BioAgents: Democratizing Bioinformatics Analysis with Multi-Agent Systems

Authors: Mehandru, Nikita, Hall, Amanda K., Melnichenko, Olesya, Dubinina, Yulia, Tsirulnikov, Daniel, Bamman, David, Alaa, Ahmed, Saponas, Scott, Malladi, Venkat S.

Subject Terms: Computer Science - Artificial Intelligence, Computer Science - Multiagent Systems

Access URL: http://arxiv.org/abs/2501.06314

Continuous Analysis: Evolution of Software Engineering and Reproducibility for Science

Authors: Malladi, Venkat S., Yazykova, Maria, Melnichenko, Olesya, Dubinina, Yulia

Subject Terms: Computer Science - Software Engineering, Computer Science - Computational Engineering, Finance, and Science

Access URL: http://arxiv.org/abs/2411.02283

The GA4GH Task Execution API: Enabling Easy Multi Cloud Task Execution

Authors: Kanitz, Alexander, McLoughlin, Matthew H., Beckman, Liam, Malladi, Venkat S., Ellrott, Kyle P.

Subject Terms: Computer Science - Distributed, Parallel, and Cluster Computing

Access URL: http://arxiv.org/abs/2405.00013

Improving Renal Tumor Biopsy Prognostication With BAP1 Analyses

Authors: Kapur, Payal, Setoodeh, Sasan, Araj, Ellen, Yan, Jingsheng, Malladi, Venkat S., Cadeddu, Jeffrey A., Christie, Alana, Brugarolas, James

Source: Archives of pathology & laboratory medicine. 146(2):154-165

Availability: http://explore.bl.uk/primo_library/libweb/action/display.do?tabs=detailsTab&gathStatTab=true&ct=display&fn=search&doc=ETOCRN631343415&indx=1&recIds=ETOCRN631343415

Germline and sporadic mTOR pathway mutations in low-grade oncocytic tumor of the kidney

Authors: Kapur, Payal, Gao, Ming, Zhong, Hua, Chintalapati, Suneetha, Mitui, Midori, Barnes, Spencer D., Zhou, Qinbo, Miyata, Jeffrey, Carrillo, Deyssy, Malladi, Venkat S., Rakheja, Dinesh, Pedrosa, Ivan, Xu, Lin, Kinch, Lisa, Brugarolas, James

Source: In Modern Pathology March 2022 35(3):333-343

Glucose starvation induces a switch in the histone acetylome for activation of gluconeogenic and fat metabolism genes

Authors: Hsieh, Wen-Chuan, Sutter, Benjamin M., Ruess, Holly, Barnes, Spencer D., Malladi, Venkat S., Tu, Benjamin P.

Source: In Molecular Cell 6 January 2022 82(1):60-74

A multi-omic single-cell landscape of human gynecologic malignancies

Authors: Regner, Matthew J., Wisniewska, Kamila, Garcia-Recio, Susana, Thennavan, Aatish, Mendez-Giraldez, Raul, Malladi, Venkat S., Hawkins, Gabrielle, Parker, Joel S., Perou, Charles M., Bae-Jump, Victoria L., Franco, Hector L.

Source: In Molecular Cell 2 December 2021 81(23):4924-4941

Single‐cell analysis of mouse and human prostate reveals novel fibroblasts with specialized distribution and microenvironment interactions

Authors: Joseph, Diya B, Henry, Gervaise H, Malewska, Alicia, Reese, Jeffrey C, Mauck, Ryan J, Gahan, Jeffrey C, Hutchinson, Ryan C, Malladi, Venkat S, Roehrborn, Claus G, Vezina, Chad M, Strand, Douglas W

Source: Journal of pathology. 255(2):141-154

Availability: http://explore.bl.uk/primo_library/libweb/action/display.do?tabs=detailsTab&gathStatTab=true&ct=display&fn=search&doc=ETOCvdc_100128818946.0x000001&indx=1&recIds=ETOCvdc_100128818946.0x000001

KLF13 promotes SLE pathogenesis by modifying chromatin accessibility of key proinflammatory cytokine genes.

Authors: Wang, Andrew, Fairhurst, Anna-Marie, Liu, Kui, Wakeland, Benjamin, Barnes, Spencer, Malladi, Venkat S., Viswanathan, Kasthuribai, Arana, Carlos, Dozmorov, Igor, Singhar, Amrita, Du, Yong, Imam, Marjaan, Moses, Angela, Chen, Christian, Sunkavalli, Ashwini, Casco, Jose, Rakheja, Dinesh, Li, Quan-Zhen, Mohan, Chandra, Clayberger, Carol

Source: Communications Biology; 11/6/2024, Vol. 7 Issue 1, p1-14, 14p

Subject Terms: MYELOID cells, SYSTEMIC lupus erythematosus, LIGANDS (Biochemistry), T cells, LUPUS nephritis

Loss of CHD1 Promotes Heterogeneous Mechanisms of Resistance to AR-Targeted Therapy via Chromatin Dysregulation

Authors: Zhang, Zeda, Zhou, Chuanli, Li, Xiaoling, Barnes, Spencer D., Deng, Su, Hoover, Elizabeth, Chen, Chi-Chao, Lee, Young Sun, Zhang, Yanxiao, Wang, Choushi, Metang, Lauren A., Wu, Chao, Tirado, Carla Rodriguez, Johnson, Nickolas A., Wongvipat, John, Navrazhina, Kristina, Cao, Zhen, Choi, Danielle, Huang, Chun-Hao, Linton, Eliot, Chen, Xiaoping, Liang, Yupu, Mason, Christopher E., de Stanchina, Elisa, Abida, Wassim, Lujambio, Amaia, Li, Sheng, Lowe, Scott W., Mendell, Joshua T., Malladi, Venkat S., Sawyers, Charles L., Mu, Ping

Source: In Cancer Cell 13 April 2020 37(4):584-598

Activation of PARP-1 by snoRNAs Controls Ribosome Biogenesis and Cell Growth via the RNA Helicase DDX21

Authors: Kim, Dae-Seok, Camacho, Cristel V., Nagari, Anusha, Malladi, Venkat S., Challa, Sridevi, Kraus, W. Lee

Source: In Molecular Cell 19 September 2019 75(6):1270-1285

Cardiac Reprogramming Factors Synergistically Activate Genome-wide Cardiogenic Stage-Specific Enhancers

Authors: Hashimoto, Hisayuki, Wang, Zhaoning, Garry, Glynnis A., Malladi, Venkat S., Botten, Giovanni A., Ye, Wenduo, Zhou, Huanyu, Osterwalder, Marco, Dickel, Diane E., Visel, Axel, Liu, Ning, Bassel-Duby, Rhonda, Olson, Eric N.

Source: In Cell Stem Cell 3 July 2019 25(1):69-86

Perivascular mesenchymal cells control adipose-tissue macrophage accrual in obesity

Authors: Shan, Bo, Shao, Mengle, Zhang, Qianbin, Hepler, Chelsea, Paschoal, Vivian A., Barnes, Spencer D., Vishvanath, Lavanya, An, Yu A., Jia, Lin, Malladi, Venkat S., Strand, Douglas W., Gupta, Olga T., Elmquist, Joel K., Oh, Dayoung, Gupta, Rana K.

Source: Nature metabolism. 2(11):1332-1349

Availability: http://explore.bl.uk/primo_library/libweb/action/display.do?tabs=detailsTab&gathStatTab=true&ct=display&fn=search&doc=ETOCvdc_100187006076.0x000001&indx=1&recIds=ETOCvdc_100187006076.0x000001

Urethral luminal epithelia are castration‐insensitive cells of the proximal prostate

Authors: Joseph, Diya B., Henry, Gervaise H., Malewska, Alicia, Iqbal, Nida S., Ruetten, Hannah M., Turco, Anne E., Abler, Lisa L., Sandhu, Simran K., Cadena, Mark T., Malladi, Venkat S., Reese, Jeffrey C., Mauck, Ryan J., Gahan, Jeffrey C., Hutchinson, Ryan C., Roehrborn, Claus G., Baker, Linda A., Vezina, Chad M., Strand, Douglas W.

Source: Prostate. 80(11):872-884

Availability: http://explore.bl.uk/primo_library/libweb/action/display.do?tabs=detailsTab&gathStatTab=true&ct=display&fn=search&doc=ETOCvdc_100107629833.0x000001&indx=1&recIds=ETOCvdc_100107629833.0x000001

Identification of a multipotent Twist2-expressing cell population in the adult heart

Authors: Min, Yi-Li, Jaichander, Priscilla, Sanchez-Ortiz, Efrain, Bezprozvannaya, Svetlana, Malladi, Venkat S., Cui, Miao, Wang, Zhaoning, Bassel-Duby, Rhonda, Olson, Eric N., Liu, Ning

Source: Proceedings of the National Academy of Sciences of the United States of America, 2018 Sep 01. 115(36), E8430-E8439.

Access URL: https://www.jstor.org/stable/26531243

A Cellular Anatomy of the Normal Adult Human Prostate and Prostatic Urethra

Authors: Henry, Gervaise H., Malewska, Alicia, Joseph, Diya B., Malladi, Venkat S., Lee, Jeon, Torrealba, Jose, Mauck, Ryan J., Gahan, Jeffrey C., Raj, Ganesh V., Roehrborn, Claus G., Hon, Gary C., MacConmara, Malcolm P., Reese, Jeffrey C., Hutchinson, Ryan C., Vezina, Chad M., Strand, Douglas W.

Source: In Cell Reports 18 December 2018 25(12):3530-3542

Twist2 amplification in rhabdomyosarcoma represses myogenesis and promotes oncogenesis by redirecting MyoD DNA binding

Authors: Li, Stephen, Chen, Kenian, Zhang, Yichi, Barnes, Spencer D., Jaichander, Priscilla, Zheng, Yanbin, Hassan, Mohammed, Malladi, Venkat S., Skapek, Stephen X., Xu, Lin

Source: Genes & development. 33(11/12):626-640

Availability: http://explore.bl.uk/primo_library/libweb/action/display.do?tabs=detailsTab&gathStatTab=true&ct=display&fn=search&doc=ETOCRN620460010&indx=1&recIds=ETOCRN620460010

High-Phosphate Diet Induces Exercise Intolerance and Impairs Fatty Acid Metabolism in Mice

Authors: Peri-Okonny, Poghni, Baskin, Kedryn K., Iwamoto, Gary, Mitchell, Jere H., Smith, Scott A., Kim, Han Kyul, Szweda, Luke I., Bassel-Duby, Rhonda, Fujikawa, Teppei, Castorena, Carlos M., Richardson, James, Shelton, John M., Ayers, Colby, Berry, Jarett D., Malladi, Venkat S., Hu, Ming-Chang, Moe, Orson W., Scherer, Philipp E., Vongpatanasin, Wanpen

Source: Circulation. 139(11):1422-1434

Availability: http://explore.bl.uk/primo_library/libweb/action/display.do?tabs=detailsTab&gathStatTab=true&ct=display&fn=search&doc=ETOCvdc_100188861548.0x000001&indx=1&recIds=ETOCvdc_100188861548.0x000001

Dynamic change of transcription pausing through modulating NELF protein stability regulates granulocytic differentiation

Authors: Liu, Xiuli, Gogate, Aishwarya A., Tastemel, Melodi, Malladi, Venkat S., Yao, Huiyu, Nguyen, Kim, Huang, Lily Jun-Shen, Bai, Xiaoying

Source: In Blood Advances 8 August 2017 1(18):1358-1367

Enhancer transcription reveals subtype-specific gene expression programs controlling breast cancer pathogenesis

Authors: Franco, Hector L., Nagari, Anusha, Malladi, Venkat S., Li, Wenqian, Xi, Yuanxin, Richardson, Dana, Allton, Kendra L., Tanaka, Kaori, Li, Jing, Murakami, Shino

Source: Genome research. 28(2):159-170

Availability: http://explore.bl.uk/primo_library/libweb/action/display.do?tabs=detailsTab&gathStatTab=true&ct=display&fn=search&doc=ETOCRN614728942&indx=1&recIds=ETOCRN614728942