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Ali Mortazavi, Ph.D. - Publications

Affiliations: 
2004-2011 Biology California Institute of Technology, Pasadena, CA 
 2011- Developmental and Cell Biology University of California, Irvine, Irvine, CA 
Area:
Functional Genomics
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65 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
2023 Pardo-Palacios FJ, Wang D, Reese F, Diekhans M, Carbonell-Sala S, Williams B, Loveland JE, De María M, Adams MS, Balderrama-Gutierrez G, Behera AK, Gonzalez JM, Hunt T, Lagarde J, Liang CE, ... ... Mortazavi A, et al. Systematic assessment of long-read RNA-seq methods for transcript identification and quantification. Biorxiv : the Preprint Server For Biology. PMID 37546854 DOI: 10.1101/2023.07.25.550582  0.66
2023 Hitz B, Lee JW, Jolanki O, Kagda M, Graham K, Sud P, Gabdank I, Strattan JS, Sloan C, Dreszer T, Rowe L, Podduturi N, Malladi V, Chan E, Davidson J, ... ... Mortazavi A, et al. The ENCODE Uniform Analysis Pipelines. Research Square. PMID 37503119 DOI: 10.21203/rs.3.rs-3111932/v1  0.612
2023 Reese F, Williams B, Balderrama-Gutierrez G, Wyman D, Çelik MH, Rebboah E, Rezaie N, Trout D, Razavi-Mohseni M, Jiang Y, Borsari B, Morabito S, Liang HY, McGill CJ, Rahmanian S, ... ... Mortazavi A, et al. The ENCODE4 long-read RNA-seq collection reveals distinct classes of transcript structure diversity. Biorxiv : the Preprint Server For Biology. PMID 37292896 DOI: 10.1101/2023.05.15.540865  0.663
2023 Hitz BC, Lee JW, Jolanki O, Kagda MS, Graham K, Sud P, Gabdank I, Seth Strattan J, Sloan CA, Dreszer T, Rowe LD, Podduturi NR, Malladi VS, Chan ET, Davidson JM, ... ... Mortazavi A, et al. The ENCODE Uniform Analysis Pipelines. Biorxiv : the Preprint Server For Biology. PMID 37066421 DOI: 10.1101/2023.04.04.535623  0.612
2023 Rozowsky J, Gao J, Borsari B, Yang YT, Galeev T, Gürsoy G, Epstein CB, Xiong K, Xu J, Li T, Liu J, Yu K, Berthel A, Chen Z, Navarro F, ... ... Mortazavi A, et al. The EN-TEx resource of multi-tissue personal epigenomes & variant-impact models. Cell. 186: 1493-1511.e40. PMID 37001506 DOI: 10.1016/j.cell.2023.02.018  0.618
2022 Moore JE, Purcaro MJ, Pratt HE, Epstein CB, Shoresh N, Adrian J, Kawli T, Davis CA, Dobin A, Kaul R, Halow J, Van Nostrand EL, Freese P, Gorkin DU, Shen Y, ... ... Mortazavi A, et al. Author Correction: Expanded encyclopaedias of DNA elements in the human and mouse genomes. Nature. PMID 35474001 DOI: 10.1038/s41586-021-04226-3  0.573
2022 Jansen C, Paraiso KD, Zhou JJ, Blitz IL, Fish MB, Charney RM, Cho JS, Yasuoka Y, Sudou N, Bright AR, Wlizla M, Veenstra GJC, Taira M, Zorn AM, Mortazavi A, et al. Uncovering the mesendoderm gene regulatory network through multi-omic data integration. Cell Reports. 38: 110364. PMID 35172134 DOI: 10.1016/j.celrep.2022.110364  0.4
2021 Moore JE, Zhang XO, Elhajjajy SI, Fan K, Pratt HE, Reese F, Mortazavi A, Weng Z. Integration of high-resolution promoter profiling assays reveals novel, cell type-specific transcription start sites across 115 human cell and tissue types. Genome Research. PMID 34949670 DOI: 10.1101/gr.275723.121  0.43
2021 Rebboah E, Reese F, Williams K, Balderrama-Gutierrez G, McGill C, Trout D, Rodriguez I, Liang H, Wold BJ, Mortazavi A. Mapping and modeling the genomic basis of differential RNA isoform expression at single-cell resolution with LR-Split-seq. Genome Biology. 22: 286. PMID 34620214 DOI: 10.1186/s13059-021-02505-w  0.655
2021 Macias-Muñoz A, Mortazavi A. A Bioinformatics Pipeline for Investigating Molecular Evolution and Gene Expression using RNA-seq. Journal of Visualized Experiments : Jove. PMID 34125087 DOI: 10.3791/61633  0.35
2021 Chang D, Serra L, Lu D, Mortazavi A, Dillman A. A Revised Adaptation of the Smart-Seq2 Protocol for Single-Nematode RNA-Seq. Methods in Molecular Biology (Clifton, N.J.). 2170: 79-99. PMID 32797452 DOI: 10.1007/978-1-0716-0743-5_6  0.685
2020 Moore JE, Purcaro MJ, Pratt HE, Epstein CB, Shoresh N, Adrian J, Kawli T, Davis CA, Dobin A, Kaul R, Halow J, Van Nostrand EL, Freese P, Gorkin DU, ... ... Mortazavi A, et al. Expanded encyclopaedias of DNA elements in the human and mouse genomes. Nature. 583: 699-710. PMID 32728249 DOI: 10.1038/S41586-020-2493-4  0.697
2020 Partridge EC, Chhetri SB, Prokop JW, Ramaker RC, Jansen CS, Goh ST, Mackiewicz M, Newberry KM, Brandsmeier LA, Meadows SK, Messer CL, Hardigan AA, Coppola CJ, Dean EC, Jiang S, ... ... Mortazavi A, et al. Occupancy maps of 208 chromatin-associated proteins in one human cell type. Nature. 583: 720-728. PMID 32728244 DOI: 10.1038/S41586-020-2023-4  0.682
2020 Jiang S, Williams K, Kong X, Zeng W, Nguyen NV, Ma X, Tawil R, Yokomori K, Mortazavi A. Single-nucleus RNA-seq identifies divergent populations of FSHD2 myotube nuclei. Plos Genetics. 16: e1008754. PMID 32365093 DOI: 10.1371/Journal.Pgen.1008754  0.312
2020 Ionkina AA, Balderrama-Gutierrez G, Phan SH, Mortazavi A, Prescher JA. Abstract 2496: Comparative transcriptome analysis of metastatic heterogeneity in a mouse model of breast cancer Cancer Research. 80: 2496-2496. DOI: 10.1158/1538-7445.Am2020-2496  0.395
2019 Macias-Muñoz A, Murad R, Mortazavi A. Molecular evolution and expression of opsin genes in Hydra vulgaris. Bmc Genomics. 20: 992. PMID 31847811 DOI: 10.1186/S12864-019-6349-Y  0.43
2019 Jansen C, Ramirez RN, El-Ali NC, Gomez-Cabrero D, Tegner J, Merkenschlager M, Conesa A, Mortazavi A. Building gene regulatory networks from scATAC-seq and scRNA-seq using Linked Self Organizing Maps. Plos Computational Biology. 15: e1006555. PMID 31682608 DOI: 10.1371/Journal.Pcbi.1006555  0.338
2019 Gomez-Cabrero D, Tarazona S, Ferreirós-Vidal I, Ramirez RN, Company C, Schmidt A, Reijmers T, Paul VVS, Marabita F, Rodríguez-Ubreva J, Garcia-Gomez A, Carroll T, Cooper L, Liang Z, Dharmalingam G, ... ... Mortazavi A, et al. STATegra, a comprehensive multi-omics dataset of B-cell differentiation in mouse. Scientific Data. 6: 256. PMID 31672995 DOI: 10.1038/S41597-019-0202-7  0.344
2019 Rahmanian S, Murad R, Breschi A, Zeng W, Mackiewicz M, Williams B, Davis CA, Roberts B, Meadows S, Moore D, Trout D, Zaleski C, Dobin A, Sei LH, Drenkow J, ... ... Mortazavi A, et al. Dynamics of microRNA expression during mouse prenatal development. Genome Research. PMID 31645363 DOI: 10.1101/Gr.248997.119  0.57
2019 Serra L, Macchietto M, Macias-Muñoz A, McGill CJ, Rodriguez IM, Rodriguez B, Murad R, Mortazavi A. Hybrid Assembly of the Genome of the Entomopathogenic Nematode Identifies the X-chromosome. G3 (Bethesda, Md.). PMID 31113823 DOI: 10.1534/g3.119.400180  0.348
2019 Chang DZ, Serra L, Lu D, Mortazavi A, Dillman AR. A core set of venom proteins is released by entomopathogenic nematodes in the genus Steinernema. Plos Pathogens. 15: e1007626. PMID 31042778 DOI: 10.1371/Journal.Ppat.1007626  0.626
2019 Fung L, Guzman H, Sevrioukov E, Idica A, Park E, Bochnakian A, Daugaard I, Jury D, Mortazavi A, Zisoulis DG, Pedersen IM. miR-128 Restriction of LINE-1 (L1) Retrotransposition Is Dependent on Targeting hnRNPA1 mRNA. International Journal of Molecular Sciences. 20. PMID 31010097 DOI: 10.3390/Ijms20081955  0.344
2019 Ferreirós-Vidal I, Carroll T, Zhang T, Lagani V, Ramirez RN, Ing-Simmons E, Garcia A, Cooper L, Liang Z, Papoutsoglou G, Dharmalingam G, Guo Y, Tarazona S, Fernandes SJ, Noori P, ... ... Mortazavi A, et al. Feedforward regulation of Myc coordinates lineage-specific with housekeeping gene expression during B cell progenitor cell differentiation. Plos Biology. 17: e2006506. PMID 30978178 DOI: 10.1371/Journal.Pbio.2006506  0.359
2018 Tardaguila M, de la Fuente L, Marti C, Pereira C, Pardo-Palacios FJ, Del Risco H, Ferrell M, Mellado M, Macchietto M, Verheggen K, Edelmann M, Ezkurdia I, Vazquez J, Tress M, Mortazavi A, et al. Corrigendum: SQANTI: extensive characterization of long-read transcript sequences for quality control in full-length transcriptome identification and quantification. Genome Research. 28: 1096. PMID 29967126 DOI: 10.1101/Gr.239137.118  0.365
2018 Wyman D, Mortazavi A. TranscriptClean: Variant-aware correction of indels, mismatches, and splice junctions in long-read transcripts. Bioinformatics (Oxford, England). PMID 29912287 DOI: 10.1093/Bioinformatics/Bty483  0.447
2018 Nguyen K, Aggarwal MB, Feng C, Balderrama G, Fazio M, Mortazavi A, Spitale RC. Spatially-Restricting Bioorthogonal Nucleoside Biosynthesis Enables Selective Metabolic Labeling of the Mitochondrial Transcriptome. Acs Chemical Biology. PMID 29756767 DOI: 10.1021/Acschembio.8B00262  0.364
2018 Jiang S, Mortazavi A. Integrating ChIP-seq with other functional genomics data. Briefings in Functional Genomics. PMID 29579165 DOI: 10.1093/bfgp/ely002  0.408
2018 Serra L, Chang DZ, Macchietto M, Williams K, Murad R, Lu D, Dillman AR, Mortazavi A. Adapting the Smart-seq2 Protocol for Robust Single Worm RNA-seq. Bio-Protocol. 8. PMID 29564372 DOI: 10.21769/BioProtoc.2729  0.674
2018 Tardaguila M, de la Fuente L, Marti C, Pereira C, Pardo-Palacios FJ, Del Risco H, Ferrell M, Mellado M, Macchietto M, Verheggen K, Edelmann M, Ezkurdia I, Vazquez J, Tress M, Mortazavi A, et al. SQANTI: extensive characterization of long-read transcript sequences for quality control in full-length transcriptome identification and quantification. Genome Research. PMID 29440222 DOI: 10.1101/Gr.222976.117  0.435
2018 Sierra RA, Hoverter NP, Ramirez RN, Vuong LM, Mortazavi A, Merrill BJ, Waterman ML, Donovan PJ. TCF7L1 suppresses primitive streak gene expression to support human embryonic stem cell pluripotency. Development (Cambridge, England). PMID 29361574 DOI: 10.1242/Dev.161075  0.359
2017 Longabaugh WJR, Zeng W, Zhang JA, Hosokawa H, Jansen CS, Li L, Romero-Wolf M, Liu P, Kueh HY, Mortazavi A, Rothenberg EV. Bcl11b and combinatorial resolution of cell fate in the T-cell gene regulatory network. Proceedings of the National Academy of Sciences of the United States of America. 114: 5800-5807. PMID 28584128 DOI: 10.1073/Pnas.1610617114  0.594
2017 Lu D, Macchietto M, Chang D, Barros MM, Baldwin J, Mortazavi A, Dillman AR. Activated entomopathogenic nematode infective juveniles release lethal venom proteins. Plos Pathogens. 13: e1006302. PMID 28426766 DOI: 10.1371/Journal.Ppat.1006302  0.652
2017 Ramirez RN, El-Ali NC, Mager MA, Wyman D, Conesa A, Mortazavi A. Dynamic Gene Regulatory Networks of Human Myeloid Differentiation. Cell Systems. PMID 28365152 DOI: 10.1016/J.Cels.2017.03.005  0.423
2017 Singh-Taylor A, Molet J, Jiang S, Korosi A, Bolton JL, Noam Y, Simeone K, Cope J, Chen Y, Mortazavi A, Baram TZ. NRSF-dependent epigenetic mechanisms contribute to programming of stress-sensitive neurons by neonatal experience, promoting resilience. Molecular Psychiatry. PMID 28070121 DOI: 10.1038/Mp.2016.240  0.314
2017 Plikus MV, Guerrero-Juarez CF, Ito M, Li YR, Dedhia PH, Zheng Y, Shao M, Gay DL, Ramos R, His TC, Oh JW, Wang X, Ramirez A, Konopelski SE, Elzein A, ... ... Mortazavi A, et al. Regeneration of fat cells from myofibroblasts during wound healing. Science (New York, N.Y.). PMID 28059714 DOI: 10.1126/Science.Aai8792  0.305
2016 Zeng W, Jiang S, Kong X, El-Ali N, Ball AR, Ma CI, Hashimoto N, Yokomori K, Mortazavi A. Single-nucleus RNA-seq of differentiating human myoblasts reveals the extent of fate heterogeneity. Nucleic Acids Research. PMID 27566152 DOI: 10.1093/Nar/Gkw739  0.402
2016 Conesa A, Madrigal P, Tarazona S, Gomez-Cabrero D, Cervera A, McPherson A, Szcześniak MW, Gaffney DJ, Elo LL, Zhang X, Mortazavi A. Erratum to: A survey of best practices for RNA-seq data analysis. Genome Biology. 17: 181. PMID 27565134 DOI: 10.1186/S13059-016-1047-4  0.345
2016 Conesa A, Madrigal P, Tarazona S, Gomez-Cabrero D, Cervera A, McPherson A, Szcześniak MW, Gaffney DJ, Elo LL, Zhang X, Mortazavi A. A survey of best practices for RNA-seq data analysis. Genome Biology. 17: 13. PMID 26813401 DOI: 10.1186/S13059-016-0881-8  0.467
2016 Blanc V, Riordan JD, Park E, Kennedy S, Madison B, Mills J, Rubin DC, Brunt E, Lee J, Ng I, Mortazavi A, Nadeau J, Davidson NO. 106 Nuclear Expression of RNA Binding Protein APOBEC-1 Complementation Factor (ACF) Regulates Liver Growth and Attenuates Tumorigenesis in Humans With Hepatocellular Carcinoma Gastroenterology. 150: S27. DOI: 10.1016/S0016-5085(16)30217-7  0.34
2015 Dillman AR, Macchietto M, Porter CF, Rogers A, Williams B, Antoshechkin I, Lee MM, Goodwin Z, Lu X, Lewis EE, Goodrich-Blair H, Stock SP, Adams BJ, Sternberg PW, Mortazavi A. Comparative genomics of Steinernema reveals deeply conserved gene regulatory networks. Genome Biology. 16: 200. PMID 26392177 DOI: 10.1186/S13059-015-0746-6  0.727
2015 Mortazavi A. Better together: multiplexing samples to improve the preparation and reliability of gene expression studies. Nature Methods. 12: 304-5. PMID 25825835 DOI: 10.1038/Nmeth.3333  0.374
2015 Blanc V, Riordan JD, Park E, Kennedy S, Brunt E, Mortazavi A, Nadeau J, Davidson NO. 800d Liver-Specific Over-Expression of Apobec 1 Complementation Factor (A1CF) Results in Spontaneous Steatosis and Hepatocellular Carcinoma Independent of RNA Editing Gastroenterology. 148: S-1192. DOI: 10.1016/S0016-5085(15)34072-5  0.308
2014 Yue F, Cheng Y, Breschi A, Vierstra J, Wu W, Ryba T, Sandstrom R, Ma Z, Davis C, Pope BD, Shen Y, Pervouchine DD, Djebali S, Thurman RE, Kaul R, ... ... Mortazavi A, et al. A comparative encyclopedia of DNA elements in the mouse genome. Nature. 515: 355-64. PMID 25409824 DOI: 10.1038/Nature13992  0.7
2014 Daniels EV, Murad R, Mortazavi A, Reed RD. Extensive transcriptional response associated with seasonal plasticity of butterfly wing patterns. Molecular Ecology. 23: 6123-34. PMID 25369871 DOI: 10.1111/Mec.12988  0.413
2014 Gerstein MB, Rozowsky J, Yan KK, Wang D, Cheng C, Brown JB, Davis CA, Hillier L, Sisu C, Li JJ, Pei B, Harmanci AO, Duff MO, Djebali S, Alexander RP, ... ... Mortazavi A, et al. Comparative analysis of the transcriptome across distant species. Nature. 512: 445-8. PMID 25164755 DOI: 10.1038/Nature13424  0.454
2014 Conesa A, Mortazavi A. The common ground of genomics and systems biology. Bmc Systems Biology. 8: S1. PMID 25033072 DOI: 10.1186/1752-0509-8-S2-S1  0.392
2014 Blanc V, Park E, Schaefer S, Miller M, Lin Y, Kennedy S, Billing AM, Ben Hamidane H, Graumann J, Mortazavi A, Nadeau JH, Davidson NO. Genome-wide identification and functional analysis of Apobec-1-mediated C-to-U RNA editing in mouse small intestine and liver. Genome Biology. 15: R79. PMID 24946870 DOI: 10.1186/Gb-2014-15-6-R79  0.468
2013 Mortazavi A, Pepke S, Jansen C, Marinov GK, Ernst J, Kellis M, Hardison RC, Myers RM, Wold BJ. Integrating and mining the chromatin landscape of cell-type specificity using self-organizing maps. Genome Research. 23: 2136-48. PMID 24170599 DOI: 10.1101/Gr.158261.113  0.655
2013 Srinivasan J, Dillman AR, Macchietto MG, Heikkinen L, Lakso M, Fracchia KM, Antoshechkin I, Mortazavi A, Wong G, Sternberg PW. The draft genome and transcriptome of Panagrellus redivivus are shaped by the harsh demands of a free-living lifestyle. Genetics. 193: 1279-95. PMID 23410827 DOI: 10.1534/Genetics.112.148809  0.748
2012 Dillman AR, Mortazavi A, Sternberg PW. Incorporating genomics into the toolkit of nematology. Journal of Nematology. 44: 191-205. PMID 23482088  0.715
2012 Park E, Williams B, Wold BJ, Mortazavi A. RNA editing in the human ENCODE RNA-seq data. Genome Research. 22: 1626-33. PMID 22955975 DOI: 10.1101/Gr.134957.111  0.681
2012 Djebali S, Davis CA, Merkel A, Dobin A, Lassmann T, Mortazavi A, Tanzer A, Lagarde J, Lin W, Schlesinger F, Xue C, Marinov GK, Khatun J, Williams BA, Zaleski C, et al. Landscape of transcription in human cells. Nature. 489: 101-8. PMID 22955620 DOI: 10.1038/Nature11233  0.658
2012 Stamatoyannopoulos JA, Snyder M, Hardison R, Ren B, Gingeras T, Gilbert DM, Groudine M, Bender M, Kaul R, Canfield T, Giste E, Johnson A, Zhang M, Balasundaram G, ... ... Mortazavi A, et al. An encyclopedia of mouse DNA elements (Mouse ENCODE). Genome Biology. 13: 418. PMID 22889292 DOI: 10.1186/Gb-2012-13-8-418  0.635
2012 Zhang JA, Mortazavi A, Williams BA, Wold BJ, Rothenberg EV. Dynamic transformations of genome-wide epigenetic marking and transcriptional control establish T cell identity. Cell. 149: 467-82. PMID 22500808 DOI: 10.1016/J.Cell.2012.01.056  0.733
2012 Reddy TE, Gertz J, Pauli F, Kucera KS, Varley KE, Newberry KM, Marinov GK, Mortazavi A, Williams BA, Song L, Crawford GE, Wold B, Willard HF, Myers RM. Effects of sequence variation on differential allelic transcription factor occupancy and gene expression. Genome Research. 22: 860-9. PMID 22300769 DOI: 10.1101/Gr.131201.111  0.662
2012 Li G, Ruan X, Auerbach RK, Sandhu KS, Zheng M, Wang P, Poh HM, Goh Y, Lim J, Zhang J, Sim HS, Peh SQ, Mulawadi FH, Ong CT, Orlov YL, ... ... Mortazavi A, et al. Extensive promoter-centered chromatin interactions provide a topological basis for transcription regulation. Cell. 148: 84-98. PMID 22265404 DOI: 10.1016/J.Cell.2011.12.014  0.652
2010 Mortazavi A, Schwarz EM, Williams B, Schaeffer L, Antoshechkin I, Wold BJ, Sternberg PW. Scaffolding a Caenorhabditis nematode genome with RNA-seq. Genome Research. 20: 1740-7. PMID 20980554 DOI: 10.1101/Gr.111021.110  0.722
2010 Trapnell C, Williams BA, Pertea G, Mortazavi A, Kwan G, van Baren MJ, Salzberg SL, Wold BJ, Pachter L. Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation. Nature Biotechnology. 28: 511-5. PMID 20436464 DOI: 10.1038/Nbt.1621  0.701
2010 Abril J, Kokocinski F, Steijger T, Williams G, Salmon M, Mortazavi A, Raetsch G, Gerstein M, Reymond A, Gingeras T, Wold B, Guigó R, Hubbard T, Harrow J. RGASP: assessment of gene-finding tools in the high-throughput era F1000research. 1. DOI: 10.7490/F1000Research.272.1  0.583
2009 Pepke S, Wold B, Mortazavi A. Computation for ChIP-seq and RNA-seq studies Nature Methods. 6: S22-32. PMID 19844228 DOI: 10.1038/Nmeth.1371  0.682
2008 Berghella L, De Angelis L, De Buysscher T, Mortazavi A, Biressi S, Forcales SV, Sirabella D, Cossu G, Wold BJ. A highly conserved molecular switch binds MSY-3 to regulate myogenin repression in postnatal muscle. Genes & Development. 22: 2125-38. PMID 18676817 DOI: 10.1101/Gad.468508  0.612
2008 Mortazavi A, Williams BA, McCue K, Schaeffer L, Wold B. Mapping and quantifying mammalian transcriptomes by RNA-Seq. Nature Methods. 5: 621-8. PMID 18516045 DOI: 10.1038/Nmeth.1226  0.674
2007 Johnson DS, Mortazavi A, Myers RM, Wold B. Genome-wide mapping of in vivo protein-DNA interactions. Science (New York, N.Y.). 316: 1497-502. PMID 17540862 DOI: 10.1126/Science.1141319  0.668
2006 Mortazavi A, Leeper Thompson EC, Garcia ST, Myers RM, Wold B. Comparative genomics modeling of the NRSF/REST repressor network: from single conserved sites to genome-wide repertoire. Genome Research. 16: 1208-21. PMID 16963704 DOI: 10.1101/Gr.4997306  0.67
2006 Roden JC, King BW, Trout D, Mortazavi A, Wold BJ, Hart CE. Mining gene expression data by interpreting principal components. Bmc Bioinformatics. 7: 194. PMID 16600052 DOI: 10.1186/1471-2105-7-194  0.699
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