2016

Van Nostrand EL, Pratt GA, Shishkin AA, et al. "Robust transcriptome-wide discovery of RNA-binding protein binding sites with enhanced CLIP (eCLIP)." Nat. Methods. 2016;13(6):508-14.
Sauls JT, Li D, Jun S. "Adder and a coarse-grained approach to cell size homeostasis in bacteria." Curr. Opin. Cell Biol.. 2016;38:38-44.
Brandler WM, Antaki D, Gujral M, et al. "Frequency and Complexity of De Novo Structural Mutation in Autism." Am. J. Hum. Genet.. 2016;98(4):667-79.
Rentas S, Holzapfel NT, Belew MS, et al. "Musashi-2 attenuates AHR signalling to expand human haematopoietic stem cells." Nature. 2016;532(7600):508-11.
Utrilla J, O'Brien EJ, Chen K, et al. "Global Rebalancing of Cellular Resources by Pleiotropic Point Mutations Illustrates a Multi-scale Mechanism of Adaptive Evolution." Cell Syst. 2016;2(4):260-71.
Gross AM, Jaeger PA, Kreisberg JF, et al. "Methylome-wide Analysis of Chronic HIV Infection Reveals Five-Year Increase in Biological Age and Epigenetic Targeting of HLA." Mol. Cell. 2016;62(2):157-68.
Conway AE, Van Nostrand EL, Pratt GA, et al. "Enhanced CLIP Uncovers IMP Protein-RNA Targets in Human Pluripotent Stem Cells Important for Cell Adhesion and Survival." Cell Rep. 2016;15(3):666-79.
Baker CW, Miller CR, Thaweethai T, et al. "Genetically Determined Variation in Lysis Time Variance in the Bacteriophage φX174." G3 (Bethesda). 2016;6(4):939-55.
Brunk E, Mih N, Monk J, et al. "Systems biology of the structural proteome." BMC Syst Biol. 2016;10:26.
Yurkovich JT, Palsson BO. "Solving Puzzles With Missing Pieces: The Power of Systems Biology." Proceedings of the IEEE. 2016;104(1):2-7. URL 

2015

Hung T, Pratt GA, Sundararaman B, et al. "The Ro60 autoantigen binds endogenous retroelements and regulates inflammatory gene expression." Science. 2015;350(6259):455-9.
Shen JPaul, Srivas R, Gross A, et al. "Chemogenetic profiling identifies RAD17 as synthetically lethal with checkpoint kinase inhibition." Oncotarget. 2015;6(34):35755-69.
Wu J, Okamura D, Li M, et al. "An alternative pluripotent state confers interspecies chimaeric competency." Nature. 2015;521(7552):316-21.
O'Brien EJ, Monk JM, Palsson BO. "Using Genome-scale Models to Predict Biological Capabilities." Cell. 2015;161(5):971-87.
Friedmann-Morvinski D, Bhargava V, Gupta S, Verma IM, Subramaniam S. "Identification of therapeutic targets for glioblastoma by network analysis." Oncogene. 2015.
Murrell B, Weaver S, Smith MD, et al. "Gene-wide identification of episodic selection." Mol. Biol. Evol.. 2015;32(5):1365-71.
Raju SC, Hauff SJ, Lemieux AJ, et al. "Combined TP53 mutation/3p loss correlates with decreased radiosensitivity and increased matrix-metalloproteinase activity in head and neck carcinoma." Oral Oncol.. 2015;51(5):470-5.
DeBoever C, Ghia EM, Shepard PJ, et al. "Transcriptome sequencing reveals potential mechanism of cryptic 3' splice site selection in SF3B1-mutated cancers." PLoS Comput. Biol.. 2015;11(3):e1004105.
He Y, Ecker JR. "Non-CG Methylation in the Human Genome." Annu Rev Genomics Hum Genet. 2015.
Taheri-Araghi S, Brown SD, Sauls JT, McIntosh DB, Jun S. "Single-Cell Physiology." Annu Rev Biophys. 2015;44:123-42.
Schultz MD, He Y, Whitaker JW, et al. "Human body epigenome maps reveal noncanonical DNA methylation variation." Nature. 2015;523(7559):212-6.
Gross AM, Ideker T. "Molecular networks in context." Nat. Biotechnol.. 2015;33(7):720-1.
Lee SR, Pratt GA, Martinez FJ, Yeo GW, Lykke-Andersen J. "Target Discrimination in Nonsense-Mediated mRNA Decay Requires Upf1 ATPase Activity." Mol. Cell. 2015;59(3):413-25.
O'Brien EJ, Palsson BO. "Computing the functional proteome: recent progress and future prospects for genome-scale models." Curr. Opin. Biotechnol.. 2015;34:125-34.
Choueiri MB, Shen JPaul, Gross AM, Huang JK, Ideker T, Fanta P. "ERCC1 and TS Expression as Prognostic and Predictive Biomarkers in Metastatic Colon Cancer." PLoS ONE. 2015;10(6):e0126898.
Gross AM, Cohen EEW. "Towards a personalized treatment of head and neck cancer." Am Soc Clin Oncol Educ Book. 2015;35:28-32.
Mukund K, Subramaniam S. "Dysregulated mechanisms underlying Duchenne muscular dystrophy from co-expression network preservation analysis." BMC Res Notes. 2015;8:182.
Singh G, Pratt G, Yeo GW, Moore MJ. "The Clothes Make the mRNA: Past and Present Trends in mRNP Fashion." Annu. Rev. Biochem.. 2015;84:325-54.
Gross AM, Kreisberg JF, Ideker T. "Analysis of Matched Tumor and Normal Profiles Reveals Common Transcriptional and Epigenetic Signals Shared across Cancer Types." PLoS ONE. 2015;10(11):e0142618.

2014

Buganim Y, Markoulaki S, van Wietmarschen N, et al. "The developmental potential of iPSCs is greatly influenced by reprogramming factor selection." Cell Stem Cell. 2014;15(3):295-309.
Gross AM, Orosco RK, Shen JP, et al. "Multi-tiered genomic analysis of head and neck cancer ties TP53 mutation to 3p loss." Nat. Genet.. 2014;46(9):939-43.
Hauff SJ, Raju SC, Orosco RK, et al. "Matrix-metalloproteinases in head and neck carcinoma-cancer genome atlas analysis and fluorescence imaging in mice." Otolaryngol Head Neck Surg. 2014;151(4):612-8.
McCorrison JM, Venepally P, Singh I, Fouts DE, Lasken RS, Methé BA. "NeatFreq: reference-free data reduction and coverage normalization for De Novo sequence assembly." BMC Bioinformatics. 2014;15(1):357. PMC 
Mukund K, Mathewson M, Minamoto V, Ward SR, Subramaniam S, Lieber RL. "Systems analysis of transcriptional data provides insights into muscle's biological response to botulinum toxin." Muscle Nerve. 2014;50(5):744-58.
Mollah SA, Dobrin JS, Feder RE, et al. "Flt3L dependence helps define an uncharacterized subset of murine cutaneous dendritic cells." J. Invest. Dermatol.. 2014;134(5):1265-75.
Wang C-C, Bajikar SS, Jamal L, Atkins KA, Janes KA. "A time- and matrix-dependent TGFBR3-JUND-KRT5 regulatory circuit in single breast epithelial cells and basal-like premalignancies." Nat. Cell Biol.. 2014. PMC 
Appleton E, Tao J, Haddock T, Densmore D. "Interactive assembly algorithms for molecular cloning." Nat. Methods. 2014;11(6):657-62.
Ma H, Morey R, O'Neil RC, et al. "Abnormalities in human pluripotent cells due to reprogramming mechanisms." Nature. 2014;511(7508):177-83.
Sauls JT, Buescher JM. "Assimilating genome-scale metabolic reconstructions with modelBorgifier." Bioinformatics. 2014.
Udpa N, Ronen R, Zhou D, et al. "Whole genome sequencing of Ethiopian highlanders reveals conserved hypoxia tolerance genes." Genome Biol.. 2014;15(2):R36. PMC 
Taheri-Araghi S, Bradde S, Sauls JT, et al. "Cell-Size Control and Homeostasis in Bacteria." Curr. Biol.. 2014.
Anandasabapathy N, Feder R, Mollah S, et al. "Classical Flt3L-dependent dendritic cells control immunity to protein vaccine." J. Exp. Med.. 2014;211(9):1875-91.
Lin MS, Cherny JJ, Fournier CT, Roth SJ, Krizanc D, Weir MP. "Assessment of MS/MS search algorithms with parent-protein profiling." J. Proteome Res.. 2014;13(4):1823-32.
Bhargava V, Head SR, Ordoukhanian P, Mercola M, Subramaniam S. "Technical Variations in Low-Input RNA-seq Methodologies." Sci Rep. 2014;4:3678. PMC 
Bean GJ, Jaeger PA, Bahr S, Ideker T. "Development of ultra-high-density screening tools for microbial "omics"." PLoS ONE. 2014;9(1):e85177. PMC 

2013

Zhou D, Udpa N, Ronen R, et al. "Whole-genome sequencing uncovers the genetic basis of chronic mountain sickness in Andean highlanders." Am. J. Hum. Genet.. 2013;93(3):452-62. PMC 
Ronen R, Udpa N, Halperin E, Bafna V. "Learning natural selection from the site frequency spectrum." Genetics. 2013;195(1):181-93. PMC 
Jung H, Bleazard T, Lee J, Hong D. "Systematic investigation of cancer-associated somatic point mutations in SNP databases." Nat. Biotechnol.. 2013;31(9):787-9.
Embree M, Nagarajan H, Movahedi N, Chitsaz H, Zengler K. "Single-cell genome and metatranscriptome sequencing reveal metabolic interactions of an alkane-degrading methanogenic community." ISME J. 2013. PMC 
Castellana NE, Shen Z, He Y, et al. "An Automated Proteogenomic Method Utilizes Mass Spectrometry to Reveal Novel Genes in Zea mays." Mol. Cell Proteomics. 2013. PMC 
Hua Z, Pool JE, Schmitz RJ, et al. "Epigenomic programming contributes to the genomic drift evolution of the F-Box protein superfamily in Arabidopsis." Proc. Natl. Acad. Sci. U.S.A.. 2013;110(42):16927-32. PMC 
Heinz S, Romanoski CE, Benner C, et al. "Effect of natural genetic variation on enhancer selection and function." Nature. 2013. PMC 
Behar M, Barken D, Werner SL, Hoffmann A. "The dynamics of signaling as a pharmacological target." Cell. 2013;155(2):448-61. PMC 
Schmitz RJ, He Y, Valdés-López O, et al. "Epigenome-wide inheritance of cytosine methylation variants in a recombinant inbred population." Genome Res.. 2013;23(10):1663-74. PMC 
Selvaraj S, Dixon JR, Bansal V, Ren B. "Whole-genome haplotype reconstruction using proximity-ligation and shotgun sequencing." Nat. Biotechnol.. 2013.
Wagner GA, Pacold ME, Kosakovsky Pond SL, et al. "Incidence and Prevalence of Intrasubtype HIV-1 Dual Infection in At-Risk Men in the United States." J. Infect. Dis.. 2013. PMC 
Nagarajan H, Embree M, Rotaru A-E, et al. "Characterization and modelling of interspecies electron transfer mechanisms and microbial community dynamics of a syntrophic association." Nat Commun. 2013;4:2809.
Jin F, Li Y, Dixon JR, et al. "A high-resolution map of the three-dimensional chromatin interactome in human cells." Nature. 2013;503(7475):290-4. PMC 
Hofree M, Shen JP, Carter H, Gross A, Ideker T. "Network-based stratification of tumor mutations." Nat. Methods. 2013;10(11):1108-15.
Xie W, Schultz MD, Lister R, et al. "Epigenomic analysis of multilineage differentiation of human embryonic stem cells." Cell. 2013;153(5):1134-48. PMC 
Fong NL, Lerman JA, Lam I, Palsson BO, Charusanti P. "Reconciling a Salmonella enterica metabolic model with experimental data confirms that overexpression of the glyoxylate shunt can rescue a lethal ppc deletion mutant." FEMS Microbiol. Lett.. 2013;342(1):62-9. PMC 
Schmitz RJ, Schultz MD, Urich MA, et al. "Patterns of population epigenomic diversity." Nature. 2013;495(7440):193-8. PMC 
Chang RL, Andrews K, Kim D, Li Z, Godzik A, Palsson BO. "Structural systems biology evaluation of metabolic thermotolerance in Escherichia coli." Science. 2013;340(6137):1220-3. PMC 
Nguyen D D, Wu C-H, Moree WJ, et al. "MS/MS networking guided analysis of molecule and gene cluster families." Proc. Natl. Acad. Sci. U.S.A.. 2013;110(28):E2611-20. PMC 
Woo S, Cha S W, Merrihew G, et al. "Proteogenomic Database Construction Driven from Large Scale RNA-seq Data." J. Proteome Res.. 2013. PMC 
Wagner GA, Pacold ME, Vigil E, et al. "Using ultradeep pyrosequencing to study HIV-1 coreceptor usage in primary and dual infection." J. Infect. Dis.. 2013;208(2):271-4. PMC 
Margeridon-Thermet S, Svarovskaia ES, Babrzadeh F, et al. "Low-level persistence of drug resistance mutations in hepatitis B virus-infected subjects with a past history of Lamivudine treatment." Antimicrob. Agents Chemother.. 2013;57(1):343-9. PMC 
Arnold ES, Ling S-C, Huelga SC, et al. "ALS-linked TDP-43 mutations produce aberrant RNA splicing and adult-onset motor neuron disease without aggregation or loss of nuclear TDP-43." Proc. Natl. Acad. Sci. U.S.A.. 2013;110(8):E736-45. PMC 
Babrzadeh F, Varghese V, Pacold M, et al. "Collinearity of protease mutations in HIV-1 samples with high-level protease inhibitor class resistance." J. Antimicrob. Chemother.. 2013;68(2):414-8. PMC 
Allison KA, Kaikkonen MU, Gaasterland T, Glass CK. "Vespucci: a system for building annotated databases of nascent transcripts." Nucleic Acids Res.. 2013. PMC 
Chaillon A, Wagner GA, Hepler LN, et al. "Dynamics of Viral Evolution and Neutralizing Antibody Response after HIV-1 Superinfection." J. Virol.. 2013;87(23):12737-44. PMC 
Lovci MT, Ghanem D, Marr H, et al. "Rbfox proteins regulate alternative mRNA splicing through evolutionarily conserved RNA bridges." Nat. Struct. Mol. Biol.. 2013;20(12):1434-42.
Lister R, Mukamel EA, Nery JR, et al. "Global epigenomic reconfiguration during mammalian brain development." Science. 2013;341(6146):1237905. PMC 
Kaikkonen MU, Spann NJ, Heinz S, et al. "Remodeling of the enhancer landscape during macrophage activation is coupled to enhancer transcription." Mol. Cell. 2013;51(3):310-25. PMC 
Lewis NE, Liu X, Li Y, et al. "Genomic landscapes of Chinese hamster ovary cell lines as revealed by the Cricetulus griseus draft genome." Nat. Biotechnol.. 2013;31(8):759-65.
Shen L, Wu H, Diep D, et al. "Genome-wide analysis reveals TET- and TDG-dependent 5-methylcytosine oxidation dynamics." Cell. 2013;153(3):692-706. PMC 
Latif H, Lerman JA, Portnoy VA, et al. "The genome organization of Thermotoga maritima reflects its lifestyle." PLoS Genet.. 2013;9(4):e1003485. PMC 
Loriaux P M, Tesler G, Hoffmann A. "Characterizing the relationship between steady state and response using analytical expressions for the steady states of mass action models." PLoS Comput. Biol.. 2013;9(2):e1002901. PMC 
Loriaux P M, Hoffmann A. "A protein turnover signaling motif controls the stimulus-sensitivity of stress response pathways." PLoS Comput. Biol.. 2013;9(2):e1002932. PMC 
Shokhirev M N, Hoffmann A. "FlowMax: A Computational Tool for Maximum Likelihood Deconvolution of CFSE Time Courses." PLoS ONE. 2013;8(6):e67620. PMC 
Feldman KE, Loriaux PM, Saito M, et al. "Ex vivo innate immune cytokine signature of enhanced risk of relapsing brucellosis." PLoS Negl Trop Dis. 2013;7(9):e2424. PMC 
Hu M, Deng K, Qin Z, et al. "Bayesian inference of spatial organizations of chromosomes." PLoS Comput. Biol.. 2013;9(1):e1002893. PMC 
Bhargava V, Ko P, Willems E, Mercola M, Subramaniam S. "Quantitative transcriptomics using designed primer-based amplification." Sci Rep. 2013;3:1740. PMC 
Ebrahim A, Lerman JA, Palsson BO, Hyduke DR. "COBRApy: COnstraints-Based Reconstruction and Analysis for Python." BMC Syst Biol. 2013;7:74. PMC 
O'Brien EJ, Lerman JA, Chang RL, Hyduke DR, Palsson BØ. "Genome-scale models of metabolism and gene expression extend and refine growth phenotype prediction." Mol. Syst. Biol.. 2013;9:693. PMC 
Chang RL, Xie L, Bourne PE, Palsson BO. "Antibacterial mechanisms identified through structural systems pharmacology." BMC Syst Biol. 2013;7:102. PMC 
Hightower GK, May SJ, Pérez-Santiago J, et al. "HIV-1 clade B pol evolution following primary infection." PLoS ONE. 2013;8(6):e68188. PMC 
Nakatsuji T, Chiang H-I, Jiang SB, Nagarajan H, Zengler K, Gallo RL. "The microbiome extends to subepidermal compartments of normal skin." Nat Commun. 2013;4:1431. PMC 
Qiu Y, Nagarajan H, Embree M, et al. "Characterizing the interplay between multiple levels of organization within bacterial sigma factor regulatory networks." Nat Commun. 2013;4:1755.
Nagarajan H, Sahin M, Nogales J, et al. "Characterizing acetogenic metabolism using a genome-scale metabolic reconstruction of Clostridium ljungdahlii." Microb. Cell Fact.. 2013;12(1):118.
DeBoever C, Reid EG, Smith EN, et al. "Whole transcriptome sequencing enables discovery and analysis of viruses in archived primary central nervous system lymphomas." PLoS ONE. 2013;8(9):e73956.

2012

Ho Sui SJ, Lo R, Fernandes AR, et al. "Raloxifene attenuates Pseudomonas aeruginosa pyocyanin production and virulence." Int. J. Antimicrob. Agents. 2012;40(3):246-51.
Wilbert ML, Huelga SC, Kapeli K, et al. "LIN28 binds messenger RNAs at GGAGA motifs and regulates splicing factor abundance." Mol. Cell. 2012;48(2):195-206. PMC 
Ruiz S, Diep D, Gore A, et al. "Identification of a specific reprogramming-associated epigenetic signature in human induced pluripotent stem cells." Proc. Natl. Acad. Sci. U.S.A.. 2012;109(40):16196-201. PMC 
Prlić A, Yates A, Bliven SE, et al. "BioJava: an open-source framework for bioinformatics in 2012." Bioinformatics. 2012;28(20):2693-5. PMC 
Baycin-Hizal D, Tabb DL, Chaerkady R, et al. "Proteomic analysis of Chinese hamster ovary cells." J. Proteome Res.. 2012;11(11):5265-76. PMC 
Lagier-Tourenne C, Polymenidou M, Hutt KR, et al. "Divergent roles of ALS-linked proteins FUS/TLS and TDP-43 intersect in processing long pre-mRNAs." Nat. Neurosci.. 2012;15(11):1488-97. PMC 
Dixon JR, Selvaraj S, Yue F, et al. "Topological domains in mammalian genomes identified by analysis of chromatin interactions." Nature. 2012;485(7398):376-80. PMC 
Bernard A, Lubbers LS, Tanis KQ, et al. "Transcriptional architecture of the primate neocortex." Neuron. 2012;73(6):1083-99. PMC 
Diep D, Plongthongkum N, Gore A, Fung H-L, Shoemaker R, Zhang K. "Library-free methylation sequencing with bisulfite padlock probes." Nat. Methods. 2012;9(3):270-2. PMC 
Ronen R, Boucher C, Chitsaz H, Pevzner P. "SEQuel: improving the accuracy of genome assemblies." Bioinformatics. 2012;28(12):i188-96. PMC 
Dixon-Salazar TJ, Silhavy JL, Udpa N, et al. "Exome sequencing can improve diagnosis and alter patient management." Sci Transl Med. 2012;4(138):138ra78.
Prindle A, Samayoa P, Razinkov I, Danino T, Tsimring LS, Hasty J. "A sensing array of radically coupled genetic 'biopixels'." Nature. 2012;481(7379):39-44. PMC 
Pacold ME, Pond S KL, Wagner GA, et al. "Clinical, virologic, and immunologic correlates of HIV-1 intraclade B dual infection among men who have sex with men." AIDS. 2012;26(2):157-65. PMC 
Panopoulos AD, Yanes O, Ruiz S, et al. "The metabolome of induced pluripotent stem cells reveals metabolic changes occurring in somatic cell reprogramming." Cell Res.. 2012;22(1):168-77. PMC 
Cho B-K, Federowicz S, Park Y-S, Zengler K, Palsson BØ. "Deciphering the transcriptional regulatory logic of amino acid metabolism." Nat. Chem. Biol.. 2012;8(1):65-71. PMC 
Huelga SC, Vu AQ, Arnold JD, et al. "Integrative genome-wide analysis reveals cooperative regulation of alternative splicing by hnRNP proteins." Cell Rep. 2012;1(2):167-178. PMC 
Gendron JM, Pruneda-Paz JL, Doherty CJ, Gross AM, S Kang E, Kay SA. "Arabidopsis circadian clock protein, TOC1, is a DNA-binding transcription factor." Proc. Natl. Acad. Sci. U.S.A.. 2012;109(8):3167-72.
Bean GJ, Ideker T. "Differential analysis of high-throughput quantitative genetic interaction data." Genome Biol.. 2012;13(12):R123. PMC 
Yamaguchi S, Hong K, Liu R, et al. "Tet1 controls meiosis by regulating meiotic gene expression." Nature. 2012;492(7429):443-7. PMC 
Hu M, Deng K, Selvaraj S, Qin Z, Ren B, Liu JS. "HiCNorm: removing biases in Hi-C data via Poisson regression." Bioinformatics. 2012;28(23):3131-3. PMC 
Shih VF-S, Davis-Turak J, Macal M, et al. "Control of RelB during dendritic cell activation integrates canonical and noncanonical NF-κB pathways." Nat. Immunol.. 2012;13(12):1162-70. PMC 
Schultz MD, Schmitz RJ, Ecker JR. "'Leveling' the playing field for analyses of single-base resolution DNA methylomes." Trends Genet.. 2012;28(12):583-5. PMC 
Nam H, Lewis NE, Lerman JA, et al. "Network context and selection in the evolution to enzyme specificity." Science. 2012;337(6098):1101-4. PMC 
Konopka G, Friedrich T, Davis-Turak J, et al. "Human-specific transcriptional networks in the brain." Neuron. 2012;75(4):601-17. PMC 
Johnson DBF, Wang C, Xu J, et al. "Release factor one is nonessential in Escherichia coli." ACS Chem. Biol.. 2012;7(8):1337-44. PMC 
Yost SE, Smith EN, Schwab RB, et al. "Identification of high-confidence somatic mutations in whole genome sequence of formalin-fixed breast cancer specimens." Nucleic Acids Res.. 2012;40(14):e107. PMC 
Lewis NE, Nagarajan H, Palsson BO. "Constraining the metabolic genotype-phenotype relationship using a phylogeny of in silico methods." Nat. Rev. Microbiol.. 2012;10(4):291-305. PMC 
Kurihara Y, Schmitz RJ, Nery JR, et al. "Surveillance of 3' Noncoding Transcripts Requires FIERY1 and XRN3 in Arabidopsis." G3 (Bethesda). 2012;2(4):487-98. PMC 
Chan JE, Kolodner RD. "Rapid analysis of Saccharomyces cerevisiae genome rearrangements by multiplex ligation-dependent probe amplification." PLoS Genet.. 2012;8(3):e1002539. PMC 
Charusanti P, Fong NL, Nagarajan H, et al. "Exploiting adaptive laboratory evolution of Streptomyces clavuligerus for antibiotic discovery and overproduction." PLoS ONE. 2012;7(3):e33727. PMC 
Loriaux PM, Hoffmann A. "A framework for modeling the relationship between cellular steady-state and stimulus-responsiveness." Methods Cell Biol.. 2012;110:81-109.
Bliven S, Prlić A. "Circular permutation in proteins." PLoS Comput. Biol.. 2012;8(3):e1002445. PMC 
Chaisson MJ, Tesler G. "Mapping single molecule sequencing reads using basic local alignment with successive refinement (BLASR): application and theory." BMC Bioinformatics. 2012;13:238. PMC 
Lerman JA, Hyduke DR, Latif H, et al. "In silico method for modelling metabolism and gene product expression at genome scale." Nat Commun. 2012;3:929. PMC 
Thiele I, Fleming RMT, Que R, Bordbar A, Diep D, Palsson BO. "Multiscale modeling of metabolism and macromolecular synthesis in E. coli and its application to the evolution of codon usage." PLoS ONE. 2012;7(9):e45635. PMC 
He Y, Zhang Y, Zheng G, Wei C. "CTF: a CRF-based transcription factor binding sites finding system." BMC Genomics. 2012;13 Suppl 8:S18. PMC 
Kim D, Hong J S-J, Qiu Y, et al. "Comparative analysis of regulatory elements between Escherichia coli and Klebsiella pneumoniae by genome-wide transcription start site profiling." PLoS Genet.. 2012;8(8):e1002867. PMC 
Ma Q, Liu W, Rosenfeld MG. "mHMM (multivariate hidden Markov model) application in studying BRD4 and JMJD6 function cooperatively on promoter-proximal polymerase-II (Pol II) pausing release.". In: Proceedings of the ACM Conference on Bioinformatics, Computational Biology and Biomedicine - BCB '12. ACM Press; 2012. URL 
Huelga SC, Yeo GW. "Genomics of Alternative Splicing in Stem Cells.". In: Computational Biology of Embryonic Stem Cells (Ming Zhan, Ed.), pp. 147-160. Oak Park, IL: Bentham Science Publishers; 2012.

2011

Tan M, Luo H, Lee S, et al. "Identification of 67 histone marks and histone lysine crotonylation as a new type of histone modification." Cell. 2011;146(6):1016-28. PMC 
Schmitz RJ, Schultz MD, Lewsey MG, et al. "Transgenerational epigenetic instability is a source of novel methylation variants." Science. 2011;334(6054):369-73. PMC 
Fox-Walsh K, Davis-Turak J, Zhou Y, Li H, Fu X-D. "A multiplex RNA-seq strategy to profile poly(A+) RNA: application to analysis of transcription response and 3' end formation." Genomics. 2011;98(4):266-71. PMC 
Hawkins DR, Hon GC, Yang C, et al. "Dynamic chromatin states in human ES cells reveal potential regulatory sequences and genes involved in pluripotency." Cell Res.. 2011;21(10):1393-409. PMC 
Johnson DBF, Xu J, Shen Z, et al. "RF1 knockout allows ribosomal incorporation of unnatural amino acids at multiple sites." Nat. Chem. Biol.. 2011;7(11):779-86. PMC 
Chan JE, Kolodner RD. "A genetic and structural study of genome rearrangements mediated by high copy repeat Ty1 elements." PLoS Genet.. 2011;7(5):e1002089. PMC 
Diep D, Zhang K. "Genome-wide mapping of the sixth base." Genome Biol.. 2011;12(6):116. PMC 
Zhou D, Udpa N, Gersten M, et al. "Experimental selection of hypoxia-tolerant Drosophila melanogaster." Proc. Natl. Acad. Sci. U.S.A.. 2011;108(6):2349-54. PMC 
Cho B-K, Federowicz SA, Embree M, Park Y-S, Kim D, Palsson BØ. "The PurR regulon in Escherichia coli K-12 MG1655." Nucleic Acids Res.. 2011;39(15):6456-64. PMC 
Hansen K D, Timp W, Bravo H C, et al. "Increased methylation variation in epigenetic domains across cancer types." Nat. Genet.. 2011;43(8):768-75. PMC 
Xu X, Nagarajan H, Lewis NE, et al. "The genomic sequence of the Chinese hamster ovary (CHO)-K1 cell line." Nat. Biotechnol.. 2011;29(8):735-41. PMC 
Gianella S, Delport W, Pacold ME, et al. "Detection of minority resistance during early HIV-1 infection: natural variation and spurious detection rather than transmission and evolution of multiple viral variants." J. Virol.. 2011;85(16):8359-67. PMC 
Liu G-H, Barkho BZ, Ruiz S, et al. "Recapitulation of premature ageing with iPSCs from Hutchinson-Gilford progeria syndrome." Nature. 2011;472(7342):221-5. PMC 
Polymenidou M, Lagier-Tourenne C, Hutt KR, et al. "Long pre-mRNA depletion and RNA missplicing contribute to neuronal vulnerability from loss of TDP-43." Nat. Neurosci.. 2011;14(4):459-68. PMC 
Chang RL, Ghamsari L, Manichaikul A, et al. "Metabolic network reconstruction of Chlamydomonas offers insight into light-driven algal metabolism." Mol. Syst. Biol.. 2011;7:518. PMC 
Orth JD, Conrad TM, Na J, et al. "A comprehensive genome-scale reconstruction of Escherichia coli metabolism--2011." Mol. Syst. Biol.. 2011;7:535. PMC 
Charusanti P, Chauhan S, McAteer K, et al. "An experimentally-supported genome-scale metabolic network reconstruction for Yersinia pestis CO92." BMC Syst Biol. 2011;5:163. PMC 
Udpa N, Zhou D, Haddad GG, Bafna V. "Tests of selection in pooled case-control data: an empirical study." Front Genet. 2011;2:83. PMC 

2010

Lerman J, Palsson BO. "Microbiology. Topping off a multiscale balancing act." Science. 2010;330(6007):1058-9.
Brinza D, Schultz M, Tesler G, Bafna V. "RAPID detection of gene-gene interactions in genome-wide association studies." Bioinformatics. 2010;26(22):2856-62. PMC 
Hawkins DR, Hon GC, Lee LK, et al. "Distinct epigenomic landscapes of pluripotent and lineage-committed human cells." Cell Stem Cell. 2010;6(5):479-91. PMC 
Feist AM, Zielinski DC, Orth JD, Schellenberger J, Herrgard MJ, Palsson BØ. "Model-driven evaluation of the production potential for growth-coupled products of Escherichia coli." Metab. Eng.. 2010;12(3):173-86. PMC 
Hughey JJ, Lee TK, Covert MW. "Computational modeling of mammalian signaling networks." Wiley Interdiscip Rev Syst Biol Med. 2010;2(2):194-209. PMC 
Lewis NE, Hixson KK, Conrad TM, et al. "Omic data from evolved E. coli are consistent with computed optimal growth from genome-scale models." Mol. Syst. Biol.. 2010;6:390. PMC 
Grubisic I, Shokhirev MN, Orzechowski M, Miyashita O, Tama F. "Biased coarse-grained molecular dynamics simulation approach for flexible fitting of X-ray structure into cryo electron microscopy maps." J. Struct. Biol.. 2010;169(1):95-105.
König R, Stertz S, Zhou Y, et al. "Human host factors required for influenza virus replication." Nature. 2010;463(7282):813-7. PMC 
Prlic A, Bliven S, Rose PW, et al. "Pre-calculated protein structure alignments at the RCSB PDB website." Bioinformatics. 2010;26(23):2983-5. PMC 
Pacold M, Smith D, Little S, et al. "Comparison of methods to detect HIV dual infection." AIDS Res. Hum. Retroviruses. 2010;26(12):1291-8. PMC 
Gay SC, Shah MB, Talakad JC, et al. "Crystal structure of a cytochrome P450 2B6 genetic variant in complex with the inhibitor 4-(4-chlorophenyl)imidazole at 2.0-A resolution." Mol. Pharmacol.. 2010;77(4):529-38. PMC 
Chang RL, Luo F, Johnson S, Scheuermann RH. "Deterministic graph-theoretic algorithm for detecting modules in biological interaction networks." Int J Bioinform Res Appl. 2010;6(2):101-19.
Nagarajan H, Butler JE, Klimes A, et al. "De Novo assembly of the complete genome of an enhanced electricity-producing variant of Geobacter sulfurreducens using only short reads." PLoS ONE. 2010;5(6):e10922. PMC 
Chang RL, Xie L, Xie L, Bourne PE, Palsson BØ. "Drug off-target effects predicted using structural analysis in the context of a metabolic network model." PLoS Comput. Biol.. 2010;6(9):e1000938. PMC 
Cohen T, G Whitfield K, Schvaneveldt RW, Mukund K, Rindflesch T. "EpiphaNet: An Interactive Tool to Support Biomedical Discoveries." J Biomed Discov Collab. 2010;5:21-49.

2009

Wang L, Rao F, Zhang K, et al. "Neuropeptide Y(1) Receptor NPY1R discovery of naturally occurring human genetic variants governing gene expression in cella as well as pleiotropic effects on autonomic activity and blood pressure in vivo." J. Am. Coll. Cardiol.. 2009;54(10):944-54. PMC 
Gupta N, Pevzner PA. "False discovery rates of protein identifications: a strike against the two-peptide rule." J. Proteome Res.. 2009;8(9):4173-81. PMC 
Fossum E, Friedel CC, Rajagopala SV, et al. "Evolutionarily conserved herpesviral protein interaction networks." PLoS Pathog.. 2009;5(9):e1000570. PMC 
Smith DM, May SJ, Pérez-Santiago J, et al. "The use of pooled viral load testing to identify antiretroviral treatment failure." AIDS. 2009;23(16):2151-8. PMC 
Hon GC, Hawkins DR, Ren B. "Predictive chromatin signatures in the mammalian genome." Hum. Mol. Genet.. 2009;18(R2):R195-201. PMC 
Tsai K-C, Teng L-W, Shao Y-M, et al. "The first pharmacophore model for potent NF-kappaB inhibitors." Bioorg. Med. Chem. Lett.. 2009;19(19):5665-9.
Terzer M, Maynard ND, Covert MW, Stelling J. "Genome-scale metabolic networks." Wiley Interdiscip Rev Syst Biol Med. 2009;1(3):285-97.
Sears DD, Hsiao G, Hsiao A, et al. "Mechanisms of human insulin resistance and thiazolidinedione-mediated insulin sensitization." Proc. Natl. Acad. Sci. U.S.A.. 2009;106(44):18745-50. PMC 
Lister R, Pelizzola M, Dowen RH, et al. "Human DNA methylomes at base resolution show widespread epigenomic differences." Nature. 2009;462(7271):315-22. PMC 
Hon G, Wang W, Ren B. "Discovery and annotation of functional chromatin signatures in the human genome." PLoS Comput. Biol.. 2009;5(11):e1000566. PMC 
Heintzman ND, Hon GC, Hawkins DR, et al. "Histone modifications at human enhancers reflect global cell-type-specific gene expression." Nature. 2009;459(7243):108-12. PMC 
Loriaux P, Hoffmann A. "Of elections and cell-death decisions." Mol. Cell. 2009;34(3):257-8. PMC 
Bushman FD, Malani N, Fernandes J, et al. "Host cell factors in HIV replication: meta-analysis of genome-wide studies." PLoS Pathog.. 2009;5(5):e1000437. PMC 
Veretnik S, Wills C, Youkharibache P, Valas RE, Bourne PE. "Sm/Lsm genes provide a glimpse into the early evolution of the spliceosome." PLoS Comput. Biol.. 2009;5(3):e1000315. PMC 
Liu W-T, Ng J, Meluzzi D, et al. "Interpretation of tandem mass spectra obtained from cyclic nonribosomal peptides." Anal. Chem.. 2009;81(11):4200-9. PMC 
Wang H, Kakaradov B, Collins SR, et al. "A complex-based reconstruction of the Saccharomyces cerevisiae interactome." Mol. Cell Proteomics. 2009;8(6):1361-81. PMC 
Valas RE, Yang S, Bourne PE. "Nothing about protein structure classification makes sense except in the light of evolution." Curr. Opin. Struct. Biol.. 2009;19(3):329-34. PMC 
Hsiao A, Kuo MD. "High-throughput biology in the postgenomic era." J Vasc Interv Radiol. 2009;20(7 Suppl):S488-96.
Horler RSP, Butcher A, Papangelopoulos N, Ashton PD, Thomas GH. "EchoLOCATION: an in silico analysis of the subcellular locations of Escherichia coli proteins and comparison with experimentally derived locations." Bioinformatics. 2009;25(2):163-6.
Smith DM, May SJ, Tweeten S, et al. "A public health model for the molecular surveillance of HIV transmission in San Diego, California." AIDS. 2009;23(2):225-32. PMC 
Kim S, Gupta N, Bandeira N, Pevzner PA. "Spectral dictionaries: Integrating de novo peptide sequencing with database search of tandem mass spectra." Mol. Cell Proteomics. 2009;8(1):53-69. PMC 
Berry RE, Shokhirev MN, Ho AYW, et al. "Effect of mutation of carboxyl side-chain amino acids near the heme on the midpoint potentials and ligand binding constants of nitrophorin 2 and its NO, histamine, and imidazole complexes." J. Am. Chem. Soc.. 2009;131(6):2313-27. PMC 
Hawkins T, Chitale M, Luban S, Kihara D. "PFP: Automated prediction of gene ontology functional annotations with confidence scores using protein sequence data." Proteins. 2009;74(3):566-82.
Chaisson MJ, Brinza D, Pevzner PA. "De novo fragment assembly with short mate-paired reads: Does the read length matter?" Genome Res.. 2009;19(2):336-46. PMC 
Feist AM, Herrgård MJ, Thiele I, Reed JL, Palsson BØ. "Reconstruction of biochemical networks in microorganisms." Nat. Rev. Microbiol.. 2009;7(2):129-43. PMC 
Li F, Thiele I, Jamshidi N, Palsson BØ. "Identification of potential pathway mediation targets in Toll-like receptor signaling." PLoS Comput. Biol.. 2009;5(2):e1000292. PMC 
Butler DM, Pacold ME, Jordan PS, Richman DD, Smith DM. "The efficiency of single genome amplification and sequencing is improved by quantitation and use of a bioinformatics tool." J. Virol. Methods. 2009;162(1-2):280-3. PMC 
Ng J, Bandeira N, Liu W-T, et al. "Dereplication and de novo sequencing of nonribosomal peptides." Nat. Methods. 2009;6(8):596-9. PMC 
Manichaikul A, Ghamsari L, Hom EFY, et al. "Metabolic network analysis integrated with transcript verification for sequenced genomes." Nat. Methods. 2009;6(8):589-92. PMC 
Pacold M. "Retroviruses and opportunistic infections--16th annual conference. Characteristics and prevention of HIV transmission. 8-11 February 2009, Montréal, QC, Canada." IDrugs. 2009;12(4):204-6.
Barrett CL, Herrgard MJ, Palsson B. "Decomposing complex reaction networks using random sampling, principal component analysis and basis rotation." BMC Syst Biol. 2009;3:30. PMC 
Mo ML, Palsson BO, Herrgård MJ. "Connecting extracellular metabolomic measurements to intracellular flux states in yeast." BMC Syst Biol. 2009;3:37. PMC 
Abdulla M-H, Ruelas DS, Wolff B, et al. "Drug discovery for schistosomiasis: hit and lead compounds identified in a library of known drugs by medium-throughput phenotypic screening." PLoS Negl Trop Dis. 2009;3(7):e478. PMC 
Seok J, Xiao W, Moldawer LL, Davis RW, Covert MW. "A dynamic network of transcription in LPS-treated human subjects." BMC Syst Biol. 2009;3:78. PMC 
Valas RE, Bourne PE. "Structural analysis of polarizing indels: an emerging consensus on the root of the tree of life." Biol. Direct. 2009;4:30. PMC 
Lee TK, Denny EM, Sanghvi JC, et al. "A noisy paracrine signal determines the cellular NF-kappaB response to lipopolysaccharide." Sci Signal. 2009;2(93):ra65. PMC 
DeBlasio D, Bruand J, Zhang S. "PMFastR: A New Approach to Multiple RNA Structure Alignment." In: Salzberg S, Warnow T, eds. Algorithms in Bioinformatics, 9th International Workshop, WABI 2009, Philadelphia, PA, USA, September 12-13, 2009. Proceedings. Springer; 2009.
Yang S, Valas R, Bourne PE. "Evolution Studied Using Protein Structure." In: Gu J, Bourne P, eds. Structural Bioinformatics (Methods of Biochemical Analysis), pp. 559-571. 2nd ed. Hoboken, N.J.: Wiley & Sons, Inc.; 2009. Publisher  Amazon 

2008

Chen WY-C, Chen P-Y, Chen CY-C, Chung J-G. "Exploring 3D-QSAR pharmacophore mapping of azaphenanthrenone derivatives for mPGES-1 inhibition Using HypoGen technique.". In: Computational Intelligence in Bioinformatics and Computational Biology, 2008. CIBCB '08. IEEE Symposium on.; 2008.
Chen OY-C, Chen G-W, Chen WY-C. "A novel strategy for the structure-based drug design of heat shock protein 90 inhibitors.". In: Neural Networks, 2008. IJCNN 2008. (IEEE World Congress on Computational Intelligence). IEEE International Joint Conference on.; 2008.
Covert MW, Xiao N, Chen TJ, Karr JR. "Integrating metabolic, transcriptional regulatory and signal transduction models in Escherichia coli." Bioinformatics. 2008;24(18):2044-50.
Dost B, Shlomi T, Gupta N, Ruppin E, Bafna V, Sharan R. "QNet: a tool for querying protein interaction networks." J. Comput. Biol.. 2008;15(7):913-25.
Shlomi T, Cabili MN, Herrgård MJ, Palsson BØ, Ruppin E. "Network-based prediction of human tissue-specific metabolism." Nat. Biotechnol.. 2008;26(9):1003-10.
König R, Zhou Y, Elleder D, et al. "Global analysis of host-pathogen interactions that regulate early-stage HIV-1 replication." Cell. 2008;135(1):49-60. PMC 
Chen Y, Rao F, Rodriguez-Flores JL, et al. "Naturally occurring human genetic variation in the 3'-untranslated region of the secretory protein chromogranin A is associated with autonomic blood pressure regulation and hypertension in a sex-dependent fashion." J. Am. Coll. Cardiol.. 2008;52(18):1468-81. PMC 
Roguev A, Bandyopadhyay S, Zofall M, et al. "Conservation and rewiring of functional modules revealed by an epistasis map in fission yeast." Science. 2008;322(5900):405-10. PMC 
Herrgård MJ, Swainston N, Dobson P, et al. "A consensus yeast metabolic network reconstruction obtained from a community approach to systems biology." Nat. Biotechnol.. 2008;26(10):1155-60. PMC 
Hon G, Ren B, Wang W. "ChromaSig: a probabilistic approach to finding common chromatin signatures in the human genome." PLoS Comput. Biol.. 2008;4(10):e1000201. PMC 
Walsh CT, Radeff-Huang J, Matteo R, et al. "Thrombin receptor and RhoA mediate cell proliferation through integrins and cysteine-rich protein 61." FASEB J.. 2008;22(11):4011-21. PMC 
Lee K, Chuang H-Y, Beyer A, et al. "Protein networks markedly improve prediction of subcellular localization in multiple eukaryotic species." Nucleic Acids Res.. 2008;36(20):e136. PMC 
Lee E, Chuang H-Y, Kim J-W, Ideker T, Lee D. "Inferring pathway activity toward precise disease classification." PLoS Comput. Biol.. 2008;4(11):e1000217. PMC 
Cheng CS, Johnson TL, Hoffmann A. "Epigenetic control: slow and global, nimble and local." Genes Dev.. 2008;22(9):1110-4. PMC 
Valas RE, Bourne PE. "Rethinking proteasome evolution: two novel bacterial proteasomes." J. Mol. Evol.. 2008;66(5):494-504. PMC 
Kang H M, Zaitlen NA, Wade CM, et al. "Efficient control of population structure in model organism association mapping." Genetics. 2008;178(3):1709-23. PMC 
Rosen RF, Farberg AS, Gearing M, et al. "Tauopathy with paired helical filaments in an aged chimpanzee." J. Comp. Neurol.. 2008;509(3):259-70. PMC 
Albuquerque CP, Smolka MB, Payne SH, Bafna V, Eng J, Zhou H. "A multidimensional chromatography technology for in-depth phosphoproteome analysis." Mol. Cell Proteomics. 2008;7(7):1389-96. PMC 
Gupta N, Benhamida J, Bhargava V, et al. "Comparative proteogenomics: combining mass spectrometry and comparative genomics to analyze multiple genomes." Genome Res.. 2008;18(7):1133-42. PMC 
Chen Y, Rao F, Rodriguez-Flores JL, et al. "Common genetic variants in the chromogranin A promoter alter autonomic activity and blood pressure." Kidney Int.. 2008;74(1):115-25. PMC 
Applebee KM, Herrgård MJ, Palsson BØ. "Impact of individual mutations on increased fitness in adaptively evolved strains of Escherichia coli." J. Bacteriol.. 2008;190(14):5087-94. PMC 
Kelley R, Feizi H, Ideker T. "Correcting for gene-specific dye bias in DNA microarrays using the method of maximum likelihood." Bioinformatics. 2008;24(1):71-7. PMC 
Tanner S, Payne SH, Dasari S, et al. "Accurate annotation of peptide modifications through unrestrictive database search." J. Proteome Res.. 2008;7(1):170-81.
Barrera LO, Li Z, Smith AD, et al. "Genome-wide mapping and analysis of active promoters in mouse embryonic stem cells and adult organs." Genome Res.. 2008;18(1):46-59. PMC 
Frank AM, Bandeira N, Shen Z, et al. "Clustering millions of tandem mass spectra." J. Proteome Res.. 2008;7(1):113-22. PMC 
Rodriguez J, Gupta N, Smith RD, Pevzner PA. "Does trypsin cut before proline?" J. Proteome Res.. 2008;7(1):300-5.
Ng J, Pevzner PA. "Algorithm for identification of fusion proteins via mass spectrometry." J. Proteome Res.. 2008;7(1):89-95.
Chaisson MJ, Pevzner PA. "Short read fragment assembly of bacterial genomes." Genome Res.. 2008;18(2):324-30. PMC 
Wilmes GM, Bergkessel M, Bandyopadhyay S, et al. "A genetic interaction map of RNA-processing factors reveals links between Sem1/Dss1-containing complexes and mRNA export and splicing." Mol. Cell. 2008;32(5):735-46. PMC 
Castellana NE, Payne SH, Shen Z, Stanke M, Bafna V, Briggs SP. "Discovery and revision of Arabidopsis genes by proteogenomics." Proc. Natl. Acad. Sci. U.S.A.. 2008;105(52):21034-8. PMC 
Portnoy VA, Herrgård MJ, Palsson BØ. "Aerobic fermentation of D-glucose by an evolved cytochrome oxidase-deficient Escherichia coli strain." Appl. Environ. Microbiol.. 2008;74(24):7561-9. PMC 
Rao F, Zhang L, Wessel J, et al. "Adrenergic polymorphism and the human stress response." Ann. N. Y. Acad. Sci.. 2008;1148:282-96. PMC 
Hsiao A, Subramaniam S. "Bivariate microarray analysis: statistical interpretation of two-channel functional genomics data." Syst Synth Biol. 2008;2(3-4):95-104. PMC 
Pevzner PA, Kim S, Ng J. "Comment on "Protein sequences from mastodon and Tyrannosaurus rex revealed by mass spectrometry"." Science. 2008;321(5892):1040; author reply 1040.
Chang MW, Belew RK, Carroll KS, Olson AJ, Goodsell DS. "Empirical entropic contributions in computational docking: evaluation in APS reductase complexes." J Comput Chem. 2008;29(11):1753-61. PMC 
Payne SH, Yau M, Smolka MB, Tanner S, Zhou H, Bafna V. "Phosphorylation-specific MS/MS scoring for rapid and accurate phosphoproteome analysis." J. Proteome Res.. 2008;7(8):3373-81. PMC 
Kim S, Gupta N, Pevzner PA. "Spectral probabilities and generating functions of tandem mass spectra: a strike against decoy databases." J. Proteome Res.. 2008;7(8):3354-63. PMC 
Cachay ER, Frost SDW, Poon AFY, et al. "Herpes simplex virus type 2 acquisition during recent HIV infection does not influence plasma HIV levels." J. Acquir. Immune Defic. Syndr.. 2008;47(5):592-6. PMC 
Pacold M, Soto P. "Retroviruses and opportunistic infections - 15th annual conference." IDrugs. 2008;11(4):233-5.
Bashir A, Volik S, Collins C, Bafna V, Raphael BJ. "Evaluation of paired-end sequencing strategies for detection of genome rearrangements in cancer." PLoS Comput. Biol.. 2008;4(4):e1000051. PMC 
Bandyopadhyay S, Kelley R, Krogan NJ, Ideker T. "Functional maps of protein complexes from quantitative genetic interaction data." PLoS Comput. Biol.. 2008;4(4):e1000065. PMC 
Young JA, Johnson JR, Benner C, et al. "In silico discovery of transcription regulatory elements in Plasmodium falciparum." BMC Genomics. 2008;9:70. PMC 
Briedis KM, Starr A, Bourne PE. "Analysis of the human kinome using methods including fold recognition reveals two novel kinases." PLoS ONE. 2008;3(2):e1597. PMC 
Suthram S, Beyer A, Karp RM, Eldar Y, Ideker T. "eQED: an efficient method for interpreting eQTL associations using protein networks." Mol. Syst. Biol.. 2008;4:162. PMC 
Raphael BJ, Volik S, Yu P, et al. "A sequence-based survey of the complex structural organization of tumor genomes." Genome Biol.. 2008;9(3):R59. PMC 
Joyce AR, Palsson BØ. "Predicting gene essentiality using genome-scale in silico models." Methods Mol. Biol.. 2008;416:433-57.
Bechtel JM, Wittenschlaeger T, Dwyer T, et al. "Genomic mid-range inhomogeneity correlates with an abundance of RNA secondary structures." BMC Genomics. 2008;9:284. PMC 
Bechtel JM, Rajesh P, Ilikchyan I, et al. "The Alternative Splicing Mutation Database: a hub for investigations of alternative splicing using mutational evidence." BMC Res Notes. 2008;1:3. PMC 
Bechtel JM, Rajesh P, Ilikchyan I, et al. "Calculation of splicing potential from the Alternative Splicing Mutation Database." BMC Res Notes. 2008;1:4. PMC 
Chen CY-C, Chen G-W, Chen WY-C. "Molecular Simulation of HER2/neu Degradation by HSP90 Inhibitors." Journal of the Chinese Chemical Society. 2008;55:297-302. Publisher 

2007

Luban S, Kihara D. "Comparative genomics of small RNAs in bacterial genomes." OMICS. 2007;11(1):58-73.
Gupta N, Tanner S, Jaitly N, et al. "Whole proteome analysis of post-translational modifications: applications of mass-spectrometry for proteogenomic annotation." Genome Res.. 2007;17(9):1362-77. PMC 
Beyer A, Bandyopadhyay S, Ideker T. "Integrating physical and genetic maps: from genomes to interaction networks." Nat. Rev. Genet.. 2007;8(9):699-710. PMC 
Zhang L, Rao F, Zhang K, et al. "Discovery of common human genetic variants of GTP cyclohydrolase 1 (GCH1) governing nitric oxide, autonomic activity, and cardiovascular risk." J. Clin. Invest.. 2007;117(9):2658-71. PMC 
Zheng M, Barrera LO, Ren B, Wu Y. "ChIP-chip: data, model, and analysis." Biometrics. 2007;63(3):787-96.
Knipp M, Yang F, Berry RE, Zhang H, Shokhirev MN, Walker AF. "Spectroscopic and functional characterization of nitrophorin 7 from the blood-feeding insect Rhodnius prolixus reveals an important role of its isoform-specific N-terminus for proper protein function." Biochemistry. 2007;46(46):13254-68. PMC 
Bashir A, Liu Y-T, Raphael BJ, Carson D, Bafna V. "Optimization of primer design for the detection of variable genomic lesions in cancer." Bioinformatics. 2007;23(21):2807-15.
Shlomi T, Herrgard M, Portnoy V, et al. "Systematic condition-dependent annotation of metabolic genes." Genome Res.. 2007;17(11):1626-33. PMC 
Xie L, Wang J, Bourne PE. "In silico elucidation of the molecular mechanism defining the adverse effect of selective estrogen receptor modulators." PLoS Comput. Biol.. 2007;3(11):e217. PMC 
Chang MW, Lindstrom W, Olson AJ, Belew RK. "Analysis of HIV wild-type and mutant structures via in silico docking against diverse ligand libraries." J Chem Inf Model. 2007;47(3):1258-62.
Kwon Y-S, Garcia-Bassets I, Hutt KR, et al. "Sensitive ChIP-DSL technology reveals an extensive estrogen receptor alpha-binding program on human gene promoters." Proc. Natl. Acad. Sci. U.S.A.. 2007;104(12):4852-7. PMC 
Heintzman ND, Stuart RK, Hon G, et al. "Distinct and predictive chromatin signatures of transcriptional promoters and enhancers in the human genome." Nat. Genet.. 2007;39(3):311-8.
Birney E, Stamatoyannopoulos JA, Dutta A, et al. "Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project." Nature. 2007;447(7146):799-816. PMC 
Berry RE, Shokhireva T K, Filippov I, Shokhirev MN, Zhang H, Walker AF. "Effect of the N-terminus on heme cavity structure, ligand equilibrium, rate constants, and reduction potentials of nitrophorin 2 from Rhodnius prolixus." Biochemistry. 2007;46(23):6830-43. PMC 
Hevener AL, Olefsky JM, Reichart D, et al. "Macrophage PPAR gamma is required for normal skeletal muscle and hepatic insulin sensitivity and full antidiabetic effects of thiazolidinediones." J. Clin. Invest.. 2007;117(6):1658-69. PMC 
Lunyak VV, Prefontaine GG, Núñez E, et al. "Developmentally regulated activation of a SINE B2 repeat as a domain boundary in organogenesis." Science. 2007;317(5835):248-51.
Hua Q, Joyce AR, Palsson BØ, Fong SS. "Metabolic characterization of Escherichia coli strains adapted to growth on lactate." Appl. Environ. Microbiol.. 2007;73(14):4639-47. PMC 
Kim T H, Barrera LO, Ren B. "ChIP-chip for genome-wide analysis of protein binding in mammalian cells." Curr Protoc Mol Biol. 2007;Chapter 21:Unit 21.13.
Zhi D, Keich U, Pevzner P, Heber S, Tang H. "Correcting base-assignment errors in repeat regions of shotgun assembly." IEEE/ACM Trans Comput Biol Bioinform. 2007;4(1):54-64.
Ye C, Eskin E. "Discovering tightly regulated and differentially expressed gene sets in whole genome expression data." Bioinformatics. 2007;23(2):e84-90.
Zhang H, Liu AY, Loriaux P, et al. "Mass spectrometric detection of tissue proteins in plasma." Mol. Cell Proteomics. 2007;6(1):64-71.
Rana BK, Insel PA, Payne SH, et al. "Population-based sample reveals gene-gender interactions in blood pressure in White Americans." Hypertension. 2007;49(1):96-106.
Garcia-Bassets I, Kwon Y-S, Telese F, et al. "Histone methylation-dependent mechanisms impose ligand dependency for gene activation by nuclear receptors." Cell. 2007;128(3):505-18. PMC 
Duarte NC, Becker SA, Jamshidi N, et al. "Global reconstruction of the human metabolic network based on genomic and bibliomic data." Proc. Natl. Acad. Sci. U.S.A.. 2007;104(6):1777-82. PMC 
Bansal V, Bashir A, Bafna V. "Evidence for large inversion polymorphisms in the human genome from HapMap data." Genome Res.. 2007;17(2):219-30. PMC 
Tanner S, Shen Z, Ng J, et al. "Improving gene annotation using peptide mass spectrometry." Genome Res.. 2007;17(2):231-9. PMC 
Sears DD, Hsiao A, Ofrecio JM, Chapman J, He W, Olefsky JM. "Selective modulation of promoter recruitment and transcriptional activity of PPARgamma." Biochem. Biophys. Res. Commun.. 2007;364(3):515-21. PMC 
Rao F, Zhang L, Wessel J, et al. "Tyrosine hydroxylase, the rate-limiting enzyme in catecholamine biosynthesis: discovery of common human genetic variants governing transcription, autonomic activity, and blood pressure in vivo." Circulation. 2007;116(9):993-1006.
Cho B-K, Charusanti P, Herrgård MJ, Palsson BO. "Microbial regulatory and metabolic networks." Curr. Opin. Biotechnol.. 2007;18(4):360-4.
Zaitlen N, Kang H M, Eskin E, Halperin E. "Leveraging the HapMap correlation structure in association studies." Am. J. Hum. Genet.. 2007;80(4):683-91. PMC 
Joyce AR, Palsson BO. "Toward whole cell modeling and simulation: comprehensive functional genomics through the constraint-based approach." Prog Drug Res. 2007;64:265, 267-309.
Becker SA, Feist AM, Mo ML, Hannum G, Palsson BØ, Herrgard MJ. "Quantitative prediction of cellular metabolism with constraint-based models: the COBRA Toolbox." Nat Protoc. 2007;2(3):727-38.
O'Dea EL, Barken D, Peralta RQ, et al. "A homeostatic model of IkappaB metabolism to control constitutive NF-kappaB activity." Mol. Syst. Biol.. 2007;3:111. PMC 
Feist AM, Henry CS, Reed JL, et al. "A genome-scale metabolic reconstruction for Escherichia coli K-12 MG1655 that accounts for 1260 ORFs and thermodynamic information." Mol. Syst. Biol.. 2007;3:121. PMC 
Parrish JR, Yu J, Liu G, et al. "A proteome-wide protein interaction map for Campylobacter jejuni." Genome Biol.. 2007;8(7):R130. PMC 
Maurya M R, Benner C, Pradervand S, Glass C, Subramaniam S. "Systems biology of macrophages." Adv. Exp. Med. Biol.. 2007;598:62-79.
Yeung M, Thiele I, Palsson BO. "Estimation of the number of extreme pathways for metabolic networks." BMC Bioinformatics. 2007;8(1):363. PMC 
Chuang H-Y, Lee E, Liu Y-T, Lee D, Ideker T. "Network-based classification of breast cancer metastasis." Mol. Syst. Biol.. 2007;3:140. PMC 
Cline MS, Smoot M, Cerami E, et al. "Integration of biological networks and gene expression data using Cytoscape." Nat Protoc. 2007;2(10):2366-82. PMC 
Aktulga H M, Kontoyiannis I, Lyznik AL, Szpankowski L, Grama AY, Szpankowski W. "Identifying statistical dependence in genomic sequences via mutual information estimates." EURASIP J Bioinform Syst Biol. 2007:14741. PMC 

2006

Wilmarth PA, Tanner S, Dasari S, et al. "Age-related changes in human crystallins determined from comparative analysis of post-translational modifications in young and aged lens: does deamidation contribute to crystallin insolubility?" J. Proteome Res.. 2006;5(10):2554-66. PMC 
Reed JL, Patel TR, Chen KH, et al. "Systems approach to refining genome annotation." Proc. Natl. Acad. Sci. U.S.A.. 2006;103(46):17480-4. PMC 
Vosseller K, Trinidad JC, Chalkley RJ, et al. "O-linked N-acetylglucosamine proteomics of postsynaptic density preparations using lectin weak affinity chromatography and mass spectrometry." Mol. Cell Proteomics. 2006;5(5):923-34.
Raetz CRH, Garrett TA, Reynolds MC, et al. "Kdo2-Lipid A of Escherichia coli, a defined endotoxin that activates macrophages via TLR-4." J. Lipid Res.. 2006;47(5):1097-111.
Herrgård MJ, Lee B-S, Portnoy V, Palsson BØ. "Integrated analysis of regulatory and metabolic networks reveals novel regulatory mechanisms in Saccharomyces cerevisiae." Genome Res.. 2006;16(5):627-35. PMC 
Gianchandani EP, Brautigan DL, Papin JA. "Systems analyses characterize integrated functions of biochemical networks." Trends Biochem. Sci.. 2006;31(5):284-91.
Joyce AR, Palsson BØ. "The model organism as a system: integrating 'omics' data sets." Nat. Rev. Mol. Cell Biol.. 2006;7(3):198-210.
Bandyopadhyay S, Sharan R, Ideker T. "Systematic identification of functional orthologs based on protein network comparison." Genome Res.. 2006;16(3):428-35. PMC 
Price ND, Thiele I, Palsson BØ. "Candidate states of Helicobacter pylori's genome-scale metabolic network upon application of "loop law" thermodynamic constraints." Biophys. J.. 2006;90(11):3919-28. PMC 
Barrera LO, Ren B. "The transcriptional regulatory code of eukaryotic cells--insights from genome-wide analysis of chromatin organization and transcription factor binding." Curr. Opin. Cell Biol.. 2006;18(3):291-8.
Hawkins T, Luban S, Kihara D. "Enhanced automated function prediction using distantly related sequences and contextual association by PFP." Protein Sci.. 2006;15(6):1550-6. PMC 
Herrgård MJ, Fong SS, Palsson BØ. "Identification of genome-scale metabolic network models using experimentally measured flux profiles." PLoS Comput. Biol.. 2006;2(7):e72. PMC 
Harish N, Gupta R, Agarwal P, Scaria V, Pillai B. "DyNAVacS: an integrative tool for optimized DNA vaccine design." Nucleic Acids Res.. 2006;34(Web Server issue):W264-6. PMC 
Jones NC, Zhi D, Raphael BJ. "AliWABA: alignment on the web through an A-Bruijn approach." Nucleic Acids Res.. 2006;34(Web Server issue):W613-6. PMC 
Hirose S, Payne SH, Loomis WF. "cis-Acting site controlling bidirectional transcription at the growth-differentiation transition in Dictyostelium discoideum." Eukaryotic Cell. 2006;5(7):1104-10. PMC 
Roepcke S, Zhi D, Vingron M, Arndt PF. "Identification of highly specific localized sequence motifs in human ribosomal protein gene promoters." Gene. 2006;365:48-56.
Allen TE, Price ND, Joyce AR, Palsson BØ. "Long-range periodic patterns in microbial genomes indicate significant multi-scale chromosomal organization." PLoS Comput. Biol.. 2006;2(1):e2. PMC 
Reed JL, Famili I, Thiele I, Palsson BO. "Towards multidimensional genome annotation." Nat. Rev. Genet.. 2006;7(2):130-41.
Payne SH, Loomis WF. "Retention and loss of amino acid biosynthetic pathways based on analysis of whole-genome sequences." Eukaryotic Cell. 2006;5(2):272-6. PMC 
Hua Q, Joyce AR, Fong SS, Palsson BØ. "Metabolic analysis of adaptive evolution for in silico-designed lactate-producing strains." Biotechnol. Bioeng.. 2006;95(5):992-1002.
Chaisson MJ, Raphael BJ, Pevzner PA. "Microinversions in mammalian evolution." Proc. Natl. Acad. Sci. U.S.A.. 2006;103(52):19824-9. PMC 
Joyce AR, Reed JL, White A, et al. "Experimental and computational assessment of conditionally essential genes in Escherichia coli." J. Bacteriol.. 2006;188(23):8259-71. PMC 
Herring CD, Raghunathan A, Honisch C, et al. "Comparative genome sequencing of Escherichia coli allows observation of bacterial evolution on a laboratory timescale." Nat. Genet.. 2006;38(12):1406-12.
Gianchandani EP, Papin JA, Price ND, Joyce AR, Palsson BO. "Matrix formalism to describe functional states of transcriptional regulatory systems." PLoS Comput. Biol.. 2006;2(8):e101. PMC 
Zhi D, Raphael BJ, Price AL, Tang H, Pevzner PA. "Identifying repeat domains in large genomes." Genome Biol.. 2006;7(1):R7. PMC 
Reguly T, Breitkreutz A, Boucher L, et al. "Comprehensive curation and analysis of global interaction networks in Saccharomyces cerevisiae." J. Biol.. 2006;5(4):11. PMC 
Suthram S, Shlomi T, Ruppin E, Sharan R, Ideker T. "A direct comparison of protein interaction confidence assignment schemes." BMC Bioinformatics. 2006;7:360. PMC 
Zhang H, Loriaux P, Eng J, et al. "UniPep--a database for human N-linked glycosites: a resource for biomarker discovery." Genome Biol.. 2006;7(8):R73. PMC 
Zhi D, Krishna SS, Cao H, Pevzner P, Godzik A. "Representing and comparing protein structures as paths in three-dimensional space." BMC Bioinformatics. 2006;7:460. PMC 
Bandyopadhyay S, Kelley R, Ideker T. "Discovering regulated networks during HIV-1 latency and reactivation." Pac Symp Biocomput. 2006:354-66. Publisher 
Tanner S, Pevzner PA, Bafna V. "Unrestrictive identification of post-translational modifications through peptide mass spectrometry." Nat Protoc. 2006;1(1):67-72.

2005

Ogawa S, Lozach J, Benner C, et al. "Molecular determinants of crosstalk between nuclear receptors and toll-like receptors." Cell. 2005;122(5):707-21. PMC 
Covert MW, Leung TH, Gaston JE, Baltimore D. "Achieving stability of lipopolysaccharide-induced NF-kappaB activation." Science. 2005;309(5742):1854-7.
Werner SL, Barken D, Hoffmann A. "Stimulus specificity of gene expression programs determined by temporal control of IKK activity." Science. 2005;309(5742):1857-61.
Fong SS, Joyce AR, Palsson BØ. "The econometrics of evolution." Nat. Chem. Biol.. 2005;1(4):191-2.
Fong SS, Joyce AR, Palsson BØ. "Parallel adaptive evolution cultures of Escherichia coli lead to convergent growth phenotypes with different gene expression states." Genome Res.. 2005;15(10):1365-72. PMC 
Suthram S, Sittler T, Ideker T. "The Plasmodium protein network diverges from those of other eukaryotes." Nature. 2005;438(7064):108-12. PMC 
Chen J, Swamidass JS, Dou Y, Bruand J, Baldi P. "ChemDB: a public database of small molecules and related chemoinformatics resources." Bioinformatics. 2005;21(22):4133-9.
Zaitlen NA, Kang H M, Feolo ML, Sherry ST, Halperin E, Eskin E. "Inference and analysis of haplotypes from combined genotyping studies deposited in dbSNP." Genome Res.. 2005;15(11):1594-600. PMC 
Kelley R, Ideker T. "Systematic interpretation of genetic interactions using protein networks." Nat. Biotechnol.. 2005;23(5):561-6. PMC 
Thiele I, Price ND, Vo TD, Palsson BØ. "Candidate metabolic network states in human mitochondria. Impact of diabetes, ischemia, and diet." J. Biol. Chem.. 2005;280(12):11683-95.
Famili I, Mahadevan R, Palsson BO. "k-Cone analysis: determining all candidate values for kinetic parameters on a network scale." Biophys. J.. 2005;88(3):1616-25. PMC 
Devaraj NK, Miller GP, Ebina W, et al. "Chemoselective covalent coupling of oligonucleotide probes to self-assembled monolayers." J. Am. Chem. Soc.. 2005;127(24):8600-1. PMC 
Kim T H, Barrera LO, Qu C, et al. "Direct isolation and identification of promoters in the human genome." Genome Res.. 2005;15(6):830-9. PMC 
Swamidass JS, Chen J, Bruand J, Phung P, Ralaivola L, Baldi P. "Kernels for small molecules and the prediction of mutagenicity, toxicity and anti-cancer activity." Bioinformatics. 2005;21 Suppl 1:i359-68.
Frank A, Tanner S, Bafna V, Pevzner P. "Peptide sequence tags for fast database search in mass-spectrometry." J. Proteome Res.. 2005;4(4):1287-95.
Tanner S, Shu H, Frank A, et al. "InsPecT: identification of posttranslationally modified peptides from tandem mass spectra." Anal. Chem.. 2005;77(14):4626-39.
Hsiao A, Ideker T, Olefsky JM, Subramaniam S. "VAMPIRE microarray suite: a web-based platform for the interpretation of gene expression data." Nucleic Acids Res.. 2005;33(Web Server issue):W627-32. PMC 
Bashir A, Ye C, Price AL, Bafna V. "Orthologous repeats and mammalian phylogenetic inference." Genome Res.. 2005;15(7):998-1006. PMC 
Tompa M, Li N, Bailey TL, et al. "Assessing computational tools for the discovery of transcription factor binding sites." Nat. Biotechnol.. 2005;23(1):137-44.
Sharan R, Suthram S, Kelley RM, et al. "Conserved patterns of protein interaction in multiple species." Proc. Natl. Acad. Sci. U.S.A.. 2005;102(6):1974-9. PMC 
Papin JA, Hunter T, Palsson BO, Subramaniam S. "Reconstruction of cellular signalling networks and analysis of their properties." Nat. Rev. Mol. Cell Biol.. 2005;6(2):99-111.
Tsur D, Tanner S, Zandi E, Bafna V, Pevzner PA. "Identification of post-translational modifications by blind search of mass spectra." Nat. Biotechnol.. 2005;23(12):1562-7.
Kim T H, Barrera LO, Zheng M, et al. "A high-resolution map of active promoters in the human genome." Nature. 2005;436(7052):876-80. PMC 
Thiele I, Vo TD, Price ND, Palsson BØ. "Expanded metabolic reconstruction of Helicobacter pylori (iIT341 GSM/GPR): an in silico genome-scale characterization of single- and double-deletion mutants." J. Bacteriol.. 2005;187(16):5818-30. PMC 
Barken D, Wang C J, Kearns J, Cheong R, Hoffmann A, Levchenko A. "Comment on "Oscillations in NF-kappaB signaling control the dynamics of gene expression"." Science. 2005;308(5718):52; author reply 52. PMC 
Herrgård MJ, Palsson BØ. "Untangling the web of functional and physical interactions in yeast." J. Biol.. 2005;4(2):5. PMC 
Overbeek R, Begley T, Butler RM, et al. "The subsystems approach to genome annotation and its use in the project to annotate 1000 genomes." Nucleic Acids Res.. 2005;33(17):5691-702. PMC 
Tsur D, Tanner S, Zandi E, Bafna V, Pevzner PA. "Identification of post-translational modifications via blind search of mass-spectra." Proc IEEE Comput Syst Bioinform Conf. 2005:157-66.
Szpankowski W, Ren W, Szpankowski L. "An optimal DNA segmentation based on the MDL principle." Int J Bioinform Res Appl. 2005;1(1):3-17. Publisher 
Payne SH. "Metabolic pathways." In: Loomis WF, Kuspa A, eds. Dictyostelium Genomics, pp. 41-57. Far Hills, N.J.: Horizon Press; 2005. Publisher  Amazon 

2004

Chaisson M, Pevzner P, Tang H. "Fragment assembly with short reads." Bioinformatics. 2004;20(13):2067-74.
Price ND, Schellenberger J, Palsson BO. "Uniform sampling of steady-state flux spaces: means to design experiments and to interpret enzymopathies." Biophys. J.. 2004;87(4):2172-86. PMC 
Hsiao A, Worrall DS, Olefsky JM, Subramaniam S. "Variance-modeled posterior inference of microarray data: detecting gene-expression changes in 3T3-L1 adipocytes." Bioinformatics. 2004;20(17):3108-27.
Raphael B, Zhi D, Tang H, Pevzner P. "A novel method for multiple alignment of sequences with repeated and shuffled elements." Genome Res.. 2004;14(11):2336-46. PMC 
Covert MW, Knight EM, Reed JL, Herrgard MJ, Palsson BO. "Integrating high-throughput and computational data elucidates bacterial networks." Nature. 2004;429(6987):92-6.
Papin JA, Palsson BO. "Topological analysis of mass-balanced signaling networks: a framework to obtain network properties including crosstalk." J. Theor. Biol.. 2004;227(2):283-97.
Wiback SJ, Famili I, Greenberg HJ, Palsson BØ. "Monte Carlo sampling can be used to determine the size and shape of the steady-state flux space." J. Theor. Biol.. 2004;228(4):437-47.
Canet-Avilés RM, Wilson MA, Miller DW, et al. "The Parkinson's disease protein DJ-1 is neuroprotective due to cysteine-sulfinic acid-driven mitochondrial localization." Proc. Natl. Acad. Sci. U.S.A.. 2004;101(24):9103-8. PMC 
Herrgård MJ, Palsson BØ. "Flagellar biosynthesis in silico: building quantitative models of regulatory networks." Cell. 2004;117(6):689-90.
Crooks GE, Hon G, Chandonia J-M, Brenner SE. "WebLogo: a sequence logo generator." Genome Res.. 2004;14(6):1188-90. PMC 
Duarte NC, Herrgård MJ, Palsson BØ. "Reconstruction and validation of Saccharomyces cerevisiae iND750, a fully compartmentalized genome-scale metabolic model." Genome Res.. 2004;14(7):1298-309. PMC 
Papin JA, Palsson BO. "The JAK-STAT signaling network in the human B-cell: an extreme signaling pathway analysis." Biophys. J.. 2004;87(1):37-46. PMC 
Chandonia J-M, Hon G, Walker NS, et al. "The ASTRAL Compendium in 2004." Nucleic Acids Res.. 2004;32(Database issue):D189-92. PMC 
Bandyopadhyay S, Cookson MR. "Evolutionary and functional relationships within the DJ1 superfamily." BMC Evol. Biol.. 2004;4:6. PMC 
Herrgård MJ, Covert MW, Palsson BØ. "Reconstruction of microbial transcriptional regulatory networks." Curr. Opin. Biotechnol.. 2004;15(1):70-7.
Zhu X, Hart R, Chang M S, et al. "Analysis of the major patterns of B cell gene expression changes in response to short-term stimulation with 33 single ligands." J. Immunol.. 2004;173(12):7141-9.
Papin JA, Reed JL, Palsson BO. "Hierarchical thinking in network biology: the unbiased modularization of biochemical networks." Trends Biochem. Sci.. 2004;29(12):641-7.
Papin JA, Stelling J, Price ND, Klamt S, Schuster S, Palsson BO. "Comparison of network-based pathway analysis methods." Trends Biotechnol.. 2004;22(8):400-5.
Barrera L, Benner C, Tao Y-C, Winzeler E, Zhou Y. "Leveraging two-way probe-level block design for identifying differential gene expression with high-density oligonucleotide arrays." BMC Bioinformatics. 2004;5:42. PMC 
Haugen AC, Kelley R, Collins JB, et al. "Integrating phenotypic and expression profiles to map arsenic-response networks." Genome Biol.. 2004;5(12):R95. PMC 

2003

Förster J, Famili I, Palsson BO, Nielsen J. "Large-scale evaluation of in silico gene deletions in Saccharomyces cerevisiae." OMICS. 2003;7(2):193-202.
Famili I, Palsson BO. "Systemic metabolic reactions are obtained by singular value decomposition of genome-scale stoichiometric matrices." J. Theor. Biol.. 2003;224(1):87-96.
Price ND, Reed JL, Papin JA, Wiback SJ, Palsson BO. "Network-based analysis of metabolic regulation in the human red blood cell." J. Theor. Biol.. 2003;225(2):185-94.
Famili I, Forster J, Nielsen J, Palsson BO. "Saccharomyces cerevisiae phenotypes can be predicted by using constraint-based analysis of a genome-scale reconstructed metabolic network." Proc. Natl. Acad. Sci. U.S.A.. 2003;100(23):13134-9. PMC 
Herrgård MJ, Covert MW, Palsson BØ. "Reconciling gene expression data with known genome-scale regulatory network structures." Genome Res.. 2003;13(11):2423-34. PMC 
Allen TE, Herrgård MJ, Liu M, et al. "Genome-scale analysis of the uses of the Escherichia coli genome: model-driven analysis of heterogeneous data sets." J. Bacteriol.. 2003;185(21):6392-9. PMC 
Palsson BO, Price ND, Papin JA. "Development of network-based pathway definitions: the need to analyze real metabolic networks." Trends Biotechnol.. 2003;21(5):195-8.
Papin JA, Price ND, Wiback SJ, Fell DA, Palsson BO. "Metabolic pathways in the post-genome era." Trends Biochem. Sci.. 2003;28(5):250-8.
Famili I, Palsson BO. "The convex basis of the left null space of the stoichiometric matrix leads to the definition of metabolically meaningful pools." Biophys. J.. 2003;85(1):16-26. PMC 
Price ND, Reed JL, Papin JA, Famili I, Palsson BO. "Analysis of metabolic capabilities using singular value decomposition of extreme pathway matrices." Biophys. J.. 2003;84(2 Pt 1):794-804. PMC 
Förster J, Famili I, Fu P, Palsson BØ, Nielsen J. "Genome-scale reconstruction of the Saccharomyces cerevisiae metabolic network." Genome Res.. 2003;13(2):244-53. PMC 
Covert MW, Famili I, Palsson BO. "Identifying constraints that govern cell behavior: a key to converting conceptual to computational models in biology?" Biotechnol. Bioeng.. 2003;84(7):763-72.
Covert MW, Palsson BO. "Constraints-based models: regulation of gene expression reduces the steady-state solution space." J. Theor. Biol.. 2003;221(3):309-25.
Price ND, Papin JA, Schilling CH, Palsson BO. "Genome-scale microbial in silico models: the constraints-based approach." Trends Biotechnol.. 2003;21(4):162-9.

2002

Price ND, Famili I, Beard DA, Palsson BØ. "Extreme pathways and Kirchhoff's second law." Biophys. J.. 2002;83(5):2879-82. PMC 
Price ND, Papin JA, Palsson BØ. "Determination of redundancy and systems properties of the metabolic network of Helicobacter pylori using genome-scale extreme pathway analysis." Genome Res.. 2002;12(5):760-9. PMC 
Papin JA, Price ND, Edwards JS, Palsson B BØ. "The genome-scale metabolic extreme pathway structure in Haemophilus influenzae shows significant network redundancy." J. Theor. Biol.. 2002;215(1):67-82.
Edwards JS, Covert M, Palsson B. "Metabolic modelling of microbes: the flux-balance approach." Environ. Microbiol.. 2002;4(3):133-40.
Papin JA, Price ND, Palsson BØ. "Extreme pathway lengths and reaction participation in genome-scale metabolic networks." Genome Res.. 2002;12(12):1889-900. PMC 
Covert MW, Palsson BØ. "Transcriptional regulation in constraints-based metabolic models of Escherichia coli." J. Biol. Chem.. 2002;277(31):28058-64.
Schilling CH, Covert MW, Famili I, Church GM, Edwards JS, Palsson BO. "Genome-scale metabolic model of Helicobacter pylori 26695." J. Bacteriol.. 2002;184(16):4582-93. PMC 

2001

Covert MW, Schilling CH, Palsson B. "Regulation of gene expression in flux balance models of metabolism." J. Theor. Biol.. 2001;213(1):73-88.
Covert MW, Schilling CH, Famili I, et al. "Metabolic modeling of microbial strains in silico." Trends Biochem. Sci.. 2001;26(3):179-86.