| Year |
Citation |
Score |
| 2024 |
Rathore U, Haas P, Easwar Kumar V, Hiatt J, Haas KM, Bouhaddou M, Swaney DL, Stevenson E, Zuliani-Alvarez L, McGregor MJ, Turner-Groth A, Ochieng' Olwal C, Bediako Y, Braberg H, Soucheray M, et al. CRISPR-Cas9 screen of E3 ubiquitin ligases identifies TRAF2 and UHRF1 as regulators of HIV latency in primary human T cells. Mbio. e0222223. PMID 38411080 DOI: 10.1128/mbio.02222-23 |
0.714 |
|
| 2023 |
Wang B, Vartak R, Zaltsman Y, Naing ZZC, Hennick KM, Polacco BJ, Bashir A, Eckhardt M, Bouhaddou M, Xu J, Sun N, Lasser M, Zhou Y, Guiley KZ, Chan U, et al. A foundational atlas of autism protein interactions reveals molecular convergence. Biorxiv : the Preprint Server For Biology. PMID 38076945 DOI: 10.1101/2023.12.03.569805 |
0.676 |
|
| 2023 |
Meyers NL, Ashuach T, Lyons DE, Khalid MM, Simoneau CR, Erickson AL, Bouhaddou M, Nguyen TT, Kumar GR, Taha TY, Natarajan V, Baron JL, Neff N, Zanini F, Mahmoudi T, et al. Hepatitis C virus infects and perturbs liver stem cells. Mbio. e0131823. PMID 37938000 DOI: 10.1128/mbio.01318-23 |
0.398 |
|
| 2023 |
Haas KM, McGregor MJ, Bouhaddou M, Polacco BJ, Kim EY, Nguyen TT, Newton BW, Urbanowski M, Kim H, Williams MAP, Rezelj VV, Hardy A, Fossati A, Stevenson EJ, Sukerman E, et al. Proteomic and genetic analyses of influenza A viruses identify pan-viral host targets. Nature Communications. 14: 6030. PMID 37758692 DOI: 10.1038/s41467-023-41442-z |
0.757 |
|
| 2023 |
Kehrer T, Cupic A, Ye C, Yildiz S, Bouhaddou M, Crossland NA, Barrall EA, Cohen P, Tseng A, Çağatay T, Rathnasinghe R, Flores D, Jangra S, Alam F, Mena I, et al. Impact of SARS-CoV-2 ORF6 and its variant polymorphisms on host responses and viral pathogenesis. Cell Host & Microbe. PMID 37738983 DOI: 10.1016/j.chom.2023.08.003 |
0.556 |
|
| 2023 |
Bouhaddou M, Reuschl AK, Polacco BJ, Thorne LG, Ummadi MR, Ye C, Rosales R, Pelin A, Batra J, Jang GM, Xu J, Moen JM, Richards AL, Zhou Y, Harjai B, et al. SARS-CoV-2 variants evolve convergent strategies to remodel the host response. Cell. PMID 37738970 DOI: 10.1016/j.cell.2023.08.026 |
0.717 |
|
| 2023 |
Mendiola AS, Yan Z, Dixit K, Johnson JR, Bouhaddou M, Meyer-Franke A, Shin MG, Yong Y, Agrawal A, MacDonald E, Muthukumar G, Pearce C, Arun N, Cabriga B, Meza-Acevedo R, et al. Defining blood-induced microglia functions in neurodegeneration through multiomic profiling. Nature Immunology. PMID 37291385 DOI: 10.1038/s41590-023-01522-0 |
0.459 |
|
| 2023 |
Muralidharan M, Krogan NJ, Bouhaddou M, Kim M. Current proteomics methods applicable to dissecting the DNA damage response. Nar Cancer. 5: zcad020. PMID 37213254 DOI: 10.1093/narcan/zcad020 |
0.441 |
|
| 2023 |
Olwal CO, Fabius JM, Zuliani-Alvarez L, Eckhardt M, Kyei GB, Quashie PK, Krogan NJ, Bouhaddou M, Bediako Y. Network modeling suggests HIV infection phenocopies PI3K-AKT pathway mutations to enhance HPV-associated cervical cancer. Molecular Omics. PMID 37204043 DOI: 10.1039/d3mo00025g |
0.412 |
|
| 2023 |
Chan GKL, Maisel S, Hwang YC, Pascual BC, Wolber RRB, Vu P, Patra KC, Bouhaddou M, Kenerson HL, Lim HC, Long D, Yeung RS, Sethupathy P, Swaney DL, Krogan NJ, et al. Oncogenic PKA signaling increases c-MYC protein expression through multiple targetable mechanisms. Elife. 12. PMID 36692000 DOI: 10.7554/eLife.69521 |
0.464 |
|
| 2022 |
Kuchina A, Yang J, Aldridge B, Janes KA, Subramanian N, Krogan NJ, Bouhaddou M, Einav S, Papin J, Germain RN. How can systems approaches help us understand and treat infectious disease? Cell Systems. 13: 945-949. PMID 36549272 DOI: 10.1016/j.cels.2022.11.009 |
0.374 |
|
| 2022 |
Sarmah D, Smith GR, Bouhaddou M, Stern AD, Erskine J, Birtwistle MR. Network inference from perturbation time course data. Npj Systems Biology and Applications. 8: 42. PMID 36316338 DOI: 10.1038/s41540-022-00253-6 |
0.545 |
|
| 2022 |
Erdem C, Mutsuddy A, Bensman EM, Dodd WB, Saint-Antoine MM, Bouhaddou M, Blake RC, Gross SM, Heiser LM, Feltus FA, Birtwistle MR. A scalable, open-source implementation of a large-scale mechanistic model for single cell proliferation and death signaling. Nature Communications. 13: 3555. PMID 35729113 DOI: 10.1038/s41467-022-31138-1 |
0.585 |
|
| 2022 |
Hiatt J, Hultquist JF, McGregor MJ, Bouhaddou M, Leenay RT, Simons LM, Young JM, Haas P, Roth TL, Tobin V, Wojcechowskyj JA, Woo JM, Rathore U, Cavero DA, Shifrut E, et al. A functional map of HIV-host interactions in primary human T cells. Nature Communications. 13: 1752. PMID 35365639 DOI: 10.1038/s41467-022-29346-w |
0.467 |
|
| 2022 |
Thorne LG, Bouhaddou M, Reuschl AK, Zuliani-Alvarez L, Polacco B, Pelin A, Batra J, Whelan MVX, Hosmillo M, Fossati A, Ragazzini R, Jungreis I, Ummadi M, Rojc A, Turner J, et al. Publisher Correction: Evolution of enhanced innate immune evasion by SARS-CoV-2. Nature. PMID 35332335 DOI: 10.1038/s41586-022-04653-w |
0.746 |
|
| 2022 |
Walz AC, Van De Vyver AJ, Yu L, Birtwistle MR, Krogan NJ, Bouhaddou M. Leveraging modeling and simulation to optimize the therapeutic window for epigenetic modifier drugs. Pharmacology & Therapeutics. 235: 108162. PMID 35189161 DOI: 10.1016/j.pharmthera.2022.108162 |
0.668 |
|
| 2022 |
Escalera A, Gonzalez-Reiche AS, Aslam S, Mena I, Laporte M, Pearl RL, Fossati A, Rathnasinghe R, Alshammary H, van de Guchte A, Farrugia K, Qin Y, Bouhaddou M, Kehrer T, Zuliani-Alvarez L, et al. Mutations in SARS-CoV-2 variants of concern link to increased spike cleavage and virus transmission. Cell Host & Microbe. PMID 35150638 DOI: 10.1016/j.chom.2022.01.006 |
0.47 |
|
| 2022 |
Varona JF, Landete P, Lopez-Martin JA, Estrada V, Paredes R, Guisado-Vasco P, Fernandez de Orueta L, Torralba M, Fortun J, Vates R, Barberan J, Clotet B, Ancochea J, Carnevali D, Cabello N, ... ... Bouhaddou M, et al. Preclinical and randomized phase I studies of plitidepsin in adults hospitalized with COVID-19. Life Science Alliance. 5. PMID 35012962 DOI: 10.26508/lsa.202101200 |
0.428 |
|
| 2021 |
Thorne LG, Bouhaddou M, Reuschl AK, Zuliani-Alvarez L, Polacco B, Pelin A, Batra J, Whelan MVX, Hosmillo M, Fossati A, Ragazzini R, Jungreis I, Ummadi M, Rojc A, Turner J, et al. Evolution of enhanced innate immune evasion by SARS-CoV-2. Nature. PMID 34942634 DOI: 10.1038/s41586-021-04352-y |
0.776 |
|
| 2021 |
Swaney DL, Ramms DJ, Wang Z, Park J, Goto Y, Soucheray M, Bhola N, Kim K, Zheng F, Zeng Y, McGregor M, Herrington KA, O'Keefe R, Jin N, VanLandingham NK, ... ... Bouhaddou M, et al. A protein network map of head and neck cancer reveals PIK3CA mutant drug sensitivity. Science (New York, N.Y.). 374: eabf2911. PMID 34591642 DOI: 10.1126/science.abf2911 |
0.445 |
|
| 2021 |
Kim M, Park J, Bouhaddou M, Kim K, Rojc A, Modak M, Soucheray M, McGregor MJ, O'Leary P, Wolf D, Stevenson E, Foo TK, Mitchell D, Herrington KA, Muñoz DP, et al. A protein interaction landscape of breast cancer. Science (New York, N.Y.). 374: eabf3066. PMID 34591612 DOI: 10.1126/science.abf3066 |
0.402 |
|
| 2021 |
Bouhaddou M, Lee RH, Li H, Bhola NE, O'Keefe RA, Naser M, Zhu TR, Nwachuku K, Duvvuri U, Olshen AB, Roy R, Hechmer A, Bolen J, Keysar SB, Jimeno A, et al. Caveolin-1 and Sox-2 are predictive biomarkers of cetuximab response in head and neck cancer. Jci Insight. PMID 34546978 DOI: 10.1172/jci.insight.151982 |
0.451 |
|
| 2021 |
Thorne LG, Bouhaddou M, Reuschl AK, Zuliani-Alvarez L, Polacco B, Pelin A, Batra J, Whelan MVX, Ummadi M, Rojc A, Turner J, Obernier K, Braberg H, Soucheray M, Richards A, et al. Evolution of enhanced innate immune evasion by the SARS-CoV-2 B.1.1.7 UK variant. Biorxiv : the Preprint Server For Biology. PMID 34127972 DOI: 10.1101/2021.06.06.446826 |
0.77 |
|
| 2021 |
Varona JF, Landete P, Lopez-Martin JA, Estrada V, Paredes R, Guisado-Vasco P, de Orueta LF, Torralba M, Fortún J, Vates R, Barberán J, Clotet B, Ancochea J, Carnevali D, Cabello N, ... ... Bouhaddou M, et al. Plitidepsin has a positive therapeutic index in adult patients with COVID-19 requiring hospitalization. Medrxiv : the Preprint Server For Health Sciences. PMID 34075384 DOI: 10.1101/2021.05.25.21257505 |
0.405 |
|
| 2021 |
Verba K, Gupta M, Azumaya C, Moritz M, Pourmal S, Diallo A, Merz G, Jang G, Bouhaddou M, Fossati A, Brilot A, Diwanji D, Hernandez E, Herrera N, Kratochvil H, et al. CryoEM and AI reveal a structure of SARS-CoV-2 Nsp2, a multifunctional protein involved in key host processes. Research Square. PMID 34031651 DOI: 10.21203/rs.3.rs-515215/v1 |
0.514 |
|
| 2021 |
Gupta M, Azumaya CM, Moritz M, Pourmal S, Diallo A, Merz GE, Jang G, Bouhaddou M, Fossati A, Brilot AF, Diwanji D, Hernandez E, Herrera N, Kratochvil HT, Lam VL, et al. CryoEM and AI reveal a structure of SARS-CoV-2 Nsp2, a multifunctional protein involved in key host processes. Biorxiv : the Preprint Server For Biology. PMID 34013269 DOI: 10.1101/2021.05.10.443524 |
0.514 |
|
| 2021 |
Reuschl AK, Thorne L, Zuliani Alvarez L, Bouhaddou M, Obernier K, Soucheray M, Turner J, Fabius J, Nguyen GT, Swaney D, Rosales R, White KM, Aviles P, Kirby IT, Melnyk JE, et al. Host-directed therapies against early-lineage SARS-CoV-2 retain efficacy against B.1.1.7 variant. Biorxiv : the Preprint Server For Biology. PMID 33501437 DOI: 10.1101/2021.01.24.427991 |
0.532 |
|
| 2021 |
White KM, Rosales R, Yildiz S, Kehrer T, Miorin L, Moreno E, Jangra S, Uccellini MB, Rathnasinghe R, Coughlan L, Martinez-Romero C, Batra J, Rojc A, Bouhaddou M, Fabius JM, et al. Plitidepsin has potent preclinical efficacy against SARS-CoV-2 by targeting the host protein eEF1A. Science (New York, N.Y.). PMID 33495306 DOI: 10.1126/science.abf4058 |
0.539 |
|
| 2020 |
Wang R, Simoneau CR, Kulsuptrakul J, Bouhaddou M, Travisano KA, Hayashi JM, Carlson-Stevermer J, Zengel JR, Richards CM, Fozouni P, Oki J, Rodriguez L, Joehnk B, Walcott K, Holden K, et al. Genetic Screens Identify Host Factors for SARS-CoV-2 and Common Cold Coronaviruses. Cell. PMID 33333024 DOI: 10.1016/j.cell.2020.12.004 |
0.517 |
|
| 2020 |
Gordon DE, Hiatt J, Bouhaddou M, Rezelj VV, Ulferts S, Braberg H, Jureka AS, Obernier K, Guo JZ, Batra J, Kaake RM, Weckstein AR, Owens TW, Gupta M, Pourmal S, et al. Comparative host-coronavirus protein interaction networks reveal pan-viral disease mechanisms. Science (New York, N.Y.). PMID 33060197 DOI: 10.1126/science.abe9403 |
0.78 |
|
| 2020 |
Wang R, Simoneau CR, Kulsuptrakul J, Bouhaddou M, Travisano K, Hayashi JM, Carlson-Stevermer J, Oki J, Holden K, Krogan NJ, Ott M, Puschnik AS. Functional genomic screens identify human host factors for SARS-CoV-2 and common cold coronaviruses. Biorxiv : the Preprint Server For Biology. PMID 32995787 DOI: 10.1101/2020.09.24.312298 |
0.515 |
|
| 2020 |
Bouhaddou M, Memon D, Meyer B, White KM, Rezelj VV, Correa Marrero M, Polacco BJ, Melnyk JE, Ulferts S, Kaake RM, Batra J, Richards AL, Stevenson E, Gordon DE, Rojc A, et al. The Global Phosphorylation Landscape of SARS-CoV-2 Infection. Cell. PMID 32645325 DOI: 10.1016/J.Cell.2020.06.034 |
0.695 |
|
| 2020 |
Gordon DE, Jang GM, Bouhaddou M, Xu J, Obernier K, O'Meara MJ, Guo JZ, Swaney DL, Tummino TA, Hüttenhain R, Kaake RM, Richards AL, Tutuncuoglu B, Foussard H, Batra J, et al. A SARS-CoV-2-Human Protein-Protein Interaction Map Reveals Drug Targets and Potential Drug-Repurposing. Biorxiv : the Preprint Server For Biology. PMID 32511329 DOI: 10.1101/2020.03.22.002386 |
0.789 |
|
| 2020 |
Tutuncuoglu B, Cakir M, Batra J, Bouhaddou M, Eckhardt M, Gordon DE, Krogan NJ. The Landscape of Human Cancer Proteins Targeted by SARS-CoV-2. Cancer Discovery. PMID 32444466 DOI: 10.1158/2159-8290.Cd-20-0559 |
0.582 |
|
| 2020 |
Gordon DE, Jang GM, Bouhaddou M, Xu J, Obernier K, White KM, O'Meara MJ, Rezelj VV, Guo JZ, Swaney DL, Tummino TA, Huettenhain R, Kaake RM, Richards AL, Tutuncuoglu B, et al. A SARS-CoV-2 protein interaction map reveals targets for drug repurposing. Nature. PMID 32353859 DOI: 10.1038/S41586-020-2286-9 |
0.786 |
|
| 2019 |
Bouhaddou M, Yu LJ, Lunardi S, Stamatelos SK, Mack F, Gallo JM, Birtwistle MR, Walz AC. Predicting In Vivo Efficacy from In Vitro Data: Quantitative Systems Pharmacology Modeling for an Epigenetic Modifier Drug in Cancer. Clinical and Translational Science. PMID 31729169 DOI: 10.1111/Cts.12727 |
0.634 |
|
| 2019 |
Bouhaddou M, Eckhardt M, Chi Naing ZZ, Kim M, Ideker T, Krogan NJ. Mapping the protein-protein and genetic interactions of cancer to guide precision medicine. Current Opinion in Genetics & Development. 54: 110-117. PMID 31288129 DOI: 10.1016/J.Gde.2019.04.005 |
0.534 |
|
| 2018 |
Holzapfel HY, Stern AD, Bouhaddou M, Anglin C, Putur D, Comer S, Birtwistle M. Fluorescence Multiplexing with Spectral Imaging and Combinatorics. Acs Combinatorial Science. PMID 30339749 DOI: 10.1021/Acscombsci.8B00101 |
0.565 |
|
| 2018 |
Koch RJ, Barrette AM, Stern AD, Hu B, Bouhaddou M, Azeloglu EU, Iyengar R, Birtwistle MR. Validating Antibodies for Quantitative Western Blot Measurements with Microwestern Array. Scientific Reports. 8: 11329. PMID 30054510 DOI: 10.1038/S41598-018-29436-0 |
0.575 |
|
| 2018 |
Bouhaddou M, Barrette AM, Stern AD, Koch RJ, DiStefano MS, Riesel EA, Santos LC, Tan AL, Mertz AE, Birtwistle MR. A mechanistic pan-cancer pathway model informed by multi-omics data interprets stochastic cell fate responses to drugs and mitogens. Plos Computational Biology. 14: e1005985. PMID 29579036 DOI: 10.1371/Journal.Pcbi.1005985 |
0.639 |
|
| 2018 |
Jones DC, Scanteianu A, DiStefano M, Bouhaddou M, Birtwistle MR. Analysis of copy number loss of the ErbB4 receptor tyrosine kinase in glioblastoma. Plos One. 13: e0190664. PMID 29342193 DOI: 10.1371/Journal.Pone.0190664 |
0.624 |
|
| 2017 |
Xiong Y, Soumillon M, Wu J, Hansen J, Hu B, van Hasselt JGC, Jayaraman G, Lim R, Bouhaddou M, Ornelas L, Bochicchio J, Lenaeus L, Stocksdale J, Shim J, Gomez E, et al. A Comparison of mRNA Sequencing with Random Primed and 3'-Directed Libraries. Scientific Reports. 7: 14626. PMID 29116112 DOI: 10.1038/S41598-017-14892-X |
0.601 |
|
| 2017 |
Barrette AM, Bouhaddou M, Birtwistle MR. Integrating Transcriptomic Data with Mechanistic Systems Pharmacology Models for Virtual Drug Combination Trials. Acs Chemical Neuroscience. PMID 28950062 DOI: 10.1021/Acschemneuro.7B00197 |
0.654 |
|
| 2017 |
Bouhaddou M, Barrette AM, Koch RJ, Birtwistle MR. Abstract 1568: Predicting stochastic proliferation and death in response to drugs with mechanistic models tailored to genomic, transcriptomic, and proteomic data Cancer Research. 77: 1568-1568. DOI: 10.1158/1538-7445.Am2017-1568 |
0.641 |
|
| 2016 |
Bouhaddou M, DiStefano MS, Riesel EA, Carrasco E, Holzapfel HY, Jones DC, Smith GR, Stern AD, Somani SS, Thompson TV, Birtwistle MR. Drug response consistency in CCLE and CGP. Nature. 540: E9-E10. PMID 27905419 DOI: 10.1038/Nature20580 |
0.61 |
|
| 2015 |
Benitez AA, Spanko LA, Bouhaddou M, Sachs D, tenOever BR. Engineered Mammalian RNAi Can Elicit Antiviral Protection that Negates the Requirement for the Interferon Response. Cell Reports. PMID 26549455 DOI: 10.1016/J.Celrep.2015.10.020 |
0.401 |
|
| 2014 |
Bouhaddou M, Birtwistle MR. Dimerization-based control of cooperativity. Molecular Biosystems. 10: 1824-32. PMID 24736836 DOI: 10.1039/C4Mb00022F |
0.59 |
|
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