Adipose Tissue Macrophage-Derived Exosomal miRNAs Can Modulate In Vivo and In Vitro Insulin Sensitivity by Ying, Wei, Riopel, Matthew, Bandyopadhyay, Gautam, Dong, Yi, Birmingham, Amanda, Seo, Jong Bae, Ofrecio, Jachelle M., Wollam, Joshua, Hernandez-Carretero, Angelina, Fu, Wenxian, Li, Pingping, Olefsky, Jerrold M.

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Normalization and microbial differential abundance strategies depend upon data characteristics by Weiss, Sophie, Xu, Zhenjiang Zech, Peddada, Shyamal, Amir, Amnon, Bittinger, Kyle, Gonzalez, Antonio, Lozupone, Catherine, Zaneveld, Jesse R, Vázquez-Baeza, Yoshiki, Birmingham, Amanda, Hyde, Embriette R, Knight, Rob

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Correlation detection strategies in microbial data sets vary widely in sensitivity and precision by Weiss, Sophie, Van Treuren, Will, Lozupone, Catherine, Faust, Karoline, Friedman, Jonathan, Deng, Ye, Xia, Li Charlie, Xu, Zhenjiang Zech, Ursell, Luke, Alm, Eric J, Birmingham, Amanda, Cram, Jacob A, Fuhrman, Jed A, Raes, Jeroen, Sun, Fengzhu, Zhou, Jizhong, Knight, Rob

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Systematic analysis of CRISPR–Cas9 mismatch tolerance reveals low levels of off-target activity by Anderson, Emily M., Haupt, Amanda, Schiel, John A., Chou, Eldon, Machado, Hidevaldo B., Strezoska, Žaklina, Lenger, Steve, McClelland, Shawn, Birmingham, Amanda, Vermeulen, Annaleen, Smith, Anja van Brabant

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Ten simple rules for writing and sharing computational analyses in Jupyter Notebooks by Rule, Adam, Birmingham, Amanda, Zuniga, Cristal, Altintas, Ilkay, Huang, Shih-Cheng, Knight, Rob, Moshiri, Niema, Nguyen, Mai H, Rosenthal, Sara Brin, Pérez, Fernando, Rose, Peter W

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Combinatorial CRISPR-Cas9 Metabolic Screens Reveal Critical Redox Control Points Dependent on the KEAP1-NRF2 Regulatory Axis by Zhao, Dongxin, Badur, Mehmet G., Luebeck, Jens, Magaña, Jose H., Birmingham, Amanda, Sasik, Roman, Ahn, Christopher S., Ideker, Trey, Metallo, Christian M., Mali, Prashant

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The ViReflow pipeline enables user friendly large scale viral consensus genome reconstruction by Moshiri, Niema, Fisch, Kathleen M., Birmingham, Amanda, DeHoff, Peter, Yeo, Gene W., Jepsen, Kristen, Laurent, Louise C., Knight, Rob

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Off-target effects by siRNA can induce toxic phenotype by Fedorov, Yuriy, Anderson, Emily M, Birmingham, Amanda, Reynolds, Angela, Karpilow, Jon, Robinson, Kathryn, Leake, Devin, Marshall, William S, Khvorova, Anastasia

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Genome Reshuffling for Advanced Intercross Permutation (GRAIP): simulation and permutation for advanced intercross population analysis by Peirce, Jeremy L, Broman, Karl W, Lu, Lu, Chesler, Elissa J, Zhou, Guomin, Airey, David C, Birmingham, Amanda E, Williams, Robert W

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Chromatin Accessibility and Transcriptional Differences in Human Stem Cell-Derived Early-Stage Retinal Organoids by Jones, Melissa K, Agarwal, Devansh, Mazo, Kevin W, Chopra, Manan, Jurlina, Shawna L, Dash, Nicholas, Xu, Qianlan, Ogata, Anna R, Chow, Melissa, Hill, Alex D, Kambli, Netra K, Xu, Guorong, Sasik, Roman, Birmingham, Amanda, Fisch, Kathleen M, Weinreb, Robert N, Enke, Ray A, Skowronska-Krawczyk, Dorota, Wahlin, Karl J

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The RNA structure alignment ontology by Brown, James W, Birmingham, Amanda, Griffiths, Paul E, Jossinet, Fabrice, Kachouri-Lafond, Rym, Knight, Rob, Lang, B Franz, Leontis, Neocles, Steger, Gerhard, Stombaugh, Jesse, Westhof, Eric

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Context and the human microbiome by McDonald, Daniel, Birmingham, Amanda, Knight, Rob

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Wastewater sequencing reveals early cryptic SARS-CoV-2 variant transmission by Karthikeyan, Smruthi, Levy, Joshua I., De Hoff, Peter, Humphrey, Greg, Birmingham, Amanda, Jepsen, Kristen, Farmer, Sawyer, Tubb, Helena M., Valles, Tommy, Tribelhorn, Caitlin E., Tsai, Rebecca, Aigner, Stefan, Moshiri, Niema, Henson, Benjamin, Mark, Adam M., Hakim, Abbas, Baer, Nathan A., Barber, Tom, Belda-Ferre, Pedro, Chacón, Marisol, Cresini, Evelyn S., Eisner, Emily R., Lastrella, Alma L., Lawrence, Elijah S., Marotz, Clarisse A., Ngo, Toan T., Ostrander, Tyler, Plascencia, Ashley, Salido, Rodolfo A., Seaver, Phoebe, Smoot, Elizabeth W., McDonald, Daniel, Neuhard, Robert M., Scioscia, Angela L., Satterlund, Alysson M., Simmons, Elizabeth H., Abelman, Dismas B., Brenner, David, Buckley, Anne, Gattas, Jeffrey, Gonias, Steven L., Hale, Matt, Ikeda, Lydia, Jhaveri, Hemlata, Kremer, Brendan, McLawhon, Ronald W., Ouillet, Pierre, Park, Daniel, Pradenas, Allorah, Riggs, Lindsay, Sanders, Alison, Sollenberger, Bradley, White, Benjamin, Winbush, Terri, Aceves, Christine M., Anderson, Catelyn, Gangavarapu, Karthik, Hufbauer, Emory, Kurzban, Ezra, Lee, Justin, Matteson, Nathaniel L., Parker, Edyth, Perkins, Sarah A., Ramesh, Karthik S., Schwab, Madison A., Wohl, Shirlee, Nicholson, Laura, McHardy, Ian H., Hobbs, Charlotte A., Bakhtar, Omid, Mendoza, Art, Becker, David, Cirulli, Elizabeth T., Isaksson, Magnus, Schiabor Barrett, Kelly M., Washington, Nicole L., Malone, John D., Schafer, Ashleigh Murphy, Fielding-Miller, Rebecca, Garfein, Richard S., Gaines, Tommi, Anderson, Cheryl, Martin, Natasha K., Schooley, Robert, Austin, Brett, Kingsmore, Stephen F., Lee, William, Shah, Seema, McDonald, Eric, Yu, Alexander T., Zeller, Mark, Fisch, Kathleen M., Longhurst, Christopher, Maysent, Patty, Pride, David, Khosla, Pradeep K., Laurent, Louise C., Yeo, Gene W., Andersen, Kristian G., Knight, Rob

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Advances in CRISPR-Cas9 genome engineering: lessons learned from RNA interference by Barrangou, Rodolphe, Birmingham, Amanda, Wiemann, Stefan, Beijersbergen, Roderick L, Hornung, Veit, Smith, Anja van Brabant

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Resurgence of SARS-CoV-2 Infection in a Highly Vaccinated Health System Workforce by Keehner, Jocelyn, Horton, Lucy E, Binkin, Nancy J, Laurent, Louise C, Pride, David, Longhurst, Christopher A, Abeles, Shira R, Torriani, Francesca J

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Interactive network visualization in Jupyter notebooks: visJS2jupyter by Rosenthal, Sara Brin, Len, Julia, Webster, Mikayla, Gary, Aaron, Birmingham, Amanda, Fisch, Kathleen M

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NoiseMaker: simulated screens for statistical assessment by Kwan, Phoenix, Birmingham, Amanda

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Interspecies transcriptome analyses identify genes that control the development and evolution of limb skeletal proportion by Cooper, Kim, Saxena, Aditya, Sharma, Virag, Neufeld, Stanley, Tran, Mai, Gutierrez, Haydee, Erberich, Joel, Birmingham, Amanda, Cobb, John, Hiller, Michael

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Interspecies transcriptomics identify genes that underlie disproportionate foot growth in jerboas by Saxena, Aditya, Sharma, Virag, Muthuirulan, Pushpanathan, Neufeld, Stanley J., Tran, Mai P., Gutierrez, Haydee L., Chen, Kevin D., Erberich, Joel M., Birmingham, Amanda, Capellini, Terence D., Cobb, John, Hiller, Michael, Cooper, Kimberly L.

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HIV-1 TAT protein enhances sensitization to methamphetamine by affecting dopaminergic function by Kesby, James P, Najera, Julia A, Romoli, Benedetto, Fang, Yiding, Basova, Liana, Birmingham, Amanda, Marcondes, Maria Cecilia G, Dulcis, Davide, Semenova, Svetlana

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