Publications
Publications by the SCORCH consortium are separated below by topic areas. Click on the topic area of interest to expand the list of publications.
HIV integration in the human brain is linked to microglial activation and 3D genome remodeling.
2023. Mol Cell.
Plaza-Jennings, Amara; Valada, Aditi; O'Shea, Callan; Iskhakova, Marina; Hu, Benxia; Javidfar, Behnam; Hutta, Gabriella Ben; Lambert, Tova Y; Murray, Jacinta; Kassim, Bibi; Chandrasekaran, Sandhya; Chen, Benjamin K; Morgello, Susan; Won, Hyejung; Akbarian, Schahram. PMID: 36525955Filgotinib suppresses HIV-1-driven gene transcription by inhibiting HIV-1 splicing and T cell activation.
2020. The Journal of Clinical Investigation.
Yeh, Yang-Hui Jimmy; Jenike, Katharine M; Calvi, Rachela M; Chiarella, Jennifer; Hoh, Rebecca; Deeks, Steven G; Ho, Ya-Chi. PMID: 32573496The Clonal Expansion Dynamics of the HIV-1 Reservoir: Mechanisms of Integration Site-Dependent Proliferation and HIV-1 Persistence.
2021. Viruses.
Yeh, Yang-Hui Jimmy; Yang, Kerui; Razmi, Anya; Ho, Ya-Chi. PMID: 34578439The single-cell landscape of immunological responses of CD4+ T cells in HIV versus severe acute respiratory syndrome coronavirus 2.
2021. Current opinion in HIV and AIDS.
Collora, Jack A; Liu, Runxia; Albrecht, Kristen; Ho, Ya-Chi. PMID: 33165008Shock-and-kill versus block-and-lock: Targeting the fluctuating and heterogeneous HIV-1 gene expression.
2021. Proceedings of the National Academy of Sciences of the United States of America.
Yeh, Yang-Hui Jimmy; Ho, Ya-Chi. PMID: 33758027Neuropathogenesis of HIV-1: insights from across the spectrum of acute through long-term treated infection.
2022. Seminars in immunopathology.
Killingsworth, Lauren; Spudich, Serena. PMID: 35882661Single-cell multiomics reveals persistence of HIV-1 in expanded cytotoxic Tcell clones.
2022. Immunity.
Collora, Jack A; Liu, Runxia; Pinto-Santini, Delia; Ravindra, Neal; Ganoza, Carmela; Lama, Javier R; Alfaro, Ricardo; Chiarella, Jennifer; Spudich, Serena; Mounzer, Karam; Tebas, Pablo; Montaner, Luis J; van Dijk, David; Duerr, Ann; Ho, Ya-Chi. PMID: 35320704Inhibition of a Chromatin and Transcription Modulator, SLTM, Increases HIV-1 Reactivation Identified by a CRISPR Inhibition Screen.
2022. Journal of virology.
Pedersen, Savannah F; Collora, Jack A; Kim, Rachel N; Yang, Kerui; Razmi, Anya; Catalano, Allison A; Yeh, Yang-Hui Jimmy; Mounzer, Karam; Tebas, Pablo; Montaner, Luis J; Ho, Ya-Chi. PMID: 35730977HIV Compartmentalization in the CNS and Its Impact in Treatment Outcomes and Cure Strategies.
2022. Current HIV/AIDS reports.
Chan, Phillip; Spudich, Serena. PMID: 35536438The loud minority: Transcriptionally active HIV-1-infected cells survive, proliferate, and persist.
2022. Cell.
Collora, Jack A; Ho, Ya-Chi. PMID: 35063069Buprenorphine reverses neurocognitive impairment in EcoHIV infected mice: A potential therapy for HIV-NCI.
2022. Frontiers in immunology.
Murphy, Aniella J; Kelschenbach, Jennifer; He, Hongxia; Chao, Wei; Kim, Boe-Hyun; Volsky, David J; Berman, Joan W. PMID: 36275760HIV viral transcription and immune perturbations in the CNS of people with HIV despite ART.
2022. JCI insight.
Farhadian, Shelli F; Lindenbaum, Ofir; Zhao, Jun; Corley, Michael J; Im, Yunju; Walsh, Hannah; Vecchio, Alyssa; Garcia-Milian, Rolando; Chiarella, Jennifer; Chintanaphol, Michelle; Calvi, Rachela; Wang, Guilin; Ndhlovu, Lishomwa C; Yoon, Jennifer; Trotta, Diane; Ma, Shuangge; Kluger, Yuval; Spudich, Serena. PMID: 35801589Induction of an immortalized songbird cell line allows for gene characterization and knockout by CRISPR-Cas9.
2022. Scientific reports.
Biegler, Matthew T; Fedrigo, Olivier; Collier, Paul; Mountcastle, Jacquelyn; Haase, Bettina; Tilgner, Hagen U; Jarvis, Erich D. PMID: 35288582Morphine suppresses peripheral responses and transforms brain myeloid gene expression to favor neuropathogenesis in SIV infection
2022. Front. Immunol.
Fox, Howard S.; Niu, Meng; Morsey, Brenda M.; Lamberty, Benjamin G.; Emanuel, Katy; Perlyasamy, Palsamy; Callen, Shannon; Acharya, Arpan; Kubik, Gregory; Eudy, James; Guda, Chittibabu; Dyavar, Shetty Ravi, Fletcher, Courtney V.; Byrareddy, Siddappa N.; Buch, Shilpa. PMID: 36466814HIV integration in the human brain is linked to microglial activation and 3D genome remodeling.
2023. Mol Cell.
Plaza-Jennings, Amara; Valada, Aditi; O'Shea, Callan; Iskhakova, Marina; Hu, Benxia; Javidfar, Behnam; Hutta, Gabriella Ben; Lambert, Tova Y; Murray, Jacinta; Kassim, Bibi; Chandrasekaran, Sandhya; Chen, Benjamin K; Morgello, Susan; Won, Hyejung; Akbarian, Schahram. PMID: 36525955Detection of differentially abundant cell subpopulations in scRNA-seq data.
2021. Proceedings of the National Academy of Sciences of the United States of America.
Zhao, Jun; Jaffe, Ariel; Li, Henry; Lindenbaum, Ofir; Sefik, Esen; Jackson, Ruaidhrí; Cheng, Xiuyuan; Flavell, Richard A; Kluger, Yuval . PMID: 34001664Computation and visualization of cell-cell signaling topologies in single-cell systems data using Connectome.
2022. Scientific reports.
Raredon, Micha Sam Brickman; Yang, Junchen; Garritano, James; Wang, Meng; Kushnir, Dan; Schupp, Jonas Christian; Adams, Taylor S; Greaney, Allison M; Leiby, Katherine L; Kaminski, Naftali; Kluger, Yuval; Levchenko, Andre; Niklason, Laura E. PMID: 35264704Induction of an immortalized songbird cell line allows for gene characterization and knockout by CRISPR-Cas9.
2022. Scientific reports.
Biegler, Matthew T; Fedrigo, Olivier; Collier, Paul; Mountcastle, Jacquelyn; Haase, Bettina; Tilgner, Hagen U; Jarvis, Erich D. PMID: 35288582Single-nuclei isoform RNA sequencing unlocks barcoded exon connectivity in frozen brain tissue.
2022. Nature biotechnology.
Hardwick, Simon A; Hu, Wen; Joglekar, Anoushka; Fan, Li; Collier, Paul G; Foord, Careen; Balacco, Jennifer; Lanjewar, Samantha; Sampson, Maureen McGuirk; Koopmans, Frank; Prjibelski, Andrey D; Mikheenko, Alla; Belchikov, Natan; Jarroux, Julien; Lucas, Anne Bergstrom; Palkovits, Miklós; Luo, Wenjie; Milner, Teresa A; Ndhlovu, Lishomwa C; Smit, August B; Trojanowski, John Q; Lee, Virginia M Y; Fedrigo, Olivier; Sloan, Steven A; Tombácz, Dóra; Ross, M Elizabeth; Jarvis, Erich; Boldogkői, Zsolt; Gan, Li; Tilgner, Hagen U. PMID: 35256815Zero-preserving imputation of single-cell RNA-seq data.
2022. Nature communications.
Linderman, George C; Zhao, Jun; Roulis, Manolis; Bielecki, Piotr; Flavell, Richard A; Nadler, Boaz; Kluger, Yuval. PMID: 35017482Forest Fire Clustering for single-cell sequencing combines iterative label propagation with parallelized Monte Carlo simulations.
2022. Nature communications.
Chen, Zhanlin; Goldwasser, Jeremy;, Philip; Liu, Jason; Zhang, Jing; Gerstein, Mark. PMID: 35725981Graph of graphs analysis for multiplexed data with application to imaging mass cytometry.
2021. PLoS computational biology.
Lin, Ya-Wei Eileen; Shnitzer, Tal; Talmon, Ronen; Villarroel-Espindola, Franz; Desai, Shruti; Schalper, Kurt; Kluger, Yuval. PMID: 33780435SCAN-IT: Domain segmentation of spatial transcriptomics images by graph neural network.
2021. BMVC : Proceddings of the British Machine Vision Conference.
Cang, Zixuan; Ning, Xinyi; Nie, Annika; Xu, Min; Zhang, Jing. PMID: 36227018Deep unsupervised feature selection by discarding nuisance and correlated features.
2022. Neural Networks.
Shaham, Uri; Lindenbaum, Ofir; Svirsky, Jonathan; Kluger, Yuval. PMID: 35500458Spectral neighbor joining for reconstruction of latent tree Models.
2021. SIAM journal on mathematics of data science.
Jaffe, Ariel; Amsel, Noah; Aizenbud, Yariv; Nadler, Boaz; Chang, Joseph T; Kluger, Yuval. PMID: 34124606The Spectral Underpinning of word2vec.
2020. Frontiers in applied mathematics and statistics.
Jaffe, Ariel; Kluger, Yuval; Lindenbaum, Ofir; Patsenker, Jonathan; Peterfreund, Erez; Steinerberger, Stefan. PMID: 34504892Doubly Stochastic Normalization of the Gaussian Kernel Is Robust to Heteroskedastic Noise.
2021. SIAM journal on mathematics of data science.
Landa, Boris; Coifman, Ronald R; Kluger, Yuval. PMID: 34124607Molecular and cellular evolution of the primate dorsolateral prefrontal cortex.
2022. Science.
Ma, Shaojie; Skarica, Mario; Li, Qian; Xu, Chuan; Risgaard, Ryan D; Tebbenkamp, Andrew T N; Mato-Blanco, Xoel; Kovner, Rothem; Krsnik, Željka; de Martin, Xabier; Luria, Victor; Martí-Pérez, Xavier; Liang, Dan; Karger, Amir; Schmidt, Danielle K; Gomez-Sanchez, Zachary; Qi, Cai; Gobeske, Kevin T; Pochareddy, Sirisha; Debnath, Ashwin; Hottman, Cade J; Spurrier, Joshua; Teo, Leon; Boghdadi, Anthony G; Homman-Ludiye, Jihane; Ely, John J; Daadi, Etienne W; Mi, Da; Daadi, Marcel; Marín, Oscar; Hof, Patrick R; Rasin, Mladen-Roko; Bourne, James; Sherwood, Chet C; Santpere, Gabriel; Girgenti, Matthew J; Strittmatter, Stephen M; Sousa, André M M; Sestan, Nenad. PMID: 36007006
