Search Results - "Wawer, Mathias J."

Harnessing Connectivity in a Large-Scale Small-Molecule Sensitivity Dataset by Seashore-Ludlow, Brinton, Rees, Matthew G, Cheah, Jaime H, Cokol, Murat, Price, Edmund V, Coletti, Matthew E, Jones, Victor, Bodycombe, Nicole E, Soule, Christian K, Gould, Joshua, Alexander, Benjamin, Li, Ava, Montgomery, Philip, Wawer, Mathias J, Kuru, Nurdan, Kotz, Joanne D, Hon, C Suk-Yee, Munoz, Benito, Liefeld, Ted, Dančík, Vlado, Bittker, Joshua A, Palmer, Michelle, Bradner, James E, Shamji, Alykhan F, Clemons, Paul A, Schreiber, Stuart L

“…Identifying genetic alterations that prime a cancer cell to respond to a particular therapeutic agent can facilitate the development of precision cancer…”
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Mapping the landscape of genetic dependencies in chordoma by Sharifnia, Tanaz, Wawer, Mathias J., Goodale, Amy, Lee, Yenarae, Kazachkova, Mariya, Dempster, Joshua M., Muller, Sandrine, Levy, Joan, Freed, Daniel M., Sommer, Josh, Kalfon, Jérémie, Vazquez, Francisca, Hahn, William C., Root, David E., Clemons, Paul A., Schreiber, Stuart L.

“…Identifying the spectrum of genes required for cancer cell survival can reveal essential cancer circuitry and therapeutic targets, but such a map remains…”
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A dataset of images and morphological profiles of 30 000 small-molecule treatments using the Cell Painting assay by Bray, Mark-Anthony, Gustafsdottir, Sigrun M, Rohban, Mohammad H, Singh, Shantanu, Ljosa, Vebjorn, Sokolnicki, Katherine L, Bittker, Joshua A, Bodycombe, Nicole E, Dančík, Vlado, Hasaka, Thomas P, Hon, Cindy S, Kemp, Melissa M, Li, Kejie, Walpita, Deepika, Wawer, Mathias J, Golub, Todd R, Schreiber, Stuart L, Clemons, Paul A, Shamji, Alykhan F, Carpenter, Anne E

“…Abstract Background Large-scale image sets acquired by automated microscopy of perturbed samples enable a detailed comparison of cell states induced by each…”
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Reference compounds for characterizing cellular injury in high-content cellular morphology assays by Dahlin, Jayme L., Hua, Bruce K., Zucconi, Beth E., Nelson, Shawn D., Singh, Shantanu, Carpenter, Anne E., Shrimp, Jonathan H., Lima-Fernandes, Evelyne, Wawer, Mathias J., Chung, Lawrence P. W., Agrawal, Ayushi, O’Reilly, Mary, Barsyte-Lovejoy, Dalia, Szewczyk, Magdalena, Li, Fengling, Lak, Parnian, Cuellar, Matthew, Cole, Philip A., Meier, Jordan L., Thomas, Tim, Baell, Jonathan B., Brown, Peter J., Walters, Michael A., Clemons, Paul A., Schreiber, Stuart L., Wagner, Bridget K.

“…Robust, generalizable approaches to identify compounds efficiently with undesirable mechanisms of action in complex cellular assays remain elusive. Such a…”
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Application of MCAT questions as a testing tool and evaluation metric for knowledge graph–based reasoning systems by Fecho, Karamarie, Balhoff, James, Bizon, Chris, Byrd, William E., Hang, Sui, Koslicki, David, Rensi, Stefano E., Schmitt, Patrick L., Wawer, Mathias J., Williams, Mark, Ahalt, Stanley C.

“…“Knowledge graphs” (KGs) have become a common approach for representing biomedical knowledge. In a KG, multiple biomedical data sets can be linked together as…”
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DNA Barcoding a Complete Matrix of Stereoisomeric Small Molecules by Gerry, Christopher J, Wawer, Mathias J, Clemons, Paul A, Schreiber, Stuart L

“…It is challenging to incorporate stereochemical diversity and topographic complexity into DNA-encoded libraries (DELs) because DEL syntheses cannot fully…”
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Synergistic Effects of Stereochemistry and Appendages on the Performance Diversity of a Collection of Synthetic Compounds by Melillo, Bruno, Zoller, Jochen, Hua, Bruce K, Verho, Oscar, Borghs, Jannik C, Nelson, Shawn D, Maetani, Micah, Wawer, Mathias J, Clemons, Paul A, Schreiber, Stuart L

“…Target- and phenotype-agnostic assessments of biological activity have emerged as viable strategies for prioritizing scaffolds, structural features, and…”
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Toward performance-diverse small-molecule libraries for cell-based phenotypic screening using multiplexed high-dimensional profiling by Wawer, Mathias J., Li, Kejie, Gustafsdottir, Sigrun M., Ljos, Vebjorn, Bodycombe, Nicole E., Marton, Melissa A., Sokolnicki, Katherine L., Bray, Mark-Anthony, Kemp, Melissa M., Winchester, Ellen, Taylor, Bradley, Grant, George B., Hon, C. Suk-Yee, Duvall, Jeremy R., Wilson, J. Anthony, Bittker, Joshua A., Dančík, Vlado, Narayan, Rajiv, Subramanian, Aravind, Winckler, Wendy, Golub, Todd R., Carpenter, Anne E., Shamji, Alykhan F., Schreiber, Stuart L., Clemons, Paul A.

“…High-throughput screening has become a mainstay of small-molecule probe and early drug discovery. The question of how to build and evolve efficient screening…”
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Genome-scale analysis identifies paralog lethality as a vulnerability of chromosome 1p loss in cancer by Viswanathan, Srinivas R., Nogueira, Marina F., Buss, Colin G., Krill-Burger, John M., Wawer, Mathias J., Malolepsza, Edyta, Berger, Ashton C., Choi, Peter S., Shih, Juliann, Taylor, Alison M., Tanenbaum, Benjamin, Pedamallu, Chandra Sekhar, Cherniack, Andrew D., Tamayo, Pablo, Strathdee, Craig A., Lage, Kasper, Carr, Steven A., Schenone, Monica, Bhatia, Sangeeta N., Vazquez, Francisca, Tsherniak, Aviad, Hahn, William C., Meyerson, Matthew

“…Functional redundancy shared by paralog genes may afford protection against genetic perturbations, but it can also result in genetic vulnerabilities due to…”
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Divergent Synthesis and Real-Time Biological Annotation of Optically Active Tetrahydrocyclopenta[c]pyranone Derivatives by Nelson, Shawn D, Wawer, Mathias J, Schreiber, Stuart L

“…Sp3-rich compounds are underrepresented in libraries for probe- and drug-discovery, despite their promise of extending the range of accessible molecular shapes…”
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Real-Time Biological Annotation of Synthetic Compounds by Gerry, Christopher J, Hua, Bruce K, Wawer, Mathias J, Knowles, Jonathan P, Nelson Jr, Shawn D, Verho, Oscar, Dandapani, Sivaraman, Wagner, Bridget K, Clemons, Paul A, Booker-Milburn, Kevin I, Boskovic, Zarko V, Schreiber, Stuart L

“…Organic chemists are able to synthesize molecules in greater number and chemical complexity than ever before. Yet, a majority of these compounds go untested in…”
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Inhibition of Dihydroorotate Dehydrogenase Overcomes Differentiation Blockade in Acute Myeloid Leukemia by Sykes, David B., Kfoury, Youmna S., Mercier, François E., Wawer, Mathias J., Law, Jason M., Haynes, Mark K., Lewis, Timothy A., Schajnovitz, Amir, Jain, Esha, Lee, Dongjun, Meyer, Hanna, Pierce, Kerry A., Tolliday, Nicola J., Waller, Anna, Ferrara, Steven J., Eheim, Ashley L., Stoeckigt, Detlef, Maxcy, Katrina L., Cobert, Julien M., Bachand, Jacqueline, Szekely, Brian A., Mukherjee, Siddhartha, Sklar, Larry A., Kotz, Joanne D., Clish, Clary B., Sadreyev, Ruslan I., Clemons, Paul A., Janzer, Andreas, Schreiber, Stuart L., Scadden, David T.

“…While acute myeloid leukemia (AML) comprises many disparate genetic subtypes, one shared hallmark is the arrest of leukemic myeloblasts at an immature and…”
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Targeted brachyury degradation disrupts a highly specific autoregulatory program controlling chordoma cell identity by Sheppard, Hadley E., Dall’Agnese, Alessandra, Park, Woojun D., Shamim, M. Hamza, Dubrulle, Julien, Johnson, Hannah L., Stossi, Fabio, Cogswell, Patricia, Sommer, Josh, Levy, Joan, Sharifnia, Tanaz, Wawer, Mathias J., Nabet, Behnam, Gray, Nathanael S., Clemons, Paul A., Schreiber, Stuart L., Workman, Paul, Young, Richard A., Lin, Charles Y.

“…Chordomas are rare spinal tumors addicted to expression of the developmental transcription factor brachyury. In chordomas, brachyury is super-enhancer…”
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Automated Structure-Activity Relationship Mining: Connecting Chemical Structure to Biological Profiles by Wawer, Mathias J, Jaramillo, David E, Dančík, Vlado, Fass, Daniel M, Haggarty, Stephen J, Shamji, Alykhan F, Wagner, Bridget K, Schreiber, Stuart L, Clemons, Paul A

“…Understanding the structure-activity relationships (SARs) of small molecules is important for developing probes and novel therapeutic agents in chemical…”
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Diversity-oriented synthesis yields novel multistage antimalarial inhibitors by Kato, Nobutaka, Comer, Eamon, Sakata-Kato, Tomoyo, Sharma, Arvind, Sharma, Manmohan, Maetani, Micah, Bastien, Jessica, Brancucci, Nicolas M., Bittker, Joshua A., Corey, Victoria, Clarke, David, Derbyshire, Emily R., Dornan, Gillian L., Duffy, Sandra, Eckley, Sean, Itoe, Maurice A., Koolen, Karin M. J., Lewis, Timothy A., Lui, Ping S., Lukens, Amanda K., Lund, Emily, March, Sandra, Meibalan, Elamaran, Meier, Bennett C., McPhail, Jacob A., Mitasev, Branko, Moss, Eli L., Sayes, Morgane, Van Gessel, Yvonne, Wawer, Mathias J., Yoshinaga, Takashi, Zeeman, Anne-Marie, Avery, Vicky M., Bhatia, Sangeeta N., Burke, John E., Catteruccia, Flaminia, Clardy, Jon C., Clemons, Paul A., Dechering, Koen J., Duvall, Jeremy R., Foley, Michael A., Gusovsky, Fabian, Kocken, Clemens H. M., Marti, Matthias, Morningstar, Marshall L., Munoz, Benito, Neafsey, Daniel E., Sharma, Amit, Winzeler, Elizabeth A., Wirth, Dyann F., Scherer, Christina A., Schreiber, Stuart L.

“…Antimalarial drugs have thus far been chiefly derived from two sources—natural products and synthetic drug-like compounds. Here we investigate whether…”
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Small-molecule targeting of brachyury transcription factor addiction in chordoma by Sharifnia, Tanaz, Wawer, Mathias J., Chen, Ting, Huang, Qing-Yuan, Weir, Barbara A., Sizemore, Ann, Lawlor, Matthew A., Goodale, Amy, Cowley, Glenn S., Vazquez, Francisca, Ott, Christopher J., Francis, Joshua M., Sassi, Slim, Cogswell, Patricia, Sheppard, Hadley E., Zhang, Tinghu, Gray, Nathanael S., Clarke, Paul A., Blagg, Julian, Workman, Paul, Sommer, Josh, Hornicek, Francis, Root, David E., Hahn, William C., Bradner, James E., Wong, Kwok K., Clemons, Paul A., Lin, Charles Y., Kotz, Joanne D., Schreiber, Stuart L.

“…Chordoma is a primary bone cancer with no approved therapy 1 . The identification of therapeutic targets in this disease has been challenging due to the…”
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Advancing Biological Understanding and Therapeutics Discovery with Small-Molecule Probes by Schreiber, Stuart L., Kotz, Joanne D., Li, Min, Aubé, Jeffrey, Austin, Christopher P., Reed, John C., Rosen, Hugh, White, E. Lucile, Sklar, Larry A., Lindsley, Craig W., Alexander, Benjamin R., Bittker, Joshua A., Clemons, Paul A., de Souza, Andrea, Foley, Michael A., Palmer, Michelle, Shamji, Alykhan F., Wawer, Mathias J., McManus, Owen, Wu, Meng, Zou, Beiyan, Yu, Haibo, Golden, Jennifer E., Schoenen, Frank J., Simeonov, Anton, Jadhav, Ajit, Jackson, Michael R., Pinkerton, Anthony B., Chung, Thomas D.Y., Griffin, Patrick R., Cravatt, Benjamin F., Hodder, Peter S., Roush, William R., Roberts, Edward, Chung, Dong-Hoon, Jonsson, Colleen B., Noah, James W., Severson, William E., Ananthan, Subramaniam, Edwards, Bruce, Oprea, Tudor I., Conn, P. Jeffrey, Hopkins, Corey R., Wood, Michael R., Stauffer, Shaun R., Emmitte, Kyle A., Brady, Linda S., Driscoll, Jamie, Li, Ingrid Y., Loomis, Carson R., Margolis, Ronald N., Michelotti, Enrique, Perry, Mary E., Pillai, Ajay, Yao, Yong

“…Small-molecule probes can illuminate biological processes and aid in the assessment of emerging therapeutic targets by perturbing biological systems in a…”
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Abstract LB216: Targeted brachyury degradation disrupts a highly specific autoregulatory program controlling chordoma cell identity by Sheppard, Hadley E., Dall'Agnese, Alessandra, Park, Woojun D., Shamim, Hamza, Dubrulle, Julien, Johnson, Hannah L., Stossi, Fabio, Cogswell, Patricia, Sommer, Josh, Levy, Joan, Sharifnia, Tanaz, Wawer, Mathias J., Clemons, Paul A., Nabet, Behnam, Gray, Nathanael S., Schreiber, Stuart L., Workman, Paul, Young, Richard A., Lin, Charles Y.

“…Abstract Chordomas are rare spinal tumors addicted to expression of the developmental transcription factor brachyury. In chordomas, brachyury is super-enhancer…”
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