Publications
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.
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