Publications
Publications by the SCORCH consortium are separated below by topic areas. SCORCH preprints on bioRxiv can be viewed here. Click on the topic area of interest to expand the list of publications.
The single-cell opioid responses in the context of HIV (SCORCH) consortium
2024.
Molecular psychiatry Ament, Seth A; Campbell, Rianne R; Lobo, Mary Kay; Receveur, Joseph P; Agrawal, Kriti; Borjabad, Alejandra; Byrareddy, Siddappa N; Chang, Linda; Clarke, Declan; Emani, Prashant; Gabuzda, Dana; Gaulton, Kyle J; Giglio, Michelle; Giorgi, Federico M; Gok, Busra; Guda, Chittibabu; Hadas, Eran; Herb, Brian R; Hu, Wen; Huttner, Anita; Ishmam, Mohammad R; Jacobs, Michelle M; Kelschenbach, Jennifer; Kim, Dong-Wook; Lee, Cheyu; Liu, Shuhui; Liu, Xiaokun; Madras, Bertha K; Mahurkar, Anup A; Mash, Deborah C; Mukamel, Eran A; Niu, Meng; O'Connor, Richard M; Pagan, Chelsea M; Pang, Alina P S; Pillai, Piya; Repunte-Canonigo, Vez; Ruzicka, W Brad; Stanley, Jay; Tickle, Timothy; Tsai, Shang-Yi A; Wang, Allen; Wills, Lauren; Wilson, Alyssa M; Wright, Susan N; Xu, Siwei; Yang, Junchen; Zand, Maryam; Zhang, Le; Zhang, Jing; Akbarian, Schahram; Buch, Shilpa; Cheng, Christine S; Corley, Michael J; Fox, Howard S; Gerstein, Mark; Gummuluru, Suryaram; Heiman, Myriam; Ho, Ya-Chi; Kellis, Manolis; Kenny, Paul J; Kluger, Yuval; Milner, Teresa A; Moore, David J; Morgello, Susan; Ndhlovu, Lishomwa C; Rana, Tariq M; Sanna, Pietro Paolo; Satterlee, John S; Sestan, Nenad; Spector, Stephen A; Spudich, Serena; Tilgner, Hagen U; Volsky, David J; White, Owen R; Williams, Dionne W; Zeng, Hongkui. PMID: 38879719Sex disparities in outcome of medication-assisted therapy of opioid use disorder: Nationally representative outpatient clinic data
2025.
Drug and alcohol dependence Butelman, Eduardo R; Huang, Yuefeng; McFarlane, Alicia; Slattery, Carolann; Goldstein, Rita Z; Volkow, Nora D; Alia-Klein, Nelly. PMID: 39788040A master regulator of opioid reward in the ventral prefrontal cortex
2024.
Science (New York, N.Y.) Smith, Alexander C W; Ghoshal, Soham; Centanni, Samuel W; Heyer, Mary P; Corona, Alberto; Wills, Lauren; Andraka, Emma; Lei, Ye; O'Connor, Richard M; Caligiuri, Stephanie P B; Khan, Sohail; Beaumont, Kristin; Sebra, Robert P; Kieffer, Brigitte L; Winder, Danny G; Ishikawa, Masago; Kenny, Paul J. PMID: 38843332Serum cytokines and inflammatory proteins in individuals with heroin use disorder: potential mechanistically based biomarkers for diagnosis
2024.
Translational psychiatry Butelman, Eduardo R; Huang, Yuefeng; Cathomas, Flurin; Gaudreault, Pierre-Olivier; Roussos, Panos; Russo, Scott J; Goldstein, Rita Z; Alia-Klein, Nelly. PMID: 39362849Drug Metabolism and Transport Capacity of Endothelial Cells, Pericytes, and Astrocytes: Implications for CNS Drug Disposition
2024.
bioRxiv : the preprint server for biology Wilkins, Hannah N; Knerler, Stephen A; Warshanna, Ahmed; Ortiz, Rodnie Colón; Haas, Kate; Orsburn, Benjamin C; Williams, Dionna W. PMID: 39149336Establishment of a Four-Cell In Vitro Blood-Brain Barrier Model With Human Primary Brain Cells
2024.
Current protocols Malik, Johid R; Modebelu, Ukamaka O; Fletcher, Courtney V; Podany, Anthony T; Scarsi, Kimberly K; Byrareddy, Siddappa N; Anand, Robbyn K; Buch, Shilpa; Sil, Susmia; Le, Jennifer; Bradley, John S; Brown, Ashley N; Sutar, Debapriya; Avedissian, Sean N. PMID: 38857108Overdose mortality rates for opioids and stimulant drugs are substantially higher in men than in women: state-level analysis
2023.
Neuropsychopharmacology : official publication of the American College of Neuropsychopharmacology Butelman, Eduardo R; Huang, Yuefeng; Epstein, David H; Shaham, Yavin; Goldstein, Rita Z; Volkow, Nora D; Alia-Klein, Nelly. PMID: 37316576Neuroimmune Mechanisms of Opioid Use Disorder and Recovery: Translatability to Human Studies, and Future Research Directions
2023.
Neuroscience Butelman, Eduardo R; Goldstein, Rita Z; Nwaneshiudu, Chinwe A; Girdhar, Kiran; Roussos, Panos; Russo, Scott J; Alia-Klein, Nelly. PMID: 37562536Cocaine Regulates Antiretroviral Therapy CNS Access Through Pregnane-X Receptor-Mediated Drug Transporter and Metabolizing Enzyme Modulation at the Blood Brain Barrier
2023.
bioRxiv : the preprint server for biology Fridman, Lisa B; Knerler, Stephen; Price, Amira-Storm; Ortiz, Rodnie Colón; Mercado, Alicia; Wilkins, Hannah; Flores, Bianca R; Orsburn, Benjamin C; Williams, Dionna W. PMID: 37546800Hedgehog-interacting protein acts in the habenula to regulate nicotine intake
2022.
Proceedings of the National Academy of Sciences of the United States of America Caligiuri, Stephanie P B; Howe, William M; Wills, Lauren; Smith, Alexander C W; Lei, Ye; Bali, Purva; Heyer, Mary P; Moen, Janna K; Ables, Jessica L; Elayouby, Karim S; Williams, Maya; Fillinger, Clementine; Oketokoun, Zainab; Lehmann, Vanessa E; DiFeliceantonio, Alexandra G; Johnson, Paul M; Beaumont, Kristin; Sebra, Robert P; Ibanez-Tallon, Ines; Kenny, Paul J. PMID: 36346845Principled PCA separates signal from noise in omics count data
2025.
bioRxiv : the preprint server for biology Stanley 3rd, Jay S; Yang, Junchen; Li, Ruiqi; Lindenbaum, Ofir; Kobak, Dmitry; Landa, Boris; Kluger, Yuval. PMID: 39975320Cluster-independent multiscale marker identification in single-cell RNA-seq data using localized marker detector (LMD)
2025.
Communications biology Li, Ruiqi; Qu, Rihao; Parisi, Fabio; Strino, Francesco; Lam, Hainan; Stanley 3rd, Jay S; Cheng, Xiuyuan; Myung, Peggy; Kluger, Yuval. PMID: 40670619Gene trajectory inference for single-cell data by optimal transport metrics
2025.
Nature biotechnology Qu, Rihao; Cheng, Xiuyuan; Sefik, Esen; Stanley Iii, Jay S; Landa, Boris; Strino, Francesco; Platt, Sarah; Garritano, James; Odell, Ian D; Coifman, Ronald; Flavell, Richard A; Myung, Peggy; Kluger, Yuval. PMID: 38580861SIMVI disentangles intrinsic and spatial-induced cellular states in spatial omics data
2025.
Nature communications Dong, Mingze; Su, David G; Kluger, Harriet; Fan, Rong; Kluger, Yuval. PMID: 40148341The Dyson equalizer: adaptive noise stabilization for low-rank signal detection and recovery
2025.
Information and inference : a journal of the IMA Landa, Boris; Kluger, Yuval. PMID: 39830802Leveraging single-cell spatial transcriptomics and connectomics to resolve brain circuit function in psychiatry
2025.
Neuropsychopharmacology : official publication of the American College of Neuropsychopharmacology Claypool, Sarah M; Kenny, Paul J. PMID: 40721521Spatial isoform sequencing at sub-micrometer single-cell resolution reveals novel patterns of spatial isoform variability in brain cell types
2025.
bioRxiv : the preprint server for biology Michielsen, Lieke; Prjibelski, Andrey; Foord, Careen; Hu, Wen; Jarroux, Julien; Hsu, Justine; Tomescu, Alexandru; Hajirasouliha, Iman; Tilgner, Hagen. PMID: 40667010Quantitative Economon Model of Transactions for Drugs and Other Commodities
2025.
bioRxiv : the preprint server for biology Haynes, Jeremy M; da Rosa, Joel Correa; Butelman, Eduardo R; Hursh, Steven R; Negus, S Stevens. PMID: 40672322SIMVI reveals intrinsic and spatial-induced states in spatial omics data
2024.
bioRxiv : the preprint server for biology Dong, Mingze; Su, David; Kluger, Harriet; Fan, Rong; Kluger, Yuval. PMID: 37693629Scaling deep identifiable models enables zero-shot characterization of single-cell biological states
2024.
bioRxiv : the preprint server for biology Dong, Mingze; Agrawal, Kriti; Fan, Rong; Sefik, Esen; Flavell, Richard A; Kluger, Yuval. PMID: 38014345FABEL: Forecasting Animal Behavioral Events with Deep Learning-Based Computer Vision
2024.
bioRxiv : the preprint server for biology Catto, Adam; O'Connor, Richard; Braunscheidel, Kevin M; Kenny, Paul J; Shen, Li. PMID: 38559273Hypometric genetics: Improved power in genetic discovery by incorporating quality control flags
2024.
American journal of human genetics Tanigawa, Yosuke; Kellis, Manolis. PMID: 39442521A polygenic score method boosted by non-additive models
2024.
Nature communications Ohta, Rikifumi; Tanigawa, Yosuke; Suzuki, Yuta; Kellis, Manolis; Morishita, Shinichi. PMID: 38811555Understanding isoform expression by pairing long-read sequencing with single-cell and spatial transcriptomics
2024.
Genome research Belchikov, Natan; Hsu, Justine; Li, Xiang Jennie; Jarroux, Julien; Hu, Wen; Joglekar, Anoushka; Tilgner, Hagen U. PMID: 39567235Comprehensive visualization of cell-cell interactions in single-cell and spatial transcriptomics with NICHES
2023.
Bioinformatics (Oxford, England) Raredon, Micha Sam Brickman; Yang, Junchen; Kothapalli, Neeharika; Lewis, Wesley; Kaminski, Naftali; Niklason, Laura E; Kluger, Yuval. PMID: 36458905Power of inclusion: Enhancing polygenic prediction with admixed individuals
2023.
American journal of human genetics Tanigawa, Yosuke; Kellis, Manolis. PMID: 37890495The variables on RNA molecules: concert or cacophony? Answers in long-read sequencing
2023.
Nature methods Foord, Careen; Hsu, Justine; Jarroux, Julien; Hu, Wen; Belchikov, Natan; Pollard, Shaun; He, Yi; Joglekar, Anoushka; Tilgner, Hagen U. PMID: 36635536Computation 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: 35264704Zero-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: 35017482Biwhitening Reveals the Rank of a Count Matrix
2022.
SIAM journal on mathematics of data science Landa, Boris; Zhang, Thomas T C K; Kluger, Yuval. PMID: 37576699Forest Fire Clustering for single-cell sequencing combines iterative label propagation with parallelized Monte Carlo simulations
2022.
Nature communications Chen, Zhanlin; Goldwasser, Jeremy; Tuckman, Philip; Liu, Jason; Zhang, Jing; Gerstein, Mark. PMID: 35725981Deep unsupervised feature selection by discarding nuisance and correlated features
2022.
Neural networks : the official journal of the International Neural Network Society Shaham, Uri; Lindenbaum, Ofir; Svirsky, Jonathan; Kluger, Yuval. PMID: 35500458DeepVelo: Single-cell transcriptomic deep velocity field learning with neural ordinary differential equations
2022.
Science advances Chen, Zhanlin; King, William C; Hwang, Aheyon; Gerstein, Mark; Zhang, Jing. PMID: 36449617Venus: An efficient virus infection detection and fusion site discovery method using single-cell and bulk RNA-seq data
2022.
PLoS computational biology Lee, Che Yu; Chen, Yuhang; Duan, Ziheng; Xu, Min; Girgenti, Matthew J; Xu, Ke; Gerstein, Mark; Zhang, Jing. PMID: 36301997Induction 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: 35288582Doubly 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: 34124607Graph 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: 33780435Spectral 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: 34124606Detection 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: 34001664SCAN-IT: Domain segmentation of spatial transcriptomics images by graph neural network
2021.
BMVC : proceedings of the British Machine Vision Conference. British Machine Vision Conference Cang, Zixuan; Ning, Xinyi; Nie, Annika; Xu, Min; Zhang, Jing. PMID: 36227018The Spectral Underpinning of word2vec
2020.
Frontiers in applied mathematics and statistics Jaffe, Ariel; Kluger, Yuval; Lindenbaum, Ofir; Patsenker, Jonathan; Peterfreund, Erez; Steinerberger, Stefan. PMID: 34504892Multi-omic Characterization of HIV Effects at Single Cell Level across Human Brain Regions
2025.
bioRxiv : the preprint server for biology Yang, Junchen; Agrawal, Kriti; Stanley 3rd, Jay; Li, Ruiqi; Jacobs, Nicholas; Wang, Haowei; Lu, Chang; Qu, Rihao; Clarke, Declan; Chen, Yuhang; Jiang, Yunzhe; Bai, Donglu; Zheng, Suchen; Fox, Howard; Ho, Ya-Chi; Huttner, Anita; Gerstein, Mark; Kluger, Yuval; Zhang, Le; Spudich, Serena. PMID: 39975288T cell-mediated SIV dissemination into the CNS: a single-cell transcriptomic analysis
2025.
Research square Xu, Xiaoke; Niu, Meng; Lamberty, Benjamin G; Emanuel, Katy; Estrella, L Daniel; Fox, Howard S. PMID: 40386405Transformation of brain myeloid cell populations by SIV in rhesus macaques revealed by multiomics
2025.
Communications biology Xu, Xiaoke; Niu, Meng; Lamberty, Benjamin G; Emanuel, Katy; Apostol, Moses Jedd Facun; Fox, Howard S. PMID: 39838075Central Nervous System Effects of Early HIV Infection and Consequences of Antiretroviral Therapy Initiation during Acute HIV
2024.
Viruses Chan, Phillip; Spudich, Serena. PMID: 39066244BACH2-driven tissue resident memory programs promote HIV-1 persistence
2024.
bioRxiv : the preprint server for biology Wei, Yulong; Ma, Haocong Katherine; Wong, Michelle E; Papasavvas, Emmanouil; Konnikova, Liza; Tebas, Pablo; Morgenstern, Ricardo; Montaner, Luis J; Ho, Ya-Chi. PMID: 39763845EcoHIV Infection of Primary Murine Brain Cell Cultures to Model HIV Replication and Neuropathogenesis
2024.
Viruses Kim, Boe-Hyun; Chao, Wei; Hadas, Eran; Borjabad, Alejandra; Potash, Mary Jane; Volsky, David J. PMID: 38793575Innate immune responses reverse HIV cognitive disease in mice: Profile by RNAseq in the brain
2024.
Virology Borjabad, Alejandra; Dong, Baojun; Chao, Wei; Volsky, David J; Potash, Mary Jane. PMID: 37951088Microglia and macrophages alterations in the CNS during acute SIV infection: A single-cell analysis in rhesus macaques
2024.
PLoS pathogens Xu, Xiaoke; Niu, Meng; Lamberty, Benjamin G; Emanuel, Katy; Ramachandran, Shawn; Trease, Andrew J; Tabassum, Mehnaz; Lifson, Jeffrey D; Fox, Howard S. PMID: 39283947All Blood Brain Barrier Cell Types Demonstrate Capability to Influence Differential Tenofovir and Emtricitabine Metabolism and Transport in the Brain
2024.
ACS pharmacology & translational science Wilkins, Hannah N; Knerler, Stephen A; Warshanna, Ahmed; Colón Ortiz, Rodnie; Haas, Kate; Orsburn, Benjamin C; Williams, Dionna W. PMID: 39539261A Transcriptional Signature of Induced Neurons Differentiates Virologically Suppressed People Living With HIV from People Without HIV
2024.
bioRxiv : the preprint server for biology Ostermann, Philipp N; Wu, Youjun; Bowler, Scott A; Siddiqui, Mohammad Adnan; Herrera, Alberto; Sidharta, Mega; Ramnarine, Kiran; Martínez-Meza, Samuel; St Bernard, Leslie Ann; Nixon, Douglas F; Jones, R Brad; Yamashita, Masahiro; Ndhlovu, Lishomwa C; Zhou, Ting; Evering, Teresa H. PMID: 39484396Integration site-dependent HIV-1 promoter activity shapes host chromatin conformation
2023.
Genome research Collora, Jack A; Ho, Ya-Chi. PMID: 37295842Single-cell epigenetic, transcriptional, and protein profiling of latent and active HIV-1 reservoir revealed that IKZF3 promotes HIV-1 persistence
2023.
Immunity Wei, Yulong; Davenport, Timothy C; Collora, Jack A; Ma, Haocong Katherine; Pinto-Santini, Delia; Lama, Javier; Alfaro, Ricardo; Duerr, Ann; Ho, Ya-Chi. PMID: 37922905Biotypes of Central Nervous System Complications in People With Human Immunodeficiency Virus: Virology, Immunology, and Neuropathology
2023.
The Journal of infectious diseases Joseph, Sarah B; Gianella, Sara; Burdo, Tricia H; Cinque, Paola; Gisslen, Magnus; Letendre, Scott; Nath, Avindra; Morgello, Susan; Ndhlovu, Lishomwa C; Spudich, Serena. PMID: 36930640Single-cell multiomic understanding of HIV-1 reservoir at epigenetic, transcriptional, and protein levels
2023.
Current opinion in HIV and AIDS Wong, Michelle; Wei, Yulong; Ho, Ya-Chi. PMID: 37535039CCL2 is required for initiation but not persistence of HIV infection mediated neurocognitive disease in mice
2023.
Scientific reports Kim, Boe-Hyun; Hadas, Eran; Kelschenbach, Jennifer; Chao, Wei; Gu, Chao-Jiang; Potash, Mary Jane; Volsky, David J. PMID: 37085605Protocol for optimizing production and quality control of infective EcoHIV virions
2023.
STAR protocols Alfar, Hammodah R; Pariser, Daphne N; Chanzu, Harry; Joshi, Smita; Coenen, Daniëlle M; Lykins, Joshua; Prakhya, Kanakanagavalli Shravani; Potash, Mary Jane; Chao, Wei; Kelschenbach, Jennifer; Volsky, David J; Metcalf-Pate, Kelly; Whiteheart, Sidney W. PMID: 37342907The latent HIV reservoir: current advances in genetic sequencing approaches
2023.
mBio Moar, Preeti; Premeaux, Thomas A; Atkins, Andrew; Ndhlovu, Lishomwa C. PMID: 37811964Single-cell multiomics reveals persistence of HIV-1 in expanded cytotoxic T cell 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: 35320704Neuropathogenesis of HIV-1: insights from across the spectrum of acute through long-term treated infection
2022.
Seminars in immunopathology Killingsworth, Lauren; Spudich, Serena. PMID: 35882661The loud minority: Transcriptionally active HIV-1-infected cells survive, proliferate, and persist
2022.
Cell Collora, Jack A; Ho, Ya-Chi. PMID: 35063069HIV Compartmentalization in the CNS and Its Impact in Treatment Outcomes and Cure Strategies
2022.
Current HIV/AIDS reports Chan, Phillip; Spudich, Serena. PMID: 35536438Interferon opens up: HIV-induced inflammation reconfigures 3D chromatin conformation and affects where HIV integrates
2022.
Molecular cell Wei, Yulong; Ho, Ya-Chi. PMID: 36525953Inhibition 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 integration in the human brain is linked to microglial activation and 3D genome remodeling
2022.
Molecular cell Plaza-Jennings, Amara L; Valada, Aditi; O'Shea, Callan; Iskhakova, Marina; Hu, Benxia; Javidfar, Behnam; Ben Hutta, Gabriella; Lambert, Tova Y; Murray, Jacinta; Kassim, Bibi; Chandrasekaran, Sandhya; Chen, Benjamin K; Morgello, Susan; Won, Hyejung; Akbarian, Schahram. PMID: 36525955Neutral sphingomyelinase 2 inhibition attenuates extracellular vesicle release and improves neurobehavioral deficits in murine HIV
2022.
Neurobiology of disease Zhu, Xiaolei; Hollinger, Kristen R; Huang, Yiyao; Borjabad, Alejandra; Kim, Boe-Hyun; Arab, Tanina; Thomas, Ajit G; Moniruzzaman, Mohammed; Lovell, Lyndah; Turchinovich, Andrey; Witwer, Kenneth W; Volsky, David J; Haughey, Norman J; Slusher, Barbara S. PMID: 35462006Buprenorphine 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: 35801589The 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: 34578439Shock-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: 33758027The 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: 33165008Filgotinib 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: 32573496ATAC-seq Assay with Low Mitochondrial DNA Contamination from Primary Human CD4+ T Lymphocytes
2019.
Journal of visualized experiments : JoVE Rickner, Hannah D; Niu, Sheng-Yong; Cheng, Christine S. PMID: 30958473Medications for opioid use disorder shape immune responses during chronic HIV infection
2025.
Cell reports. Medicine Collora, Jack A; Steinhauser, Savannah F; Davenport, Timothy C; Lin, Daniel C; Eshetu, Amare; Zeidi, Samana; Kim, Rachel; Frank, Cynthia; Kluger, Yuval; Springer, Sandra A; Ho, Ya-Chi. PMID: 40460829Transcriptional impacts of substance use disorder and HIV on human ventral midbrain neurons and microglia
2025.
bioRxiv : the preprint server for biology Wilson, Alyssa M; Jacobs, Michelle M; Lambert, Tova Y; Valada, Aditi; Meloni, Gregory; Gilmore, Evan; Murray, Jacinta; Morgello, Susan; Akbarian, Schahram. PMID: 39974894Virally Suppressed People Living with HIV Who Use Opioids Have Diminished Latency Reversal
2023.
Viruses Basukala, Binita; Rossi, Sarah; Bendiks, Sally; Gnatienko, Natalia; Patts, Gregory; Krupitsky, Evgeny; Lioznov, Dmitry; So-Armah, Kaku; Sagar, Manish; Cheng, Christine; Henderson, Andrew J. PMID: 36851631Morphine suppresses peripheral responses and transforms brain myeloid gene expression to favor neuropathogenesis in SIV infection
2022.
Frontiers in immunology Fox, Howard S; Niu, Meng; Morsey, Brenda M; Lamberty, Benjamin G; Emanuel, Katy; Periyasamy, Palsamy; Callen, Shannon; Acharya, Arpan; Kubik, Gregory; Eudy, James; Guda, Chittibabu; Dyavar, Shetty Ravi; Fletcher, Courtney V; Byrareddy, Siddappa N; Buch, Shilpa. PMID: 36466814Early developmental origins of cortical disorders modeled in human neural stem cells
2025.
Nature communications Mato-Blanco, Xoel; Kim, Suel-Kee; Jourdon, Alexandre; Ma, Shaojie; Choi, Sang-Hun; Giani, Alice M; Paredes, Miguel I; Tebbenkamp, Andrew T N; Liu, Fuchen; Duque, Alvaro; Vaccarino, Flora M; Sestan, Nenad; Colantuoni, Carlo; Rakic, Pasko; Santpere, Gabriel; Micali, Nicola. PMID: 40634286Dysregulation of mTOR signalling is a converging mechanism in lissencephaly
2025.
Nature Zhang, Ce; Liang, Dan; Ercan-Sencicek, A Gulhan; Bulut, Aybike S; Cortes, Joelly; Cheng, Iris Q; Henegariu, Octavian; Nishimura, Sayoko; Wang, Xinyuan; Peksen, A Buket; Takeo, Yutaka; Caglar, Caner; Lam, TuKiet T; Koroglu, Merve Nur; Narayanan, Anand; Lopez-Giraldez, Francesc; Miyagishima, Danielle F; Mishra-Gorur, Ketu; Barak, Tanyeri; Yasuno, Katsuhito; Erson-Omay, E Zeynep; Yalcinkaya, Cengiz; Wang, Guilin; Mane, Shrikant; Kaymakcalan, Hande; Guzel, Aslan; Caglayan, A Okay; Tuysuz, Beyhan; Sestan, Nenad; Gunel, Murat; Louvi, Angeliki; Bilguvar, Kaya. PMID: 39743596Cell type-specific contributions to impaired blood-brain barrier and cerebral metabolism in presymptomatic 5XFAD mice
2025.
bioRxiv : the preprint server for biology Yao, Minmin; Sun, Na; Linville, Raleigh; Wei, Zhiliang; Kakazu, Aaron; Ouyang, Yuxiao; Li, Ruoxuan; Du, Lida; Wang, Haitong; Zhou, Yuan; Jiang, Yanli; Zhang, Ziqin; Li, Anna; Lu, Hanzhang; Xu, Jiadi; Kellis, Manolis; Heiman, Myriam; Duan, Wenzhen. PMID: 40635873Combined single-cell profiling of chromatin-transcriptome and splicing across brain cell types, regions and disease state
2025.
Nature biotechnology Hu, Wen; Foord, Careen; Hsu, Justine; Fan, Li; Corley, Michael J; Lanjewar, Samantha N; Xu, Siwei; Belchikov, Natan; He, Yi; Pang, Alina P S; Bhatia, Tarun N; Jarroux, Julien; Joglekar, Anoushka; Milner, Teresa A; Ndhlovu, Lishomwa C; Zhang, Jing; Butelman, Eduardo; Sloan, Steven A; Lee, Virginia M Y; Gan, Li; Tilgner, Hagen U. PMID: 40696189A spatial long-read approach at near-single-cell resolution reveals developmental regulation of splicing and polyadenylation sites in distinct cortical layers and cell types
2025.
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