Troyanskaya O. "Getting started in. ": a series not to miss. PLoS Comput Biol. 2007;3(10):1841.

Koivunen P, Fell SM, Lu W, Rabinowitz JD, Kung AL, Schlisio S. The 2-oxoglutarate analog 3-oxoglutarate decreases normoxic hypoxia-inducible factor-1α in cancer cells, induces cell death, and reduces tumor xenograft growth. Hypoxia (Auckl). 2016;4:15–27. PMCID: PMC4981084

Rodan LH, Qi W, Ducker GS, Demirbas D, Laine R, Yang E, Walker MA, Eichler F, Rabinowitz JD, Anselm I, Berry GT, Network UD. 5,10-methenyltetrahydrofolate synthetase deficiency causes a neurometabolic disorder associated with microcephaly, epilepsy, and cerebral hypomyelination. Mol Genet Metab. 2018;125(1-2):118–126. PMCID: PMC6557438

Reaves ML, Sinha S, Rabinowitz JD, Kruglyak L, Redfield RJ. Absence of detectable arsenate in DNA from arsenate-grown GFAJ-1 cells. Science. 2012;337(6093):470–3.

Webber AL, Tilghman SM. The absence of enhancer competition between Igf2 and H19 following transfer into differentiated cells. Mol Cell Biol. 1998;18(4):1903–10.

Bennett BD, Kimball EH, Gao M, Osterhout R, Van Dien SJ, Rabinowitz JD. Absolute metabolite concentrations and implied enzyme active site occupancy in Escherichia coli. Nat Chem Biol. 2009;5(8):593–9.

Bennett BD, Yuan J, Kimball EH, Rabinowitz JD. Absolute quantitation of intracellular metabolite concentrations by an isotope ratio-based approach. Nat Protoc. 2008;3(8):1299–311.

Heck JA, Gresham D, Botstein D, Alani E. Accumulation of recessive lethal mutations in Saccharomyces cerevisiae mlh1 mismatch repair mutants is not associated with gross chromosomal rearrangements. Genetics. 2006;174(1):519–23.

Endres RG, Wingreen NS. Accuracy of direct gradient sensing by cell-surface receptors. Prog Biophys Mol Biol. 2009;100(1-3):33–9.

Endres RG, Wingreen NS. Accuracy of direct gradient sensing by single cells. Proc Natl Acad Sci U S A. 2008;105(41):15749–54.

Myers CL, Dunham M, Kung SY, Troyanskaya OG. Accurate detection of aneuploidies in array CGH and gene expression microarray data. Bioinformatics. 2004;20(18):3533–43.

Greene CS, Troyanskaya OG. Accurate evaluation and analysis of functional genomics data and methods. Ann N Y Acad Sci. 2012;1260:95–100.

Zhou J, Schor IE, Yao V, Theesfeld CL, Marco-Ferreres R, Tadych A, Furlong EEM, Troyanskaya OG. Accurate genome-wide predictions of spatio-temporal gene expression during embryonic development. PLoS Genet. 2019;15(9):e1008382. PMCID: PMC6779412

Dubuis J, Samanta R, Gregor T. Accurate measurements of dynamics and reproducibility in small genetic networks. Mol Syst Biol. 2013;9:639.

Khan Z, Amini S, Bloom JS, Ruse C, Caudy AA, Kruglyak L, Singh M, Perlman DH, Tavazoie S. Accurate proteome-wide protein quantification from high-resolution 15N mass spectra. Genome Biol. 2011;12(12):R122.

Chikina MD, Troyanskaya OG. Accurate quantification of functional analogy among close homologs. PLoS Comput Biol. 2011;7(2):e1001074.

Goyal S, Yuan J, Chen T, Rabinowitz JD, Wingreen NS. Achieving optimal growth through product feedback inhibition in metabolism. PLoS Comput Biol. 2010;6(6):e1000802.

Rabinowitz JD, Kimball E. Acidic acetonitrile for cellular metabolome extraction from Escherichia coli. Anal Chem. 2007;79(16):6167–73.

Wang S, Arellano-Santoyo H, Combs PA, Shaevitz JW. Actin-like cytoskeleton filaments contribute to cell mechanics in bacteria. Proc Natl Acad Sci U S A. 2010;107(20):9182–5.

Mignot T, Shaevitz JW. Active and passive mechanisms of intracellular transport and localization in bacteria. Curr Opin Microbiol. 2008;11(6):580–5.

Swanson D, Wingreen NS. Active biopolymers confer fast reorganization kinetics. Phys Rev Lett. 2011;107(21):218103.

Teng S-W, Schaffer JN, Tu KC, Mehta P, Lu W, Ong NP, Bassler BL, Wingreen NS. Active regulation of receptor ratios controls integration of quorum-sensing signals in Vibrio harveyi. Mol Syst Biol. 2011;7:491.

Gresham D, Usaite R, Germann SM, Lisby M, Botstein D, Regenberg B. Adaptation to diverse nitrogen-limited environments by deletion or extrachromosomal element formation of the GAP1 locus. Proc Natl Acad Sci U S A. 2010;107(43):18551–6.

Andolfatto P. Adaptive evolution of non-coding DNA in Drosophila. Nature. 2005;437(7062):1149–52.

Murphy CT. Aging: miRacles of longevity?. Curr Biol. 2010;20(24):R1076–8.

Morozova T V, Ayroles J, Jordan KW, Duncan L, Carbone MA, Lyman RF, Stone EA, Govindaraju DR, Ellison C, Mackay TFC, Anholt R. Alcohol sensitivity in Drosophila: translational potential of systems genetics. Genetics. 2009;183(2):733–45, 1SI.

Pfeifer K, Tilghman SM. Allele-specific gene expression in mammals: the curious case of the imprinted RNAs. Genes Dev. 1994;8(16):1867–74.

O’Neill MJ, Ingram RS, Vrana PB, Tilghman SM. Allelic expression of IGF2 in marsupials and birds. Dev Genes Evol. 2000;210(1):18–20.

Hess DC, Lu W, Rabinowitz JD, Botstein D. Ammonium toxicity and potassium limitation in yeast. PLoS Biol. 2006;4(11):e351.

Goodwin M, Zhang X, Shekleton T, Kirr D, Hannon H, Harbron E. Amplifying the reactivity of BODIPY photoremovable protecting groups. Chemical Communications. 2021;57:10059–10062.

Browning SR, Browning BL, Zhou Y, Tucci S, Akey J. Analysis of Human Sequence Data Reveals Two Pulses of Archaic Denisovan Admixture. Cell. 2018;173(1):53–61.e9. PMCID: PMC5866234

Chi A, Huttenhower C, Geer LY, Coon JJ, Syka JEP, Bai DL, Shabanowitz J, Burke DJ, Troyanskaya OG, Hunt DF. Analysis of phosphorylation sites on proteins from Saccharomyces cerevisiae by electron transfer dissociation (ETD) mass spectrometry. Proc Natl Acad Sci U S A. 2007;104(7):2193–8.

Ayroles J, Gibson G. Analysis of variance of microarray data. Methods Enzymol. 2006;411:214–33.

Zhou J, Troyanskaya O. An analytical framework for interpretable and generalizable single-cell data analysis. Nature methods. 2021;18(11):1317–1321. PMCID: PMC8959118

Lu W, Bennett BD, Rabinowitz JD. Analytical strategies for LC-MS-based targeted metabolomics. J Chromatogr B Analyt Technol Biomed Life Sci. 2008;871(2):236–42.

Di Gregorio A, Levine M. Analyzing gene regulation in ascidian embryos: new tools for new perspectives. Differentiation. 2002;70(4-5):132–9.

Sharpee T, Rust NC, Bialek W. Analyzing neural responses to natural signals: maximally informative dimensions. Neural Comput. 2004;16(2):223–50.

Barutcuoglu Z, Airoldi EM, Dumeaux V, Schapire RE, Troyanskaya OG. Aneuploidy prediction and tumor classification with heterogeneous hidden conditional random fields. Bioinformatics. 2009;25(10):1307–13.

Kwon YK, Higgins MB, Rabinowitz JD. Antifolate-induced depletion of intracellular glycine and purines inhibits thymineless death in E. coli. ACS Chem Biol. 2010;5(8):787–95.

He B, Doubrovinski K, Polyakov O, Wieschaus E. Apical constriction drives tissue-scale hydrodynamic flow to mediate cell elongation. Nature. 2014;508(7496):392–6.

Mehta P, Gregor T. Approaching the molecular origins of collective dynamics in oscillating cell populations. Curr Opin Genet Dev. 2010;20(6):574–80.

Jensen JD, Thornton KR, Andolfatto P. An approximate bayesian estimator suggests strong, recurrent selective sweeps in Drosophila. PLoS Genet. 2008;4(9):e1000198.

Thornton K, Andolfatto P. Approximate Bayesian inference reveals evidence for a recent, severe bottleneck in a Netherlands population of Drosophila melanogaster. Genetics. 2006;172(3):1607–19.

Grady SL, Purdy JG, Rabinowitz JD, Shenk T. Argininosuccinate synthetase 1 depletion produces a metabolic state conducive to herpes simplex virus 1 infection. Proc Natl Acad Sci U S A. 2013;110(51):E5006–15.

Klein DE, Nappi VM, Reeves GT, Shvartsman SY, Lemmon MA. Argos inhibits epidermal growth factor receptor signalling by ligand sequestration. Nature. 2004;430(7003):1040–4.

Tolwinski NS, Wieschaus E. Armadillo nuclear import is regulated by cytoplasmic anchor Axin and nuclear anchor dTCF/Pan. Development. 2001;128(11):2107–17.

Müller HA, Wieschaus E. armadillo, bazooka, and stardust are critical for early stages in formation of the zonula adherens and maintenance of the polarized blastoderm epithelium in Drosophila. J Cell Biol. 1996;134(1):149–63.

Pavlova NN, Hui S, Ghergurovich JM, Fan J, Intlekofer AM, White RM, Rabinowitz JD, Thompson CB, Zhang J. As Extracellular Glutamine Levels Decline, Asparagine Becomes an Essential Amino Acid. Cell Metab. 2018;27(2):428–438.e5. PMCID: PMC5803449

Zhang J, Fan J, Venneti S, Cross JR, Takagi T, Bhinder B, Djaballah H, Kanai M, Cheng EH, Judkins AR, Pawel B, Baggs J, Cherry S, Rabinowitz JD, Thompson CB. Asparagine plays a critical role in regulating cellular adaptation to glutamine depletion. Mol Cell. 2014;56(2):205–18.

Huttenhower C, Troyanskaya OG. Assessing the functional structure of genomic data. Bioinformatics. 2008;24(13):i330–8.