Francisca Vazquez

Publication Activity (10 Years)

Years Active: 2018-2024
Publications (10 Years): 36

Top Topics

Transcription Factor

High Throughput Sequencing

Top Venues

Nature communications

Cancer discovery

Cancer research

This page only lists publications with an associated author ORCID identifier.

Publications

Alessandro Vinceti, Raffaele M Iannuzzi, Isabella Boyle, Lucia Trastulla, Catarina D Campbell, Francisca Vazquez, Joshua M Dempster, Francesco Iorio
A benchmark of computational methods for correcting biases of established and unknown origin in CRISPR-Cas9 screening data. Genome biology 25 (1) (2024)
Johanna Zerbib, Marica Rosaria Ippolito, Yonatan Eliezer, Giuseppina De Feudis, Eli Reuveni, Anouk Savir Kadmon, Sara Martin, Sonia Viganò, Gil Leor, James Berstler, Julia Muenzner, Michael Mulleder, Emma M Campagnolo, Eldad David Shulman, Tian-Gen Chang, Carmela Rubolino, Kathrin Laue, Yael Cohen-Sharir, Simone Scorzoni, Silvia Taglietti, Alice Ratti, Chani Stossel, Talia Golan, Francesco Nicassio, Eytan Ruppin, Markus Ralser, Francisca Vazquez, Uri Ben-David, Stefano Santaguida
Human aneuploid cells depend on the RAF/MEK/ERK pathway for overcoming increased DNA damage. Nature communications 15 (1) (2024)
Alessandro Vinceti, Raffaele M Iannuzzi, Isabella Boyle, Lucia Trastulla, Catarina D Campbell, Francisca Vazquez, Joshua M Dempster, Francesco Iorio
A benchmark of computational methods for correcting biases of established and unknown origin in CRISPR-Cas9 screening data. Genome biology 25 (1) (2024)
Alessandro Vinceti, Raffaele M Iannuzzi, Isabella Boyle, Lucia Trastulla, Catarina D Campbell, Francisca Vazquez, Joshua M Dempster, Francesco Iorio
A benchmark of computational methods for correcting biases of established and unknown origin in CRISPR-Cas9 screening data. Genome biology 25 (1) (2024)
Qian Qin, Victoria Popic, Houlin Yu, Emily White, Akanksha Khorgade, Asa Shin, Kirsty Wienand, Arthur Dondi, Niko Beerenwinkel, Francisca Vazquez, Aziz M Al'Khafaji, Brian J Haas
CTAT-LR-fusion: accurate fusion transcript identification from long and short read isoform sequencing at bulk or single cell resolution. bioRxiv : the preprint server for biology (2024)
Marica Rosaria Ippolito, Johanna Zerbib, Yonatan Eliezer, Eli Reuveni, Sonia Viganò, Giuseppina De Feudis, Eldad David Shulman, Anouk Savir Kadmon, Rachel Slutsky, Tian-Gen Chang, Emma M Campagnolo, Silvia Taglietti, Simone Scorzoni, Sara Gianotti, Sara Martin, Julia Muenzner, Michael Mulleder, Nir Rozenblum, Carmela Rubolino, Tal Ben-Yishay, Kathrin Laue, Yael Cohen-Sharir, Ilaria Vigorito, Francesco Nicassio, Eytan Ruppin, Markus Ralser, Francisca Vazquez, Stefano Santaguida, Uri Ben-David
Increased RNA and protein degradation is required for counteracting transcriptional burden and proteotoxic stress in human aneuploid cells. Cancer discovery (2024)
Qian Qin, Victoria Popic, Houlin Yu, Emily White, Akanksha Khorgade, Asa Shin, Kirsty Wienand, Arthur Dondi, Niko Beerenwinkel, Francisca Vazquez, Aziz M AlKhafaji, Brian J Haas
CTAT-LR-fusion: accurate fusion transcript identification from long and short read isoform sequencing at bulk or single cell resolution. bioRxiv : the preprint server for biology (2024)
Lisa D Cervia, Tsukasa Shibue, Ashir A Borah, Benjamin Gaeta, Linh He, Lisa Leung, Naomi Li, Sydney M Moyer, Brian H Shim, Nancy Dumont, Alfredo E Gonzalez, Nolan R Bick, Mariya Kazachkova, Joshua M Dempster, John Michael Krill-Burger, Frederica Piccioni, Namrata D Udeshi, Meagan E Olive, Steven A Carr, David E Root, James M McFarland, Francisca Vazquez, William C Hahn
A Ubiquitination Cascade Regulating the Integrated Stress Response and Survival in Carcinomas. Cancer discovery 13 (3) (2023)
J Michael Krill-Burger, Joshua M Dempster, Ashir A Borah, Brenton R Paolella, David E Root, Todd R Golub, Jesse S Boehm, William C Hahn, James M McFarland, Francisca Vazquez, Aviad Tsherniak
Partial gene suppression improves identification of cancer vulnerabilities when CRISPR-Cas9 knockout is pan-lethal. Genome biology 24 (1) (2023)
Ricardo de Matos Simoes, Ryosuke Shirasaki, Sondra L Downey-Kopyscinski, Geoffrey M Matthews, Benjamin G Barwick, Vilas A Gupta, Daphné Dupéré-Richer, Shizuka Yamano, Yiguo Hu, Michal Sheffer, Eugen Dhimolea, Olga Dashevsky, Sara Gandolfi, Kazuya Ishiguro, Robin M Meyers, Jordan G Bryan, Neekesh V Dharia, Paul J Hengeveld, Johanna B Brüggenthies, Huihui Tang, Andrew J Aguirre, Quinlan L Sievers, Benjamin L Ebert, Brian J Glassner, Christopher J Ott, James E Bradner, Nicholas P Kwiatkowski, Daniel Auclair, Joan Levy, Jonathan J Keats, Richard W J Groen, Nathanael S Gray, Aedin C Culhane, James M McFarland, Joshua M Dempster, Jonathan D Licht, Lawrence H Boise, William C Hahn, Francisca Vazquez, Aviad Tsherniak, Constantine S Mitsiades
Genome-scale functional genomics identify genes preferentially essential for multiple myeloma cells compared to other neoplasias. Nature cancer 4 (5) (2023)
Lisa D Cervia, Tsukasa Shibue, Ashir A Borah, Benjamin Gaeta, Linh He, Lisa Leung, Naomi Li, Sydney M Moyer, Brian H Shim, Nancy Dumont, Alfredo E Gonzalez, Nolan R Bick, Mariya Kazachkova, Joshua M Dempster, John Michael Krill-Burger, Frederica Piccioni, Namrata D Udeshi, Meagan E Olive, Steven A Carr, David E Root, James M McFarland, Francisca Vazquez, William C Hahn
A Ubiquitination Cascade Regulating the Integrated Stress Response and Survival in Carcinomas. Cancer discovery 13 (3) (2023)
Lisa D Cervia, Tsukasa Shibue, Ashir A Borah, Benjamin Gaeta, Linh He, Lisa Leung, Naomi Li, Sydney M Moyer, Brian H Shim, Nancy Dumont, Alfredo E Gonzalez, Nolan R Bick, Mariya Kazachkova, Joshua M Dempster, John Michael Krill-Burger, Frederica Piccioni, Namrata D Udeshi, Meagan E Olive, Steven A Carr, David E Root, James M McFarland, Francisca Vazquez, William C Hahn
A Ubiquitination Cascade Regulating the Integrated Stress Response and Survival in Carcinomas. Cancer discovery 13 (3) (2023)
Hugh S Gannon, Tao Zou, Michael K Kiessling, Galen F Gao, Diana Cai, Peter S Choi, Alexandru P Ivan, Ilana Buchumenski, Ashton C Berger, Jonathan T Goldstein, Andrew D Cherniak, Francisca Vazquez, Aviad Tsherniak, Erez Y Levanon, William C Hahn, Matthew L Meyerson
Author Correction: Identification of ADAR1 adenosine deaminase dependency in a subset of cancer cells. Nature communications 13 (1) (2022)
Lisa D Cervia, Tsukasa Shibue, Ashir A Borah, Benjamin Gaeta, Linh He, Lisa Leung, Naomi Li, Sydney M Moyer, Brian H Shim, Nancy Dumont, Alfredo E Gonzalez, Nolan R Bick, Mariya Kazachkova, Joshua M Dempster, John Michael Krill-Burger, Frederica Piccioni, Namrata D Udeshi, Meagan E Olive, Steven A Carr, David E Root, James M McFarland, Francisca Vazquez, William C Hahn
A ubiquitination cascade regulating the integrated stress response and survival in carcinomas. Cancer discovery (2022)
Eshini Panditharatna, Joana G Marques, Tingjian Wang, Maria C Trissal, Ilon Liu, Li Jiang, Alexander Beck, Andrew Groves, Neekesh V Dharia, Deyao Li, Samantha E Hoffman, Guillaume Kugener, McKenzie L Shaw, Hafsa M Mire, Olivia A Hack, Joshua M Dempster, Caleb A Lareau, Lingling Dai, Logan H Sigua, Michael A Quezada, Ann-Catherine J Stanton, Meghan Wyatt, Zohra Kalani, Amy Goodale, Francisca Vazquez, Frederica Piccioni, John G Doench, David E Root, Jamie N Anastas, Kristen L Jones, Amy Saur Conway, Sylwia A Stopka, Michael S Regan, Yu Liang, Hyuk-Soo Seo, Kijun Song, Puspalata Bashyal, William P Jerome, Nathan D Mathewson, Sirano Dhe-Paganon, Mario L Suvà, Angel Montero Carcaboso, Cinzia Lavarino, Jaume Catala-Mora, Quang-De Nguyen, Keith L Ligon, Yang Shi, Sameer Agnihotri, Nathalie Y R Agar, Kimberly Stegmaier, Charles D Stiles, Michelle Monje, Todd R Golub, Jun Qi, Mariella G Filbin
BAF Complex Maintains Glioma Stem Cells in Pediatric H3K27M Glioma. Cancer discovery 12 (12) (2022)
Treg Grubb, Smruthi Maganti, John Michael Krill-Burger, Cameron S Fraser, Laura Stransky, Tomas Radivoyevitch, Kristopher A Sarosiek, Francisca Vazquez, William G Kaelin, Abhishek A Chakraborty
A Mesenchymal Tumor Cell State Confers Increased Dependency on the BCL-XL Antiapoptotic Protein in Kidney Cancer. Clinical cancer research : an official journal of the American Association for Cancer Research 28 (21) (2022)
Francisca Vazquez, William R Sellers
Are CRISPR Screens Providing the Next Generation of Therapeutic Targets? Cancer research 81 (23) (2022)
Daniel P Bondeson, Brenton R Paolella, Adhana Asfaw, Michael V Rothberg, Thomas A Skipper, Carly Langan, Gabriel Mesa, Alfredo Gonzalez, Lauren E Surface, Kentaro Ito, Mariya Kazachkova, William N Colgan, Allison Warren, Joshua M Dempster, John Michael Krill-Burger, Maria Ericsson, Andrew A Tang, Iris Fung, Emily S Chambers, Mai Abdusamad, Nancy Dumont, John G Doench, Federica Piccioni, David E Root, Jesse S Boehm, William C Hahn, Michael Mannstadt, James M McFarland, Francisca Vazquez, Todd R Golub
Phosphate dysregulation via the XPR1-KIDINS220 protein complex is a therapeutic vulnerability in ovarian cancer. Nature cancer 3 (6) (2022)
Riaz Gillani, Bo Kyung Alex Seong, Jett Crowdis, Jake R Conway, Neekesh V Dharia, Saif Alimohamed, Brian J Haas, Kyuho Han, Jihye Park, Felix Dietlein, Meng Xiao He, Alma Imamovic, Clement Ma, Michael C Bassik, Jesse S Boehm, Francisca Vazquez, Alexander Gusev, David R Liu, Katherine A Janeway, James M McFarland, Kimberly Stegmaier, Eliezer M Van Allen
Gene Fusions Create Partner and Collateral Dependencies Essential to Cancer Cell Survival. Cancer research 81 (15) (2021)
Allison Warren, Yejia Chen, Andrew Jones, Tsukasa Shibue, William C Hahn, Jesse S Boehm, Francisca Vazquez, Aviad Tsherniak, James M McFarland
Global computational alignment of tumor and cell line transcriptional profiles. Nature communications 12 (1) (2021)
Clare F Malone, Neekesh V Dharia, Guillaume Kugener, Alexandra B Forman, Michael V Rothberg, Mai Abdusamad, Alfredo Gonzalez, Miljan Kuljanin, Amanda L Robichaud, Amy Saur Conway, Joshua M Dempster, Brenton R Paolella, Nancy Dumont, Volker Hovestadt, Joseph D Mancias, Scott T Younger, David E Root, Todd R Golub, Francisca Vazquez, Kimberly Stegmaier
Selective Modulation of a Pan-Essential Protein as a Therapeutic Strategy in Cancer. Cancer discovery 11 (9) (2021)
Takahiro Ito, Michael J Young, Ruitong Li, Sidharth S Jain, Andreas Wernitznig, John Michael Krill-Burger, Christopher T Lemke, Davide Monducci, Diego J Rodriguez, Liang Chang, Sanjukta Dutta, Debjani Pal, Brenton R Paolella, Michael V Rothberg, David E Root, Cory M Johannessen, Laxmi Parida, Gad A Getz, Francisca Vazquez, John G Doench, Mahdi Zamanighomi, William R Sellers
Paralog knockout profiling identifies DUSP4 and DUSP6 as a digenic dependence in MAPK pathway-driven cancers. Nature genetics 53 (12) (2021)
Neekesh V Dharia, Guillaume Kugener, Lillian M Guenther, Clare F Malone, Adam D Durbin, Andrew L Hong, Thomas P Howard, Pratiti Bandopadhayay, Caroline S Wechsler, Iris Fung, Allison C Warren, Joshua M Dempster, John Michael Krill-Burger, Brenton R Paolella, Phoebe Moh, Nishant Jha, Andrew Tang, Phillip G Montgomery, Jesse S Boehm, William C Hahn, Charles W M Roberts, James M McFarland, Aviad Tsherniak, Todd R Golub, Francisca Vazquez, Kimberly Stegmaier
A first-generation pediatric cancer dependency map. Nature genetics 53 (4) (2021)
Francisca Vazquez, Jesse S Boehm
The Cancer Dependency Map enables drug mechanism-of-action investigations. Molecular systems biology 16 (7) (2020)
James M McFarland, Brenton R Paolella, Allison Warren, Kathryn R Geiger-Schuller, Tsukasa Shibue, Michael Rothberg, Olena Kuksenko, William N Colgan, Andrew Jones, Emily Chambers, Danielle Dionne, Samantha Bender, Brian M Wolpin, Mahmoud Ghandi, Itay Tirosh, Orit Rozenblatt-Rosen, Jennifer A Roth, Todd R Golub, Aviv Regev, Andrew J Aguirre, Francisca Vazquez, Aviad Tsherniak
Multiplexed single-cell transcriptional response profiling to define cancer vulnerabilities and therapeutic mechanism of action. Nature communications 11 (1) (2020)
Haoxin Li, Shaoyang Ning, Mahmoud Ghandi, Gregory V Kryukov, Shuba Gopal, Amy Deik, Amanda Souza, Kerry Pierce, Paula Keskula, Desiree Hernandez, Julie Ann, Dojna Shkoza, Verena Apfel, Yilong Zou, Francisca Vazquez, Jordi Barretina, Raymond A Pagliarini, Giorgio G Galli, David E Root, William C Hahn, Aviad Tsherniak, Marios Giannakis, Stuart L Schreiber, Andrew T Chan, Levi A Garraway, William R Sellers
The landscape of cancer cell line metabolism. Nature medicine 25 (5) (2019)
Pratiti Bandopadhayay, Frederica Piccioni, Ryan O'Rourke, Patricia Ho, Elizabeth M Gonzalez, Graham Buchan, Kenin Qian, Gabrielle Gionet, Emily Girard, Margo Coxon, Matthew G Rees, Lisa Brenan, Frank Dubois, Ofer Shapira, Noah F Greenwald, Melanie Pages, Amanda Balboni Iniguez, Brenton R Paolella, Alice Meng, Claire Sinai, Giovanni Roti, Neekesh V Dharia, Amanda Creech, Benjamin Tanenbaum, Prasidda Khadka, Adam Tracy, Hong L Tiv, Andrew L Hong, Shannon Coy, Rumana Rashid, Jia-Ren Lin, Glenn S Cowley, Fred C Lam, Amy Goodale, Yenarae Lee, Kathleen Schoolcraft, Francisca Vazquez, William C Hahn, Aviad Tsherniak, James E Bradner, Michael B Yaffe, Till Milde, Stefan M Pfister, Jun Qi, Monica Schenone, Steven A Carr, Keith L Ligon, Mark W Kieran, Sandro Santagata, James M Olson, Prafulla C Gokhale, Jacob D Jaffe, David E Root, Kimberly Stegmaier, Cory M Johannessen, Rameen Beroukhim
Neuronal differentiation and cell-cycle programs mediate response to BET-bromodomain inhibition in MYC-driven medulloblastoma. Nature communications 10 (1) (2019)
Xiaofeng Wang, Su Wang, Emma C Troisi, Thomas P Howard, Jeffrey R Haswell, Bennett K Wolf, William H Hawk, Pilar Ramos, Elaine M Oberlick, Evgeni P Tzvetkov, Aaron Ross, Francisca Vazquez, William C Hahn, Peter J Park, Charles W M Roberts
Author Correction: BRD9 defines a SWI/SNF sub-complex and constitutes a specific vulnerability in malignant rhabdoid tumors. Nature communications 10 (1) (2019)
Joshua M Dempster, Clare Pacini, Sasha Pantel, Fiona M Behan, Thomas Green, John Michael Krill-Burger, Charlotte M Beaver, Scott T Younger, Victor Zhivich, Hanna Najgebauer, Felicity Allen, Emanuel Gonçalves, Rebecca Shepherd, John G Doench, Kosuke Yusa, Francisca Vazquez, Leopold Parts, Jesse S Boehm, Todd R Golub, William C Hahn, David E Root, Mathew J Garnett, Aviad Tsherniak, Francesco Iorio
Agreement between two large pan-cancer CRISPR-Cas9 gene dependency data sets. Nature communications 10 (1) (2019)
Colles Price, Stanley Gill, Zandra V Ho, Shawn M Davidson, Erin Merkel, James M McFarland, Lisa Leung, Andrew Tang, Maria Kost-Alimova, Aviad Tsherniak, Oliver Jonas, Francisca Vazquez, William C Hahn
Genome-Wide Interrogation of Human Cancers Identifies EGLN1 Dependency in Clear Cell Ovarian Cancers. Cancer research 79 (10) (2019)
Thomas P Howard, Taylor E Arnoff, Melinda R Song, Andrew O Giacomelli, Xiaofeng Wang, Andrew L Hong, Neekesh V Dharia, Su Wang, Francisca Vazquez, Minh-Tam Pham, Ann M Morgan, Franziska Wachter, Gregory H Bird, Guillaume Kugener, Elaine M Oberlick, Matthew G Rees, Hong L Tiv, Justin H Hwang, Katherine H Walsh, April Cook, John Michael Krill-Burger, Aviad Tsherniak, Prafulla C Gokhale, Peter J Park, Kimberly Stegmaier, Loren D Walensky, William C Hahn, Charles W M Roberts
MDM2 and MDM4 Are Therapeutic Vulnerabilities in Malignant Rhabdoid Tumors. Cancer research 79 (9) (2019)
Xiaofeng Wang, Su Wang, Emma C Troisi, Thomas P Howard, Jeffrey R Haswell, Bennett K Wolf, William H Hawk, Pilar Ramos, Elaine M Oberlick, Evgeni P Tzvetkov, Aaron Ross, Francisca Vazquez, William C Hahn, Peter J Park, Charles W M Roberts
BRD9 defines a SWI/SNF sub-complex and constitutes a specific vulnerability in malignant rhabdoid tumors. Nature communications 10 (1) (2019)
Tanaz Sharifnia, Mathias J Wawer, Ting Chen, Qing-Yuan Huang, Barbara A Weir, Ann Sizemore, Matthew A Lawlor, Amy Goodale, Glenn S Cowley, Francisca Vazquez, Christopher J Ott, Joshua M Francis, Slim Sassi, Patricia Cogswell, Hadley E Sheppard, Tinghu Zhang, Nathanael S Gray, Paul Andrew Clarke, Julian Blagg, Paul Workman, Josh Sommer, Francis Hornicek, David E Root, William C Hahn, James E Bradner, Kwok K Wong, Paul A Clemons, Charles Y Lin, Joanne D Kotz, Stuart L Schreiber
Small-molecule targeting of brachyury transcription factor addiction in chordoma. Nature medicine 25 (2) (2019)
Adam D Durbin, Mark W Zimmerman, Neekesh V Dharia, Brian J Abraham, Amanda Balboni Iniguez, Nina Weichert-Leahey, Shuning He, John M Krill-Burger, David E Root, Francisca Vazquez, Aviad Tsherniak, William C Hahn, Todd R Golub, Richard A Young, A Thomas Look, Kimberly Stegmaier
Selective gene dependencies in MYCN-amplified neuroblastoma include the core transcriptional regulatory circuitry. Nature genetics 50 (9) (2018)
Hugh S Gannon, Tao Zou, Michael K Kiessling, Galen F Gao, Diana Cai, Peter S Choi, Alexandru P Ivan, Ilana Buchumenski, Ashton C Berger, Jonathan T Goldstein, Andrew D Cherniak, Francisca Vazquez, Aviad Tsherniak, Erez Y Levanon, William C Hahn, Matthew L Meyerson
Identification of ADAR1 adenosine deaminase dependency in a subset of cancer cells. Nature communications 9 (1) (2018)
Andrew O Giacomelli, Xiaoping Yang, Robert E Lintner, James M McFarland, Marc Duby, Jaegil Kim, Thomas P Howard, David Y Takeda, Seav Huong Ly, Eejung Kim, Hugh S Gannon, Brian Hurhula, Ted Sharpe, Amy Goodale, Briana Fritchman, Scott Steelman, Francisca Vazquez, Aviad Tsherniak, Andrew J Aguirre, John G Doench, Frederica Piccioni, Charles W M Roberts, Matthew L Meyerson, Gad A Getz, Cory M Johannessen, David E Root, William C Hahn
Mutational processes shape the landscape of TP53 mutations in human cancer. Nature genetics 50 (10) (2018)