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Jason Daniel Buenrostro, Ph.D.

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Research
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  1. DP2HL151353 (BUENROSTRO, JASON DANIEL) Sep 15, 2019 - Apr 30, 2024
    NIH/NHLBI
    Single-cell epigenomic and cellular plasticity
    Role: Principal Investigator
  2. R21HG009749 (BUENROSTRO, JASON DANIEL) Aug 18, 2017 - May 31, 2019
    NIH/NHGRI
    In situ ATAC-seq, a novel technology for structural epigenomics
    Role: Principal Investigator

Bibliographic
Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Faculty can login to make corrections and additions.
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PMC Citations indicate the number of times the publication was cited by articles in PubMed Central, and the Altmetric score represents citations in news articles and social media. (Note that publications are often cited in additional ways that are not shown here.) Fields are based on how the National Library of Medicine (NLM) classifies the publication's journal and might not represent the specific topic of the publication. Translation tags are based on the publication type and the MeSH terms NLM assigns to the publication. Some publications (especially newer ones and publications not in PubMed) might not yet be assigned Field or Translation tags.) Click a Field or Translation tag to filter the publications.
  1. Lareau CA, Ludwig LS, Muus C, Gohil SH, Zhao T, Chiang Z, Pelka K, Verboon JM, Luo W, Christian E, Rosebrock D, Getz G, Boland GM, Chen F, Buenrostro JD, Hacohen N, Wu CJ, Aryee MJ, Regev A, Sankaran VG. Massively parallel single-cell mitochondrial DNA genotyping and chromatin profiling. Nat Biotechnol. 2020 Aug 12. PMID: 32788668.
    Citations:    
  2. Agbleke AA, Amitai A, Buenrostro JD, Chakrabarti A, Chu L, Hansen AS, Koenig KM, Labade AS, Liu S, Nozaki T, Ovchinnikov S, Seeber A, Shaban HA, Spille JH, Stephens AD, Su JH, Wadduwage D. Advances in Chromatin and Chromosome Research: Perspectives from Multiple Fields. Mol Cell. 2020 09 17; 79(6):881-901. PMID: 32768408.
    Citations:    
  3. LaFave LM, Kartha VK, Ma S, Meli K, Del Priore I, Lareau C, Naranjo S, Westcott PMK, Duarte FM, Sankar V, Chiang Z, Brack A, Law T, Hauck H, Okimoto A, Regev A, Buenrostro JD, Jacks T. Epigenomic State Transitions Characterize Tumor Progression in Mouse Lung Adenocarcinoma. Cancer Cell. 2020 Aug 10; 38(2):212-228.e13. PMID: 32707078.
    Citations:    
  4. Sarikhani M, Garbern JC, Ma S, Sereda R, Conde J, Krähenbühl G, Escalante GO, Ahmed A, Buenrostro JD, Lee RT. Sustained Activation of AMPK Enhances Differentiation of Human iPSC-Derived Cardiomyocytes via Sirtuin Activation. Stem Cell Reports. 2020 08 11; 15(2):498-514. PMID: 32649901.
    Citations:    
  5. Lareau CA, Ma S, Duarte FM, Buenrostro JD. Inference and effects of barcode multiplets in droplet-based single-cell assays. Nat Commun. 2020 02 13; 11(1):866. PMID: 32054859.
    Citations:    
  6. Zhang B, Ma S, Rachmin I, He M, Baral P, Choi S, Gonçalves WA, Shwartz Y, Fast EM, Su Y, Zon LI, Regev A, Buenrostro JD, Cunha TM, Chiu IM, Fisher DE, Hsu YC. Hyperactivation of sympathetic nerves drives depletion of melanocyte stem cells. Nature. 2020 01; 577(7792):676-681. PMID: 31969699.
    Citations:    
  7. Chen H, Lareau C, Andreani T, Vinyard ME, Garcia SP, Clement K, Andrade-Navarro MA, Buenrostro JD, Pinello L. Assessment of computational methods for the analysis of single-cell ATAC-seq data. Genome Biol. 2019 11 18; 20(1):241. PMID: 31739806.
    Citations:    
  8. Lareau CA, Duarte FM, Chew JG, Kartha VK, Burkett ZD, Kohlway AS, Pokholok D, Aryee MJ, Steemers FJ, Lebofsky R, Buenrostro JD. Droplet-based combinatorial indexing for massive-scale single-cell chromatin accessibility. Nat Biotechnol. 2019 08; 37(8):916-924. PMID: 31235917.
    Citations:    
  9. Ludwig LS, Lareau CA, Bao EL, Nandakumar SK, Muus C, Ulirsch JC, Chowdhary K, Buenrostro JD, Mohandas N, An X, Aryee MJ, Regev A, Sankaran VG. Transcriptional States and Chromatin Accessibility Underlying Human Erythropoiesis. Cell Rep. 2019 06 11; 27(11):3228-3240.e7. PMID: 31189107.
    Citations:    
  10. Chen H, Albergante L, Hsu JY, Lareau CA, Lo Bosco G, Guan J, Zhou S, Gorban AN, Bauer DE, Aryee MJ, Langenau DM, Zinovyev A, Buenrostro JD, Yuan GC, Pinello L. Single-cell trajectories reconstruction, exploration and mapping of omics data with STREAM. Nat Commun. 2019 04 23; 10(1):1903. PMID: 31015418.
    Citations:    
  11. Ulirsch JC, Lareau CA, Bao EL, Ludwig LS, Guo MH, Benner C, Satpathy AT, Kartha VK, Salem RM, Hirschhorn JN, Finucane HK, Aryee MJ, Buenrostro JD, Sankaran VG. Interrogation of human hematopoiesis at single-cell and single-variant resolution. Nat Genet. 2019 04; 51(4):683-693. PMID: 30858613.
    Citations:    
  12. Ludwig LS, Lareau CA, Ulirsch JC, Christian E, Muus C, Li LH, Pelka K, Ge W, Oren Y, Brack A, Law T, Rodman C, Chen JH, Boland GM, Hacohen N, Rozenblatt-Rosen O, Aryee MJ, Buenrostro JD, Regev A, Sankaran VG. Lineage Tracing in Humans Enabled by Mitochondrial Mutations and Single-Cell Genomics. Cell. 2019 03 07; 176(6):1325-1339.e22. PMID: 30827679.
    Citations:    
  13. Yoshida H, Lareau CA, Ramirez RN, Rose SA, Maier B, Wroblewska A, Desland F, Chudnovskiy A, Mortha A, Dominguez C, Tellier J, Kim E, Dwyer D, Shinton S, Nabekura T, Qi Y, Yu B, Robinette M, Kim KW, Wagers A, Rhoads A, Nutt SL, Brown BD, Mostafavi S, Buenrostro JD, Benoist C. The cis-Regulatory Atlas of the Mouse Immune System. Cell. 2019 02 07; 176(4):897-912.e20. PMID: 30686579.
    Citations:    Fields:    
  14. Shema E, Bernstein BE, Buenrostro JD. Single-cell and single-molecule epigenomics to uncover genome regulation at unprecedented resolution. Nat Genet. 2019 01; 51(1):19-25. PMID: 30559489.
    Citations:    Fields:    
  15. Zviran A, Mor N, Rais Y, Gingold H, Peles S, Chomsky E, Viukov S, Buenrostro JD, Scognamiglio R, Weinberger L, Manor YS, Krupalnik V, Zerbib M, Hezroni H, Jaitin DA, Larastiaso D, Gilad S, Benjamin S, Gafni O, Mousa A, Ayyash M, Sheban D, Bayerl J, Aguilera-Castrejon A, Massarwa R, Maza I, Hanna S, Stelzer Y, Ulitsky I, Greenleaf WJ, Tanay A, Trumpp A, Amit I, Pilpel Y, Novershtern N, Hanna JH. Deterministic Somatic Cell Reprogramming Involves Continuous Transcriptional Changes Governed by Myc and Epigenetic-Driven Modules. Cell Stem Cell. 2019 02 07; 24(2):328-341.e9. PMID: 30554962.
    Citations:    
  16. Mor N, Rais Y, Sheban D, Peles S, Aguilera-Castrejon A, Zviran A, Elinger D, Viukov S, Geula S, Krupalnik V, Zerbib M, Chomsky E, Lasman L, Shani T, Bayerl J, Gafni O, Hanna S, Buenrostro JD, Hagai T, Masika H, Vainorius G, Bergman Y, Greenleaf WJ, Esteban MA, Elling U, Levin Y, Massarwa R, Merbl Y, Novershtern N, Hanna JH. Neutralizing Gatad2a-Chd4-Mbd3/NuRD Complex Facilitates Deterministic Induction of Naive Pluripotency. Cell Stem Cell. 2018 09 06; 23(3):412-425.e10. PMID: 30122475.
    Citations:    
  17. Chihara N, Madi A, Kondo T, Zhang H, Acharya N, Singer M, Nyman J, Marjanovic ND, Kowalczyk MS, Wang C, Kurtulus S, Law T, Etminan Y, Nevin J, Buckley CD, Burkett PR, Buenrostro JD, Rozenblatt-Rosen O, Anderson AC, Regev A, Kuchroo VK. Induction and transcriptional regulation of the co-inhibitory gene module in T cells. Nature. 2018 06; 558(7710):454-459. PMID: 29899446.
    Citations:    Fields:    Translation:AnimalsCells
  18. Buenrostro JD, Corces MR, Lareau CA, Wu B, Schep AN, Aryee MJ, Majeti R, Chang HY, Greenleaf WJ. Integrated Single-Cell Analysis Maps the Continuous Regulatory Landscape of Human Hematopoietic Differentiation. Cell. 2018 05 31; 173(6):1535-1548.e16. PMID: 29706549.
    Citations: 5     Fields:    
  19. Satpathy AT, Saligrama N, Buenrostro JD, Wei Y, Wu B, Rubin AJ, Granja JM, Lareau CA, Li R, Qi Y, Parker KR, Mumbach MR, Serratelli WS, Gennert DG, Schep AN, Corces MR, Khodadoust MS, Kim YH, Khavari PA, Greenleaf WJ, Davis MM, Chang HY. Transcript-indexed ATAC-seq for precision immune profiling. Nat Med. 2018 05; 24(5):580-590. PMID: 29686426.
    Citations:    
  20. Finucane HK, Reshef YA, Anttila V, Slowikowski K, Gusev A, Byrnes A, Gazal S, Loh PR, Lareau C, Shoresh N, Genovese G, Saunders A, Macosko E, Pollack S, Perry JRB, Buenrostro JD, Bernstein BE, Raychaudhuri S, McCarroll S, Neale BM, Price AL. Heritability enrichment of specifically expressed genes identifies disease-relevant tissues and cell types. Nat Genet. 2018 04; 50(4):621-629. PMID: 29632380.
    Citations: 3     Fields:    
  21. Koh AS, Miller EL, Buenrostro JD, Moskowitz DM, Wang J, Greenleaf WJ, Chang HY, Crabtree GR. Rapid chromatin repression by Aire provides precise control of immune tolerance. Nat Immunol. 2018 02; 19(2):162-172. PMID: 29335648.
    Citations:    
  22. Daugherty AC, Yeo RW, Buenrostro JD, Greenleaf WJ, Kundaje A, Brunet A. Chromatin accessibility dynamics reveal novel functional enhancers in C. elegans. Genome Res. 2017 12; 27(12):2096-2107. PMID: 29141961.
    Citations:    
  23. Schep AN, Wu B, Buenrostro JD, Greenleaf WJ. chromVAR: inferring transcription-factor-associated accessibility from single-cell epigenomic data. Nat Methods. 2017 Oct; 14(10):975-978. PMID: 28825706.
    Citations:    
  24. Soto-Feliciano YM, Bartlebaugh JME, Liu Y, Sánchez-Rivera FJ, Bhutkar A, Weintraub AS, Buenrostro JD, Cheng CS, Regev A, Jacks TE, Young RA, Hemann MT. PHF6 regulates phenotypic plasticity through chromatin organization within lineage-specific genes. Genes Dev. 2017 05 15; 31(10):973-989. PMID: 28607179.
    Citations:    
  25. She R, Chakravarty AK, Layton CJ, Chircus LM, Andreasson JO, Damaraju N, McMahon PL, Buenrostro JD, Jarosz DF, Greenleaf WJ. Comprehensive and quantitative mapping of RNA-protein interactions across a transcribed eukaryotic genome. Proc Natl Acad Sci U S A. 2017 04 04; 114(14):3619-3624. PMID: 28325876.
    Citations:    
  26. Miller EL, Hargreaves DC, Kadoch C, Chang CY, Calarco JP, Hodges C, Buenrostro JD, Cui K, Greenleaf WJ, Zhao K, Crabtree GR. TOP2 synergizes with BAF chromatin remodeling for both resolution and formation of facultative heterochromatin. Nat Struct Mol Biol. 2017 04; 24(4):344-352. PMID: 28250416.
    Citations: 9     Fields:    Translation:AnimalsCells
  27. Moskowitz DM, Zhang DW, Hu B, Le Saux S, Yanes RE, Ye Z, Buenrostro JD, Weyand CM, Greenleaf WJ, Goronzy JJ. Epigenomics of human CD8 T cell differentiation and aging. Sci Immunol. 2017 Feb; 2(8). PMID: 28439570.
    Citations:    
  28. Litzenburger UM, Buenrostro JD, Wu B, Shen Y, Sheffield NC, Kathiria A, Greenleaf WJ, Chang HY. Single-cell epigenomic variability reveals functional cancer heterogeneity. Genome Biol. 2017 01 24; 18(1):15. PMID: 28118844.
    Citations:    
  29. Guo MH, Nandakumar SK, Ulirsch JC, Zekavat SM, Buenrostro JD, Natarajan P, Salem RM, Chiarle R, Mitt M, Kals M, Pärn K, Fischer K, Milani L, Mägi R, Palta P, Gabriel SB, Metspalu A, Lander ES, Kathiresan S, Hirschhorn JN, Esko T, Sankaran VG. Comprehensive population-based genome sequencing provides insight into hematopoietic regulatory mechanisms. Proc Natl Acad Sci U S A. 2017 01 17; 114(3):E327-E336. PMID: 28031487.
    Citations: 10     Fields:    Translation:HumansCells
  30. Chen X, Shen Y, Draper W, Buenrostro JD, Litzenburger U, Cho SW, Satpathy AT, Carter AC, Ghosh RP, East-Seletsky A, Doudna JA, Greenleaf WJ, Liphardt JT, Chang HY. ATAC-see reveals the accessible genome by transposase-mediated imaging and sequencing. Nat Methods. 2016 Dec; 13(12):1013-1020. PMID: 27749837.
    Citations:    
  31. Corces MR, Buenrostro JD, Wu B, Greenside PG, Chan SM, Koenig JL, Snyder MP, Pritchard JK, Kundaje A, Greenleaf WJ, Majeti R, Chang HY. Lineage-specific and single-cell chromatin accessibility charts human hematopoiesis and leukemia evolution. Nat Genet. 2016 10; 48(10):1193-203. PMID: 27526324.
    Citations:    
  32. Mazumdar C, Shen Y, Xavy S, Zhao F, Reinisch A, Li R, Corces MR, Flynn RA, Buenrostro JD, Chan SM, Thomas D, Koenig JL, Hong WJ, Chang HY, Majeti R. Leukemia-Associated Cohesin Mutants Dominantly Enforce Stem Cell Programs and Impair Human Hematopoietic Progenitor Differentiation. Cell Stem Cell. 2015 Dec 03; 17(6):675-688. PMID: 26607380.
    Citations:    
  33. Schep AN, Buenrostro JD, Denny SK, Schwartz K, Sherlock G, Greenleaf WJ. Structured nucleosome fingerprints enable high-resolution mapping of chromatin architecture within regulatory regions. Genome Res. 2015 Nov; 25(11):1757-70. PMID: 26314830.
    Citations:    
  34. Maza I, Caspi I, Zviran A, Chomsky E, Rais Y, Viukov S, Geula S, Buenrostro JD, Weinberger L, Krupalnik V, Hanna S, Zerbib M, Dutton JR, Greenleaf WJ, Massarwa R, Novershtern N, Hanna JH. Transient acquisition of pluripotency during somatic cell transdifferentiation with iPSC reprogramming factors. Nat Biotechnol. 2015 Jul; 33(7):769-74. PMID: 26098448.
    Citations:    
  35. Buenrostro JD, Wu B, Litzenburger UM, Ruff D, Gonzales ML, Snyder MP, Chang HY, Greenleaf WJ. Single-cell chromatin accessibility reveals principles of regulatory variation. Nature. 2015 Jul 23; 523(7561):486-90. PMID: 26083756.
    Citations:    
  36. Buenrostro JD, Wu B, Chang HY, Greenleaf WJ. ATAC-seq: A Method for Assaying Chromatin Accessibility Genome-Wide. Curr Protoc Mol Biol. 2015 Jan 05; 109:21.29.1-21.29.9. PMID: 25559105.
    Citations:    
  37. Buenrostro JD, Araya CL, Chircus LM, Layton CJ, Chang HY, Snyder MP, Greenleaf WJ. Quantitative analysis of RNA-protein interactions on a massively parallel array reveals biophysical and evolutionary landscapes. Nat Biotechnol. 2014 Jun; 32(6):562-8. PMID: 24727714.
    Citations:    
  38. Couthouis J, Raphael AR, Siskind C, Findlay AR, Buenrostro JD, Greenleaf WJ, Vogel H, Day JW, Flanigan KM, Gitler AD. Exome sequencing identifies a DNAJB6 mutation in a family with dominantly-inherited limb-girdle muscular dystrophy. Neuromuscul Disord. 2014 May; 24(5):431-5. PMID: 24594375.
    Citations:    
  39. Carpenter ML, Buenrostro JD, Valdiosera C, Schroeder H, Allentoft ME, Sikora M, Rasmussen M, Gravel S, Guillén S, Nekhrizov G, Leshtakov K, Dimitrova D, Theodossiev N, Pettener D, Luiselli D, Sandoval K, Moreno-Estrada A, Li Y, Wang J, Gilbert MT, Willerslev E, Greenleaf WJ, Bustamante CD. Pulling out the 1%: whole-genome capture for the targeted enrichment of ancient DNA sequencing libraries. Am J Hum Genet. 2013 Nov 07; 93(5):852-64. PMID: 24568772.
    Citations:    
  40. Buenrostro JD, Giresi PG, Zaba LC, Chang HY, Greenleaf WJ. Transposition of native chromatin for fast and sensitive epigenomic profiling of open chromatin, DNA-binding proteins and nucleosome position. Nat Methods. 2013 Dec; 10(12):1213-8. PMID: 24097267.
    Citations:    
  41. Myllykangas S, Buenrostro JD, Natsoulis G, Bell JM, Ji HP. Efficient targeted resequencing of human germline and cancer genomes by oligonucleotide-selective sequencing. Nat Biotechnol. 2011 Oct 23; 29(11):1024-7. PMID: 22020387.
    Citations:    
  42. Flaherty P, Natsoulis G, Muralidharan O, Winters M, Buenrostro J, Bell J, Brown S, Holodniy M, Zhang N, Ji HP. Ultrasensitive detection of rare mutations using next-generation targeted resequencing. Nucleic Acids Res. 2012 Jan; 40(1):e2. PMID: 22013163.
    Citations:    
  43. Natsoulis G, Bell JM, Xu H, Buenrostro JD, Ordonez H, Grimes S, Newburger D, Jensen M, Zahn JM, Zhang N, Ji HP. A flexible approach for highly multiplexed candidate gene targeted resequencing. PLoS One. 2011; 6(6):e21088. PMID: 21738606.
    Citations:    
  44. Dick CA, Buenrostro J, Butler T, Carlson ML, Kliebenstein DJ, Whittall JB. Arctic mustard flower color polymorphism controlled by petal-specific downregulation at the threshold of the anthocyanin biosynthetic pathway. PLoS One. 2011 Apr 07; 6(4):e18230. PMID: 21490971.
    Citations:    
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Funded by the NIH National Center for Advancing Translational Sciences through its Clinical and Translational Science Awards Program, grant number UL1TR002541.