Search Results - "Kaminow, Benjamin"

Pan-human consensus genome significantly improves the accuracy of RNA-seq analyses by Kaminow, Benjamin, Ballouz, Sara, Gillis, Jesse, Dobin, Alexander

“…The Human Reference Genome serves as the foundation for modern genomic analyses. However, in its present form, it does not adequately represent the vast…”
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EspalomaCharge: Machine Learning-Enabled Ultrafast Partial Charge Assignment by Wang, Yuanqing, Pulido, Iván, Takaba, Kenichiro, Kaminow, Benjamin, Scheen, Jenke, Wang, Lily, Chodera, John D.

“…Atomic partial charges are crucial parameters in molecular dynamics simulation, dictating the electrostatic contributions to intermolecular energies and…”
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Open science discovery of potent noncovalent SARS-CoV-2 main protease inhibitors by Boby, Melissa L, Fearon, Daren, Ferla, Matteo, Filep, Mihajlo, Koekemoer, Lizbé, Robinson, Matthew C, Chodera, John D, Lee, Alpha A, London, Nir, von Delft, Annette, von Delft, Frank, Achdout, Hagit, Aimon, Anthony, Alonzi, Dominic S, Arbon, Robert, Aschenbrenner, Jasmin C, Balcomb, Blake H, Bar-David, Elad, Barr, Haim, Ben-Shmuel, Amir, Bennett, James, Bilenko, Vitaliy A, Borden, Bruce, Boulet, Pascale, Bowman, Gregory R, Brewitz, Lennart, Brun, Juliane, Bvnbs, Sarma, Calmiano, Mark, Carbery, Anna, Carney, Daniel W, Cattermole, Emma, Chang, Edcon, Chernyshenko, Eugene, Clyde, Austin, Coffland, Joseph E, Cohen, Galit, Cole, Jason C, Contini, Alessandro, Cox, Lisa, Croll, Tristan Ian, Cvitkovic, Milan, De Jonghe, Steven, Dias, Alex, Donckers, Kim, Dotson, David L, Douangamath, Alice, Duberstein, Shirly, Dudgeon, Tim, Dunnett, Louise E, Eastman, Peter, Erez, Noam, Eyermann, Charles J, Fairhead, Michael, Fate, Gwen, Fedorov, Oleg, Fernandes, Rafaela S, Ferrins, Lori, Foster, Richard, Foster, Holly, Fraisse, Laurent, Gabizon, Ronen, García-Sastre, Adolfo, Gawriljuk, Victor O, Gehrtz, Paul, Gileadi, Carina, Giroud, Charline, Glass, William G, Glen, Robert C, Glinert, Itai, Godoy, Andre S, Gorichko, Marian, Gorrie-Stone, Tyler, Griffen, Ed J, Haneef, Amna, Hassell Hart, Storm, Heer, Jag, Henry, Michael, Hill, Michelle, Horrell, Sam, Huang, Qiu Yu Judy, Huliak, Victor D, Hurley, Matthew F D, Israely, Tomer, Jajack, Andrew, Jansen, Jitske, Jnoff, Eric, Jochmans, Dirk, John, Tobias, Kaminow, Benjamin, Kang, Lulu, Kantsadi, Anastassia L, Kenny, Peter W, Kiappes, J L, Kinakh, Serhii O, Kovar, Boris, Krojer, Tobias, La, Van Ngoc Thuy, Laghnimi-Hahn, Sophie, Lefker, Bruce A

“…We report the results of the COVID Moonshot, a fully open-science, crowdsourced, and structure-enabled drug discovery campaign targeting the severe acute…”
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End-to-end differentiable construction of molecular mechanics force fields by Wang, Yuanqing, Fass, Josh, Kaminow, Benjamin, Herr, John E, Rufa, Dominic, Zhang, Ivy, Pulido, Iván, Henry, Mike, Bruce Macdonald, Hannah E, Takaba, Kenichiro, Chodera, John D

“…Molecular mechanics (MM) potentials have long been a workhorse of computational chemistry. Leveraging accuracy and speed, these functional forms find use in a…”
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Abstract C084: Oncogenic KRAS signaling drives the activation of tissue-resident fibroblasts and is required to maintain CAF heterogeneity in pancreatic cancer by Caligiuri, Giuseppina, Thalappillil, Jennifer S., Shakiba, Mojdeh, Nadella, Sandeep, Hinds, Juliene, Courtois, Elise, Flynn, William F., Alagesan, Brinda, Yordanov, Georgi N., Kaminow, Benjamin, Robson, Paul, Perez-Mancera, Pedro A., Preall, Jonathan, Dobin, Alexander, Park, Youngku, Tuveson, David A.

“…Abstract The complexity of the tumor microenvironment (TME) is one of the distinguishing features of pancreatic ductal adenocarcinoma (PDA) and is responsible…”
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Abstract 3647: Oncogenic Kras drives cancer-associated fibroblast heterogeneity and substate changes in pancreatic cancer by Thalappillil, Jennifer S., Caligiuri, Giuseppina, Nadella, Sandeep, Alagesan, Brinda, Yordanov, Georgi N., Shakiba, Mojdeh, Kaminow, Benjamin, Hinds, Juliene, Perez-Mancera, Pedro A., Preall, Jonathan, Dobin, Alexander, Park, Youngkyu, Tuveson, David A.

“…Abstract Pancreatic ductal adenocarcinoma (PDAC) is currently the third-leading cause of cancer-related deaths in the United States with no effective or…”
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EspalomaCharge: Machine learning-enabled ultra-fast partial charge assignment by Wang, Yuanqing, Pulido, Iván, Takaba, Kenichiro, Kaminow, Benjamin, Scheen, Jenke, Wang, Lily, Chodera, John D

“…Atomic partial charges are crucial parameters in molecular dynamics (MD) simulation, dictating the electrostatic contributions to intermolecular energies, and…”
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End-to-End Differentiable Molecular Mechanics Force Field Construction by Wang, Yuanqing, Fass, Josh, Kaminow, Benjamin, Herr, John E, Rufa, Dominic, Zhang, Ivy, Pulido, Iván, Henry, Mike, Chodera, John D

“…Molecular mechanics (MM) potentials have long been a workhorse of computational chemistry. Leveraging accuracy and speed, these functional forms find use in a…”
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