhihui; Jafarah, Hilda M; Lei, Haiyan; Jones, Paige; Sayers, Carly M; Yohe, Marielle E; Chittiboina, Prashant; Widemann, Brigitte C; Thiele, Carol J; Kelly,Michael; Hannenhalli, Sridhar; Shern, Jack F
  3. Cell Reports. 2022, Sep 20; 40(12): 111363.
  1. 15.   Inhibition of HSP 90 is associated with potent anti-tumor activity in Papillary Renal Cell Carcinoma
  2. Pahwa, Roma; Dubhashi, Janhavi; Singh, Anand; Jailwala, Parthav; Lobanov,Alexei; Thomas, Craig J; Ceribelli, Michele; Wilson, Kelli; Ricketts, Christopher J; Vocke, Cathy D; Wells, Catherine; Bottaro, Donald P; Linehan, W Marston; Neckers, Len; Srinivasan, Ramaprasad
  3. Journal of Experimental & Clinical Cancer Research : CR. 2022, Jun 27; 41(1): 208.
  1. 16.   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. 17.   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. 18.   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. 19.   A Phase II Study of Pembrolizumab in Combination with Capecitabine and Oxaliplatin with Molecular Profiling in Patients with Advanced Biliary Tract Carcinoma
  2. Monge, Cecilia; Pehrsson,Erica; Xie, Changqing; Duffy, Austin G; Mabry, Donna; Wood, Bradford J; Kleiner, David E; Steinberg, Seth M; Figg, William D; Redd, Bernadette; Budhu, Anuradha; Wang, Sophie; Tandon,Mayank; Ma, Lichun; Wei Wang, Xin; Greten, Tim F
  3. The Oncologist. 2022, Mar 11; 27(3): e273-e285.
  1. 20.   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. 21.   Molecular Signature and Immune Landscape of HCV-Associated Hepatocellular Carcinoma (HCC): Differences and Similarities with HBV-HCC
  2. De Battista, Davide; Zamboni, Fausto; Gerstein, Hannah; Sato, Shinya; Markowitz,Tovah; Lack,Justin; Engle, Ronald E; Farci, Patrizia
  3. Journal of hepatocellular carcinoma. 2021, Nov 21; 8: 1399-1413.
  1. 22.   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. 23.   Source identification of HIV-1 transmission in three lawsuits Using Ultra-Deep pyrosequencing and phylogenetic analysis
  2. Li, Wei-You; Huang,Szu-Wei; Wang, Sheng-Fan; Liu, Hsin-Fu; Chou, Chih-Hung; Wu, Shang-Jung; Huang, Hsien-Da; Lu, Po-Liang; Fann, Cathy S J; Chen, Marcelo; Chen, Yen-Hsu; Chen, Yi-Ming Arthur
  3. Journal of microbiology, immunology, and infection = Wei mian yu gan ran za zhi. 2021, Aug; 54(4): 596-605.
  1. 24.   Verification of CRISPR editing and finding transgenic inserts by Xdrop indirect sequence capture followed by short- and long-read sequencing
  2. Blondal, Thorarinn; Gamba, Cristina; Jagd, Lea Moller; Su,Ling; Demirov,Dimiter; Guo,Amber; Johnston, Camille M.; Riising, Eva M.; Wu,Xiaolin; Mikkelsen, Marie J.; Szabova,Ludmila; Mouritzen, Peter
  3. Methods. 2021, Jul; 191: 68-77.
  1. 25.   TPM, FPKM, or Normalized Counts? A Comparative Study of Quantification Measures for the Analysis of RNA-seq Data from the NCI Patient-Derived Models Repository
  2. Zhao, Yingdong; Li, Ming-Chung; Konaté, Mariam M; Chen,Li; Das,Biswajit; Karlovich,Chris; Williams,Mickey; Evrard,Yvonne; Doroshow, James H; McShane, Lisa M
  3. Journal of translational medicine. 2021, Jun 22; 19(1): 269.
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