Bouhaddou Lab Publications

June 3, 2025.

Kareem Alba, Declan M. Winters, Sara K. Makanani, Prashant Kaushal, Yennifer Delgado, Immy A. Ashley, Shipra Sharma, Sophie F. Blanc, Erin Kim, Tomer Yaron, Jared L. Johnson, Justin Selby, Min Hur, Jocelyn Ni, Jasmine Nguyen, Marc H. Brent, Elaine Yip, Ahmad Kassem, James Wohlschlegel, Oliver I. Fregoso, Ting-Ting Wu, Melody MH Li, Mehdi Bouhaddou. 2025. “Global Landscape of Human Kinase Motifs in Viral Proteomes.” bioRxiv.

June 7, 2025.

Charles Ochieng’ Olwal, Ujjwal Rathore, Sara Makanani, Prashant Kaushal, Immy A. Ashley, Manisha R. Ummadi, Vincent Appiah, Alexandra Lindsey Djomkam Zune, Sophie Blanc, Declan Winters, Yennifer Delgado, Kapten Muthoka, Jacqueline M. Fabius, Manon Eckhardt, Robyn M. Kaake, Maureen Su, Oliver I. Fregoso, Judd F. Hultquist, Elkanah Omenge Orang’o, Danielle L. Swaney, George Boateng Kyei, Nevan J. Krogan, Peter Kojo Quashie, Yaw Bediako, Mehdi Bouhaddou. 2025. “Paracrine Signals from HIV-1 Infected Immune Cells Reprogram Cervical Cancer Pathways.“ bioRxiv.

May 15, 2024.

Prashant Kaushal, Manisha R. Ummadi, Gwendolyn M. Jang, Yennifer Delgado, Sara K. Makanani, Sophie F. Blanc, Decan M. Winters, Jiewei Xu, Benjamin Polacco, Yuan Zhou, Erica Stevenson, Manon Eckhardt, Lorena Zuliani-Alvarez, Robyn Kaake, Danielle L. Swaney, Nevan Krogan, Mehdi Bouhaddou. 2024. “Mapping Differential Protein-Protein Interaction Networks using Affinity Purification Mass Spectrometry.” STAR Protocols.

Sept 21, 2023. Volume 186, Issue 21, p4597-4614.e26

Bouhaddou M, Reuschl AK, Polacco BJ, Thorne LG, Ummadi MR, Ye C, Rosales R, Adrian Pelin, Jyoti Batra, Gwendolyn M. Jang, Jiewei Xu, Jack M. Moen, Alicia L. Richards, Yuan Zhou, Bhavya Harjai, Erica Stevenson, Ajda Rojc, Roberta Ragazzini, Matthew V.X. Whelan, Wilhelm Furnon, Giuditta De Lorenzo, Vanessa Cowton, Abdullah M. Syed, Alison Ciling, Noa Deutsch, Nevan J. Krogan, 2024. “SARS-CoV-2 variants evolve convergent strategies to remodel the host response.” Cell

Dec 23, 2021. Volume 602, Issue 7898, p487–495

Lucy G. Thorne, Mehdi Bouhaddou, Ann-Kathrin Reuschl, Lorena Zuliani-Alvarez, Ben Polacco, Adrian Pelin, Jyoti Batra, Matthew V. X. Whelan, Myra Hosmillo, Andrea Fossati, Roberta Ragazzini, Irwin Jungreis, Manisha Ummadi, Ajda Rojc, Jane Turner, Marie L. Bischof, Kirsten Obernier, Hannes Braberg, Margaret Soucheray, Alicia Richards, Kuei-Ho Chen, Bhavya Harjai, Danish Memon, Joseph Hiatt, …Nevan J. Krogan, 2022. “Evolution of Enhanced Innate Immune Evasion by SARS-CoV-2.” Nature

Oct 22, 2021. Volume 6, Issue 20

Mehdi Bouhaddou, Rex H. Lee, Hua Li, Neil E. Bhola, Rachel A. O’Keefe, Mohammad Naser, Tian Ran Zhu, Kelechi Nwachuku, Umamaheswar Duvvuri, Adam B. Olshen, Ritu Roy, Aaron Hechmer, Jennifer Bolen, Stephen B. Keysar, Antonio Jimeno, Gordon B. Mills, Scott Vandenberg, Danielle L. Swaney, Daniel E. Johnson, Nevan J. Krogan, Jennifer R. Grandis, 2021. “Caveolin-1 and Sox-2 Are Predictive Biomarkers of Cetuximab Response in Head and Neck Cancer.” JCI Insight

Oct 1, 2021. Volume 374, Issue 6563

Minkyu Kim, Jisoo Park, Mehdi Bouhaddou, Kyumin Kim, Ajda Rojc, Maya Modak, Margaret Soucheray, Michael J. McGregor, Patrick O’Leary, Denise Wolf, Erica Stevenson, Tzeh Keong Foo, Dominique Mitchell, Kari A. Herrington, Denise P. Muñoz, Beril Tutuncuoglu, Kuei-Ho Chen, Fan Zheng, Jason F. Kreisberg, Morgan E. Diolaiti, John D. Gordan, Jean-Philippe Coppé, Danielle L. Swaney, Bing Xia, Laura van ’t Veer, Alan Ashworth, Trey Ideker, Nevan J. Krogan, 2021. “A Protein Interaction Landscape of Breast Cancer.” Science

Jan 07, 2021. Volume 184, Issue 1, p106-119.e14

Ruofan Wang, Camille R. Simoneau, Jessie Kulsuptrakul, Mehdi Bouhaddou, Katherine A. Travisano, Jennifer M. Hayashi, Jared Carlson-Stevermer, James R. Zengel, Christopher M. Richards, Parinaz Fozouni, Jennifer Oki, Lauren Rodriguez, Bastian Joehnk, Keith Walcott, Kevin Holden, Anita Sil, Jan E. Carette, Nevan J. Krogan, Melanie Ott, Andreas S. Puschnik , 2021. “Genetic Screens Identify Host Factors for SARS-CoV-2 and Common Cold Coronaviruses.” Cell

Oct 15, 2020. Volume 270, Issue 6521

David E. Gordon, Joseph Hiatt, Mehdi Bouhaddou, Veronica V. Rezelj, Svenja Ulferts, Hannes Braberg, Alexander S. Jureka, Kirsten Obernier, Jeffrey Z. Guo, Jyoti Batra, Robyn M. Kaake, Andrew R. Weckstein, Tristan W. Owens, Meghna Gupta, Sergei Pourmal, Erron W. Titus, Merve Cakir, Margaret Soucheray, Michael McGregor, Zeynep Cakir, Gwendolyn Jang, Matthew J. O’Meara, Tia A. Tummino, Ziyang Zhang, Helene Foussard, Ajda Rojc, Dmitry Kuchenov, Ruth Hüttenhain, …, Nevan J. Krogan, 2020. “Comparative Host-Coronavirus Protein Interaction Networks Reveal Pan-Viral Disease Mechanisms.” Science

Aug 06, 2020. Volume 182, Issue 3, p533-786

Mehdi Bouhaddou, Danish Memon, Bjoern Meyer, Kris M. White, Veronica V. Rezelj, Miguel Correa Marrero, Benjamin J. Polacco, James E. Melnyk 21, Svenja Ulferts, Robyn M. Kaake, Jyoti Batra, Alicia L. Richards, Erica Stevenson, David E. Gordon, Ajda Rojc, Kirsten Obernier, Jacqueline M. Fabius, Margaret Soucheray, Lisa Miorin, Elena Moreno, Cassandra Koh, …, Nevan J. Krogan, 2020. “The Global Phosphorylation Landscape of SARS-CoV-2 Infection.” Cell

Apr 30, 2020. Volume 583, Issue 7816, p459–468

David E. Gordon, Gwendolyn M. Jang, Mehdi Bouhaddou, Jiewei Xu, Kirsten Obernier, Kris M. White, Matthew J. O’Meara, Veronica V. Rezelj, Jeffrey Z. Guo, Danielle L. Swaney, Tia A. Tummino, Ruth Hüttenhain, Robyn M. Kaake, Alicia L. Richards, Beril Tutuncuoglu, Helene Foussard, Jyoti Batra, Kelsey Haas, Maya Modak, Minkyu Kim, Paige Haas, Benjamin J. Polacco, Hannes Braberg, Jacqueline M. Fabius, Manon Eckhardt, Margaret Soucheray, Melanie J. Bennett, Merve Cakir, Michael J. McGregor, Qiongyu Li, …, Nevan J. Krogan, 2020. “A SARS-CoV-2 Protein Interaction Map Reveals Targets for Drug Repurposing.” Nature

Mar 26, 2018.

Mehdi Bouhaddou, Anne Marie Barrette, Alan D. Stern, Rick J. Koch, Matthew S. DiStefano, Eric A. Riesel, Luis C. Santos, Annie L. Tan, Alex E. Mertz, and Marc R. Birtwistle. 2018. “A Mechanistic Pan-Cancer Pathway Model Informed by Multi-Omics Data Interprets Stochastic Cell Fate Responses to Drugs and Mitogens.” PLoS Computational Biology

Collaborative Publications

  1. Arjit Vijey Jeyachandran, Anne K. Zaiss, Nikhil Chakravarty, Sneha Singh, Yennifer Delgado, Ramya Paravastu, Nivedha Satheeshkumar, Ephrem Gerald, Aakash Jeysankar, Joshua Thomas, Lilly Fuller, Noella Lee, Cameron Taylor, Shantanu Joshi, Mark Parcells, Samuel W. French, Abhijit Date, Mehdi Bouhaddou, Gustavo Garcia Jr, Ashok Kumar, Robert Damoiseaux and Vaithilingaraja Arumugaswami. ”Drug screen reveals new potent host-targeted antivirals against Mpox virus.” May 7, 2025. bioRxiv. Link

  2. Pablo A. Alvarez, Ashley Tang, Declan M. Winters, Prashant Kaushal, Angelica Medina, Karolina E. Kaczor-Urbanowicz, Bryan Ramirez Reyes, Robyn M. Kaake, Oliver I. Fregoso, April D. Pyle, Mehdi Bouhaddou, Hengli Tang and Melody M.H. Li. “Old World alphaviruses use distinct mechanisms to infect brain microvascular endothelial cells for neuroinvasion.” Jan 24, 2025. bioRxiv. Link

  3. Karly A Nisson, Rishi S Patel, Yennifer Delgado, Mehdi Bouhaddou, Lucie Etienne and Oliver I Fregoso. “HIV Vpr activates a nucleolar-specific ATR pathway to degrade the nucleolar stress sensor CCDC137.” Sep 13, 2024. bioRxiv. Link

  4. Zhenlan Yao, Sangeetha Ramachandran, Serina Huang, Erin Kim, Yasaman Jami-Alahmadi, Prashant Kaushal, Mehdi Bouhaddou, James A Wohlschlegel, and Melody MH Li. Sep 11, 2024. “Interaction of chikungunya virus glycoproteins with macrophage factors controls virion production.” EMBO J. Link

  5. Ryu, J. K., Yan, Z., Montano, M., Sozmen, E. G., Dixit, K., Suryawanshi, R. K., Matsui, Y., Helmy, E., Kaushal, P., Makanani, S. K., Deerinck, T. J., Meyer-Franke, A., Rios Coronado, P. E., Trevino, T. N., Shin, M. G., Tognatta, R., Liu, Y., Schuck, R., Le, L., Miyajima, H., Bouhaddou, M.,… Akassoglou, K. “Fibrin drives thromboinflammation and neuropathology in COVID-19.” Aug 28, 2024. Nature. Link

For a full list of publications, check out our Google Scholar page.