Genomics, computation and sequencing

Mortazavi Lab at UC Irvine

Publications

  • Occupancy maps of 208 chromatin-associated proteins in one human cell type

    Partridge, E Christopher and Chhetri, Surya B and Prokop, Jeremy W and Ramaker, Ryne C and Jansen, Camden S and Goh, Say-Tar and Mackiewicz, Mark and Newberry, Kimberly M and Brandsmeier, Laurel A and Meadows, Sarah K and others

    Nature, 2020


  • Expanded encyclopaedias of DNA elements in the human and mouse genomes

    Moore, Jill E and Purcaro, Michael J and Pratt, Henry E and Epstein, Charles B and Shoresh, Noam and Adrian, Jessika and Kawli, Trupti and Davis, Carrie A and Dobin, Alexander and Kaul, Rajinder and others

    Nature, 2020


  • Swan; a library for the analysis and visualization of long-read transcriptomes

    Reese, Fairlie and Mortazavi, Ali

    bioRxiv, 2020


  • Relationship of DUX4 and target gene expression in FSHD myocytes

    Chau, Jonathan and Kong, Xiangduk and Nguyen, Nam Viet and Williams, Katherine and Tawil, Rabi and Kiyono, Tohru and Mortazavi, Ali and Yokomori, Kyoko

    bioRxiv, 2020


  • Long-TUC-seq is a robust method for quantification of metabolically labeled full-length isoforms

    Rahmanian, Sorena and Balderrama-Gutierrez, Gabriela and Wyman, Dana and McGill, Cassandra Joan and Nguyen, Kim and Spitale, Robert and Mortazavi, Ali

    bioRxiv, 2020


  • Transcriptome-Wide Combinatorial RNA Structure Probing in Living Cells

    Chan, Dalen and Feng, Chao and England, Whitney and Wyman, Dana and Flynn, Ryan and Wang, Xiuye and Shi, Yongsheng and Mortazavi, Ali and Spitale, Robert

    bioRxiv, 2020


  • Single-nucleus RNA-seq identifies divergent populations of FSHD2 myotube nuclei

    Jiang, Shan and Williams, Katherine and Kong, Xiangduo and Zeng, Weihua and Nguyen, Nam Viet and Ma, Xinyi and Tawil, Rabi and Yokomori, Kyoko and Mortazavi, Ali

    PLoS genetics, 2020


  • A core set of venom proteins is released by entomopathogenic nematodes in the genus Steinernema

    Chang, Dennis Z and Serra, Lorrayne and Lu, Dihong and Mortazavi, Ali and Dillman, Adler R

    PLoS pathogens, 2019


  • Building gene regulatory networks from scATAC-seq and scRNA-seq using Linked Self Organizing Maps

    Jansen, Camden and Ramirez, Ricardo N and El-Ali, Nicole C and Gomez-Cabrero, David and Tegner, Jesper and Merkenschlager, Matthias and Conesa, Ana and Mortazavi, Ali

    PLoS computational biology, 2019


  • Intra-individual methylomics detects the impact of early-life adversity

    Jiang, Shan and Kamei, Noriko and Bolton, Jessica L and Ma, Xinyi and Stern, Hal S and Baram, Tallie Z and Mortazavi, Ali

    Life science alliance, 2019


  • Integrative analysis of Hydra head regeneration reveals activation of distal enhancer-like elements

    Murad, Rabi and Macias-Munoz, Aide and Wong, Ashley and Ma, Xinyi and Mortazavi, Ali

    bioRxiv, 2019


  • Feedforward regulation of Myc coordinates lineage-specific with housekeeping gene expression during B cell progenitor cell differentiation

    Ferreir{\'o}s-Vidal, Isabel and Carroll, Thomas and Zhang, Tianyi and Lagani, Vincenzo and Ramirez, Ricardo N and Ing-Simmons, Elizabeth and G{\'o}mez-Valad{\'e}s, Alicia G and Cooper, Lee and Liang, Ziwei and Papoutsoglou, Georgios and others

    PLoS biology, 2019


  • miR-128 Restriction of LINE-1 (L1) Retrotransposition Is Dependent on Targeting hnRNPA1 mRNA

    Fung, Lianna and Guzman, Herlinda and Sevrioukov, Evgueni and Idica, Adam and Park, Eddie and Bochnakian, Aurore and Daugaard, Iben and Jury, Douglas and Mortazavi, Ali and Zisoulis, Dimitrios G and others

    International journal of molecular sciences, 2019


  • Hybrid assembly of the genome of the entomopathogenic nematode Steinernema carpocapsae identifies the X-chromosome

    Serra, Lorrayne and Macchietto, Marissa and Macias-Mu{\~n}oz, Aide and McGill, Cassandra Joan and Rodriguez, Isaryhia Maya and Rodriguez, Bryan and Murad, Rabi and Mortazavi, Ali

    G3; Genes, Genomes, Genetics, 2019


  • Progressive Clustering and Characterization of Increasingly Higher Dimensional Datasets with Living Self-organizing Maps

    Jansen, Camden and Mortazavi, Ali

    , 2019


  • The genome of Peromyscus leucopus, natural host for Lyme disease and other emerging infections

    Long, Anthony D and Baldwin-Brown, James and Tao, Yuan and Cook, Vanessa J and Balderrama-Gutierrez, Gabriela and Corbett-Detig, Russell and Mortazavi, Ali and Barbour, Alan G

    Science Advances, 2019


  • Molecular evolution and expression of opsin genes in Hydra vulgaris

    Macias-Mu{\~n}oz, Aide and Murad, Rabi and Mortazavi, Ali

    BMC Genomics, 2019


  • STATegra, a comprehensive multi-omics dataset of B-cell differentiation in mouse

    Gomez-Cabrero, David and Tarazona, Sonia and Ferreir{\'o}s-Vidal, Isabel and Ramirez, Ricardo N and Company, Carlos and Schmidt, Andreas and Reijmers, Theo and von Saint Paul, Veronica and Marabita, Francesco and Rodr{\'\i}guez-Ubreva, Javier and others

    Scientific data, 2019


  • Intra-individual changes in methylome profiles; an epigenetic'scar'of early-life adversity?

    Mortazavi, Ali and Baram, Tallie Z

    , 2019


  • A technology-agnostic long-read analysis pipeline for transcriptome discovery and quantification

    Wyman, Dana and Balderrama-Gutierrez, Gabriela and Reese, Fairlie and Jiang, Shan and Rahmanian, Sorena and Zeng, Weihua and Williams, Brian A and Trout, Diane and England, Whitney and Chu, Sophie and others

    BioRxiv, 2019


  • Disrupting $\beta$-catenin dependent Wnt signaling activates an invasive gene program predictive of colon cancer progression

    Chen, George T and Tifrea, Delia F and Murad, Rabi and Lyou, Yung and Mortazavi, Ali and Edwards, Robert A and Waterman, Marian L

    bioRxiv, 2019


  • Dynamics of microRNA expression during mouse prenatal development

    Murad, Rabi and Rahmanian, Sorena and Breschi, Alessandra and Zeng, Weihua and Mackiewicz, Mark and Williams, Brian and Davis, Carrie and Roberts, Brian and Meadows, Sarah and Moore, Dianne and others

    , 2018


  • Blocking NRSF Function Rescues Spatial Memory Impaired by Early-Life Adversity and Reveals Unexpected Underlying Transcriptional Programs

    Schulmann, Anton and Bolton, Jessica L and Curran, Megan M and Regev, Limor and Kamei, Noriko and Singh-Taylor, Akanksha and Jiang, Shan and Molet, Jenny and Mortazavi, Ali and Baram, Tallie Z

    Available at SSRN 3284454, 2018


  • Occupancy patterns of 208 DNA-associated proteins in a single human cell type

    Partridge, E Christopher and Chhetri, Surya B and Prokop, Jeremy W and Ramaker, Ryne C and Jansen, Camden S and Goh, Say-Tar and Mackiewicz, Mark and Newberry, Kimberly M and Brandsmeier, Laurel A and Meadows, Sarah K and others

    bioRxiv, 2018


  • A limited capacity for microglial repopulation in the adult brain

    Najafi, Allison R and Crapser, Joshua and Jiang, Shan and Ng, Winnie and Mortazavi, Ali and West, Brian L and Green, Kim N

    Glia, 2018


  • Spatially Restricting Bioorthogonal Nucleoside Biosynthesis Enables Selective Metabolic Labeling of the Mitochondrial Transcriptome

    Nguyen, Kim and Aggarwal, Mahima B and Feng, Chao and Balderrama, Gabriela and Fazio, Michael and Mortazavi, Ali and Spitale, Robert C

    ACS chemical biology, 2018


  • TranscriptClean; Variant-aware correction of indels, mismatches, and splice junctions in long-read transcripts

    Wyman, Dana and Mortazavi, Ali

    Bioinformatics, 2018


  • SQANTI; extensive characterization of long-read transcript sequences for quality control in full-length transcriptome identification and quantification

    Tardaguila, Manuel and de la Fuente, Lorena and Marti, Cristina and Pereira, C{\'e}cile and Pardo-Palacios, Francisco Jose and del Risco, Hector and Ferrell, Marc and Mellado, Maravillas and Macchietto, Marissa and Verheggen, Kenneth and others

    Genome research, 2018


  • Adapting the Smart-seq2 Protocol for Robust Single Worm RNA-seq

    Serra, Lorrayne and Chang, Dennis Z and Macchietto, Marissa and Williams, Katherine and Murad, Rabi and Lu, Dihong and Dillman, Adler R and Mortazavi, Ali

    Bio-protocol, 2018


  • NRSF-dependent epigenetic mechanisms contribute to programming of stress-sensitive neurons by neonatal experience, promoting resilience

    Singh-Taylor, Akanksha and Molet, Jenny and Jiang, Shan and Korosi, Aniko and Bolton, Jessica L and Noam, Yoav and Simeone, Kristina and Cope, Jessica and Chen, Yuncai and Mortazavi, Ali and others

    Molecular psychiatry, 2018


  • Integrating ChIP-seq with other functional genomics data

    Jiang, Shan and Mortazavi, Ali

    Briefings in functional genomics, 2018


  • TCF7L1 suppresses primitive streak gene expression to support human embryonic stem cell pluripotency

    Sierra, Robert A and Hoverter, Nathan P and Ramirez, Ricardo N and Vuong, Linh M and Mortazavi, Ali and Merrill, Bradley J and Waterman, Marian L and Donovan, Peter J

    Development, 2018


  • Wound regeneration deficit in rats correlates with low morphogenetic potential and distinct transcriptome profile of epidermis

    Guerrero-Juarez, Christian F and Astrowski, Aliaksandr A and Murad, Rabi and Dang, Christina T and Shatrova, Vera O and Astrowskaja, Aksana and Lim, Chae Ho and Ramos, Raul and Wang, Xiaojie and Liu, Yuchen and others

    Journal of Investigative Dermatology, 2018


  • Comparative transcriptomics of Steinernema and Caenorhabditis single embryos reveals orthologous gene expression convergence during late embryogenesis

    Macchietto, Marissa and Angdembey, Dristi and Heidarpour, Negar and Serra, Lorrayne and Rodriguez, Bryan and El-Ali, Nicole and Mortazavi, Ali

    Genome Biology and Evolution, 2017


  • Prostaglandin E2 leads to the acquisition of DNMT3A-dependent tolerogenic functions in human myeloid-derived suppressor cells

    Rodr{\'\i}guez-Ubreva, Javier and Catal{\`a}-Moll, Francesc and Obermajer, Nata{\v{s}}a and {\'A}lvarez-Errico, Damiana and Ramirez, Ricardo N and Company, Carlos and Vento-Tormo, Roser and Moreno-Bueno, Gema and Edwards, Robert P and Mortazavi, Ali and others

    Cell reports, 2017


  • Prevention of C5aR1 signaling delays microglial inflammatory polarization, favors clearance pathways and suppresses cognitive loss

    Hernandez, Michael X and Jiang, Shan and Cole, Tracy A and Chu, Shu-Hui and Fonseca, Maria I and Fang, Melody J and Hohsfield, Lindsay A and Torres, Maria D and Green, Kim N and Wetsel, Rick A and others

    Molecular Neurodegeneration, 2017


  • iPSC-Derived Human Microglia-like Cells to Study Neurological Diseases

    Abud, Edsel M and Ramirez, Ricardo N and Martinez, Eric S and Healy, Luke M and Nguyen, Cecilia HH and Newman, Sean A and Yeromin, Andriy V and Scarfone, Vanessa M and Marsh, Samuel E and Fimbres, Cristhian and others

    Neuron, 2017


  • Activated entomopathogenic nematode infective juveniles release lethal venom proteins

    Lu, Dihong and Macchietto, Marissa and Chang, Dennis and Barros, Mirayana M and Baldwin, James and Mortazavi, Ali and Dillman, Adler R

    PLoS Pathogens, 2017


  • Dynamic Gene Regulatory Networks of Human Myeloid Differentiation

    Ramirez, Ricardo N and El-Ali, Nicole C and Mager, Mikayla Anne and Wyman, Dana and Conesa, Ana and Mortazavi, Ali

    Cell Systems, 2017


  • Regeneration of fat cells from myofibroblasts during wound healing

    Plikus, Maksim V and Guerrero-Juarez, Christian F and Ito, Mayumi and Li, Yun Rose and Dedhia, Priya H and Zheng, Ying and Shao, Mengle and Gay, Denise L and Ramos, Raul and Hsi, Tsai-Ching and others

    Science, 2017


  • Bcl11b and combinatorial resolution of cell fate in the T-cell gene regulatory network

    Longabaugh, William JR and Zeng, Weihua and Zhang, Jingli A and Hosokawa, Hiroyuki and Jansen, Camden S and Li, Long and Romero-Wolf, Maile and Liu, Pentao and Kueh, Hao Yuan and Mortazavi, Ali and others

    Proceedings of the National Academy of Sciences, 2017


  • Single-nucleus RNA-seq of differentiating human myoblasts reveals the extent of fate heterogeneity

    Zeng, Weihua and Jiang, Shan and Kong, Xiangduo and El-Ali, Nicole and Ball Jr, Alexander R and Ma, Christopher I-Hsing and Hashimoto, Naohiro and Yokomori, Kyoko and Mortazavi, Ali

    Nucleic acids research, 2016


  • A survey of best practices for RNA-seq data analysis

    Conesa, Ana and Madrigal, Pedro and Tarazona, Sonia and Gomez-Cabrero, David and Cervera, Alejandra and McPherson, Andrew and Szcze{\'s}niak, Micha{\l} Wojciech and Gaffney, Daniel J and Elo, Laura L and Zhang, Xuegong and others

    Genome biology, 2016


  • Comparative genomics of Steinernema reveals deeply conserved gene regulatory networks

    Dillman, Adler R and Macchietto, Marissa and Porter, Camille F and Rogers, Alicia and Williams, Brian and Antoshechkin, Igor and Lee, Ming-Min and Goodwin, Zane and Lu, Xiaojun and Lewis, Edwin E and others

    Genome biology, 2015


  • Better together; multiplexing samples to improve the preparation and reliability of gene expression studies

    Mortazavi, Ali

    Nature methods, 2015


  • Genetic and Epigenetic Characteristics of FSHD-Associated 4q and 10q D4Z4 that are Distinct from Non-4q/10q D4Z4 Homologs

    Zeng, Weihua and Chen, Yen-Yun and Newkirk, Daniel A and Wu, Beibei and Balog, Judit and Kong, Xiangduo and Ball Jr, Alexander R and Zanotti, Simona and Tawil, Rabi and Hashimoto, Naohiro and others

    Human mutation, 2014


  • Genome-wide identification and functional analysis of Apobec-1-mediated C-to-U RNA editing in mouse small intestine and liver

    Blanc, Valerie and Park, Eddie and Schaefer, Sabine and Miller, Melanie and Lin, Yiing and Kennedy, Susan and Billing, Anja M and Hamidane, Hisham Ben and Graumann, Johannes and Mortazavi, Ali and others

    Genome biology, 2014


  • A comparative encyclopedia of DNA elements in the mouse genome

    Yue, Feng and Cheng, Yong and Breschi, Alessandra and Vierstra, Jeff and Wu, Weisheng and Ryba, Tyrone and Sandstrom, Richard and Ma, Zhihai and Davis, Carrie and Pope, Benjamin D and others

    Nature, 2014


  • Extensive transcriptional response associated with seasonal plasticity of butterfly wing patterns

    Daniels, Emily V and Murad, Rabi and Mortazavi, Ali and Reed, Robert D

    Molecular ecology, 2014


  • Comparative analysis of the transcriptome across distant species

    Gerstein, Mark B and Rozowsky, Joel and Yan, Koon-Kiu and Wang, Daifeng and Cheng, Chao and Brown, James B and Davis, Carrie A and Hillier, LaDeana and Sisu, Cristina and Li, Jingyi Jessica and others

    Nature, 2014


  • The common ground of genomics and systems biology

    Conesa, Ana and Mortazavi, Ali

    BMC systems biology, 2014


  • The draft genome and transcriptome of Panagrellus redivivus are shaped by the harsh demands of a free-living lifestyle

    Srinivasan, Jagan and Dillman, Adler R and Macchietto, Marissa G and Heikkinen, Liisa and Lakso, Merja and Fracchia, Kelley M and Antoshechkin, Igor and Mortazavi, Ali and Wong, Garry and Sternberg, Paul W

    Genetics, 2013


  • Integrating and mining the chromatin landscape of cell-type specificity using self-organizing maps

    Mortazavi, Ali and Pepke, Shirley and Jansen, Camden and Marinov, Georgi K and Ernst, Jason and Kellis, Manolis and Hardison, Ross C and Myers, Richard M and Wold, Barbara J

    Genome research, 2013


  • Assessment of transcript reconstruction methods for RNA-seq

    Steijger, Tamara and Abril, Josep F and Engstr{\"o}m, P{\"a}r G and Kokocinski, Felix and Akerman, Martin and Alioto, Tyler and Ambrosini, Giovanna and Antonarakis, Stylianos E and Behr, Jonas and Bertone, Paul and others

    Nature methods, 2013


  • An integrated encyclopedia of DNA elements in the human genome

    ENCODE Project Consortium and others

    Nature, 2012


  • Incorporating Genomics into the Toolkit of Nematology

    Dillman, Adler R and Mortazavi, Ali and Sternberg, Paul W

    Journal of Nematology, 2012


  • An encyclopedia of mouse DNA elements (Mouse ENCODE)

    Stamatoyannopoulos, John A and Snyder, Michael and Hardison, Ross and Ren, Bing and Gingeras, Thomas and Gilbert, David M and Groudine, Mark and Bender, Michael and Kaul, Rajinder and Canfield, Theresa and others

    Genome Biology, 2012


  • RNA editing in the human ENCODE RNA-seq data

    Park, Eddie and Williams, Brian and Wold, Barbara J and Mortazavi, Ali

    Genome Research, 2012


  • Landscape of transcription in human cells

    Djebali, Sarah and Davis, Carrie A and Merkel, Angelika and Dobin, Alex and Lassmann, Timo and Mortazavi, Ali and Tanzer, Andrea and Lagarde, Julien and Lin, Wei and Schlesinger, Felix and others

    Nature, 2012


  • Technical considerations for functional sequencing assays

    Zeng, Weihua and Mortazavi, Ali

    Nature immunology, 2012


  • Effects of sequence variation on differential allelic transcription factor occupancy and gene expression

    Reddy, Timothy E and Gertz, Jason and Pauli, Florencia and Kucera, Katerina S and Varley, Katherine E and Newberry, Kimberly M and Marinov, Georgi K and Mortazavi, Ali and Williams, Brian A and Song, Lingyun and others

    Genome research, 2012


  • Dynamic Transformations of Genome-wide Epigenetic Marking and Transcriptional Control Establish T Cell Identity

    Zhang, Jingli A and Mortazavi, Ali and Williams, Brian A and Wold, Barbara J and Rothenberg, Ellen V

    Cell, 2012


  • Extensive promoter-centered chromatin interactions provide a topological basis for transcription regulation

    Li, Guoliang and Ruan, Xiaoan and Auerbach, Raymond K and Sandhu, Kuljeet Singh and Zheng, Meizhen and Wang, Ping and Poh, Huay Mei and Goh, Yufen and Lim, Joanne and Zhang, Jingyao and others

    Cell, 2012


  • A user's guide to the encyclopedia of DNA elements (ENCODE)

    ENCODE Project Consortium and others

    PLoS biology, 2011


  • Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation

    Trapnell, Cole and Williams, Brian A and Pertea, Geo and Mortazavi, Ali and Kwan, Gordon and Van Baren, Marijke J and Salzberg, Steven L and Wold, Barbara J and Pachter, Lior

    Nature biotechnology, 2010


  • Scaffolding a Caenorhabditis nematode genome with RNA-seq

    Mortazavi, Ali and Schwarz, Erich M and Williams, Brian and Schaeffer, Lorian and Antoshechkin, Igor and Wold, Barbara J and Sternberg, Paul W

    Genome research, 2010


  • Computation for ChIP-seq and RNA-seq studies

    Pepke, Shirley and Wold, Barbara and Mortazavi, Ali

    Nature methods, 2009


  • Mapping and quantifying mammalian transcriptomes by RNA-Seq

    Mortazavi, Ali and Williams, Brian A and McCue, Kenneth and Schaeffer, Lorian and Wold, Barbara

    Nature methods, 2008


  • A highly conserved molecular switch binds MSY-3 to regulate myogenin repression in postnatal muscle

    Berghella, Libera and De Angelis, Luciana and De Buysscher, Tristan and Mortazavi, Ali and Biressi, Stefano and Forcales, Sonia V and Sirabella, Dario and Cossu, Giulio and Wold, Barbara J

    Genes \& development, 2008


  • Genome-wide mapping of in vivo protein-DNA interactions

    Johnson, David S and Mortazavi, Ali and Myers, Richard M and Wold, Barbara

    Science, 2007


  • Comparative genomics modeling of the NRSF/REST repressor network; from single conserved sites to genome-wide repertoire

    Mortazavi, Ali and Thompson, Evonne Chen Leeper and Garcia, Sarah T and Myers, Richard M and Wold, Barbara

    Genome research, 2006


  • Mining gene expression data by interpreting principal components

    Roden, Joseph C and King, Brandon W and Trout, Diane and Mortazavi, Ali and Wold, Barbara J and Hart, Christopher E

    BMC bioinformatics, 2006