Bibliotecas PUC-SP - Busca Integrada

Chromatin-bound protein colocalization analysis using bedGraph2Cluster and PanChIP

Por Hanjun Lee, Ioannis Sanidas, Nicholas J. Dyson, Michael S. Lawrence
Publicado no STAR Protocols (2023-03-01)

Single-cell transcriptomic profiling for inferring tumor origin and mechanisms of therapeutic resistance

Por Maoxuan Lin, Moshe Sade-Feldman, Lori Wirth, Michael S. Lawrence, Daniel L. Faden
Publicado no npj Precision Oncology (2022-10-01)

Distinguishing preferences of human APOBEC3A and APOBEC3B for cytosines in hairpin loops, and reflection of these preferences in APOBEC-signature cancer genome mutations

Por Yasha Butt, Ramin Sakhtemani, Rukshana Mohamad-Ramshan, Michael S. Lawrence, Ashok S. Bhagwat
Publicado no Nature Communications (2024-03-01)

An extended APOBEC3A mutation signature in cancer

Por Adam Langenbucher, Danae Bowen, Ramin Sakhtemani, Elodie Bournique, Jillian F. Wise, Lee Zou, Ashok S. Bhagwat, Rémi Buisson, Michael S. Lawrence
Publicado no Nature Communications (2021-03-01)

Quantification of ongoing APOBEC3A activity in tumor cells by monitoring RNA editing at hotspots

Por Pégah Jalili, Danae Bowen, Adam Langenbucher, Shinho Park, Kevin Aguirre, Ryan B. Corcoran, Angela G. Fleischman, Michael S. Lawrence, Lee Zou, Rémi Buisson
Publicado no Nature Communications (2020-06-01)

The RNA m5C modification in R-loops as an off switch of Alt-NHEJ

Por Haibo Yang, Emily M. Lachtara, Xiaojuan Ran, Jessica Hopkins, Parasvi S. Patel, Xueping Zhu, Yao Xiao, Laiyee Phoon, Boya Gao, Lee Zou, Michael S. Lawrence, Li Lan
Publicado no Nature Communications (2023-09-01)

Mesoscale DNA features impact APOBEC3A and APOBEC3B deaminase activity and shape tumor mutational landscapes

Por Ambrocio Sanchez, Pedro Ortega, Ramin Sakhtemani, Lavanya Manjunath, Sunwoo Oh, Elodie Bournique, Alexandrea Becker, Kyumin Kim, Cameron Durfee, Nuri Alpay Temiz, Xiaojiang S. Chen, Reuben S. Harris, Michael S. Lawrence, Rémi Buisson
Publicado no Nature Communications (2024-03-01)

APOBEC Mutagenesis Is Concordant between Tumor and Viral Genomes in HPV-Positive Head and Neck Squamous Cell Carcinoma

Por Daniel L. Faden, Krystle A. Lang Kuhs, Maoxuan Lin, Adam Langenbucher, Maisa Pinheiro, Meredith Yeager, Michael Cullen, Joseph F. Boland, Mia Steinberg, Sara Bass, James S. Lewis, Michael S. Lawrence, Robert L. Ferris, Lisa Mirabello
Publicado no Viruses (2021-08-01)

A pan-cancer analysis of transcriptome changes associated with somatic mutations in U2AF1 reveals commonly altered splicing events.

Por Angela N Brooks, Peter S Choi, Luc de Waal, Tanaz Sharifnia, Marcin Imielinski, Gordon Saksena, Chandra Sekhar Pedamallu, Andrey Sivachenko, Mara Rosenberg, Juliann Chmielecki, Michael S Lawrence, David S DeLuca, Gad Getz, Matthew Meyerson
Publicado no PLoS ONE (2014-01-01)

YAP1 maintains active chromatin state in head and neck squamous cell carcinomas that promotes tumorigenesis through cooperation with BRD4

Por Nana Chen, Gabriel Golczer, Subhoshree Ghose, Brian Lin, Adam Langenbucher, Jason Webb, Haymanti Bhanot, Nicholas B. Abt, Derrick Lin, Mark Varvares, Martin Sattler, Ann Marie Egloff, Richard Joh, Ravindra Uppaluri, Kevin S. Emerick, Michael S. Lawrence, Srinivas Vinod Saladi
Publicado no Cell Reports (2022-06-01)

TGF-β in the microenvironment induces a physiologically occurring immune-suppressive senescent state

Por Satoru Matsuda, Ajinkya Revandkar, Taronish D. Dubash, Arvind Ravi, Ben S. Wittner, Maoxuan Lin, Robert Morris, Risa Burr, Hongshan Guo, Karsen Seeger, Annamaria Szabolcs, Dante Che, Linda Nieman, Gad A. Getz, David T. Ting, Michael S. Lawrence, Justin Gainor, Daniel A. Haber, Shyamala Maheswaran
Publicado no Cell Reports (2023-03-01)

Multi-omics profiling of longitudinal samples reveals early genomic changes in follicular lymphoma

Por Baoyan Bai, Jillian F. Wise, Daniel Vodák, Sigve Nakken, Ankush Sharma, Yngvild Nuvin Blaker, Marianne Brodtkorb, Vera Hilden, Gunhild Trøen, Weicheng Ren, Susanne Lorenz, Michael S. Lawrence, Ola Myklebost, Eva Kimby, Qiang Pan-Hammarström, Chloé B. Steen, Leonardo A. Meza-Zepeda, Klaus Beiske, Erlend B. Smeland, Eivind Hovig, Ole Christian Lingjærde, Harald Holte, June Helen Myklebust
Publicado no Blood Cancer Journal (2024-08-01)

A post-transcriptional program of chemoresistance by AU-rich elements and TTP in quiescent leukemic cells

Por Sooncheol Lee, Douglas Micalizzi, Samuel S. Truesdell, Syed I. A. Bukhari, Myriam Boukhali, Jennifer Lombardi-Story, Yasutaka Kato, Min-Kyung Choo, Ipsita Dey-Guha, Fei Ji, Benjamin T. Nicholson, David T. Myers, Dongjun Lee, Maria A. Mazzola, Radhika Raheja, Adam Langenbucher, Nicholas J. Haradhvala, Michael S. Lawrence, Roopali Gandhi, Christopher Tiedje, Manuel D. Diaz-Muñoz, David A. Sweetser, Ruslan Sadreyev, David Sykes, Wilhelm Haas, Daniel A. Haber, Shyamala Maheswaran, Shobha Vasudevan
Publicado no Genome Biology (2020-02-01)

Author Correction: Pathway and network analysis of more than 2500 whole cancer genomes

Por Matthew A. Reyna, David Haan, Marta Paczkowska, Lieven P. C. Verbeke, Miguel Vazquez, Abdullah Kahraman, Sergio Pulido-Tamayo, Jonathan Barenboim, Lina Wadi, Priyanka Dhingra, Raunak Shrestha, Gad Getz, Michael S. Lawrence, Jakob Skou Pedersen, Mark A. Rubin, David A. Wheeler, Søren Brunak, Jose M. G. Izarzugaza, Ekta Khurana, Kathleen Marchal, Christian von Mering, S. Cenk Sahinalp, Alfonso Valencia, PCAWG Drivers and Functional Interpretation Working Group, Jüri Reimand, Joshua M. Stuart, Benjamin J. Raphael, PCAWG Consortium
Publicado no Nature Communications (2022-12-01)

Pathway and network analysis of more than 2500 whole cancer genomes

Por Matthew A. Reyna, David Haan, Marta Paczkowska, Lieven P. C. Verbeke, Miguel Vazquez, Abdullah Kahraman, Sergio Pulido-Tamayo, Jonathan Barenboim, Lina Wadi, Priyanka Dhingra, Raunak Shrestha, Gad Getz, Michael S. Lawrence, Jakob Skou Pedersen, Mark A. Rubin, David A. Wheeler, Søren Brunak, Jose M. G. Izarzugaza, Ekta Khurana, Kathleen Marchal, Christian von Mering, S. Cenk Sahinalp, Alfonso Valencia, PCAWG Drivers and Functional Interpretation Working Group, Jüri Reimand, Joshua M. Stuart, Benjamin J. Raphael, PCAWG Consortium
Publicado no Nature Communications (2020-02-01)

Genomic Correlates of Immune-Cell Infiltrates in Colorectal Carcinoma

Por Marios Giannakis, Xinmeng Jasmine Mu, Sachet A. Shukla, Zhi Rong Qian, Ofir Cohen, Reiko Nishihara, Samira Bahl, Yin Cao, Ali Amin-Mansour, Mai Yamauchi, Yasutaka Sukawa, Chip Stewart, Mara Rosenberg, Kosuke Mima, Kentaro Inamura, Katsuhiko Nosho, Jonathan A. Nowak, Michael S. Lawrence, Edward L. Giovannucci, Andrew T. Chan, Kimmie Ng, Jeffrey A. Meyerhardt, Eliezer M. Van Allen, Gad Getz, Stacey B. Gabriel, Eric S. Lander, Catherine J. Wu, Charles S. Fuchs, Shuji Ogino, Levi A. Garraway
Publicado no Cell Reports (2016-04-01)

Genomic Correlates of Immune-Cell Infiltrates in Colorectal Carcinoma

Por Marios Giannakis, Xinmeng Jasmine Mu, Sachet A. Shukla, Zhi Rong Qian, Ofir Cohen, Reiko Nishihara, Samira Bahl, Yin Cao, Ali Amin-Mansour, Mai Yamauchi, Yasutaka Sukawa, Chip Stewart, Mara Rosenberg, Kosuke Mima, Kentaro Inamura, Katsuhiko Nosho, Jonathan A. Nowak, Michael S. Lawrence, Edward L. Giovannucci, Andrew T. Chan, Kimmie Ng, Jeffrey A. Meyerhardt, Eliezer M. Van Allen, Gad Getz, Stacey B. Gabriel, Eric S. Lander, Catherine J. Wu, Charles S. Fuchs, Shuji Ogino, Levi A. Garraway
Publicado no Cell Reports (2016-10-01)

Tumor cell-based liquid biopsy using high-throughput microfluidic enrichment of entire leukapheresis product

Por Avanish Mishra, Shih-Bo Huang, Taronish Dubash, Risa Burr, Jon F. Edd, Ben S. Wittner, Quinn E. Cunneely, Victor R. Putaturo, Akansha Deshpande, Ezgi Antmen, Kaustav A. Gopinathan, Keisuke Otani, Yoshiyuki Miyazawa, Ji Eun Kwak, Sara Y. Guay, Justin Kelly, John Walsh, Linda T. Nieman, Isabella Galler, PuiYee Chan, Michael S. Lawrence, Ryan J. Sullivan, Aditya Bardia, Douglas S. Micalizzi, Lecia V. Sequist, Richard J. Lee, Joseph W. Franses, David T. Ting, Patricia A. R. Brunker, Shyamala Maheswaran, David T. Miyamoto, Daniel A. Haber, Mehmet Toner
Publicado no Nature Communications (2025-01-01)

Dissection of <i>PIK3CA</i> Aberration for Cervical Adenocarcinoma Outcomes

Por Tony K. H. Chung, Graeme Doran, Tak-Hong Cheung, So-Fan Yim, Mei-Yung Yu, Michael J. Worley, Kevin M. Elias, Aaron R. Thorner, Chandra Sekhar Pedamallu, Akinyemi I. Ojesina, Kei-Man Lau, Matthew D. Ducar, Raymond R. Y. Wong, Vivian W. Wang, Anwesha Nag, Bruce M. Wollison, Audrey Dalgarno, Jacqueline H. S. Lee, Suet-Ying Yeung, Lo Wong, Neil S. Horowitz, Michelle R. Davis, Shuk-On A. Leung, Yi Mu, Samuel C. Mok, Paul K. S. Chan, Michael S. Lawrence, Christopher P. Crum, Rossa W. K. Chiu, Ross S. Berkowitz, Yick-Fu Wong
Publicado no Cancers (2021-06-01)

Integrative Genomic Analysis of Cholangiocarcinoma Identifies Distinct IDH-Mutant Molecular Profiles

Por Farshad Farshidfar, Siyuan Zheng, Marie-Claude Gingras, Yulia Newton, Juliann Shih, A. Gordon Robertson, Toshinori Hinoue, Katherine A. Hoadley, Ewan A. Gibb, Jason Roszik, Kyle R. Covington, Chia-Chin Wu, Eve Shinbrot, Nicolas Stransky, Apurva Hegde, Ju Dong Yang, Ed Reznik, Sara Sadeghi, Chandra Sekhar Pedamallu, Akinyemi I. Ojesina, Julian M. Hess, J. Todd Auman, Suhn K. Rhie, Reanne Bowlby, Mitesh J. Borad, Rehan Akbani, Loretta K. Allotey, Adrian Ally, Domenico Alvaro, Jesper B. Andersen, Elizabeth L. Appelbaum, Arshi Arora, J. Todd Auman, Miruna Balasundaram, Saianand Balu, Nabeel Bardeesy, Oliver F. Bathe, Stephen B. Baylin, Rameen Beroukhim, Mario Berrios, Tom Bodenheimer, Lori Boice, Moiz S. Bootwalla, Mitesh J. Borad, Jay Bowen, Reanne Bowlby, Maria Consiglia Bragazzi, Denise Brooks, Vincenzo Cardinale, Rebecca Carlsen, Guido Carpino, Andre L. Carvalho, Roongruedee Chaiteerakij, Vishal C. Chandan, Andrew D. Cherniack, Lynda Chin, Juok Cho, Gina Choe, Eric Chuah, Sudha Chudamani, Carrie Cibulskis, Matthew G. Cordes, Kyle R. Covington, Daniel Crain, Erin Curley, Agostino Maria De Rose, Timothy Defreitas, John A. Demchok, Vikram Deshpande, Noreen Dhalla, Li Ding, Kimberley Evason, Farshad Farshidfar, Ina Felau, Martin L. Ferguson, Wai Chin Foo, Antonio Franchitto, Scott Frazer, Catrina C. Fronick, Lucinda A. Fulton, Robert S. Fulton, Stacey B. Gabriel, Johanna Gardner, Julie M. Gastier-Foster, Eugenio Gaudio, Nils Gehlenborg, Giannicola Genovese, Mark Gerken, Gad Getz, Nasra H. Giama, Richard A. Gibbs, Marie-Claude Gingras, Felice Giuliante, Gian Luca Grazi, D. Neil Hayes, Apurva M. Hegde, David I. Heiman, Julian M. Hess, Toshinori Hinoue, Katherine A. Hoadley, Andrea Holbrook, Robert A. Holt, Alan P. Hoyle, Mei Huang, Carolyn M. Hutter, Stuart R. Jefferys, Steven J.M. Jones, Corbin D. Jones, Katayoon Kasaian, Robin K. Kelley, Jaegil Kim, David E. Kleiner, Jean-Pierre A. Kocher, Lawrence N. Kwong, Phillip H. Lai, Peter W. Laird, Michael S. Lawrence, Kristen M. Leraas, Tara M. Lichtenberg, Pei Lin, Wenbin Liu, Jia Liu, Laxmi Lolla, Yiling Lu, Yussanne Ma, David Mallery, Elaine R. Mardis, Marco A. Marra, Marcus M. Matsushita, Michael Mayo, Michael D. McLellan, Autumn J. McRee, Sam Meier, Shaowu Meng, Matthew Meyerson, Piotr A. Mieczkowski, Christopher A. Miller, Gordon B. Mills, Richard A. Moore, Scott Morris, Lisle E. Mose, Catherine D. Moser, Taofic Mounajjed, Andrew J. Mungall, Karen Mungall, Bradley A. Murray, Rashi Naresh, Yulia Newton, Michael S. Noble, Daniel R. O’Brien, Akinyemi I. Ojesina, Joel S. Parker, Tushar C. Patel, Joseph Paulauskis, Chandra Sekhar Pedamallu, Robert Penny, Charles M. Perou, Amy H. Perou, Todd Pihl, Amie J. Radenbaugh, Nilsa C. Ramirez, W. Kimryn Rathmell, Ed Reznik, Suhn K. Rhie, Jeffrey Roach, Lewis R. Roberts, A. Gordon Robertson, Sara Sadeghi, Gordon Saksena, Chris Sander, Jacqueline E. Schein, Heather K. Schmidt, Steven E. Schumacher, Candace Shelton, Troy Shelton, Ronglai Shen, Margi Sheth, Yan Shi, Juliann Shih, Eve Shinbrot, Rachna Shroff, Janae V. Simons, Payal Sipahimalani, Tara Skelly, Heidi J. Sofia, Matthew G. Soloway, Hubert Stoppler, Nicolas Stransky, Josh Stuart, Qiang Sun, Angela Tam, Donghui Tan, Roy Tarnuzzer, Nina Thiessen, Leigh B. Thorne, Michael S. Torbenson, David J. Van Den Berg, Umadevi Veluvolu, Roel G.W. Verhaak, Doug Voet, Yunhu Wan, Zhining Wang, John N. Weinstein, Daniel J. Weisenberger, David A. Wheeler, Richard K. Wilson, Lisa Wise, Tina Wong, Chia-Chin Wu, Ye Wu, Liu Xi, Ju Dong Yang, Liming Yang, Jean C. Zenklusen, Hailei Zhang, Jiashan (Julia) Zhang, Siyuan Zheng, Erik Zmuda
Publicado no Cell Reports (2017-06-01)