Mass Spectrometry-Based Proteogenomics: New Therapeutic Opportunities for Precision Medicine by Joshi, Sunil K, Piehowski, Paul, Liu, Tao, Gosline, Sara J.C, McDermott, Jason E, Druker, Brian J, Traer, Elie, Tyner, Jeffrey W, Agarwal, Anupriya, Tognon, Cristina E, Rodland, Karin D

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Spatiotemporal Loss of NF1 in Schwann Cell Lineage Leads to Different Types of Cutaneous Neurofibroma Susceptible to Modification by the Hippo Pathway by Chen, Zhiguo, Mo, Juan, Brosseau, Jean-Philippe, Shipman, Tracey, Wang, Yong, Liao, Chung-Ping, Cooper, Jonathan M, Allaway, Robert J, Gosline, Sara J C, Guinney, Justin, Carroll, Thomas J, Le, Lu Q

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Quantitative Proteomics Analysis of the Secretory Pathway by Gilchrist, Annalyn, Au, Catherine E., Hiding, Johan, Bell, Alexander W., Fernandez-Rodriguez, Julia, Lesimple, Souad, Nagaya, Hisao, Roy, Line, Gosline, Sara J.C., Hallett, Michael, Paiement, Jacques, Kearney, Robert E., Nilsson, Tommy, Bergeron, John J.M.

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Elucidating MicroRNA Regulatory Networks Using Transcriptional, Post-transcriptional, and Histone Modification Measurements by Gosline, Sara J.C., Gurtan, Allan M., JnBaptiste, Courtney K., Bosson, Andrew, Milani, Pamela, Dalin, Simona, Matthews, Bryan J., Yap, Yoon S., Sharp, Phillip A., Fraenkel, Ernest

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Linking proteomic and transcriptional data through the interactome and epigenome reveals a map of oncogene-induced signaling by Huang, Shao-shan Carol, Clarke, David C, Gosline, Sara J C, Labadorf, Adam, Chouinard, Candace R, Gordon, William, Lauffenburger, Douglas A, Fraenkel, Ernest

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Chromosome 8 gain is associated with high-grade transformation in MPNST by Dehner, Carina, Moon, Chang In, Zhang, Xiyuan, Zhou, Zhaohe, Miller, Chris, Xu, Hua, Wan, Xiaodan, Yang, Kuangying, Mashl, Jay, Gosline, Sara Jc, Wang, Yuxi, Zhang, Xiaochun, Godec, Abigail, Jones, Paul A, Dahiya, Sonika, Bhatia, Himanshi, Primeau, Tina, Li, Shunqiang, Pollard, Kai, Rodriguez, Fausto J, Ding, Li, Pratilas, Christine A, Shern, Jack F, Hirbe, Angela C

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Network-Based Interpretation of Diverse High-Throughput Datasets through the Omics Integrator Software Package by Tuncbag, Nurcan, Gosline, Sara J C, Kedaigle, Amanda, Soltis, Anthony R, Gitter, Anthony, Fraenkel, Ernest

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The AML microenvironment catalyzes a stepwise evolution to gilteritinib resistance by Joshi, Sunil K., Nechiporuk, Tamilla, Bottomly, Daniel, Piehowski, Paul D., Reisz, Julie A., Pittsenbarger, Janét, Kaempf, Andy, Gosline, Sara J.C., Wang, Yi-Ting, Hansen, Joshua R., Gritsenko, Marina A., Hutchinson, Chelsea, Weitz, Karl K., Moon, Jamie, Cendali, Francesca, Fillmore, Thomas L., Tsai, Chia-Feng, Schepmoes, Athena A., Shi, Tujin, Arshad, Osama A., McDermott, Jason E., Babur, Ozgun, Watanabe-Smith, Kevin, Demir, Emek, D'Alessandro, Angelo, Liu, Tao, Tognon, Cristina E., Tyner, Jeffrey W., McWeeney, Shannon K., Rodland, Karin D., Druker, Brian J., Traer, Elie

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Cutaneous neurofibromas in the genomics era: current understanding and open questions by Allaway, Robert J., Gosline, Sara J. C., La Rosa, Salvatore, Knight, Pamela, Bakker, Annette, Guinney, Justin, Le, Lu Q.

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Posttranscriptional Regulation of PER1 Underlies the Oncogenic Function of IREα by PLUQUET, Olivier, DEJEANS, Nicolas, DUGOT-SENANT, Nathalie, VITAL, Anne, LOISEAU, Hugues, GOSLINE, Sara J. C, TAOUJI, Said, HALLETT, Michael, SARKARIA, Jann N, ANDERSON, Keith, WENTING WU, RODRIGUEZ, Fausto J, BOUCHECAREILH, Marion, ROSENBAUM, Jean, SALTEL, Frédéric, FERNANDEZ-ZAPICO, Martin E, CHEVET, Eric, LHOMOND, Stephanie, PINEAU, Raphael, HIGA, Arisa, DELUGIN, Maylis, COMBE, Chantal, LORIOT, Sandrine, CUBEL, Gaelle

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A field guide to cultivating computational biology by Way, Gregory P, Greene, Casey S, Carninci, Piero, Carvalho, Benilton S, de Hoon, Michiel, Finley, Stacey D, Gosline, Sara J C, Lȇ Cao, Kim-Anh, Lee, Jerry S H, Marchionni, Luigi, Robine, Nicolas, Sindi, Suzanne S, Theis, Fabian J, Yang, Jean Y H, Carpenter, Anne E, Fertig, Elana J

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leapR: An R Package for Multiomic Pathway Analysis by Danna, Vincent, Mitchell, Hugh, Anderson, Lindsey, Godinez, Iobani, Gosline, Sara J. C, Teeguarden, Justin, McDermott, Jason E

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The evolution and multi-molecular properties of NF1 cutaneous neurofibromas originating from C-fiber sensory endings and terminal Schwann cells at normal sites of sensory terminati... by Rice, Frank L, Houk, George, Wymer, James P, Gosline, Sara J C, Guinney, Justin, Wu, Jianqiang, Ratner, Nancy, Jankowski, Michael P, La Rosa, Salvo, Dockum, Marilyn, Storey, James R, Carroll, Steven L, Albrecht, Phillip J, Riccardi, Vincent M

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Targeting CCL2/CCR2 Signaling Overcomes MEK Inhibitor Resistance in Acute Myeloid Leukemia by Modak, Rucha V, de Oliveira Rebola, Katia G, McClatchy, John, Mohammadhosseini, Mona, Damnernsawad, Alisa, Kurtz, Stephen E, Eide, Christopher A, Wu, Guanming, Laderas, Ted, Nechiporuk, Tamilla, Gritsenko, Marina A, Hansen, Joshua R, Hutchinson, Chelsea, Gosline, Sara J C, Piehowski, Paul, Bottomly, Daniel, Short, Nicholas, Rodland, Karin, McWeeney, Shannon K, Tyner, Jeffrey W, Agarwal, Anupriya

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Proteome Mapping of the Human Pancreatic Islet Microenvironment Reveals Endocrine–Exocrine Signaling Sphere of Influence by Gosline, Sara J.C., Velickovic, Marija, Pino, James, Day, Le Z., Attah, Isaac K., Swensen, Adam C., Danna, Vincent, Posso, Camilo, Rodland, Karin D., Chen, Jing, Matthews, Clayton E., Campbell-Thompson, Martha, Laskin, Julia, Burnum-Johnson, Kristin, Zhu, Ying, Piehowski, Paul D.

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Knowledge-based classification of fine-grained immune cell types in single-cell RNA-Seq data by Liu, Xuan, Gosline, Sara J C, Pflieger, Lance T, Wallet, Pierre, Iyer, Archana, Guinney, Justin, Bild, Andrea H, Chang, Jeffrey T

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Proteogenomic data and resources for pan-cancer analysis by Dou, Yongchao, Da Veiga Leprevost, Felipe, Geffen, Yifat, Calinawan, Anna P., Aguet, François, Birger, Chet, Cao, Song, Chaudhary, Rekha, Cieslik, Marcin, Colaprico, Antonio, Zhou, Daniel Cui, Day, Corbin, Domagalski, Marcin J., Fenyö, David, Foltz, Steven M., Gonzalez-Robles, Tania, Gümüş, Zeynep H., Heiman, David, Hong, Runyu, Hu, Yingwei, Jaehnig, Eric J., Ji, Jiayi, Jiang, Wen, Ketchum, Karen A., Klein, Robert J., Liao, Yuxing, Lindgren, Caleb M., Ma, Weiping, Ma, Lei, MacCoss, Michael J., Martins Rodrigues, Fernanda, Nguyen, Ngoc, Oldroyd, Robert, Reva, Boris, Rudnick, Paul, Savage, Sara R., Schnaubelt, Michael, Schraink, Tobias, Shi, Zhiao, Singhal, Deepak, Storrs, Erik, Thangudu, Ratna R., Thiagarajan, Mathangi, Wang, Liang-Bo, Wang, Joshua M., Wen, Bo, Wu, Yige, Wyczalkowski, Matthew A., Xin, Yi, Yao, Lijun, Zhang, Hui, Zhang, Qing, Getz, Gad, Ding, Li, Nesvizhskii, Alexey I., Robles, Ana I., Payne, Samuel H., Lazar, Alexander J., Paulovich, Amanda G., Iavarone, Antonio, Chinnaiyan, Arul M., Druker, Brian J., Kumar-Sinha, Chandan, Newton, Chelsea J., Smith, Richard D., Huntsman, Emily, Schadt, Eric E., An, Eunkyung, Petralia, Francesca, Cho, Hanbyul, Rodriguez, Henry, Zhang, Hui, Kolodziejczak, Iga, Johnson, Jared L., Bavarva, Jasmin, Tan, Jimin, Clauser, Karl R., Krug, Karsten, Cantley, Lewis C., Wiznerowicz, Maciej, Anurag, Meenakshi, Mesri, Mehdi, Gillette, Michael A., Birrer, Michael J., Ceccarelli, Michele, Dhanasekaran, Saravana M., Edwards, Nathan, Tignor, Nicole, Babur, Özgün, Pugliese, Pietro, Jewell, Scott D., Satpathy, Shankha, Chowdhury, Shrabanti, Schürer, Stephan, Carr, Steven A., Hiltke, Tara, Yaron, Tomer M., Liu, Wenke, Song, Yizhe, Zhang, Zhen

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Pan-cancer analysis of post-translational modifications reveals shared patterns of protein regulation by Geffen, Yifat, Anand, Shankara, Akiyama, Yo, Yaron, Tomer M., Song, Yizhe, Johnson, Jared L., Govindan, Akshay, Li, Yize, Huntsman, Emily, Wang, Liang-Bo, Birger, Chet, Heiman, David I., Zhang, Qing, Miller, Mendy, Calinawan, Anna, Belkin, Saveliy, Kerelsky, Alexander, Clauser, Karl R., Krug, Karsten, Satpathy, Shankha, Payne, Samuel H., Mani, D.R., Gillette, Michael A., Dhanasekaran, Saravana M., Thiagarajan, Mathangi, Mesri, Mehdi, Rodriguez, Henry, Robles, Ana I., Lazar, Alexander J., Ding, Li, Getz, Gad, An, Eunkyung, Anurag, Meenakshi, Bavarva, Jasmin, Birrer, Michael J., Cao, Song, Ceccarelli, Michele, Chinnaiyan, Arul M., Chowdhury, Shrabanti, Colaprico, Antonio, Carr, Steven A., da Veiga Leprevost, Felipe, Day, Corbin, Domagalski, Marcin J., Ellis, Matthew J., Fenyo, David, Foltz, Steven M., Francis, Alicia, Gonzalez Robles, Tania J., Gosline, Sara J.C., Gümüş, Zeynep H., Hiltke, Tara, Hong, Runyu, Hu, Yingwei, Huang, Chen, Iavarone, Antonio, Jewel, Scott D., Katsnelson, Lizabeth, Ketchum, Karen A., Kolodziejczak, Iga, Kumar-Sinha, Chandan, Krug, Karsten, Lei, Jonathan T., Liang, Wen-Wei, Liao, Yuxing, Lindgren, Caleb M., Liu, Tao, Liu, Wenke, Ma, Weiping, McKerrow, Wilson, Mesri, Mehdi, Newton, Chelsea, Omenn, Gilbert S., Paulovich, Amanda G., Petralia, Francesca, Pugliese, Pietro, Reva, Boris, Rodland, Karin D., Ruggles, Kelly V., Rodrigues, Fernanda Martins, Savage, Sara R., Schadt, Eric E., Schnaubelt, Michael, Schraink, Tobias, Shi, Zhiao, Smith, Richard D., Stathias, Vasileios, Storrs, Erik P., Selvan, Myvizhi Esai, Tan, Jimin, Thangudu, Ratna R., Wang, Joshua M., Wang, Pei, Wang, Ying (Cindy), Wen, Bo, Wu, Yige, Yi, Xinpei, Zhang, Bing, Zhang, Xu, Zhang, Zhen

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Pan-cancer proteogenomics connects oncogenic drivers to functional states by Porta-Pardo, Eduard, Bailey, Matthew H., Yaron, Tomer M., Stathias, Vasileios, Geffen, Yifat, Imbach, Kathleen J., Cao, Song, Anand, Shankara, Akiyama, Yo, Liu, Wenke, Wyczalkowski, Matthew A., Song, Yizhe, Storrs, Erik P., Wendl, Michael C., Zhang, Wubing, Sibai, Mustafa, Ruiz-Serra, Victoria, Terekhanova, Nadezhda V., Rodrigues, Fernanda Martins, Clauser, Karl R., Heiman, David I., Zhang, Qing, Aguet, Francois, Calinawan, Anna P., Birger, Chet, Satpathy, Shankha, Zhou, Daniel Cui, Wang, Liang-Bo, Baral, Jessika, Johnson, Jared L., Huntsman, Emily M., Pugliese, Pietro, Colaprico, Antonio, Iavarone, Antonio, Ricketts, Christopher J., Fenyö, David, Payne, Samuel H., Kumar-Sinha, Chandan, Lazar, Alexander J., Getz, Gad, An, Eunkyung, Anurag, Meenakshi, Bavarva, Jasmin, Birrer, Michael J., Calinawan, Anna, Ceccarelli, Michele, Chan, Daniel W., Chinnaiyan, Arul M., Cho, Hanbyul, Chowdhury, Shrabanti, Day, Corbin, Domagalski, Marcin J., Dou, Yongchao, Druker, Brian J., Edwards, Nathan, Selvan, Myvizhi Esai, Foltz, Steven M., Gonzalez Robles, Tania J., Gümüş, Zeynep H., Hiltke, Tara, Hostetter, Galen, Hu, Yingwei, Huang, Chen, Huntsman, Emily, Jaehnig, Eric J., Jewel, Scott D., Ji, Jiayi, Jiang, Wen, Katsnelson, Lizabeth, Ketchum, Karen A., Kolodziejczak, Iga, Lei, Jonathan T., Liao, Yuxing, Lindgren, Caleb M., Liu, Tao, Ma, Weiping, McKerrow, Wilson, Nesvizhskii, Alexey I., Oldroyd, Robert, Omenn, Gilbert S., Petralia, Francesca, Reva, Boris, Rodland, Karin D., Ruggles, Kelly V., Rykunov, Dmitry, Savage, Sara R., Schadt, Eric E., Schraink, Tobias, Shi, Zhiao, Smith, Richard D., Song, Xiaoyu, Tan, Jimin, Wang, Joshua M., Wang, Pei, Wen, Bo, Wiznerowicz, Maciej, Yi, Xinpei, Zhang, Bing, Zhang, Xu, Zhang, Zhen

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SAMNetWeb: identifying condition-specific networks linking signaling and transcription by Gosline, Sara J C, Oh, Coyin, Fraenkel, Ernest

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