Search Results - "Donghia, Nina M"

A Deep Learning Approach to Antibiotic Discovery by Stokes, Jonathan M., Yang, Kevin, Swanson, Kyle, Jin, Wengong, Cubillos-Ruiz, Andres, Donghia, Nina M., MacNair, Craig R., French, Shawn, Carfrae, Lindsey A., Bloom-Ackermann, Zohar, Tran, Victoria M., Chiappino-Pepe, Anush, Badran, Ahmed H., Andrews, Ian W., Chory, Emma J., Church, George M., Brown, Eric D., Jaakkola, Tommi S., Barzilay, Regina, Collins, James J.

“…Due to the rapid emergence of antibiotic-resistant bacteria, there is a growing need to discover new antibiotics. To address this challenge, we trained a deep…”
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Minimally instrumented SHERLOCK (miSHERLOCK) for CRISPR-based point-of-care diagnosis of SARS-CoV-2 and emerging variants by de Puig, Helena, Lee, Rose A., Najjar, Devora, Tan, Xiao, Soenksen, Luis R., Angenent-Mari, Nicolaas M., Donghia, Nina M., Weckman, Nicole E., Ory, Audrey, Ng, Carlos F., Nguyen, Peter Q., Mao, Angelo S., Ferrante, Thomas C., Lansberry, Geoffrey, Sallum, Hani, Niemi, James, Collins, James J.

“…An integrated, low-cost, sample-to-answer, CRISPR-based diagnostic detects SARS-CoV-2 and variants from unprocessed saliva. The COVID-19 pandemic highlights…”
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A Deep Learning Approach to Antibiotic Discovery by Stokes, Jonathan M., Yang, Kevin, Swanson, Kyle, Jin, Wengong, Cubillos-Ruiz, Andres, Donghia, Nina M., MacNair, Craig R., French, Shawn, Carfrae, Lindsey A., Bloom-Ackermann, Zohar, Tran, Victoria M., Chiappino-Pepe, Anush, Badran, Ahmed H., Andrews, Ian W., Chory, Emma J., Church, George M., Brown, Eric D., Jaakkola, Tommi S., Barzilay, Regina, Collins, James J.

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Widespread genomic breaks generated by activation-induced cytidine deaminase are prevented by homologous recombination by Donghia, Nina M, Coffey, Eliot, He, Yishu, Wilpan, Robert Y, Ames, Jacquelyn, Mills, Kevin D, Maynard, Jane, King, Benjamin L, Hasham, Muneer G, Snow, Kathy J

“…Activation-induced cytidine deaminase triggers somatic hypermutation and immunoglobulin class switching. Mills and colleagues show that it can also cause…”
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Laboratory-Generated DNA Can Cause Anomalous Pathogen Diagnostic Test Results by Robinson-McCarthy, Lindsey R, Mijalis, Alexander J, Filsinger, Gabriel T, de Puig, Helena, Donghia, Nina M, Schaus, Thomas E, Rasmussen, Robert A, Ferreira, Raphael, Lunshof, Jeantine E, Chao, George, Ter-Ovanesyan, Dmitry, Dodd, Oliver, Kuru, Erkin, Sesay, Adama M, Rainbow, Joshua, Pawlowski, Andrew C, Wannier, Timothy M, Angenent-Mari, Nicolaas M, Najjar, Devora, Yin, Peng, Ingber, Donald E, Tam, Jenny M, Church, George M

“…The coronavirus disease 2019 (COVID-19) pandemic has brought about the unprecedented expansion of highly sensitive molecular diagnostics as a primary infection…”
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Wearable materials with embedded synthetic biology sensors for biomolecule detection by Nguyen, Peter Q., Soenksen, Luis R., Donghia, Nina M., Angenent-Mari, Nicolaas M., de Puig, Helena, Huang, Ally, Lee, Rose, Slomovic, Shimyn, Galbersanini, Tommaso, Lansberry, Geoffrey, Sallum, Hani M., Zhao, Evan M., Niemi, James B., Collins, James J.

“…Integrating synthetic biology into wearables could expand opportunities for noninvasive monitoring of physiological status, disease states and exposure to…”
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Ultrasensitive CRISPR-based diagnostic for field-applicable detection of Plasmodium species in symptomatic and asymptomatic malaria by Lee, Rose A., De Puig, Helena, Nguyen, Peter Q., Angenent-Mari, Nicolaas M., Donghia, Nina M., McGee, James P., Dvorin, Jeffrey D., Klapperich, Catherine M., Pollock, Nira R., Collins, James J.

“…Asymptomatic carriers of Plasmodium parasites hamper malaria control and eradication. Achieving malaria eradication requires ultrasensitive diagnostics for low…”
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Discovery of a structural class of antibiotics with explainable deep learning by Wong, Felix, Zheng, Erica J., Valeri, Jacqueline A., Donghia, Nina M., Anahtar, Melis N., Omori, Satotaka, Li, Alicia, Cubillos-Ruiz, Andres, Krishnan, Aarti, Jin, Wengong, Manson, Abigail L., Friedrichs, Jens, Helbig, Ralf, Hajian, Behnoush, Fiejtek, Dawid K., Wagner, Florence F., Soutter, Holly H., Earl, Ashlee M., Stokes, Jonathan M., Renner, Lars D., Collins, James J.

“…The discovery of novel structural classes of antibiotics is urgently needed to address the ongoing antibiotic resistance crisis 1 – 9 . Deep learning…”
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An engineered live biotherapeutic for the prevention of antibiotic-induced dysbiosis by Cubillos-Ruiz, Andrés, Alcantar, Miguel A., Donghia, Nina M., Cárdenas, Pablo, Avila-Pacheco, Julian, Collins, James J.

“…Antibiotic-induced alterations in the gut microbiota are implicated in many metabolic and inflammatory diseases, increase the risk of secondary infections and…”
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Discovering small-molecule senolytics with deep neural networks by Wong, Felix, Omori, Satotaka, Donghia, Nina M, Zheng, Erica J, Collins, James J

“…The accumulation of senescent cells is associated with aging, inflammation and cellular dysfunction. Senolytic drugs can alleviate age-related comorbidities by…”
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ARTEMIS stabilizes the genome and modulates proliferative responses in multipotent mesenchymal cells by Maas, Sarah A, Donghia, Nina M, Tompkins, Kathleen, Foreman, Oded, Mills, Kevin D

“…Unrepaired DNA double-stranded breaks (DSBs) cause chromosomal rearrangements, loss of genetic information, neoplastic transformation or cell death. The…”
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Anomalous COVID-19 tests hinder researchers by Robinson-McCarthy, Lindsey R, Mijalis, Alexander J, Filsinger, Gabriel T, de Puig, Helena, Donghia, Nina M, Schaus, Thomas E, Rasmussen, Robert A, Ferreira, Raphael, Lunshof, Jeantine E, Chao, George, Ter-Ovanesyan, Dmitry, Dodd, Oliver, Kuru, Erkin, Sesay, Adama M, Rainbow, Joshua, Pawlowski, Andrew C, Wannier, Timothy M, Yin, Peng, Collins, James J, Ingber, Donald E, Church, George M, Tam, Jenny M

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A DNA break– and phosphorylation-dependent positive feedback loop promotes immunoglobulin class-switch recombination by Vuong, Bao Q, Herrick-Reynolds, Kayleigh, Vaidyanathan, Bharat, Pucella, Joseph N, Ucher, Anna J, Donghia, Nina M, Gu, Xiwen, Nicolas, Laura, Nowak, Urszula, Rahman, Numa, Strout, Matthew P, Mills, Kevin D, Stavnezer, Janet, Chaudhuri, Jayanta

“…The cytidine deaminase AID mediates immunoglobulin class-switch recombination. Chaudhuri and colleagues show that a phosphorylation-dependent positive feedback…”
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Attenuating homologous recombination stimulates an AID-induced antileukemic effect by Lamont, Kristin R, Hasham, Muneer G, Donghia, Nina M, Branca, Jane, Chavaree, Margaret, Chase, Betsy, Breggia, Anne, Hedlund, Jacquelyn, Emery, Ivette, Cavallo, Francesca, Jasin, Maria, Rüter, Jens, Mills, Kevin D

“…Activation-induced cytidine deaminase (AID) is critical in normal B cells to initiate somatic hypermutation and immunoglobulin class switch recombination…”
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Activation-induced cytidine deaminase-initiated off-target DNA breaks are detected and resolved during S phase by Hasham, Muneer G, Snow, Kathy J, Donghia, Nina M, Branca, Jane A, Lessard, Mark D, Stavnezer, Janet, Shopland, Lindsay S, Mills, Kevin D

“…Activation-induced cytidine deaminase (AID) initiates DNA double-strand breaks (DSBs) in the IgH gene (Igh) to stimulate isotype class switch recombination…”
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AID-Initiated Off-Target DNA Breaks are Detected and Resolved During S-Phase by Hasham, Muneer G., Snow, Kathy J., Donghia, Nina M., Branca, Jane A., Lessard, Mark D., Stavnezer, Janet, Shopland, Lindsay S., Mills, Kevin D.

“…Activation-induced cytidine deaminase (AID) initiates DNA double strand breaks (DSBs) in the immunoglobulin heavy chain gene ( Igh ) to stimulate isotype class…”
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Widespread genomic breaks from activation-induced cytidine deaminase are prevented by homologous recombination by Hasham, Muneer G., Donghia, Nina M., Coffey, Eliot, Maynard, Jane, Snow, Kathy J., Ames, Jacquelyn, Wilpan, Robert Y., He, Yishu, King, Benjamin L., Mills, Kevin D.

“…Activation induced cytidine deaminase (AID) is required for somatic hypermutation and immunoglobulin class switching in activated B cells. Because AID…”
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