Robustness and applicability of transcription factor and pathway analysis tools on single-cell RNA-seq data von Holland, Christian H., Tanevski, Jovan, Perales-Paton, Javier, Gleixner, Jan, Kumar, Manu P., Mereu, Elisabetta, Joughin, Brian A., Stegle, Oliver, Lauffenburger, Douglas A., Heyn, Holger, Szalai, Bence, Saez-Rodriguez, Julio

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Multiplexed relative and absolute quantitative immunopeptidomics reveals MHC I repertoire alterations induced by CDK4/6 inhibition von Stopfer, Lauren E., Mesfin, Joshua M., Joughin, Brian A., Lauffenburger, Douglas A., White, Forest M.

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DNA Repair Capacity in Multiple Pathways Predicts Chemoresistance in Glioblastoma Multiforme von Nagel, Zachary D, Kitange, Gaspar J, Gupta, Shiv K, Joughin, Brian A, Chaim, Isaac A, Mazzucato, Patrizia, Lauffenburger, Douglas A, Sarkaria, Jann N, Samson, Leona D

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ROS and Oxidative Stress Are Elevated in Mitosis during Asynchronous Cell Cycle Progression and Are Exacerbated by Mitotic Arrest von Patterson, Jesse C., Joughin, Brian A., van de Kooij, Bert, Lim, Daniel C., Lauffenburger, Douglas A., Yaffe, Michael B.

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The Fanconi anemia core complex promotes CtIP-dependent end resection to drive homologous recombination at DNA double-strand breaks von van de Kooij, Bert, van der Wal, Fenna J., Rother, Magdalena B., Wiegant, Wouter W., Creixell, Pau, Stout, Merula, Joughin, Brian A., Vornberger, Julia, Altmeyer, Matthias, van Vugt, Marcel A. T. M., Yaffe, Michael B., van Attikum, Haico

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Low Doses of Arsenic in a Mouse Model of Human Exposure and in Neuronal Culture Lead to S-Nitrosylation of Synaptic Proteins and Apoptosis via Nitric Oxide von Amal, Haitham, Gong, Guanyu, Yang, Hongmei, Joughin, Brian A., Wang, Xin, Knutson, Charles G., Kartawy, Maryam, Khaliulin, Igor, Wishnok, John S., Tannenbaum, Steven R.

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Phosphoproteomics identifies microglial Siglec‐F inflammatory response during neurodegeneration von Morshed, Nader, Ralvenius, William T, Nott, Alexi, Watson, L Ashley, Rodriguez, Felicia H, Akay, Leyla A, Joughin, Brian A, Pao, Ping‐Chieh, Penney, Jay, LaRocque, Lauren, Mastroeni, Diego, Tsai, Li‐Huei, White, Forest M

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Transite: A Computational Motif-Based Analysis Platform That Identifies RNA-Binding Proteins Modulating Changes in Gene Expression von Krismer, Konstantin, Bird, Molly A., Varmeh, Shohreh, Handly, Erika D., Gattinger, Anna, Bernwinkler, Thomas, Anderson, Daniel A., Heinzel, Andreas, Joughin, Brian A., Kong, Yi Wen, Cannell, Ian G., Yaffe, Michael B.

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A genome-scale in vivo loss-of-function screen identifies Phf6 as a lineage-specific regulator of leukemia cell growth von Meacham, Corbin E, Lawton, Lee N, Soto-Feliciano, Yadira M, Pritchard, Justin R, Joughin, Brian A, Ehrenberger, Tobias, Fenouille, Nina, Zuber, Johannes, Williams, Richard T, Young, Richard A, Hemann, Michael T

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Comprehensive substrate specificity profiling of the human Nek kinome reveals unexpected signaling outputs von van de Kooij, Bert, Creixell, Pau, van Vlimmeren, Anne, Joughin, Brian A, Miller, Chad J, Haider, Nasir, Simpson, Craig D, Linding, Rune, Stambolic, Vuk, Turk, Benjamin E, Yaffe, Michael B

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An in vitro intestinal model captures immunomodulatory properties of the microbiota in inflammation von Lock, Jaclyn Y., Caboni, Mariaelena, Strandwitz, Philip, Morrissette, Madeleine, DiBona, Kevin, Joughin, Brian A., Lewis, Kim, Carrier, Rebecca L.

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Tandem phosphorylation within an intrinsically disordered region regulates ACTN4 function von Travers, Timothy, Shao, Hanshuang, Joughin, Brian A, Lauffenburger, Douglas A, Wells, Alan, Camacho, Carlos J

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Quantitative Phospho-proteomics to Investigate the Polo-like Kinase 1-Dependent Phospho-proteome von Grosstessner-Hain, Karin, Hegemann, Björn, Novatchkova, Maria, Rameseder, Jonathan, Joughin, Brian A., Hudecz, Otto, Roitinger, Elisabeth, Pichler, Peter, Kraut, Norbert, Yaffe, Michael B., Peters, Jan-Michael, Mechtler, Karl

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PTP1B-dependent regulation of receptor tyrosine kinase signaling by the actin-binding protein Mena von Hughes, Shannon K, Oudin, Madeleine J, Tadros, Jenny, Neil, Jason, Del Rosario, Amanda, Joughin, Brian A, Ritsma, Laila, Wyckoff, Jeff, Vasile, Eliza, Eddy, Robert, Philippar, Ulrike, Lussiez, Alisha, Condeelis, John S, van Rheenen, Jacco, White, Forest, Lauffenburger, Douglas A, Gertler, Frank B

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Cancer-Associated Fibroblasts and Squamous Epithelial Cells Constitute a Unique Microenvironment in a Mouse Model of Inflammation-Induced Colon Cancer von Vega, Paige N, Nilsson, Avlant, Kumar, Manu P, Niitsu, Hiroaki, Simmons, Alan J, Ro, James, Wang, Jiawei, Chen, Zhengyi, Joughin, Brian A, Li, Wei, McKinley, Eliot T, Liu, Qi, Roland, Joseph T, Washington, M Kay, Coffey, Robert J, Lauffenburger, Douglas A, Lau, Ken S

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Acidification of Tumor at Stromal Boundaries Drives Transcriptome Alterations Associated with Aggressive Phenotypes von Rohani, Nazanin, Hao, Liangliang, Alexis, Maria S, Joughin, Brian A, Krismer, Konstantin, Moufarrej, Mira N, Soltis, Anthony R, Lauffenburger, Douglas A, Yaffe, Michael B, Burge, Christopher B, Bhatia, Sangeeta N, Gertler, Frank B

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Shank3 mutation in a mouse model of autism leads to changes in the S-nitroso-proteome and affects key proteins involved in vesicle release and synaptic function von Amal, Haitham, Barak, Boaz, Bhat, Vadiraja, Gong, Guanyu, Joughin, Brian A., Wang, Xin, Wishnok, John S., Feng, Guoping, Tannenbaum, Steven R.

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Proteomics of Coagulopathy Following Injury Reveals Limitations of Using Laboratory Assessment to Define Trauma-Induced Coagulopathy to Predict Massive Transfusion von Moore, Hunter B, Neal, Matthew D, Bertolet, Marnie, Joughin, Brian A, Yaffe, Michael B, Barrett, Christopher D, Bird, Molly A, Tracy, Russell P, Moore, Ernest E, Sperry, Jason L, Zuckerbraun, Brian S, Park, Myung S, Cohen, Mitchell J, Wisniewski, Stephen R, Morrissey, James H

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The injury response to DNA damage in live tumor cells promotes antitumor immunity von Sriram, Ganapathy, Milling, Lauren E., Chen, Jung-Kuei, Kong, Yi Wen, Joughin, Brian A., Abraham, Wuhbet, Swartwout, Susanne, Handly, Erika D., Irvine, Darrell J., Yaffe, Michael B.

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The intrinsic substrate specificity of the human tyrosine kinome von Yaron-Barir, Tomer M., Joughin, Brian A., Huntsman, Emily M., Kerelsky, Alexander, Cizin, Daniel M., Cohen, Benjamin M., Regev, Amit, Song, Junho, Vasan, Neil, Lin, Ting-Yu, Orozco, Jose M., Schoenherr, Christina, Sagum, Cari, Bedford, Mark T., Wynn, R. Max, Tso, Shih-Chia, Chuang, David T., Li, Lei, Li, Shawn S.-C., Creixell, Pau, Krismer, Konstantin, Takegami, Mina, Lee, Harin, Zhang, Bin, Lu, Jingyi, Cossentino, Ian, Landry, Sean D., Uduman, Mohamed, Blenis, John, Elemento, Olivier, Frame, Margaret C., Hornbeck, Peter V., Cantley, Lewis C., Turk, Benjamin E., Yaffe, Michael B., Johnson, Jared L.

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