Columbia University in the City of New York

Tavazoie Lab


Systematic assessment of prognostic molecular features across cancers
Cell Genomics 3, 100262 2023
Santhanam, B., Oiknomou, P. Tavazoie, S.

OxPhos defects cause hypermetabolism and reduce lifespan in cells and in patients with mitochondrial diseases.
Communication Biology 6(1):22 2023
Sturm, G. et al.

Arginine limitation drives a directed codon-dependent DNA sequence evolution response in colorectal cancer cells
Science Advances 9(1):eade9120 2023
Hsu D.J., Gao, J., Yamaguchi, N., Pinzaru, Al., Wu, Q., Mandayam, N., Liberti, M., Heissel, S., Alwaseem, H., Tavazoie, S., Tavazoie, S.F.

Intracellular acidification is a hallmark of thymineless death in E. coli
PLoS Genetics 180(10):e1010456 2022
Ketcham, A., Freddolino, P.L. Tavazoie, S.

Functional genetic screen identifies ITPR3/calcium/RELB axis as a driver of colorectal
cancer metastasis liver colonization
Developmental Cell 57(9):1146-1159:e7 2022
Moy, R.H. et al.

Dynamic landscape of protein occupancy across the Escherichia coli chromosome.
PLoS Biology 19(6):e3001306 2021
Freddolino, P., Amemiya, H.M., Goss, T.J., Tavazoie, S.

Molecular topography of an entire nervous system.
Cell Jul 2:S0092-8674(21)00758-3 2021
Taylor, S.R. et al.

An inducible CRISPR interference library for genetic interrogation of Sacharomyces cerevisiae biology.
Communications Biology 3(1):723 2020
Momen-Roknabadi, A., Oikonomou, P., Tavazoie, S.

In vivo mRNA display enables large-scale proteomics by next generation sequencing.
PNAS 117(43):26710 2020
Oikonomou, P., Salatino, R., Tavazoie, S.

Research Highlight: Nucleic-acid sequencing of proteomes Nature Reviews Genetics

Regulatory and evolutionary adaptation of yeast to acute lethal ethanol stress.
PLoS One e0239528 2020
Yang, J., Tavazoie, S.

Prokaryotic Single-Cell RNA Sequencing by in Situ Combinatorial Indexing.
Nature Microbiology May 25, 2020
Blattman, S.B., Jiang, W., Oikonomou, P., Tavazoie, S.

Comprehensive genome-wide perturbations via CRISPR adaptation reveal complex genetics of antibiotic sensitivity.
Cell 180(5):1002 2020
Jiang, W, Oikonomou, P., Tavazoie, S.

Dynamic landscape of protein occupancy across the Escherichia coli chromosome.
BioRxiv Januray 30, 2020
Freddolino, P., Gross, TJ, Amemiya, M., Tavazoie, S.

Extreme Antibiotic Persistence via Heterogeneity-Generating Mutations Targeting Translation.
mSystems 5(1), pii: e00847-19 Januray 21, 2020
Khare, A., Tavazoie, S.

Genome wide analysis of 3' UTR sequence elements and proteins regulating mRNA stability during maternal-to-zygotic transition in zebrafish.
Genome Research 2019 29(7):1100-1114 (2019)
Vejnar CE, Abdel Messih M, Takacs CM, Yartseva V, Oikonomou P, Christiano R, Stoeckius M, Lau S, Lee MT, Beaudoin JD, Musaev D, Darwich-Codore H, Walther TC, Tavazoie S, Cifuentes D, Giraldez AJ.

Unconventional function of an Achaete-Scute homolog as a terminal selector of nociceptive neuron identity.
PLoS Biology 16(4):e2004979 2018
Masoudi, N., Tavazoie, S., Glenwinkel, L., Ryu, L., Kim, K., Hobert, O.

Stochastic tuning of gene expression enables cellular adaptation in the absence of pre-existing regulatory circuitry.
eLife 2018;7:e31867 DOI: 10.7554/eLife.31867
Freddolino, P., Yang, J., Momen-Roknabadi, A., Tavazoie, S.

Cellular adaptation by fitness-directed transcriptional tuning.
BioRxiv May 14, 2017
Freddolino, P., Yang, J., Tavazoie, S.

Multifactorial competition and resistance in a two-species bacterial system.
PLoS Genetics 2015 11(12):e1005715
Khare, A., Tavazoie, S.

HNRNPA2B1 is a mediator of m6A-dependent nuclear RNA processing events.
Cell 2015 162(6):1299-308
Alarcon, C.R., Goodarzi, H., Lee, H, Liu, X., Tavazoie, S., Tavazoie, S.F.

TARBP2 binding structured RNA elements drives metastasis.
Cell Cycle. 2014 13(18):2799-2800
Goodarzi, H., Tavazoie, S.F., & Tavazoie, S.

Metastasis-suppressor transcript destabilization through TARBP2 binding of mRNA hairpins.
Nature. 2014 513, 255-260
Goodarzi, H., Zhang, S., Buss, C.G., Fish, L., Tavazoie, S., & Tavazoie, S.F.

Systematic Identification of Regulatory Elements in Conserved 3′ UTRs of Human Transcripts.
Cell Reports. 2014 Mar 20.
Oikonomou, P., Goodarzi, H. & Tavazoie, S.

Revealing the genetic basis of natural bacterial phenotypic divergence.
J Bacteriol. 2013 [Epub ahead of print] PDF
Freddolino, P.L., Goodarzi, H. & Tavazoie, S.

Synaptic state matching: a dynamical architecture for predictive internal representation and feature detection..
PLoS One. 2013 Aug 26;8(8):e72865. doi: 10.1371/journal.pone.0072865.
Tavazoie, S.

Bacterial adaptation through loss of function.
PLoS Genet. 2013;9(7):e1003617. doi: 10.1371/journal.pgen.1003617.
Hottes, A.K., Freddolino, P.L., Khare, A., Donnell, Z.N., Liu, J.C., & Tavazoie, S.

A neurodegeneration-specific gene-expression signature of acutely isolated microglia from an amyotrophic lateral sclerosis mouse model.
Cell Rep. 2013 Jul 25;4(2):385-401. doi: 10.1016/j.celrep.2013.06.018.
Chiu, I.M., Morimoto, E.T., Goodarzi, H., Liao, J.T., O'Keeffe, S., Phatnani, H.P., Muratet, M., Carroll, M.C., Levy, S., Tavazoie, S., Myers, R.M., & Maniatis, T.

The dawn of virtual cell biology.
Cell. 2012 Jul 20;150(2):248-50. PDF
Freddolino, P. & Tavazoie, S.

Beyond homeostasis: a predictive-dynamic framework for understanding cellular behavior.
Annu Rev Cell Biol 2012. Vol. 28: 363-384
Freddolino, P.L., & Tavazoie, S.

Large mutational target size for rapid emergence of bacterial persistence.
Proc Natl Acad Sci U S A. 2012 Jul 16. [Epub ahead of print] PDF
Girgis, H.S., Harris, K., & Tavazoie, S.

Fitness landscape transformation through a single amino acid change in the Rho terminator
PLoS Genetics, Vol. 8, No. 5. (2012), e1002744
Freddolino, P., Goodarzi, H., & Tavazoie, S.

Systematic discovery of structural elements governing stability of mammalian messenger RNAs
Nature 485, 264-268 (2012) PDF
Goodarzi, H., Najafabadi, H.S., Oikonomou, P., Greco, T.M., Fish, L., Salavati, R., Cristea, I.M., & Tavazoie, S.

Accurate proteome-wide protein quantification from high-resolution 15N mass spectra
Genome Biology 12:R122 (2011) PDF
Khan, Z., Amini, S., Bloom, J.S., Ruse, C., Caudy, A.A., Kruglyak, L., Singh, M., Perlman, D.H., & Tavazoie, S.

Newly Identified Genetic Variations in Common Escherichia coli MG1655 Stock Cultures
Journal of Bacteriology 2011 Nov 11. [Epub ahead of print] PDF
Freddolino, P.L., Amini, S. & Tavazoie, S.

Analysis of gene networks in white adipose tissue development reveals a role for ETS2 in adipogenesis
Development. Nov;138(21):4709-19 (2011). PDF
Birsoy K, Berry R, Wang T, Ceyhan O, Tavazoie S, Friedman JM, Rodeheffer MS.

Antibiotics and the post-genome revolution
Current Opinion in Microbiology 14 (2011). PDF
Amini S. & Tavazoie, S.

Microarray-based genetic footprinting strategy to identify strain improvement genes after competitive selection of transposon libraries
Methods Mol Biol. 765:83-97 (2011). PDF
Hottes, A.K. & Tavazoie, S.

Fitness Landscape of Antibiotic Tolerance in Pseudomonas aeruginosa Biofilms
PLoS Pathogens 7(10):e1002298 (2011). PDF
Amini S., Hottes, A.K., Tavazoie, S.

Large-scale discovery and characterization of protein regulatory motifs in eukaryotes
PLoS One. 2010 December 29;5(12):e14444. PDF
Lieber DS, Elemento O, Tavazoie S

Regulatory and metabolic rewiring during laboratory evolution of ethanol tolerance in E. coli
Mol Syst Biol. 2010 Jun 8; 6:378. PDF
Goodarzi H, Bennett BD, Amini S, Reaves ML, Hottes AK, Rabinowitz JD, Tavazoie S

Revealing global regulatory perturbations across human cancers
Molecular Cell. 2009 Dec 11; 36:900-911. PDF
Goodarzi, H, Elemento, O, Tavazoie S
Preview in same issue: A FIRE-y PAGE in computational analysis of cancer profiles by Prensner JR, Chinnaiyan AM ( PDF )

Global protein occupancy landscape of a bacterial genome
Molecular Cell. 2009 Jul 31;35(2):247-53. PDF
Vora T, Hottes AK, Tavazoie S

Global discovery of adaptive mutations
Nature Methods. 2009 Aug; 6(8):581-3. PDF
Goodarzi H, Hottes AK, Tavazoie S

Coupling of zygotic transcription to mitotic control at the Drosophila mid-blastula transition.
Development. 2009 Jun;136(12):2101-10. PDF
Lu X, Li JM, Elemento O, Tavazoie S, Wieschaus EF

Genetic architecture of intrinsic antibiotic susceptibility.
PLoS ONE. 2009 May 20;4(5):e5629. PDF
Girgis HS, Hottes AK, Tavazoie S

Genetic dissection of an exogenously induced biofilm in laboratory and clinical isolates of E. coli.
PLoS Pathog. 2009 May;5(5):e1000432. Epub 2009 May 15. PDF
Amini S, Goodarzi H, Tavazoie S

Microarray profiling of phage-display selections for rapid mapping of transcription factor-DNA interactions.
PLoS Genet. 2009 Apr;5(4):e1000449. Epub 2009 Apr 10. PDF
Freckleton G, Lippman SI, Broach JR, Tavazoie S

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.
J Biol Chem. 2009 Mar 13;284(11):6605-9. Epub 2009 Jan 6. PDF
Legesse-Miller A, Elemento O, Pfau SJ, Forman JJ, Tavazoie S, Coller HA

Predictive behavior within microbial genetic networks
Science (2008) 320:1313-1317, Epub 2008 May 8. PDF
Tagkopoulos I, Liu Y, Tavazoie S

A universal framework for regulatory element discovery across all genomes and data-types
Molecular Cell (2007) 28(2):337-50. PDF
Elemento O, Slonim N, Tavazoie S
Highlight in Nature Reviews Genetics 8:908-909 ( PDF )

A comprehensive genetic characterization of bacterial motility
PLoS Genetics (2007) 3 (9): e154. PDF
Girgis H, Liu Y, Ryu W, Tavazoie S
Highlight in Nature Reviews Genetics 8:653-653 ( PDF )

Unmasking the zygotic genome using chromosome deletion in the Drosophila embryo.
PLoS Biology (2007) 5(5): e117. PDF
De Renzis S, Elemento O, Tavazoie S, Wieschaus EF

Fastcompare: A non-alignment approach for genome-scale discovery of DNA and mRNA regulatory elements using network-level conservation
Methods in Mol. Biol., Comparative Genomics, 2007
Elemento O, Tavazoie S.

Role of transcription factor Kar4 in regulating downstream events in the Saccharomyces cerevisiae pheromone response pathway.
Mol. Cell Biol. 2006 Nov. 13, Epub. PDF
Lahav R, Gammie A, Tavazoie S, Rose MD

Ab initio genotype-phenotype association reveals the intrinsic modularity of genetic networks.
Molecular Systems Biology 2006; 2:2006.0005. Epub 2006 Jan 31. PDF
(Slonim N, Elemento O, equal contribution) and Tavazoie S

Revealing posttranscriptional regulatory elements through network-level conservation.
PLoS Computational Biology 2005 Dec; 1(7): e69 Epub 2005 Dec. 9. PDF
(Chan S, Elemento O, equal contribution) and Tavazoie S

Fast and systematic genome-wide discovery of conserved regulatory elements using a non-alignment based approach.
Genome Biology (2005) 6(2):R18. Epub 2005 Jan 26. PDF
Elemento O, Tavazoie S

Mapping global histone acetylation patterns to gene expression.
Cell 2004 Jun 11; 117(6):721-33. PDF
Kurdistani SK, Tavazoie S, Grunstein M

Predicting gene expression from sequence.
Cell 2004 Apr 16; 117(2):185-98. PDF
Beer MA, Tavazoie S
Highlight in Nature Reviews Genetics ( PDF )

A cross-genomic approach for systematic mapping of phenotypic traits to genes.
Genome Research 2004 Jan; 14(1):109-15. PDF
Jim K, Parmar K, Singh M, Tavazoie S

Whole-genome discovery of transcription factor binding sites by network-level conservation.
Genome Research 2004 Jan; 14(1):99-108. PDF
Pritsker M, Liu Y, Beer M, Tavazoie S

Ras and Gpa2 mediate one branch of a redundant glucose signaling pathway in yeast.
PLoS Biology 2004 May; 2 (5): Epub 2004 May 11. PDF
Wang Y, Pierce M, Schneper L, Güldal CG, Zhang X, Tavazoie S, Broach JR

Genomewide binding map of RPD3 histone deacetylase in yeast.
Nature Genetics 2002 31: 248-254. PDF
Kurdistani S, Robyr D, Tavazoie S, Grunstein M

Selection analyses of insertional mutants using subgenic-resolution arrays.
Nature Biotechnology 2001 19: 1060-1065. PDF
Badarinarayana V, Estep PW 3rd, Shendure J, Edwards J, Tavazoie S, Lam F, Church GM

Computational identification of cis-regulatory elements within functionally related groups of genes in Saccharomyces cerevisiae.
Journal of Molecular Biology 2000 296: 1205-1214. PDF
Hughes JD, Estep PW, Tavazoie S, Church GM

Systematic determination of genetic network architecture.
Nature Genetics 1999 22: 281-285. PDF
Tavazoie S, Hughes JD, Campbell MJ, Cho RJ, Church GM

Quantitative whole-genome analysis of DNA-protein interactions by in vivo methylase protection in E. coli.
Nature Biotechnology 1998 16: 566-571. PDF
Tavazoie S, Church GM

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