Publications

The single-cell opioid responses in the context of HIV (SCORCH) consortium

2024. Mol Psychiatry.

Seth A. Ament, Rianne R. Campbell, Mary Kay Lobo, Joseph P. Receveur, Kriti Agrawal, Alejandra Borjabad, Siddappa N. Byrareddy, Linda Chang, Declan Clarke, Prashant Emani, Dana Gabuzda, Kyle J. Gaulton, Michelle Giglio, Federico M. Giorgi, Busra Gok, Chittibabu Guda, Eran Hadas, Brian R. Herb, Wen Hu, Anita Huttner, Mohammad R. Ishmam, Michelle M. Jacobs, Jennifer Kelschenbach, Dong-Wook Kim, Cheyu Lee, Shuhui Liu, Xiaokun Liu, Bertha K. Madras, Anup A. Mahurkar, Deborah C. Mash, Eran A. Mukamel, Meng Niu, Richard M. O’Connor, Chelsea M. Pagan, Alina P. S. Pang, Piya Pillai, Vez Repunte-Canonigo, W. Brad Ruzicka, Jay Stanley, Timothy Tickle, Shang-Yi A. Tsai, Allen Wang, Lauren Wills, Alyssa M. Wilson, Susan N. Wright, Siwei Xu, Junchen Yang, Maryam Zand, Le Zhang, Jing Zhang, Schahram Akbarian, Shilpa Buch, Christine S. Cheng, Michael J. Corley, Howard S. Fox, Mark Gerstein, Suryaram Gummuluru, Myriam Heiman, Ya-Chi Ho, Manolis Kellis, Paul J. Kenny, Yuval Kluger, Teresa A. Milner, David J. Moore, Susan Morgello, Lishomwa C. Ndhlovu, Tariq M. Rana, Pietro Paolo Sanna, John S. Satterlee, Nenad Sestan, Stephen A. Spector, Serena Spudich, Hagen U. Tilgner, David J. Volsky, Owen R. White, Dionne W. Williams & Hongkui Zeng. PMID: 38879719

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: 36525955

Filgotinib 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: 32573496

The 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: 34578439

The 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: 33165008

Shock-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: 33758027

Neuropathogenesis of HIV-1: insights from across the spectrum of acute through long-term treated infection.

2022. Seminars in immunopathology.

Killingsworth, Lauren; Spudich, Serena. PMID: 35882661

Single-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: 35320704

Inhibition 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: 35730977

HIV Compartmentalization in the CNS and Its Impact in Treatment Outcomes and Cure Strategies.

2022. Current HIV/AIDS reports.

Chan, Phillip; Spudich, Serena. PMID: 35536438

The loud minority: Transcriptionally active HIV-1-infected cells survive, proliferate, and persist.

2022. Cell.

Collora, Jack A; Ho, Ya-Chi. PMID: 35063069

Buprenorphine 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: 36275760

HIV 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: 35801589

Induction 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: 35288582

Coming Soon

Morphine 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: 36466814

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: 36525955

Detection 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: 34001664

Computation 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: 35264704

Induction 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: 35288582

Single-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: 35256815

Zero-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: 35017482

Forest 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: 35725981

Graph 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: 33780435

SCAN-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: 36227018

Deep unsupervised feature selection by discarding nuisance and correlated features.

2022. Neural Networks.

Shaham, Uri; Lindenbaum, Ofir; Svirsky, Jonathan; Kluger, Yuval. PMID: 35500458

Spectral 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: 34124606

The Spectral Underpinning of word2vec.

2020. Frontiers in applied mathematics and statistics.

Jaffe, Ariel; Kluger, Yuval; Lindenbaum, Ofir; Patsenker, Jonathan; Peterfreund, Erez; Steinerberger, Stefan. PMID: 34504892

Doubly 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: 34124607

Molecular 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