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

32 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
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  0.4
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  0.64
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  0.36
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  0.36
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  0.64
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  0.4
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  0.64
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  0.36
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  0.64
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  0.36
2018 Guerrero-Juarez CF, Astrowski AA, Murad R, Dang CT, Shatrova VO, Astrowskaja A, Lim CH, Ramos R, Wang X, Liu Y, Lee HL, Pham KT, Hsi TC, Oh JW, Crocker D, ... Mortazavi A, et al. Wound regeneration deficit in rats correlates with low morphogenetic potential and distinct transcriptome profile of epidermis. The Journal of Investigative Dermatology. PMID 29317265 DOI: 10.1016/j.jid.2017.12.030  0.36
2017 Macchietto M, Angdembey D, Heidarpour N, Serra L, Rodriguez B, El-Ali N, Mortazavi A. Comparative Transcriptomics of Steinernema and Caenorhabditis Single Embryos Reveals Orthologous Gene Expression Convergence during Late Embryogenesis. Genome Biology and Evolution. 9: 2681-2696. PMID 29048526 DOI: 10.1093/gbe/evx195  0.4
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  0.68
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  0.64
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  0.36
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  0.64
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  0.36
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  0.36
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  0.64
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  0.64
2012 Dillman AR, Mortazavi A, Sternberg PW. Incorporating genomics into the toolkit of nematology. Journal of Nematology. 44: 191-205. PMID 23482088  0.64
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  0.64
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  0.64
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  0.64
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  0.68
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  0.64
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  0.64
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  0.64
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  0.64
2009 Pepke S, Wold B, Mortazavi A. Computation for ChIP-seq and RNA-seq studies Nature Methods. 6: S22-32. PMID 19844228  0.64
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  0.64
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  0.64
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