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Joshua Levin - Publications

Affiliations: 
Broad Institute, Cambridge, MA, United States 
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30 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2024 Simmons SK, Adiconis X, Haywood N, Parker J, Lin Z, Liao Z, Tuncali I, Al'Khafaji A, Shin A, Jagadeesh K, Gosik K, Gatzen M, Smith JT, El Kodsi DN, Kuras Y, ... ... Levin JZ, et al. Experimental and Computational Methods for Allelic Imbalance Analysis from Single-Nucleus RNA-seq Data. Biorxiv : the Preprint Server For Biology. PMID 39185246 DOI: 10.1101/2024.08.13.607784  0.338
2024 Antón-Bolaños N, Faravelli I, Faits T, Andreadis S, Kastli R, Trattaro S, Adiconis X, Wei A, Sampath Kumar A, Di Bella DJ, Tegtmeyer M, Nehme R, Levin JZ, Regev A, Arlotta P. Brain Chimeroids reveal individual susceptibility to neurotoxic triggers. Nature. PMID 38926573 DOI: 10.1038/s41586-024-07578-8  0.39
2024 Zheng X, Wu B, Liu Y, Simmons SK, Kim K, Clarke GS, Ashiq A, Park J, Li J, Wang Z, Tong L, Wang Q, Rajamani KT, Muñoz-Castañeda R, Mu S, ... ... Levin JZ, et al. Massively parallel in vivo Perturb-seq reveals cell-type-specific transcriptional networks in cortical development. Cell. PMID 38772369 DOI: 10.1016/j.cell.2024.04.050  0.357
2023 Zheng X, Wu B, Liu Y, Simmons SK, Kim K, Clarke GS, Ashiq A, Park J, Wang Z, Tong L, Wang Q, Xu X, Levin JZ, Jin X. Massively parallel Perturb-seq reveals cell type-specific transcriptional networks in cortical development. Biorxiv : the Preprint Server For Biology. PMID 37790302 DOI: 10.1101/2023.09.18.558077  0.379
2023 Pigoni M, Uzquiano A, Paulsen B, Kedaigle A, Yang SM, Symvoulidis P, Adiconis X, Velasco S, Sartore R, Kim K, Tucewicz A, Tropp SY, Tsafou K, Jin X, Barrett L, ... ... Levin JZ, et al. Cell-type specific defects in PTEN-mutant cortical organoids converge on abnormal circuit activity. Human Molecular Genetics. PMID 37384417 DOI: 10.1093/hmg/ddad107  0.71
2023 Janssen P, Kliesmete Z, Vieth B, Adiconis X, Simmons S, Marshall J, McCabe C, Heyn H, Levin JZ, Enard W, Hellmann I. The effect of background noise and its removal on the analysis of single-cell expression data. Genome Biology. 24: 140. PMID 37337297 DOI: 10.1186/s13059-023-02978-x  0.3
2022 Uzquiano A, Kedaigle AJ, Pigoni M, Paulsen B, Adiconis X, Kim K, Faits T, Nagaraja S, Antón-Bolaños N, Gerhardinger C, Tucewicz A, Murray E, Jin X, Buenrostro J, Chen F, ... ... Levin JZ, et al. Proper acquisition of cell class identity in organoids allows definition of fate specification programs of the human cerebral cortex. Cell. 185: 3770-3788.e27. PMID 36179669 DOI: 10.1016/j.cell.2022.09.010  0.704
2022 Simmons SK, Lithwick-Yanai G, Adiconis X, Oberstrass F, Iremadze N, Geiger-Schuller K, Thakore PI, Frangieh CJ, Barad O, Almogy G, Rozenblatt-Rosen O, Regev A, Lipson D, Levin JZ. Mostly natural sequencing-by-synthesis for scRNA-seq using Ultima sequencing. Nature Biotechnology. PMID 36109685 DOI: 10.1038/s41587-022-01452-6  0.312
2022 Paulsen B, Velasco S, Kedaigle AJ, Pigoni M, Quadrato G, Deo AJ, Adiconis X, Uzquiano A, Sartore R, Yang SM, Simmons SK, Symvoulidis P, Kim K, Tsafou K, Podury A, ... ... Levin JZ, et al. Autism genes converge on asynchronous development of shared neuron classes. Nature. PMID 35110736 DOI: 10.1038/s41586-021-04358-6  0.711
2021 Mifflin L, Hu Z, Dufort C, Hession CC, Walker AJ, Niu K, Zhu H, Liu N, Liu JS, Levin JZ, Stevens B, Yuan J, Zou C. A RIPK1-regulated inflammatory microglial state in amyotrophic lateral sclerosis. Proceedings of the National Academy of Sciences of the United States of America. 118. PMID 33766915 DOI: 10.1073/pnas.2025102118  0.465
2020 Zou C, Mifflin L, Hu Z, Zhang T, Shan B, Wang H, Xing X, Zhu H, Adiconis X, Levin JZ, Li F, Liu CF, Liu JS, Yuan J. Reduction of mNAT1/hNAT2 Contributes to Cerebral Endothelial Necroptosis and Aβ Accumulation in Alzheimer's Disease. Cell Reports. 33: 108447. PMID 33296651 DOI: 10.1016/j.celrep.2020.108447  0.441
2020 Jin X, Simmons SK, Guo A, Shetty AS, Ko M, Nguyen L, Jokhi V, Robinson E, Oyler P, Curry N, Deangeli G, Lodato S, Levin JZ, Regev A, Zhang F, et al. In vivo Perturb-Seq reveals neuronal and glial abnormalities associated with autism risk genes. Science (New York, N.Y.). 370. PMID 33243861 DOI: 10.1126/science.aaz6063  0.386
2020 Mereu E, Lafzi A, Moutinho C, Ziegenhain C, McCarthy DJ, Álvarez-Varela A, Batlle E, Sagar, Grün D, Lau JK, Boutet SC, Sanada C, Ooi A, Jones RC, Kaihara K, ... ... Levin JZ, et al. Benchmarking single-cell RNA-sequencing protocols for cell atlas projects. Nature Biotechnology. 38: 747-755. PMID 32518403 DOI: 10.1038/S41587-020-0469-4  0.373
2020 Ding J, Adiconis X, Simmons SK, Kowalczyk MS, Hession CC, Marjanovic ND, Hughes TK, Wadsworth MH, Burks T, Nguyen LT, Kwon JYH, Barak B, Ge W, Kedaigle AJ, Carroll S, ... ... Levin JZ, et al. Author Correction: Systematic comparison of single-cell and single-nucleus RNA-sequencing methods. Nature Biotechnology. PMID 32341567 DOI: 10.1038/S41587-020-0534-Z  0.682
2020 Ding J, Adiconis X, Simmons SK, Kowalczyk MS, Hession CC, Marjanovic ND, Hughes TK, Wadsworth MH, Burks T, Nguyen LT, Kwon JYH, Barak B, Ge W, Kedaigle AJ, Carroll S, ... ... Levin JZ, et al. Systematic comparison of single-cell and single-nucleus RNA-sequencing methods. Nature Biotechnology. PMID 32341560 DOI: 10.1038/S41587-020-0465-8  0.698
2019 Du J, Simmons S, Brunklaus A, Adiconis X, Hession CC, Fu Z, Li Y, Shema R, Møller RS, Barak B, Feng G, Meisler M, Sanders S, Lerche H, Campbell AJ, ... ... Levin JZ, et al. Differential excitatory vs inhibitory SCN expression at single cell level regulates brain sodium channel function in neurodevelopmental disorders. European Journal of Paediatric Neurology : Ejpn : Official Journal of the European Paediatric Neurology Society. PMID 31928904 DOI: 10.1016/J.Ejpn.2019.12.019  0.306
2019 Ximerakis M, Lipnick SL, Innes BT, Simmons SK, Adiconis X, Dionne D, Mayweather BA, Nguyen L, Niziolek Z, Ozek C, Butty VL, Isserlin R, Buchanan SM, Levine SS, Regev A, ... ... Levin JZ, et al. Single-cell transcriptomic profiling of the aging mouse brain. Nature Neuroscience. 22: 1696-1708. PMID 31551601 DOI: 10.1038/S41593-019-0491-3  0.323
2019 Velasco S, Kedaigle AJ, Simmons SK, Nash A, Rocha M, Quadrato G, Paulsen B, Nguyen L, Adiconis X, Regev A, Levin JZ, Arlotta P. Individual brain organoids reproducibly form cell diversity of the human cerebral cortex. Nature. PMID 31168097 DOI: 10.1038/S41586-019-1289-X  0.711
2018 Tekin H, Simmons S, Cummings B, Gao L, Adiconis X, Hession CC, Ghoshal A, Dionne D, Choudhury SR, Yesilyurt V, Sanjana NE, Shi X, Lu C, Heidenreich M, Pan JQ, ... Levin JZ, et al. Effects of 3D culturing conditions on the transcriptomic profile of stem-cell-derived neurons. Nature Biomedical Engineering. 2: 540-554. PMID 30271673 DOI: 10.1038/S41551-018-0219-9  0.335
2018 Xu D, Jin T, Zhu H, Chen H, Ofengeim D, Zou C, Mifflin L, Pan L, Amin P, Li W, Shan B, Naito MG, Meng H, Li Y, Pan H, ... ... Levin JZ, et al. TBK1 Suppresses RIPK1-Driven Apoptosis and Inflammation during Development and in Aging. Cell. PMID 30146158 DOI: 10.1016/J.Cell.2018.07.041  0.444
2018 Adiconis X, Haber AL, Simmons SK, Levy Moonshine A, Ji Z, Busby MA, Shi X, Jacques J, Lancaster MA, Pan JQ, Regev A, Levin JZ. Comprehensive comparative analysis of 5'-end RNA-sequencing methods. Nature Methods. PMID 29867192 DOI: 10.1038/S41592-018-0014-2  0.31
2017 Ofengeim D, Mazzitelli S, Ito Y, DeWitt JP, Mifflin L, Zou C, Das S, Adiconis X, Chen H, Zhu H, Kelliher MA, Levin JZ, Yuan J. RIPK1 mediates a disease-associated microglial response in Alzheimer's disease. Proceedings of the National Academy of Sciences of the United States of America. PMID 28904096 DOI: 10.1073/Pnas.1714175114  0.45
2016 Shekhar K, Lapan SW, Whitney IE, Tran NM, Macosko EZ, Kowalczyk M, Adiconis X, Levin JZ, Nemesh J, Goldman M, McCarroll SA, Cepko CL, Regev A, Sanes JR. Comprehensive Classification of Retinal Bipolar Neurons by Single-Cell Transcriptomics. Cell. 166: 1308-1323.e30. PMID 27565351 DOI: 10.1016/J.Cell.2016.07.054  0.302
2013 Shalek AK, Satija R, Adiconis X, Gertner RS, Gaublomme JT, Raychowdhury R, Schwartz S, Yosef N, Malboeuf C, Lu D, Trombetta JJ, Gennert D, Gnirke A, Goren A, Hacohen N, ... Levin JZ, et al. Single-cell transcriptomics reveals bimodality in expression and splicing in immune cells. Nature. 498: 236-40. PMID 23685454 DOI: 10.1038/Nature12172  0.389
2013 Slavoff SA, Mitchell AJ, Schwaid AG, Cabili MN, Ma J, Levin JZ, Karger AD, Budnik BA, Rinn JL, Saghatelian A. Peptidomic discovery of short open reading frame-encoded peptides in human cells. Nature Chemical Biology. 9: 59-64. PMID 23160002 DOI: 10.1038/Nchembio.1120  0.343
2010 Guttman M, Garber M, Levin JZ, Donaghey J, Robinson J, Adiconis X, Fan L, Koziol MJ, Gnirke A, Nusbaum C, Rinn JL, Lander ES, Regev A. Ab initio reconstruction of cell type-specific transcriptomes in mouse reveals the conserved multi-exonic structure of lincRNAs. Nature Biotechnology. 28: 503-10. PMID 20436462 DOI: 10.1038/nbt.1633  0.341
2010 Ciulla D, Giannoukos G, Earl A, Feldgarden M, Gevers D, Levin J, Livny J, Ward D, Gnirke A, Nusbaum C, Birren B. Evaluation of bacterial ribosomal RNA (rRNA) depletion methods for sequencing microbial community transcriptomes Genome Biology. 11: 9. DOI: 10.1186/Gb-2010-11-S1-P9  0.325
2010 Henn MR, Lennon NJ, Newman R, Charlebois P, Boutwell C, OhAinle M, Berlin A, Ryan E, Malboeuf C, Macalalad A, Casali M, Erlich R, Bigelow H, Green L, Gnerre S, ... ... Levin J, et al. Sensitive population profiling and genome assembly of HIV and Flaviviruses using ultra-deep sequencing technologies Genome Biology. 11: P18. DOI: 10.1186/Gb-2010-11-S1-P18  0.314
2003 de la Cruz IP, Levin JZ, Cummins C, Anderson P, Horvitz HR. sup-9, sup-10, and unc-93 may encode components of a two-pore K+ channel that coordinates muscle contraction in Caenorhabditis elegans. The Journal of Neuroscience : the Official Journal of the Society For Neuroscience. 23: 9133-45. PMID 14534247 DOI: 10.1523/Jneurosci.23-27-09133.2003  0.4
1992 Levin JZ, Horvitz HR. The Caenorhabditis elegans unc-93 gene encodes a putative transmembrane protein that regulates muscle contraction. The Journal of Cell Biology. 117: 143-55. PMID 1313436 DOI: 10.1083/Jcb.117.1.143  0.496
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