Search Results - "Ingraham, John"

Deep generative models of genetic variation capture the effects of mutations by Riesselman, Adam J., Ingraham, John B., Marks, Debora S.

“…The functions of proteins and RNAs are defined by the collective interactions of many residues, and yet most statistical models of biological sequences…”
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Mutation effects predicted from sequence co-variation by Hopf, Thomas A, Ingraham, John B, Poelwijk, Frank J, Schärfe, Charlotta P I, Springer, Michael, Sander, Chris, Marks, Debora S

“…The global effects of epistasis on protein and RNA function are revealed by an unsupervised model of amino acid co-conservation in evolutionary sequence…”
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3D RNA and Functional Interactions from Evolutionary Couplings by Weinreb, Caleb, Riesselman, Adam J., Ingraham, John B., Gross, Torsten, Sander, Chris, Marks, Debora S.

“…Non-coding RNAs are ubiquitous, but the discovery of new RNA gene sequences far outpaces the research on the structure and functional interactions of these RNA…”
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The EVcouplings Python framework for coevolutionary sequence analysis by Hopf, Thomas A, Green, Anna G, Schubert, Benjamin, Mersmann, Sophia, Schärfe, Charlotta P I, Ingraham, John B, Toth-Petroczy, Agnes, Brock, Kelly, Riesselman, Adam J, Palmedo, Perry, Kang, Chan, Sheridan, Robert, Draizen, Eli J, Dallago, Christian, Sander, Chris, Marks, Debora S

“…Coevolutionary sequence analysis has become a commonly used technique for de novo prediction of the structure and function of proteins, RNA, and protein…”
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Illuminating protein space with a programmable generative model by Ingraham, John B., Baranov, Max, Costello, Zak, Barber, Karl W., Wang, Wujie, Ismail, Ahmed, Frappier, Vincent, Lord, Dana M., Ng-Thow-Hing, Christopher, Van Vlack, Erik R., Tie, Shan, Xue, Vincent, Cowles, Sarah C., Leung, Alan, Rodrigues, João V., Morales-Perez, Claudio L., Ayoub, Alex M., Green, Robin, Puentes, Katherine, Oplinger, Frank, Panwar, Nishant V., Obermeyer, Fritz, Root, Adam R., Beam, Andrew L., Poelwijk, Frank J., Grigoryan, Gevorg

“…Three billion years of evolution has produced a tremendous diversity of protein molecules 1 , but the full potential of proteins is likely to be much greater…”
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Structured States of Disordered Proteins from Genomic Sequences by Toth-Petroczy, Agnes, Palmedo, Perry, Ingraham, John, Hopf, Thomas A., Berger, Bonnie, Sander, Chris, Marks, Debora S.

“…Protein flexibility ranges from simple hinge movements to functional disorder. Around half of all human proteins contain apparently disordered regions with…”
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Galactose metabolic genes in yeast respond to a ratio of galactose and glucose by Escalante-Chong, Renan, Savir, Yonatan, Carroll, Sean M., Ingraham, John B., Wang, Jue, Marx, Christopher J., Springer, Michael

“…Natural environments are filled with multiple, often competing, signals. In contrast, biological systems are often studied in “well-controlled” environments…”
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Basketball teams as strategic networks by Fewell, Jennifer H, Armbruster, Dieter, Ingraham, John, Petersen, Alexander, Waters, James S

“…We asked how team dynamics can be captured in relation to function by considering games in the first round of the NBA 2010 play-offs as networks. Defining…”
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Simultaneous enhancement of multiple functional properties using evolution-informed protein design by Fram, Benjamin, Su, Yang, Truebridge, Ian, Riesselman, Adam J., Ingraham, John B., Passera, Alessandro, Napier, Eve, Thadani, Nicole N., Lim, Samuel, Roberts, Kristen, Kaur, Gurleen, Stiffler, Michael A., Marks, Debora S., Bahl, Christopher D., Khan, Amir R., Sander, Chris, Gauthier, Nicholas P.

“…A major challenge in protein design is to augment existing functional proteins with multiple property enhancements. Altering several properties likely…”
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The Cost Does Not Outweigh the Benefit: Pathologic Evaluation of Wrist Ganglion Cysts Should Not Be Routine by McLaughlin, Caroline M., LePere, Darren, Candela, Xavier, Ingraham, John M.

“…Background: As health care costs in the United States continue to rise, there is increasing attention on cost-saving measures. One area of investigation is the…”
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The state of remote learning in plastic surgery: A systematic review of modalities by Patel, Akshilkumar, Massand, Sameer, Ingraham, John

“…Objective: To systematically review the published literature describing remote alternative educational modalities for plastic surgery residents. Design:…”
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200 kHz commercial sonar systems generate lower frequency side lobes audible to some marine mammals by Deng, Z Daniel, Southall, Brandon L, Carlson, Thomas J, Xu, Jinshan, Martinez, Jayson J, Weiland, Mark A, Ingraham, John M

“…The spectral properties of pulses transmitted by three commercially available 200 kHz echo sounders were measured to assess the possibility that marine mammals…”
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The Teaching of Ethics and Professionalism in Plastic Surgery Residency: A Cross-Sectional Survey by Bennett, Katelyn G, Ingraham, John M, Schneider, Lisa F, Saadeh, Pierre B, Vercler, Christian J

“…BACKGROUNDThe ethical practice of medicine has always been of utmost importance, and plastic surgery is no exception. The literature is devoid of information…”
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The surprising Rut pathway: an unexpected way to derive nitrogen from pyrimidines by Parales, Rebecca E, Ingraham, John L

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Feasibility of Tracking Fish with Acoustic Transmitters in the Ice Harbor Dam Tailrace by Ingraham, John M., Deng, Z. Daniel, Martinez, Jayson J., Trumbo, Bradly A., Mueller, Robert P., Weiland, Mark A.

“…The Juvenile Salmon Acoustic Telemetry System (JSATS) has been used at many dams but has never been deployed in the near-dam tailrace environment. The use of…”
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31. Which Characteristics of Applicants and Medical Schools Produce the Most Integrated Plastic Surgery Residents? An Analysis of the 2016-2022 Cohort by Oxford, Madison A., Ryu, Grace, Borusiewicz, Mikayla, Ingraham, John M.

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The sternocleidomastoid myocutaneous “patch esophagoplasty” for cervical esophageal stricture by Noland, Shelley S., Ingraham, John M., Lee, Gordon K.

“…Esophageal strictures may be caused by many etiologies. Patients suffer from dysphagia and many are tube‐feed dependent. Cervical esophageal reconstruction is…”
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How We Teach Tendon Repairs Outside the Operating Room by Ingraham, John M., Weber, Robert A., Weber, Robert A.

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Rapidly Involuting Congenital Hemangioma of the Hand by Delgadillo, 3rd, Daniel, Carr, Logan W, Brgoch, Morgan S, Ingraham, John M

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Utility of Routine Pathologic Specimens in Ganglion Wrist Excisions by LePere, Darren B., Bickham, Rebecca S., Ingraham, John M.

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