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  1. 1.   TRAIL induces cytokine production via the NFkB2 pathway promoting neutrophil chemotaxis and neutrophil-mediated immune-suppression in triple negative breast cancer cells
  2. Kundu, Manjari; Greer, Yoshimi E; Lobanov, Alexei; Ridnour, Lisa; Donahue, Renee N; Ng, Yeap; Ratnayake, Shashi; White, Karley; Voeller, Donna; Weltz, Sarah; Chen, Qingrong; Lockett,Stephen; Cam, Maggie; Meerzaman, Daoud; Wink, David A; Weigert, Roberto; Lipkowitz, Stanley
  3. Cancer Letters. 2025, Jun 28; 620: 217692.
  1. 2.   Expression of HIV from a 1-LTR circular DNA in the absence of integration
  2. Gurgo, Corrado; Fenizia, Claudio; McKinnon, Katherine; Hsia,Ru-Ching; Franchini, Genoveffa
  3. Retrovirology. 2025, Mar 17; 22(1): 2.
  1. 3.   Data imbalance in drug response prediction: multi-objective optimization approach in deep learning setting
  2. Narykov, Oleksandr; Zhu, Yitan; Brettin, Thomas; Evrard,Yvonne; Partin, Alexander; Xia, Fangfang; Shukla, Maulik; Vasanthakumari, Priyanka; Doroshow, James H; Stevens, Rick L
  3. Briefings in Bioinformatics. 2025, Mar 04; 26(2):
  1. 4.   Deletion of a single CTCF motif at the boundary of a chromatin domain with three FGF genes disrupts gene expression and embryonic development
  2. Chakraborty, Shreeta; Wenzlitschke, Nina; Anderson,Matthew; Eraso, Ariel; Baudic, Manon; Thompson, Joyce J; Evans, Alicia A; Shatford-Adams, Lilly M; Chari,Raj; Awasthi,Roackie; Dale, Ryan K; Lewandoski,Mark; Petros, Timothy J; Rocha, Pedro P
  3. Developmental Cell. 2025, Feb 24;
  1. 5.   HIF1a Plays a Crucial Role in the Development of TFE3-Rearranged Renal Cell Carcinoma by Orchestrating a Metabolic Shift Toward Fatty Acid Synthesis
  2. Nishizawa, Hidekazu; Funasaki, Shintaro; Ma, Wenjuan; Kubota, Yoshiaki; Watanabe, Kazuhide; Arima, Yuichiro; Kuroda, Shoichiro; Ito, Takaaki; Furuya, Mitsuko; Motoshima, Takanobu; Nishiyama, Akira; Mehanna, Sally; Satou, Yorifumi; Hasumi, Hisashi; Jikuya, Ryosuke; Makiyama, Kazuhide; Tamura, Tomohiko; Oike, Yuichi; Tanaka, Yasuhito; Suda, Toshio; Schmidt,Laura; Linehan, W Marston; Baba, Masaya; Kamba, Tomomi
  3. Genes to Cells : devoted to molecular & cellular mechanisms. 2025, Jan; 30(1): e13195.
  1. 6.   Associations Between Mosaic Loss of Sex Chromosomes and Incident Hospitalization for Atrial Fibrillation in the United Kingdom
  2. Lim, Jungeun; Hubbard, Aubrey K; Blechter, Batel; Shi, Jianxin; Zhou,Weiyin; Loftfield, Erikka; Machiela, Mitchell J; Wong, Jason Y Y
  3. Journal of the American Heart Association. 2024, Nov 19; 13(22): e036984.
  1. 7.   Analytical measuring interval, linearity, and precision of serology assays for detection of SARS-CoV-2 antibodies according to CLSI guidelines
  2. Haynesworth,Katrina; Kemp,Troy; Loftus,Sarah; Metz,Jordan; Castro, Nicholas C; Bullock, Jimmie; Fetterer, David; Pinto,Ligia
  3. mSphere. 2024, Oct 31; e0039324.
  1. 8.   A novel pathogenic germline chromosome 3 inversion in von Hippel-Lindau disease
  2. Vocke, Cathy D; Ricketts, Christopher J; Pack, Svetlana; Raffeld, Mark; Hewitt, Stephen; Lebensohn, Alexandra P; O'Brien, Lidenys; Gautam, Rabindra; Reynolds, Krista; Schmidt,Laura; Choo, Kristin; Kenigsberg, Alex; Gurram, Sandeep; Chew, Emily Y; Nilubol, Naris; Chittaboina, Prashant; Merino, Maria J; Ball, Mark W; Linehan, W Marston
  3. Journal of Medical Genetics. 2024, Sep 24;
  1. 9.   Novel mechanisms of MITF regulation identified in a mouse suppressor screen
  2. Vu, Hong Nhung; Valdimarsson, Matti Már; Sigurbjörnsdóttir, Sara; Bergsteinsdóttir, Kristín; Debbache, Julien; Bismuth, Keren; Swing, Deborah A; Hallsson, Jón H; Larue, Lionel; Arnheiter, Heinz; Copeland, Neal G; Jenkins, Nancy A; Heidarsson, Petur O; Steingrímsson, Eiríkur
  3. EMBO Reports. 2024, Aug 21;
  1. 10.   Near-infrared duocarmycin photorelease from a Treg-targeted antibody-drug conjugate improves efficacy of PD-1 blockade in syngeneic murine tumor models
  2. Fukushima, Hiroshi; Furusawa, Aki; Takao, Seiichiro; Thankarajan Mini Mablet,Ebaston; Luciano, Michael P; Usama, Syed Muhammad; Kano, Makoto; Okuyama, Shuhei; Yamamoto, Hiroshi; Suzuki, Motofumi; Kano, Miyu; Choyke, Peter L; Schnermann,Martin; Kobayashi, Hisataka
  3. Oncoimmunology. 2024, Jun 20; 13(1): 2370544.
  1. 11.   Microenvironment shapes small-cell lung cancer neuroendocrine states and presents therapeutic opportunities
  2. Desai, Parth; Takahashi, Nobuyuki; Kumar, Rajesh; Nichols, Samantha; Malin, Justin; Hunt, Allison; Schultz, Christopher; Cao, Yingying; Tillo, Desiree; Nousome, Darryl; Chauhan, Lakshya; Sciuto, Linda; Jordan, Kimberly; Rajapakse, Vinodh; Tandon, Mayank; Lissa, Delphine; Zhang, Yang; Kumar, Suresh; Pongor, Lorinc; Singh, Abhay; Schroder, Brett; Sharma, Ajit Kumar; Chang, Tiangen; Vilimas, Rasa; Pinkiert, Danielle; Graham, Chante; Butcher,Donna; Warner,Andrew; Sebastian, Robin; Mahon, Mimi; Baker, Karen; Cheng, Jennifer; Berger, Ann; Lake, Ross; Abel, Melissa; Krishnamurthy, Manan; Chrisafis, George; Fitzgerald, Peter; Nirula, Micheal; Goyal, Shubhank; Atkinson, Devon; Bateman, Nicholas W; Abulez, Tamara; Nair, Govind; Apolo, Andrea; Guha, Udayan; Karim,Baktiar; El Meskini,Rajaa; Ohler,Zoe; Jolly, Mohit Kumar; Schaffer, Alejandro; Ruppin, Eytan; Kleiner, David; Miettinen, Markku; Brown, G Tom; Hewitt, Stephen; Conrads, Thomas; Thomas, Anish
  3. Cell Reports. Medicine. 2024, Jun 18; 5(6): 101610.
  1. 12.   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. 13.   Systematic characterization of multi-omics landscape between gut microbial metabolites and GPCRome in Alzheimer's disease
  2. Qiu, Yunguang; Hou, Yuan; Gohel, Dhruv; Zhou, Yadi; Xu, Jielin; Bykova, Marina; Yang, Yuxin; Leverenz, James B; Pieper, Andrew A; Nussinov,Ruth; Caldwell, Jessica Z K; Brown, J Mark; Cheng, Feixiong
  3. Cell Reports. 2024, Apr 21; 43(5): 114128.
  1. 14.   Germline pathogenic variants associated with triple-negative breast cancer in US Hispanic and Guatemalan women using hospital and community-based recruitment strategies
  2. Godinez Paredes, Jesica M; Rodriguez, Isabel; Ren, Megan; Orozco, Anali; Ortiz, Jeremy; Albanez, Anaseidy; Jones, Catherine; Nahleh, Zeina; Barreda, Lilian; Garland,Lisa; Torres-Gonzalez, Edmundo; Wu,Dongjing; Luo,Wen; Liu,Jia; Argueta, Victor; Orozco, Roberto; Gharzouzi, Eduardo; Dean, Michael
  3. Breast Cancer Research and Treatment. 2024, Mar 23;
  1. 15.   Phototruncation cell tracking with near-infrared photoimmunotherapy using heptamethine cyanine dye to visualise migratory dynamics of immune cells
  2. Fukushima, Hiroshi; Furusawa, Aki; Takao, Seiichiro; Matikonda, Siddharth S; Kano, Makoto; Okuyama, Shuhei; Yamamoto, Hiroshi; Choyke, Peter L; Schnermann,Martin; Kobayashi, Hisataka
  3. EBioMedicine. 2024, Mar 14; 102: 105050.
  1. 16.   A Comprehensive Investigation of Active Learning Strategies for Conducting Anti-Cancer Drug Screening
  2. Vasanthakumari, Priyanka; Zhu, Yitan; Brettin, Thomas; Partin, Alexander; Shukla, Maulik; Xia, Fangfang; Narykov, Oleksandr; Weil,Michael; Stevens, Rick L
  3. Cancers. 2024, Jan 26; 16(3):
  1. 17.   Tumor Suppression by Anti-Fibroblast Activation Protein Near-Infrared Photoimmunotherapy Targeting Cancer-Associated Fibroblasts
  2. Glabman, Raisa A; Olkowski, Colleen P; Minor, Hannah A; Bassel,Laura; Kedei, Noemi; Choyke, Peter L; Sato, Noriko
  3. Cancers. 2024, Jan 20; 16(2):
  1. 18.   Recommendations for assessing appearance concerns related to plexiform and cutaneous neurofibromas in neurofibromatosis 1 clinical trials
  2. Merker, Vanessa L; Thompson, Heather L; Wolters, Pamela L; Buono, Frank D; Hingtgen, Cynthia M; Rosser, Tena; Barton, Belinda; Barnett, Carolina; Smith, Taylor; Haberkamp, Diana; McManus, Miranda L; Baldwin,Andrea; Moss, Irene P; Röhl, Claas; Martin, Staci
  3. Clinical Trials (London, England). 2023, Dec 23; 17407745231205577.
  1. 19.   Integration of Computational Docking into Anti-Cancer Drug Response Prediction Models
  2. Narykov, Oleksandr; Zhu, Yitan; Brettin, Thomas; Evrard,Yvonne; Partin, Alexander; Shukla, Maulik; Xia, Fangfang; Clyde, Austin; Vasanthakumari, Priyanka; Doroshow, James H; Stevens, Rick L
  3. Cancers. 2023, Dec 21; 16(1):
  1. 20.   Can incorporating genotyping data into efficacy estimators improve efficiency of early phase malaria vaccine trials?
  2. Potter, Gail E; Callier,Viviane; Shrestha, Biraj; Joshi, Sudhaunshu; Dwivedi, Ankit; Silva, Joana C; Laurens, Matthew B; Follmann, Dean A; Deye, Gregory A
  3. Malaria Journal. 2023, Dec 19; 22(1): 383.
  1. 21.   Deep learning-based segmentation of multisite disease in ovarian cancer
  2. Buddenkotte, Thomas; Rundo, Leonardo; Woitek, Ramona; Escudero Sanchez, Lorena; Beer, Lucian; Crispin-Ortuzar, Mireia; Etmann, Christian; Mukherjee, Subhadip; Bura, Vlad; McCague, Cathal; Sahin, Hilal; Pintican, Roxana; Zerunian, Marta; Allajbeu, Iris; Singh, Naveena; Sahdev, Anju; Havrilesky, Laura; Cohn, David E; Bateman, Nicholas W; Conrads, Thomas P; Darcy, Kathleen M; Maxwell, G Larry; Freymann,John; Öktem, Ozan; Brenton, James D; Sala, Evis; Schönlieb, Carola-Bibiane
  3. European Radiology Experimental. 2023, Dec 07; 7(1): 77.
  1. 22.   Genome-wide profiling of transcription factor activity in primary liver cancer using single-cell ATAC sequencing
  2. Craig, Amanda J; Silveira, Maruhen A Datsch; Ma, Lichun; Revsine, Mahler; Wang, Limin; Heinrich, Sophia; Rae, Zachary; Ruchinskas, Allison; Dadkhah,Kimia; Do, Whitney; Behrens, Shay; Mehrabadi, Farid R; Dominguez, Dana A; Forgues, Marshonna; Budhu, Anuradha; Chaisaingmongkol, Jittiporn; Hernandez, Jonathan M; Davis, Jeremy L; Tran,Bao; Marquardt, Jens U; Ruchirawat, Mathuros; Kelly, Michael; Greten, Tim F; Wang, Xin W
  3. Cell Reports. 2023, Nov 17; 42(11): 113446.
  1. 23.   Abundant binary promoter switches in lineage-determining transcription factors indicate a digital component of cell fate determination
  2. Li,Hongchuan; Rahman, Md Ahasanur; Ruesch, Michael; Eisele, Caprice D; Anderson,Erik; Wright,Paul; Cao, Jennie; Ratnayake, Shashikala; Chen, Qingrong; Yan, Chunhua; Meerzaman, Daoud; Abraham, Roshini S; Freud, Aharon G; Anderson,Steve
  3. Cell Reports. 2023, Nov 16; 42(11): 113454.
  1. 24.   DOCK 6: Incorporating hierarchical traversal through precomputed ligand conformations to enable large-scale docking
  2. Balius,Trent; Tan, Y Stanley; Chakrabarti,Mayukh
  3. Journal of Computational Chemistry. 2023, Sep 25;
  1. 25.   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.
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