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Saeed Tavazoie, Ph.D. - Publications

Affiliations: 
Biological Sciences, Biochemistry and Molecular Biophysics, Systems Biology Columbia University, New York, NY 
 2000 Harvard University, Cambridge, MA, United States 
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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
2022 Ketcham A, Freddolino PL, Tavazoie S. Intracellular acidification is a hallmark of thymineless death in E. coli. Plos Genetics. 18: e1010456. PMID 36279294 DOI: 10.1371/journal.pgen.1010456  0.588
2022 Freddolino PL, Amemiya HM, Goss TJ, Tavazoie S. Correction: Dynamic landscape of protein occupancy across the Escherichia coli chromosome. Plos Biology. 20: e3001557. PMID 35476699 DOI: 10.1371/journal.pbio.3001557  0.528
2021 Freddolino PL, Amemiya HM, Goss TJ, Tavazoie S. Dynamic landscape of protein occupancy across the Escherichia coli chromosome. Plos Biology. 19: e3001306. PMID 34170902 DOI: 10.1371/journal.pbio.3001306  0.649
2021 Freddolino PL, Amemiya HM, Goss TJ, Tavazoie S. Dynamic landscape of protein occupancy across the Escherichia coli chromosome. Plos Biology. 19: e3001306. PMID 34170902 DOI: 10.1371/journal.pbio.3001306  0.649
2020 Momen-Roknabadi A, Oikonomou P, Zegans M, Tavazoie S. An inducible CRISPR interference library for genetic interrogation of Saccharomyces cerevisiae biology. Communications Biology. 3: 723. PMID 33247197 DOI: 10.1038/s42003-020-01452-9  0.323
2020 Blattman SB, Jiang W, Oikonomou P, Tavazoie S. Prokaryotic single-cell RNA sequencing by in situ combinatorial indexing. Nature Microbiology. PMID 32451472 DOI: 10.1038/S41564-020-0729-6  0.38
2020 Jiang W, Oikonomou P, Tavazoie S. Comprehensive Genome-wide Perturbations via CRISPR Adaptation Reveal Complex Genetics of Antibiotic Sensitivity. Cell. PMID 32109417 DOI: 10.1016/J.Cell.2020.02.007  0.421
2020 Khare A, Tavazoie S. Extreme Antibiotic Persistence via Heterogeneity-Generating Mutations Targeting Translation. Msystems. 5. PMID 31964772 DOI: 10.1128/mSystems.00847-19  0.777
2019 Vejnar CE, Abdelmessih M, Takacs C, Yartseva V, Oikonomou P, Christiano R, Stoeckius M, Lau S, Lee M, Beaudoin JD, Musaev D, Darwich-Codore H, Walther T, Tavazoie S, Cifuentes D, et al. Genome wide analysis of 3'-UTR sequence elements and proteins regulating mRNA stability during maternal-to-zygotic transition in zebrafish. Genome Research. PMID 31227602 DOI: 10.1101/Gr.245159.118  0.406
2018 Masoudi N, Tavazoie S, Glenwinkel L, Ryu L, Kim K, Hobert O. Unconventional function of an Achaete-Scute homolog as a terminal selector of nociceptive neuron identity. Plos Biology. 16: e2004979. PMID 29672507 DOI: 10.1371/Journal.Pbio.2004979  0.329
2018 Freddolino PL, Yang J, Momen-Roknabadi A, Tavazoie S. Stochastic tuning of gene expression enables cellular adaptation in the absence of pre-existing regulatory circuitry. Elife. 7. PMID 29620524 DOI: 10.7554/Elife.31867  0.67
2018 Freddolino PL, Yang J, Momen-Roknabadi A, Tavazoie S. Author response: Stochastic tuning of gene expression enables cellular adaptation in the absence of pre-existing regulatory circuitry Elife. DOI: 10.7554/Elife.31867.052  0.645
2016 Fish L, Pencheva N, Goodarzi H, Tran H, Yoshida M, Tavazoie SF. Muscleblind-like 1 suppresses breast cancer metastatic colonization and stabilizes metastasis suppressor transcripts. Genes & Development. 30: 386-98. PMID 26883358 DOI: 10.1101/Gad.270645.115  0.62
2015 Khare A, Tavazoie S. Multifactorial Competition and Resistance in a Two-Species Bacterial System. Plos Genetics. 11: e1005715. PMID 26647077 DOI: 10.1371/Journal.Pgen.1005715  0.777
2015 Alarcón CR, Goodarzi H, Lee H, Liu X, Tavazoie S, Tavazoie SF. HNRNPA2B1 Is a Mediator of m(6)A-Dependent Nuclear RNA Processing Events. Cell. PMID 26321680 DOI: 10.1016/J.Cell.2015.08.011  0.622
2015 Furlow PW, Zhang S, Soong TD, Halberg N, Goodarzi H, Mangrum C, Wu YG, Elemento O, Tavazoie SF. Mechanosensitive pannexin-1 channels mediate microvascular metastatic cell survival. Nature Cell Biology. PMID 26098574 DOI: 10.1038/ncb3194  0.64
2015 Goodarzi H, Liu X, Nguyen HC, Zhang S, Fish L, Tavazoie SF. Endogenous tRNA-Derived Fragments Suppress Breast Cancer Progression via YBX1 Displacement. Cell. 161: 790-802. PMID 25957686 DOI: 10.1016/J.Cell.2015.02.053  0.608
2015 Alarcón CR, Lee H, Goodarzi H, Halberg N, Tavazoie SF. N6-methyladenosine marks primary microRNAs for processing. Nature. 519: 482-5. PMID 25799998 DOI: 10.1038/Nature14281  0.561
2014 Goodarzi H, Tavazoie SF, Tavazoie S. TARBP2 binding structured RNA elements drives metastasis. Cell Cycle (Georgetown, Tex.). 13: 2799-800. PMID 25486461 DOI: 10.4161/15384101.2014.954453  0.701
2014 Goodarzi H, Zhang S, Buss CG, Fish L, Tavazoie S, Tavazoie SF. Metastasis-suppressor transcript destabilization through TARBP2 binding of mRNA hairpins. Nature. 513: 256-60. PMID 25043050 DOI: 10.1038/Nature13466  0.673
2014 Oikonomou P, Goodarzi H, Tavazoie S. Systematic identification of regulatory elements in conserved 3' UTRs of human transcripts. Cell Reports. 7: 281-92. PMID 24656821 DOI: 10.1016/J.Celrep.2014.03.001  0.77
2014 Freddolino PL, Goodarzi H, Tavazoie S. Revealing the genetic basis of natural bacterial phenotypic divergence. Journal of Bacteriology. 196: 825-39. PMID 24317396 DOI: 10.1128/Jb.01039-13  0.73
2013 Hottes AK, Freddolino PL, Khare A, Donnell ZN, Liu JC, Tavazoie S. Bacterial adaptation through loss of function. Plos Genetics. 9: e1003617. PMID 23874220 DOI: 10.1371/Journal.Pgen.1003617  0.758
2013 Chiu IM, Morimoto ET, Goodarzi H, Liao JT, O'Keeffe S, Phatnani HP, Muratet M, Carroll MC, Levy S, Tavazoie S, Myers RM, Maniatis T. A neurodegeneration-specific gene-expression signature of acutely isolated microglia from an amyotrophic lateral sclerosis mouse model. Cell Reports. 4: 385-401. PMID 23850290 DOI: 10.1016/J.Celrep.2013.06.018  0.628
2013 Freddolino P, Tavazoie S. Genome-Wide Measurement of Bacterial Transcriptional Regulatory States Biophysical Journal. 104: 328a. DOI: 10.1016/J.Bpj.2012.11.1820  0.691
2012 Freddolino PL, Tavazoie S. The dawn of virtual cell biology. Cell. 150: 248-50. PMID 22817888 DOI: 10.1016/J.Cell.2012.07.001  0.593
2012 Girgis HS, Harris K, Tavazoie S. Large mutational target size for rapid emergence of bacterial persistence. Proceedings of the National Academy of Sciences of the United States of America. 109: 12740-5. PMID 22802628 DOI: 10.1073/Pnas.1205124109  0.369
2012 Freddolino PL, Goodarzi H, Tavazoie S. Fitness landscape transformation through a single amino acid change in the rho terminator. Plos Genetics. 8: e1002744. PMID 22693458 DOI: 10.1371/Journal.Pgen.1002744  0.75
2012 Freddolino PL, Tavazoie S. Beyond homeostasis: a predictive-dynamic framework for understanding cellular behavior. Annual Review of Cell and Developmental Biology. 28: 363-84. PMID 22559263 DOI: 10.1146/Annurev-Cellbio-092910-154129  0.611
2012 Goodarzi H, Najafabadi HS, Oikonomou P, Greco TM, Fish L, Salavati R, Cristea IM, Tavazoie S. Systematic discovery of structural elements governing stability of mammalian messenger RNAs. Nature. 485: 264-8. PMID 22495308 DOI: 10.1038/Nature11013  0.769
2012 Freddolino PL, Amini S, Tavazoie S. Newly identified genetic variations in common Escherichia coli MG1655 stock cultures. Journal of Bacteriology. 194: 303-6. PMID 22081388 DOI: 10.1128/Jb.06087-11  0.636
2011 Amini S, Hottes AK, Smith LE, Tavazoie S. Fitness landscape of antibiotic tolerance in Pseudomonas aeruginosa biofilms. Plos Pathogens. 7: e1002298. PMID 22028649 DOI: 10.1371/Journal.Ppat.1002298  0.322
2011 Birsoy K, Berry R, Wang T, Ceyhan O, Tavazoie S, Friedman JM, Rodeheffer MS. Analysis of gene networks in white adipose tissue development reveals a role for ETS2 in adipogenesis. Development (Cambridge, England). 138: 4709-19. PMID 21989915 DOI: 10.1242/Jcs.101436  0.386
2011 Amini S, Tavazoie S. Antibiotics and the post-genome revolution. Current Opinion in Microbiology. 14: 513-8. PMID 21816663 DOI: 10.1016/J.Mib.2011.07.017  0.359
2011 Hottes AK, Tavazoie S. Microarray-based genetic footprinting strategy to identify strain improvement genes after competitive selection of transposon libraries. Methods in Molecular Biology (Clifton, N.J.). 765: 83-97. PMID 21815088 DOI: 10.1007/978-1-61779-197-0_6  0.356
2010 Lieber DS, Elemento O, Tavazoie S. Large-scale discovery and characterization of protein regulatory motifs in eukaryotes. Plos One. 5: e14444. PMID 21206902 DOI: 10.1371/Journal.Pone.0014444  0.535
2010 Goodarzi H, Bennett BD, Amini S, Reaves ML, Hottes AK, Rabinowitz JD, Tavazoie S. Regulatory and metabolic rewiring during laboratory evolution of ethanol tolerance in E. coli. Molecular Systems Biology. 6: 378. PMID 20531407 DOI: 10.1038/Msb.2010.33  0.619
2009 Goodarzi H, Elemento O, Tavazoie S. Revealing global regulatory perturbations across human cancers. Molecular Cell. 36: 900-11. PMID 20005852 DOI: 10.1016/J.Molcel.2009.11.016  0.716
2009 Vora T, Hottes AK, Tavazoie S. Protein occupancy landscape of a bacterial genome. Molecular Cell. 35: 247-53. PMID 19647521 DOI: 10.1016/J.Molcel.2009.06.035  0.376
2009 Goodarzi H, Hottes AK, Tavazoie S. Global discovery of adaptive mutations. Nature Methods. 6: 581-3. PMID 19597501 DOI: 10.1038/Nmeth.1352  0.641
2009 Lu X, Li JM, Elemento O, Tavazoie S, Wieschaus EF. Coupling of zygotic transcription to mitotic control at the Drosophila mid-blastula transition. Development (Cambridge, England). 136: 2101-10. PMID 19465600 DOI: 10.1242/Dev.034421  0.521
2009 Girgis HS, Hottes AK, Tavazoie S. Genetic architecture of intrinsic antibiotic susceptibility. Plos One. 4: e5629. PMID 19462005 DOI: 10.1371/Journal.Pone.0005629  0.307
2009 Amini S, Goodarzi H, Tavazoie S. Genetic dissection of an exogenously induced biofilm in laboratory and clinical isolates of E. coli. Plos Pathogens. 5: e1000432. PMID 19436718 DOI: 10.1371/Journal.Ppat.1000432  0.622
2009 Freckleton G, Lippman SI, Broach JR, Tavazoie S. Microarray profiling of phage-display selections for rapid mapping of transcription factor-DNA interactions. Plos Genetics. 5: e1000449. PMID 19360118 DOI: 10.1371/Journal.Pgen.1000449  0.391
2009 Legesse-Miller A, Elemento O, Pfau SJ, Forman JJ, Tavazoie S, Coller HA. let-7 Overexpression leads to an increased fraction of cells in G2/M, direct down-regulation of Cdc34, and stabilization of Wee1 kinase in primary fibroblasts. The Journal of Biological Chemistry. 284: 6605-9. PMID 19126550 DOI: 10.1074/Jbc.C900002200  0.53
2008 Tagkopoulos I, Liu YC, Tavazoie S. Predictive behavior within microbial genetic networks. Science (New York, N.Y.). 320: 1313-7. PMID 18467556 DOI: 10.3731/Topologica.2.018  0.652
2007 Elemento O, Tavazoie S. Fastcompare: a nonalignment approach for genome-scale discovery of DNA and mRNA regulatory elements using network-level conservation. Methods in Molecular Biology (Clifton, N.J.). 395: 349-66. PMID 17993685 DOI: 10.1385/1-59745-514-8:349  0.517
2007 Elemento O, Slonim N, Tavazoie S. A universal framework for regulatory element discovery across all genomes and data types. Molecular Cell. 28: 337-50. PMID 17964271 DOI: 10.1016/J.Molcel.2007.09.027  0.774
2007 Girgis HS, Liu Y, Ryu WS, Tavazoie S. A comprehensive genetic characterization of bacterial motility. Plos Genetics. 3: 1644-60. PMID 17941710 DOI: 10.1371/Journal.Pgen.0030154  0.429
2007 De Renzis S, Elemento O, Tavazoie S, Wieschaus EF. Unmasking activation of the zygotic genome using chromosomal deletions in the Drosophila embryo. Plos Biology. 5: e117. PMID 17456005 DOI: 10.1371/Journal.Pbio.0050117  0.56
2007 Lahav R, Gammie A, Tavazoie S, Rose MD. Role of transcription factor Kar4 in regulating downstream events in the Saccharomyces cerevisiae pheromone response pathway. Molecular and Cellular Biology. 27: 818-29. PMID 17101777 DOI: 10.1128/Mcb.00439-06  0.431
2006 Slonim N, Elemento O, Tavazoie S. Ab initio genotype-phenotype association reveals intrinsic modularity in genetic networks. Molecular Systems Biology. 2: 2006.0005. PMID 16732191 DOI: 10.1038/Msb4100047  0.745
2005 Chan CS, Elemento O, Tavazoie S. Revealing posttranscriptional regulatory elements through network-level conservation. Plos Computational Biology. 1: e69. PMID 16355253 DOI: 10.1371/Journal.Pcbi.0010069  0.681
2005 Elemento O, Tavazoie S. Fast and systematic genome-wide discovery of conserved regulatory elements using a non-alignment based approach. Genome Biology. 6: R18. PMID 15693947 DOI: 10.1186/Gb-2005-6-2-R18  0.548
2005 Chan C, Elemento O, Tavazoie S. Revealing post-transcriptional regulatory interactions through network-level conservation Plos Computational Biology. DOI: 10.1371/Journal.Pcbi.0010069.Eor  0.337
2004 Kurdistani SK, Tavazoie S, Grunstein M. Mapping global histone acetylation patterns to gene expression. Cell. 117: 721-33. PMID 15186774 DOI: 10.1016/J.Cell.2004.05.023  0.373
2004 Wang Y, Pierce M, Schneper L, Güldal CG, Zhang X, Tavazoie S, Broach JR. Ras and Gpa2 mediate one branch of a redundant glucose signaling pathway in yeast. Plos Biology. 2: E128. PMID 15138498 DOI: 10.1371/Journal.Pbio.0020128  0.332
2004 Beer MA, Tavazoie S. Predicting gene expression from sequence. Cell. 117: 185-98. PMID 15084257 DOI: 10.1016/S0092-8674(04)00304-6  0.651
2004 Jim K, Parmar K, Singh M, Tavazoie S. A cross-genomic approach for systematic mapping of phenotypic traits to genes. Genome Research. 14: 109-15. PMID 14707173 DOI: 10.1101/Gr.1586704  0.388
2004 Pritsker M, Liu YC, Beer MA, Tavazoie S. Whole-genome discovery of transcription factor binding sites by network-level conservation. Genome Research. 14: 99-108. PMID 14672978 DOI: 10.1101/Gr.1739204  0.63
2002 Kurdistani SK, Robyr D, Tavazoie S, Grunstein M. Genome-wide binding map of the histone deacetylase Rpd3 in yeast. Nature Genetics. 31: 248-54. PMID 12089521 DOI: 10.1038/Ng907  0.427
2001 Badarinarayana V, Estep PW, Shendure J, Edwards J, Tavazoie S, Lam F, Church GM. Selection analyses of insertional mutants using subgenic-resolution arrays. Nature Biotechnology. 19: 1060-5. PMID 11689852 DOI: 10.1038/Nbt1101-1060  0.777
2000 Hughes JD, Estep PW, Tavazoie S, Church GM. Computational identification of cis-regulatory elements associated with groups of functionally related genes in Saccharomyces cerevisiae. Journal of Molecular Biology. 296: 1205-14. PMID 10698627 DOI: 10.1006/Jmbi.2000.3519  0.784
1999 Tavazoie S, Hughes JD, Campbell MJ, Cho RJ, Church GM. Systematic determination of genetic network architecture. Nature Genetics. 22: 281-5. PMID 10391217 DOI: 10.1038/10343  0.698
1998 Tavazoie S, Church GM. Quantitative whole-genome analysis of DNA-protein interactions by in vivo methylase protection in E. coli. Nature Biotechnology. 16: 566-71. PMID 9624689 DOI: 10.1038/Nbt0698-566  0.549
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