H2A.Z landscapes and dual modifications in pluripotent and multipotent stem cells underlie complex genome regulatory functions

por Ku, Manching, Jaffe, Jacob D, Koche, Richard P, Rheinbay, Esther, Endoh, Mitsuhiro, Koseki, Haruhiko, Carr, Steven A, Bernstein, Bradley E
Publicado 2012

Study of mitotic chromatin supports a model of bookmarking by histone modifications and reveals nucleosome deposition patterns

por Javasky, Elisheva, Shamir, Inbal, Gandhi, Shashi, Egri, Shawn, Sandler, Oded, Rothbart, Scott B., Kaplan, Noam, Jaffe, Jacob D., Goren, Alon, Simon, Itamar
Publicado 2018

Specter: linear deconvolution for targeted analysis of data-independent acquisition mass spectrometry proteomics

por Peckner, Ryan, Myers, Samuel A, Jacome, Alvaro Sebastian Vaca, Egertson, Jarrett D, Abelin, Jennifer G., MacCoss, Michael J., Carr, Steven A, Jaffe, Jacob D
Publicado 2018

Avant-garde: An automated data-driven DIA data curation tool.

por Jacome, Alvaro Sebastian Vaca, Peckner, Ryan, Shulman, Nicholas, Krug, Karsten, DeRuff, Katherine C., Officer, Adam, Christianson, Karen E., MacLean, Brendan, MacCoss, Michael J., Carr, Steven A., Jaffe, Jacob D.
Publicado 2020

Causal interactions from proteomic profiles: Molecular data meet pathway knowledge

por Babur, Özgün, Luna, Augustin, Korkut, Anil, Durupinar, Funda, Siper, Metin Can, Dogrusoz, Ugur, Vaca Jacome, Alvaro Sebastian, Peckner, Ryan, Christianson, Karen E., Jaffe, Jacob D., Spellman, Paul T., Aslan, Joseph E., Sander, Chris, Demir, Emek
Publicado 2021

The nucleosome acidic patch and H2A ubiquitination underlie mSWI/SNF recruitment in synovial sarcoma

por McBride, Matthew J., Mashtalir, Nazar, Winter, Evan B., Dao, Hai T., Filipovski, Martin, D’Avino, Andrew R., Seo, Hyuk-Soo, Umbreit, Neil T., St. Pierre, Roodolph, Valencia, Alfredo M., Qian, Kristin, Zullow, Hayley J., Jaffe, Jacob D., Dhe-Paganon, Sirano, Muir, Tom W., Kadoch, Cigall
Publicado 2020

Author Correction: The nucleosome acidic patch and H2A ubiquitination underlie mSWI/SNF recruitment in synovial sarcoma

por McBride, Matthew J., Mashtalir, Nazar, Winter, Evan B., Dao, Hai T., Filipovski, Martin, D’Avino, Andrew R., Seo, Hyuk-Soo, Umbreit, Neil T., St. Pierre, Roodolph, Valencia, Alfredo M., Qian, Kristin, Zullow, Hayley J., Jaffe, Jacob D., Dhe-Paganon, Sirano, Muir, Tom W., Kadoch, Cigall
Publicado 2020

Panorama: A Targeted Proteomics Knowledge Base

por Sharma, Vagisha, Eckels, Josh, Taylor, Greg K., Shulman, Nicholas J., Stergachis, Andrew B., Joyner, Shannon A., Yan, Ping, Whiteaker, Jeffrey R., Halusa, Goran N., Schilling, Birgit, Gibson, Bradford W., Colangelo, Christopher M., Paulovich, Amanda G., Carr, Steven A., Jaffe, Jacob D., MacCoss, Michael J., MacLean, Brendan
Publicado 2014

An Unbiased Approach To Identify Endogenous Substrates of “Histone” Deacetylase 8

por Olson, David E., Udeshi, Namrata D., Wolfson, Noah A., Pitcairn, Carol Ann, Sullivan, Eric D., Jaffe, Jacob D., Svinkina, Tanya, Natoli, Ted, Lu, Xiaodong, Paulk, Joshiawa, McCarren, Patrick, Wagner, Florence F., Barker, Doug, Howe, Eleanor, Lazzaro, Fanny, Gale, Jennifer P., Zhang, Yan-Ling, Subramanian, Aravind, Fierke, Carol A., Carr, Steven A., Holson, Edward B.
Publicado 2014

ZBED6, a Novel Transcription Factor Derived from a Domesticated DNA Transposon Regulates IGF2 Expression and Muscle Growth

por Markljung, Ellen, Jiang, Lin, Jaffe, Jacob D., Mikkelsen, Tarjei S., Wallerman, Ola, Larhammar, Martin, Zhang, Xiaolan, Wang, Li, Saenz-Vash, Veronica, Gnirke, Andreas, Lindroth, Anders M., Barrés, Romain, Yan, Jie, Strömberg, Sara, De, Sachinandan, Pontén, Fredrik, Lander, Eric S., Carr, Steven A., Zierath, Juleen R., Kullander, Klas, Wadelius, Claes, Lindblad-Toh, Kerstin, Andersson, Göran, Hjälm, Göran, Andersson, Leif
Publicado 2009

Proteomic profiling dataset of chemical perturbations in multiple biological backgrounds

por Dele-Oni, Deborah O., Christianson, Karen E., Egri, Shawn B., Vaca Jacome, Alvaro Sebastian, DeRuff, Katherine C., Mullahoo, James, Sharma, Vagisha, Davison, Desiree, Ko, Tak, Bula, Michael, Blanchard, Joel, Young, Jennie Z., Litichevskiy, Lev, Lu, Xiaodong, Lam, Daniel, Asiedu, Jacob K., Toder, Caidin, Officer, Adam, Peckner, Ryan, MacCoss, Michael J., Tsai, Li-Huei, Carr, Steven A., Papanastasiou, Malvina, Jaffe, Jacob D.
Publicado 2021

JAK–STAT Signaling in Inflammatory Breast Cancer Enables Chemotherapy-Resistant Cell States

por Stevens, Laura E., Peluffo, Guillermo, Qiu, Xintao, Temko, Daniel, Fassl, Anne, Li, Zheqi, Trinh, Anne, Seehawer, Marco, Jovanović, Bojana, Alečković, Maša, Wilde, Callahan M., Geck, Renee C., Shu, Shaokun, Kingston, Natalie L., Harper, Nicholas W., Almendro, Vanessa, Pyke, Alanna L., Egri, Shawn B., Papanastasiou, Malvina, Clement, Kendell, Zhou, Ningxuan, Walker, Sarah, Salas, Jacqueline, Park, So Yeon, Frank, David A., Meissner, Alexander, Jaffe, Jacob D., Sicinski, Piotr, Toker, Alex, Michor, Franziska, Long, Henry W., Overmoyer, Beth A., Polyak, Kornelia
Publicado 2023

Triplication of a 21q22 region contributes to B cell transformation through HMGN1 overexpression and loss of histone H3 lysine 27 trimethylation

por Lane, Andrew A., Chapuy, Bjoern, Lin, Charles Y., Tivey, Trevor, Li, Hubo, Townsend, Elizabeth C., van Bodegom, Diederik, Day, Tovah A., Wu, Shuo-Chieh, Liu, Huiyun, Yoda, Akinori, Alexe, Gabriela, Schinzel, Anna C., Sullivan, Timothy J., Malinge, Sébastien, Taylor, Jordan E., Stegmaier, Kimberly, Jaffe, Jacob D., Bustin, Michael, te Kronnie, Geertruy, Izraeli, Shai, Harris, Marian, Stevenson, Kristen E., Neuberg, Donna, Silverman, Lewis B., Sallan, Stephen E., Bradner, James E., Hahn, William C., Crispino, John D., Pellman, David, Weinstock, David M.
Publicado 2014

High-fat diet fuels prostate cancer progression by rewiring the metabolome and amplifying the MYC program

por Labbé, David P., Zadra, Giorgia, Yang, Meng, Reyes, Jaime M., Lin, Charles Y., Cacciatore, Stefano, Ebot, Ericka M., Creech, Amanda L., Giunchi, Francesca, Fiorentino, Michelangelo, Elfandy, Habiba, Syamala, Sudeepa, Karoly, Edward D., Alshalalfa, Mohammed, Erho, Nicholas, Ross, Ashley, Schaeffer, Edward M., Gibb, Ewan A., Takhar, Mandeep, Den, Robert B., Lehrer, Jonathan, Karnes, R. Jeffrey, Freedland, Stephen J., Davicioni, Elai, Spratt, Daniel E., Ellis, Leigh, Jaffe, Jacob D., DʼAmico, Anthony V., Kantoff, Philip W., Bradner, James E., Mucci, Lorelei A., Chavarro, Jorge E., Loda, Massimo, Brown, Myles
Publicado 2019

Performance Metrics for Liquid Chromatography-Tandem Mass Spectrometry Systems in Proteomics Analyses

por Rudnick, Paul A., Clauser, Karl R., Kilpatrick, Lisa E., Tchekhovskoi, Dmitrii V., Neta, Pedatsur, Blonder, Nikša, Billheimer, Dean D., Blackman, Ronald K., Bunk, David M., Cardasis, Helene L., Ham, Amy-Joan L., Jaffe, Jacob D., Kinsinger, Christopher R., Mesri, Mehdi, Neubert, Thomas A., Schilling, Birgit, Tabb, David L., Tegeler, Tony J., Vega-Montoto, Lorenzo, Variyath, Asokan Mulayath, Wang, Mu, Wang, Pei, Whiteaker, Jeffrey R., Zimmerman, Lisa J., Carr, Steven A., Fisher, Susan J., Gibson, Bradford W., Paulovich, Amanda G., Regnier, Fred E., Rodriguez, Henry, Spiegelman, Cliff, Tempst, Paul, Liebler, Daniel C., Stein, Stephen E.
Publicado 2010

A Library of Phosphoproteomic and Chromatin Signatures for Characterizing Cellular Responses to Drug Perturbations

por Litichevskiy, Lev, Peckner, Ryan, Abelin, Jennifer G., Asiedu, Jacob K., Creech, Amanda L., Davis, John F., Davison, Desiree, Dunning, Caitlin M., Egertson, Jarrett D., Egri, Shawn, Gould, Joshua, Ko, Tak, Johnson, Sarah A., Lahr, David L., Lam, Daniel, Liu, Zihan, Lyons, Nicholas J., Lu, Xiaodong, MacLean, Brendan X., Mungenast, Alison E., Officer, Adam, Natoli, Ted E., Papanastasiou, Malvina, Patel, Jinal, Sharma, Vagisha, Toder, Courtney, Tubelli, Andrew A., Young, Jennie Z., Carr, Steven A., Golub, Todd R., Subramanian, Aravind, MacCoss, Michael J., Tsai, Li-Huei, Jaffe, Jacob D.
Publicado 2018

The genome of the green anole lizard and a comparative analysis with birds and mammals

por Alföldi, Jessica, Di Palma, Federica, Grabherr, Manfred, Williams, Christina, Kong, Lesheng, Mauceli, Evan, Russell, Pamela, Lowe, Craig B., Glor, Richard, Jaffe, Jacob D., Ray, David A., Boissinot, Stephane, Shedlock, Andrew M., Botka, Christopher, Castoe, Todd A., Colbourne, John K., Fujita, Matthew K., Moreno, Ricardo Godinez, ten Hallers, Boudewijn F., Haussler, David, Heger, Andreas, Heiman, David, Janes, Daniel E., Johnson, Jeremy, de Jong, Pieter J., Koriabine, Maxim Y., Novick, Peter, Organ, Chris L., Peach, Sally E., Poe, Steven, Pollock, David D., de Queiroz, Kevin, Sanger, Thomas, Searle, Steve, Smith, Jeremy D., Smith, Zachary, Swofford, Ross, Turner-Maier, Jason, Wade, Juli, Young, Sarah, Zadissa, Amonida, Edwards, Scott V., Glenn, Travis C., Schneider, Christopher J., Losos, Jonathan B., Lander, Eric S., Breen, Matthew, Ponting, Chris P., Lindblad-Toh, Kerstin
Publicado 2011

Neuronal differentiation and cell-cycle programs mediate response to BET-bromodomain inhibition in MYC-driven medulloblastoma

por Bandopadhayay, Pratiti, Piccioni, Federica, O’Rourke, Ryan, Ho, Patricia, Gonzalez, Elizabeth M., Buchan, Graham, Qian, Kenin, Gionet, Gabrielle, Girard, Emily, Coxon, Margo, Rees, Matthew G., Brenan, Lisa, Dubois, Frank, Shapira, Ofer, Greenwald, Noah F., Pages, Melanie, Balboni Iniguez, Amanda, Paolella, Brenton R., Meng, Alice, Sinai, Claire, Roti, Giovanni, Dharia, Neekesh V., Creech, Amanda, Tanenbaum, Benjamin, Khadka, Prasidda, Tracy, Adam, Tiv, Hong L., Hong, Andrew L., Coy, Shannon, Rashid, Rumana, Lin, Jia-Ren, Cowley, Glenn S., Lam, Fred C., Goodale, Amy, Lee, Yenarae, Schoolcraft, Kathleen, Vazquez, Francisca, Hahn, William C., Tsherniak, Aviad, Bradner, James E., Yaffe, Michael B., Milde, Till, Pfister, Stefan M., Qi, Jun, Schenone, Monica, Carr, Steven A., Ligon, Keith L., Kieran, Mark W., Santagata, Sandro, Olson, James M., Gokhale, Prafulla C., Jaffe, Jacob D., Root, David E., Stegmaier, Kimberly, Johannessen, Cory M., Beroukhim, Rameen
Publicado 2019