Human Proteomic Variation Revealed by Combining RNA-Seq Proteogenomics and Global Post-Translational Modification (G-PTM) Search Strategy

por Cesnik, Anthony J., Shortreed, Michael R., Sheynkman, Gloria M., Frey, Brian L., Smith, Lloyd M.
Publicado 2015

AD-Syn-Net: systematic identification of Alzheimer’s disease-associated mutation and co-mutation vulnerabilities via deep learning

por Pan, Xingxin, Coban Akdemir, Zeynep H, Gao, Ruixuan, Jiang, Xiaoqian, Sheynkman, Gloria M, Wu, Erxi, Huang, Jason H, Sahni, Nidhi, Yi, S Stephen
Publicado 2023

Using Galaxy-P to leverage RNA-Seq for the discovery of novel protein variations

por Sheynkman, Gloria M, Johnson, James E, Jagtap, Pratik D, Shortreed, Michael R, Onsongo, Getiria, Frey, Brian L, Griffin, Timothy J, Smith, Lloyd M
Publicado 2014

Global Identification of Protein Post-translational Modifications in a Single-Pass Database Search

por Shortreed, Michael R., Wenger, Craig D., Frey, Brian L., Sheynkman, Gloria M., Scalf, Mark, Keller, Mark P., Attie, Alan D., Smith, Lloyd M.
Publicado 2015

Characterization of protein isoform diversity in human umbilical vein endothelial cells via long-read proteogenomics

por Mehlferber, Madison M., Jeffery, Erin D., Saquing, Jamie, Jordan, Ben T., Sheynkman, Leon, Murali, Mayank, Genet, Gael, Acharya, Bipul R., Hirschi, Karen K., Sheynkman, Gloria M.
Publicado 2022

Connexin 37 sequestering of activated-ERK in the cytoplasm promotes p27-mediated endothelial cell cycle arrest

por Acharya, Bipul R, Fang, Jennifer S, Jeffery, Erin D, Chavkin, Nicholas W, Genet, Gael, Vasavada, Hema, Nelson, Elizabeth A, Sheynkman, Gloria M, Humphries, Martin J, Hirschi, Karen K
Publicado 2023

Full-length mRNA sequencing uncovers a widespread coupling between transcription initiation and mRNA processing

por Anvar, Seyed Yahya, Allard, Guy, Tseng, Elizabeth, Sheynkman, Gloria M., de Klerk, Eleonora, Vermaat, Martijn, Yin, Raymund H., Johansson, Hans E., Ariyurek, Yavuz, den Dunnen, Johan T., Turner, Stephen W., ‘t Hoen, Peter A. C.
Publicado 2018

ORF Capture-Seq as a versatile method for targeted identification of full-length isoforms

por Sheynkman, Gloria M., Tuttle, Katharine S., Laval, Florent, Tseng, Elizabeth, Underwood, Jason G., Yu, Liang, Dong, Da, Smith, Melissa L., Sebra, Robert, Willems, Luc, Hao, Tong, Calderwood, Michael A., Hill, David E., Vidal, Marc
Publicado 2020

Endothelial cell cycle state determines propensity for arterial-venous fate

por Chavkin, Nicholas W., Genet, Gael, Poulet, Mathilde, Jeffery, Erin D., Marziano, Corina, Genet, Nafiisha, Vasavada, Hema, Nelson, Elizabeth A., Acharya, Bipul R., Kour, Anupreet, Aragon, Jordon, McDonnell, Stephanie P., Huba, Mahalia, Sheynkman, Gloria M., Walsh, Kenneth, Hirschi, Karen K.
Publicado 2022

Enhanced protein isoform characterization through long-read proteogenomics

por Miller, Rachel M., Jordan, Ben T., Mehlferber, Madison M., Jeffery, Erin D., Chatzipantsiou, Christina, Kaur, Simi, Millikin, Robert J., Dai, Yunxiang, Tiberi, Simone, Castaldi, Peter J., Shortreed, Michael R., Luckey, Chance John, Conesa, Ana, Smith, Lloyd M., Deslattes Mays, Anne, Sheynkman, Gloria M.
Publicado 2022

Full-length transcript sequencing of human and mouse cerebral cortex identifies widespread isoform diversity and alternative splicing

por Leung, Szi Kay, Jeffries, Aaron R., Castanho, Isabel, Jordan, Ben T., Moore, Karen, Davies, Jonathan P., Dempster, Emma L., Bray, Nicholas J., O’Neill, Paul, Tseng, Elizabeth, Ahmed, Zeshan, Collier, David A., Jeffery, Erin D., Prabhakar, Shyam, Schalkwyk, Leonard, Jops, Connor, Gandal, Michael J., Sheynkman, Gloria M., Hannon, Eilis, Mill, Jonathan
Publicado 2021

The Transcription Factor Nfatc2 Regulates β-Cell Proliferation and Genes Associated with Type 2 Diabetes in Mouse and Human Islets

por Keller, Mark P., Paul, Pradyut K., Rabaglia, Mary E., Stapleton, Donnie S., Schueler, Kathryn L., Broman, Aimee Teo, Ye, Shuyun Isabella, Leng, Ning, Brandon, Christopher J., Neto, Elias Chaibub, Plaisier, Christopher L., Simonett, Shane P., Kebede, Melkam A., Sheynkman, Gloria M., Klein, Mark A., Baliga, Nitin S., Smith, Lloyd M., Broman, Karl W., Yandell, Brian S., Kendziorski, Christina, Attie, Alan D.
Publicado 2016

Systematic assessment of long-read RNA-seq methods for transcript identification and quantification

por Pardo-Palacios, Francisco J., Wang, Dingjie, Reese, Fairlie, Diekhans, Mark, Carbonell-Sala, Sílvia, Williams, Brian, Loveland, Jane E., De María, Maite, Adams, Matthew S., Balderrama-Gutierrez, Gabriela, Behera, Amit K., Gonzalez, Jose M., Hunt, Toby, Lagarde, Julien, Liang, Cindy E., Li, Haoran, Jerryd Meade, Marcus, Moraga Amador, David A., Prjibelski, Andrey D., Birol, Inanc, Bostan, Hamed, Brooks, Ashley M., Hasan Çelik, Muhammed, Chen, Ying, Du, Mei R,M., Felton, Colette, Göke, Jonathan, Hafezqorani, Saber, Herwig, Ralf, Kawaji, Hideya, Lee, Joseph, Liang Li, Jian, Lienhard, Matthias, Mikheenko, Alla, Mulligan, Dennis, Ming Nip, Ka, Pertea, Mihaela, Ritchie, Matthew E., Sim, Andre D., Tang, Alison D., Kei Wan, Yuk, Wang, Changqing, Wong, Brandon Y., Yang, Chen, Barnes, If, Berry, Andrew, Capella, Salvador, Dhillon, Namrita, Fernandez-Gonzalez, Jose M., Ferrández-Peral, Luis, Garcia-Reyero, Natàlia, Goetz, Stefan, Hernández-Ferrer, Carles, Kondratova, Liudmyla, Liu, Tianyuan, Martinez-Martin, Alessandra, Menor, Carlos, Mestre-Tomás, Jorge, Mudge, Jonathan M., Panayotova, Nedka G., Paniagua, Alejandro, Repchevsky, Dmitry, Rouchka, Eric, Saint-John, Brandon, Sapena, Enrique, Sheynkman, Leon, Laird Smith, Melissa, Suner, Marie-Marthe, Takahashi, Hazuki, Youngworth, Ingrid Ashley., Carninci, Piero, Denslow, Nancy D., Guigó, Roderic, Hunter, Margaret E., Tilgner, Hagen U., Wold, Barbara J., Vollmers, Christopher, Frankish, Adam, Fai Au, Kin, Sheynkman, Gloria M., Mortazavi, Ali, Conesa, Ana, Brooks, Angela N.
Publicado 2023

A reference map of the human binary protein interactome

por Luck, Katja, Kim, Dae-Kyum, Lambourne, Luke, Spirohn, Kerstin, Begg, Bridget E., Bian, Wenting, Brignall, Ruth, Cafarelli, Tiziana, Campos-Laborie, Francisco J., Charloteaux, Benoit, Choi, Dongsic, Coté, Atina G., Daley, Meaghan, Deimling, Steven, Desbuleux, Alice, Dricot, Amélie, Gebbia, Marinella, Hardy, Madeleine F., Kishore, Nishka, Knapp, Jennifer J., Kovács, István A., Lemmens, Irma, Mee, Miles W., Mellor, Joseph C., Pollis, Carl, Pons, Carles, Richardson, Aaron D., Schlabach, Sadie, Teeking, Bridget, Yadav, Anupama, Babor, Mariana, Balcha, Dawit, Basha, Omer, Bowman-Colin, Christian, Chin, Suet-Feung, Choi, Soon Gang, Colabella, Claudia, Coppin, Georges, D’Amata, Cassandra, Ridder, David De, Rouck, Steffi De, Duran-Frigola, Miquel, Ennajdaoui, Hanane, Goebels, Florian, Goehring, Liana, Gopal, Anjali, Haddad, Ghazal, Hatchi, Elodie, Helmy, Mohamed, Jacob, Yves, Kassa, Yoseph, Landini, Serena, Li, Roujia, van Lieshout, Natascha, MacWilliams, Andrew, Markey, Dylan, Paulson, Joseph N., Rangarajan, Sudharshan, Rasla, John, Rayhan, Ashyad, Rolland, Thomas, San-Miguel, Adriana, Shen, Yun, Sheykhkarimli, Dayag, Sheynkman, Gloria M., Simonovsky, Eyal, Taşan, Murat, Tejeda, Alexander, Tropepe, Vincent, Twizere, Jean-Claude, Wang, Yang, Weatheritt, Robert J., Weile, Jochen, Xia, Yu, Yang, Xinping, Yeger-Lotem, Esti, Zhong, Quan, Aloy, Patrick, Bader, Gary D., Rivas, Javier De Las, Gaudet, Suzanne, Hao, Tong, Rak, Janusz, Tavernier, Jan, Hill, David E., Vidal, Marc, Roth, Frederick P., Calderwood, Michael A.
Publicado 2020