2016
Robust transcriptome-wide discovery of RNA-binding protein binding sites with enhanced CLIP (eCLIP)." Nat. Methods. 2016;13(6):508-14. "
Adder and a coarse-grained approach to cell size homeostasis in bacteria." Curr. Opin. Cell Biol.. 2016;38:38-44. "
Frequency and Complexity of De Novo Structural Mutation in Autism." Am. J. Hum. Genet.. 2016;98(4):667-79. "
Musashi-2 attenuates AHR signalling to expand human haematopoietic stem cells." Nature. 2016;532(7600):508-11. "
Global Rebalancing of Cellular Resources by Pleiotropic Point Mutations Illustrates a Multi-scale Mechanism of Adaptive Evolution." Cell Syst. 2016;2(4):260-71. "
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. "
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. "
Genetically Determined Variation in Lysis Time Variance in the Bacteriophage φX174." G3 (Bethesda). 2016;6(4):939-55. "
Systems biology of the structural proteome." BMC Syst Biol. 2016;10:26. "
Solving Puzzles With Missing Pieces: The Power of Systems Biology." Proceedings of the IEEE. 2016;104(1):2-7. "
URL
2015
The Ro60 autoantigen binds endogenous retroelements and regulates inflammatory gene expression." Science. 2015;350(6259):455-9. "
Chemogenetic profiling identifies RAD17 as synthetically lethal with checkpoint kinase inhibition." Oncotarget. 2015;6(34):35755-69. "
An alternative pluripotent state confers interspecies chimaeric competency." Nature. 2015;521(7552):316-21. "
Using Genome-scale Models to Predict Biological Capabilities." Cell. 2015;161(5):971-87. "
Identification of therapeutic targets for glioblastoma by network analysis." Oncogene. 2015. "
Gene-wide identification of episodic selection." Mol. Biol. Evol.. 2015;32(5):1365-71. "
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. "
Transcriptome sequencing reveals potential mechanism of cryptic 3' splice site selection in SF3B1-mutated cancers." PLoS Comput. Biol.. 2015;11(3):e1004105. "
Non-CG Methylation in the Human Genome." Annu Rev Genomics Hum Genet. 2015. "
Single-Cell Physiology." Annu Rev Biophys. 2015;44:123-42. "
Human body epigenome maps reveal noncanonical DNA methylation variation." Nature. 2015;523(7559):212-6. "
Molecular networks in context." Nat. Biotechnol.. 2015;33(7):720-1. "
Target Discrimination in Nonsense-Mediated mRNA Decay Requires Upf1 ATPase Activity." Mol. Cell. 2015;59(3):413-25. "
Computing the functional proteome: recent progress and future prospects for genome-scale models." Curr. Opin. Biotechnol.. 2015;34:125-34. "
ERCC1 and TS Expression as Prognostic and Predictive Biomarkers in Metastatic Colon Cancer." PLoS ONE. 2015;10(6):e0126898. "
Towards a personalized treatment of head and neck cancer." Am Soc Clin Oncol Educ Book. 2015;35:28-32. "
Dysregulated mechanisms underlying Duchenne muscular dystrophy from co-expression network preservation analysis." BMC Res Notes. 2015;8:182. "
The Clothes Make the mRNA: Past and Present Trends in mRNP Fashion." Annu. Rev. Biochem.. 2015;84:325-54. "
Analysis of Matched Tumor and Normal Profiles Reveals Common Transcriptional and Epigenetic Signals Shared across Cancer Types." PLoS ONE. 2015;10(11):e0142618. "
2014
The developmental potential of iPSCs is greatly influenced by reprogramming factor selection." Cell Stem Cell. 2014;15(3):295-309. "
Multi-tiered genomic analysis of head and neck cancer ties TP53 mutation to 3p loss." Nat. Genet.. 2014;46(9):939-43. "
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. "
NeatFreq: reference-free data reduction and coverage normalization for De Novo sequence assembly." BMC Bioinformatics. 2014;15(1):357. "
PMC
Systems analysis of transcriptional data provides insights into muscle's biological response to botulinum toxin." Muscle Nerve. 2014;50(5):744-58. "
Flt3L dependence helps define an uncharacterized subset of murine cutaneous dendritic cells." J. Invest. Dermatol.. 2014;134(5):1265-75. "
A time- and matrix-dependent TGFBR3-JUND-KRT5 regulatory circuit in single breast epithelial cells and basal-like premalignancies." Nat. Cell Biol.. 2014. "
PMC
Interactive assembly algorithms for molecular cloning." Nat. Methods. 2014;11(6):657-62. "
Abnormalities in human pluripotent cells due to reprogramming mechanisms." Nature. 2014;511(7508):177-83. "
Assimilating genome-scale metabolic reconstructions with modelBorgifier." Bioinformatics. 2014. "
Whole genome sequencing of Ethiopian highlanders reveals conserved hypoxia tolerance genes." Genome Biol.. 2014;15(2):R36. "
PMC
Cell-Size Control and Homeostasis in Bacteria." Curr. Biol.. 2014. "
Classical Flt3L-dependent dendritic cells control immunity to protein vaccine." J. Exp. Med.. 2014;211(9):1875-91. "
Assessment of MS/MS search algorithms with parent-protein profiling." J. Proteome Res.. 2014;13(4):1823-32. "
Technical Variations in Low-Input RNA-seq Methodologies." Sci Rep. 2014;4:3678. "
PMC
Development of ultra-high-density screening tools for microbial "omics"." PLoS ONE. 2014;9(1):e85177. "
PMC
2013
Whole-genome sequencing uncovers the genetic basis of chronic mountain sickness in Andean highlanders." Am. J. Hum. Genet.. 2013;93(3):452-62. "
PMC
Learning natural selection from the site frequency spectrum." Genetics. 2013;195(1):181-93. "
PMC
Systematic investigation of cancer-associated somatic point mutations in SNP databases." Nat. Biotechnol.. 2013;31(9):787-9. "
Single-cell genome and metatranscriptome sequencing reveal metabolic interactions of an alkane-degrading methanogenic community." ISME J. 2013. "
PMC
An Automated Proteogenomic Method Utilizes Mass Spectrometry to Reveal Novel Genes in Zea mays." Mol. Cell Proteomics. 2013. "
PMC
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
The dynamics of signaling as a pharmacological target." Cell. 2013;155(2):448-61. "
PMC
Epigenome-wide inheritance of cytosine methylation variants in a recombinant inbred population." Genome Res.. 2013;23(10):1663-74. "
PMC
Whole-genome haplotype reconstruction using proximity-ligation and shotgun sequencing." Nat. Biotechnol.. 2013. "
Incidence and Prevalence of Intrasubtype HIV-1 Dual Infection in At-Risk Men in the United States." J. Infect. Dis.. 2013. "
PMC
Characterization and modelling of interspecies electron transfer mechanisms and microbial community dynamics of a syntrophic association." Nat Commun. 2013;4:2809. "
A high-resolution map of the three-dimensional chromatin interactome in human cells." Nature. 2013;503(7475):290-4. "
PMC
Network-based stratification of tumor mutations." Nat. Methods. 2013;10(11):1108-15. "
Epigenomic analysis of multilineage differentiation of human embryonic stem cells." Cell. 2013;153(5):1134-48. "
PMC
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
Patterns of population epigenomic diversity." Nature. 2013;495(7440):193-8. "
PMC
Structural systems biology evaluation of metabolic thermotolerance in Escherichia coli." Science. 2013;340(6137):1220-3. "
PMC
MS/MS networking guided analysis of molecule and gene cluster families." Proc. Natl. Acad. Sci. U.S.A.. 2013;110(28):E2611-20. "
PMC
Proteogenomic Database Construction Driven from Large Scale RNA-seq Data." J. Proteome Res.. 2013. "
PMC
Using ultradeep pyrosequencing to study HIV-1 coreceptor usage in primary and dual infection." J. Infect. Dis.. 2013;208(2):271-4. "
PMC
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
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
Collinearity of protease mutations in HIV-1 samples with high-level protease inhibitor class resistance." J. Antimicrob. Chemother.. 2013;68(2):414-8. "
PMC
Vespucci: a system for building annotated databases of nascent transcripts." Nucleic Acids Res.. 2013. "
PMC
Dynamics of Viral Evolution and Neutralizing Antibody Response after HIV-1 Superinfection." J. Virol.. 2013;87(23):12737-44. "
PMC
Rbfox proteins regulate alternative mRNA splicing through evolutionarily conserved RNA bridges." Nat. Struct. Mol. Biol.. 2013;20(12):1434-42. "
Global epigenomic reconfiguration during mammalian brain development." Science. 2013;341(6146):1237905. "
PMC
Remodeling of the enhancer landscape during macrophage activation is coupled to enhancer transcription." Mol. Cell. 2013;51(3):310-25. "
PMC
Genomic landscapes of Chinese hamster ovary cell lines as revealed by the Cricetulus griseus draft genome." Nat. Biotechnol.. 2013;31(8):759-65. "
Genome-wide analysis reveals TET- and TDG-dependent 5-methylcytosine oxidation dynamics." Cell. 2013;153(3):692-706. "
PMC
The genome organization of Thermotoga maritima reflects its lifestyle." PLoS Genet.. 2013;9(4):e1003485. "
PMC
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
A protein turnover signaling motif controls the stimulus-sensitivity of stress response pathways." PLoS Comput. Biol.. 2013;9(2):e1002932. "
PMC
FlowMax: A Computational Tool for Maximum Likelihood Deconvolution of CFSE Time Courses." PLoS ONE. 2013;8(6):e67620. "
PMC
Ex vivo innate immune cytokine signature of enhanced risk of relapsing brucellosis." PLoS Negl Trop Dis. 2013;7(9):e2424. "
PMC
Bayesian inference of spatial organizations of chromosomes." PLoS Comput. Biol.. 2013;9(1):e1002893. "
PMC
Quantitative transcriptomics using designed primer-based amplification." Sci Rep. 2013;3:1740. "
PMC
COBRApy: COnstraints-Based Reconstruction and Analysis for Python." BMC Syst Biol. 2013;7:74. "
PMC
Genome-scale models of metabolism and gene expression extend and refine growth phenotype prediction." Mol. Syst. Biol.. 2013;9:693. "
PMC
Antibacterial mechanisms identified through structural systems pharmacology." BMC Syst Biol. 2013;7:102. "
PMC
HIV-1 clade B pol evolution following primary infection." PLoS ONE. 2013;8(6):e68188. "
PMC
The microbiome extends to subepidermal compartments of normal skin." Nat Commun. 2013;4:1431. "
PMC
Characterizing the interplay between multiple levels of organization within bacterial sigma factor regulatory networks." Nat Commun. 2013;4:1755. "
Characterizing acetogenic metabolism using a genome-scale metabolic reconstruction of Clostridium ljungdahlii." Microb. Cell Fact.. 2013;12(1):118. "
Whole transcriptome sequencing enables discovery and analysis of viruses in archived primary central nervous system lymphomas." PLoS ONE. 2013;8(9):e73956. "
2012
Raloxifene attenuates Pseudomonas aeruginosa pyocyanin production and virulence." Int. J. Antimicrob. Agents. 2012;40(3):246-51. "
LIN28 binds messenger RNAs at GGAGA motifs and regulates splicing factor abundance." Mol. Cell. 2012;48(2):195-206. "
PMC
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
BioJava: an open-source framework for bioinformatics in 2012." Bioinformatics. 2012;28(20):2693-5. "
PMC
Proteomic analysis of Chinese hamster ovary cells." J. Proteome Res.. 2012;11(11):5265-76. "
PMC
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
Topological domains in mammalian genomes identified by analysis of chromatin interactions." Nature. 2012;485(7398):376-80. "
PMC
Transcriptional architecture of the primate neocortex." Neuron. 2012;73(6):1083-99. "
PMC
Library-free methylation sequencing with bisulfite padlock probes." Nat. Methods. 2012;9(3):270-2. "
PMC
SEQuel: improving the accuracy of genome assemblies." Bioinformatics. 2012;28(12):i188-96. "
PMC
Exome sequencing can improve diagnosis and alter patient management." Sci Transl Med. 2012;4(138):138ra78. "
A sensing array of radically coupled genetic 'biopixels'." Nature. 2012;481(7379):39-44. "
PMC
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
The metabolome of induced pluripotent stem cells reveals metabolic changes occurring in somatic cell reprogramming." Cell Res.. 2012;22(1):168-77. "
PMC
Deciphering the transcriptional regulatory logic of amino acid metabolism." Nat. Chem. Biol.. 2012;8(1):65-71. "
PMC
Integrative genome-wide analysis reveals cooperative regulation of alternative splicing by hnRNP proteins." Cell Rep. 2012;1(2):167-178. "
PMC
Arabidopsis circadian clock protein, TOC1, is a DNA-binding transcription factor." Proc. Natl. Acad. Sci. U.S.A.. 2012;109(8):3167-72. "
Differential analysis of high-throughput quantitative genetic interaction data." Genome Biol.. 2012;13(12):R123. "
PMC
Tet1 controls meiosis by regulating meiotic gene expression." Nature. 2012;492(7429):443-7. "
PMC
HiCNorm: removing biases in Hi-C data via Poisson regression." Bioinformatics. 2012;28(23):3131-3. "
PMC
Control of RelB during dendritic cell activation integrates canonical and noncanonical NF-κB pathways." Nat. Immunol.. 2012;13(12):1162-70. "
PMC
'Leveling' the playing field for analyses of single-base resolution DNA methylomes." Trends Genet.. 2012;28(12):583-5. "
PMC
Network context and selection in the evolution to enzyme specificity." Science. 2012;337(6098):1101-4. "
PMC
Human-specific transcriptional networks in the brain." Neuron. 2012;75(4):601-17. "
PMC
Release factor one is nonessential in Escherichia coli." ACS Chem. Biol.. 2012;7(8):1337-44. "
PMC
Identification of high-confidence somatic mutations in whole genome sequence of formalin-fixed breast cancer specimens." Nucleic Acids Res.. 2012;40(14):e107. "
PMC
Constraining the metabolic genotype-phenotype relationship using a phylogeny of in silico methods." Nat. Rev. Microbiol.. 2012;10(4):291-305. "
PMC
Surveillance of 3' Noncoding Transcripts Requires FIERY1 and XRN3 in Arabidopsis." G3 (Bethesda). 2012;2(4):487-98. "
PMC
Rapid analysis of Saccharomyces cerevisiae genome rearrangements by multiplex ligation-dependent probe amplification." PLoS Genet.. 2012;8(3):e1002539. "
PMC
Exploiting adaptive laboratory evolution of Streptomyces clavuligerus for antibiotic discovery and overproduction." PLoS ONE. 2012;7(3):e33727. "
PMC
A framework for modeling the relationship between cellular steady-state and stimulus-responsiveness." Methods Cell Biol.. 2012;110:81-109. "
Circular permutation in proteins." PLoS Comput. Biol.. 2012;8(3):e1002445. "
PMC
Mapping single molecule sequencing reads using basic local alignment with successive refinement (BLASR): application and theory." BMC Bioinformatics. 2012;13:238. "
PMC
In silico method for modelling metabolism and gene product expression at genome scale." Nat Commun. 2012;3:929. "
PMC
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
CTF: a CRF-based transcription factor binding sites finding system." BMC Genomics. 2012;13 Suppl 8:S18. "
PMC
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
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
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
Identification of 67 histone marks and histone lysine crotonylation as a new type of histone modification." Cell. 2011;146(6):1016-28. "
PMC
Transgenerational epigenetic instability is a source of novel methylation variants." Science. 2011;334(6054):369-73. "
PMC
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
Dynamic chromatin states in human ES cells reveal potential regulatory sequences and genes involved in pluripotency." Cell Res.. 2011;21(10):1393-409. "
PMC
RF1 knockout allows ribosomal incorporation of unnatural amino acids at multiple sites." Nat. Chem. Biol.. 2011;7(11):779-86. "
PMC
A genetic and structural study of genome rearrangements mediated by high copy repeat Ty1 elements." PLoS Genet.. 2011;7(5):e1002089. "
PMC
Genome-wide mapping of the sixth base." Genome Biol.. 2011;12(6):116. "
PMC
Experimental selection of hypoxia-tolerant Drosophila melanogaster." Proc. Natl. Acad. Sci. U.S.A.. 2011;108(6):2349-54. "
PMC
The PurR regulon in Escherichia coli K-12 MG1655." Nucleic Acids Res.. 2011;39(15):6456-64. "
PMC
Increased methylation variation in epigenetic domains across cancer types." Nat. Genet.. 2011;43(8):768-75. "
PMC
The genomic sequence of the Chinese hamster ovary (CHO)-K1 cell line." Nat. Biotechnol.. 2011;29(8):735-41. "
PMC
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
Recapitulation of premature ageing with iPSCs from Hutchinson-Gilford progeria syndrome." Nature. 2011;472(7342):221-5. "
PMC
Long pre-mRNA depletion and RNA missplicing contribute to neuronal vulnerability from loss of TDP-43." Nat. Neurosci.. 2011;14(4):459-68. "
PMC
Metabolic network reconstruction of Chlamydomonas offers insight into light-driven algal metabolism." Mol. Syst. Biol.. 2011;7:518. "
PMC
A comprehensive genome-scale reconstruction of Escherichia coli metabolism--2011." Mol. Syst. Biol.. 2011;7:535. "
PMC
An experimentally-supported genome-scale metabolic network reconstruction for Yersinia pestis CO92." BMC Syst Biol. 2011;5:163. "
PMC
Tests of selection in pooled case-control data: an empirical study." Front Genet. 2011;2:83. "
PMC
2010
Microbiology. Topping off a multiscale balancing act." Science. 2010;330(6007):1058-9. "
RAPID detection of gene-gene interactions in genome-wide association studies." Bioinformatics. 2010;26(22):2856-62. "
PMC
Distinct epigenomic landscapes of pluripotent and lineage-committed human cells." Cell Stem Cell. 2010;6(5):479-91. "
PMC
Model-driven evaluation of the production potential for growth-coupled products of Escherichia coli." Metab. Eng.. 2010;12(3):173-86. "
PMC
Computational modeling of mammalian signaling networks." Wiley Interdiscip Rev Syst Biol Med. 2010;2(2):194-209. "
PMC
Omic data from evolved E. coli are consistent with computed optimal growth from genome-scale models." Mol. Syst. Biol.. 2010;6:390. "
PMC
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. "
Human host factors required for influenza virus replication." Nature. 2010;463(7282):813-7. "
PMC
Pre-calculated protein structure alignments at the RCSB PDB website." Bioinformatics. 2010;26(23):2983-5. "
PMC
Comparison of methods to detect HIV dual infection." AIDS Res. Hum. Retroviruses. 2010;26(12):1291-8. "
PMC
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
Deterministic graph-theoretic algorithm for detecting modules in biological interaction networks." Int J Bioinform Res Appl. 2010;6(2):101-19. "
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
Drug off-target effects predicted using structural analysis in the context of a metabolic network model." PLoS Comput. Biol.. 2010;6(9):e1000938. "
PMC
EpiphaNet: An Interactive Tool to Support Biomedical Discoveries." J Biomed Discov Collab. 2010;5:21-49. "
2009
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
False discovery rates of protein identifications: a strike against the two-peptide rule." J. Proteome Res.. 2009;8(9):4173-81. "
PMC
Evolutionarily conserved herpesviral protein interaction networks." PLoS Pathog.. 2009;5(9):e1000570. "
PMC
The use of pooled viral load testing to identify antiretroviral treatment failure." AIDS. 2009;23(16):2151-8. "
PMC
Predictive chromatin signatures in the mammalian genome." Hum. Mol. Genet.. 2009;18(R2):R195-201. "
PMC
The first pharmacophore model for potent NF-kappaB inhibitors." Bioorg. Med. Chem. Lett.. 2009;19(19):5665-9. "
Genome-scale metabolic networks." Wiley Interdiscip Rev Syst Biol Med. 2009;1(3):285-97. "
Mechanisms of human insulin resistance and thiazolidinedione-mediated insulin sensitization." Proc. Natl. Acad. Sci. U.S.A.. 2009;106(44):18745-50. "
PMC
Human DNA methylomes at base resolution show widespread epigenomic differences." Nature. 2009;462(7271):315-22. "
PMC
Discovery and annotation of functional chromatin signatures in the human genome." PLoS Comput. Biol.. 2009;5(11):e1000566. "
PMC
Histone modifications at human enhancers reflect global cell-type-specific gene expression." Nature. 2009;459(7243):108-12. "
PMC
Of elections and cell-death decisions." Mol. Cell. 2009;34(3):257-8. "
PMC
Host cell factors in HIV replication: meta-analysis of genome-wide studies." PLoS Pathog.. 2009;5(5):e1000437. "
PMC
Sm/Lsm genes provide a glimpse into the early evolution of the spliceosome." PLoS Comput. Biol.. 2009;5(3):e1000315. "
PMC
Interpretation of tandem mass spectra obtained from cyclic nonribosomal peptides." Anal. Chem.. 2009;81(11):4200-9. "
PMC
A complex-based reconstruction of the Saccharomyces cerevisiae interactome." Mol. Cell Proteomics. 2009;8(6):1361-81. "
PMC
Nothing about protein structure classification makes sense except in the light of evolution." Curr. Opin. Struct. Biol.. 2009;19(3):329-34. "
PMC
High-throughput biology in the postgenomic era." J Vasc Interv Radiol. 2009;20(7 Suppl):S488-96. "
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. "
A public health model for the molecular surveillance of HIV transmission in San Diego, California." AIDS. 2009;23(2):225-32. "
PMC
Spectral dictionaries: Integrating de novo peptide sequencing with database search of tandem mass spectra." Mol. Cell Proteomics. 2009;8(1):53-69. "
PMC
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
PFP: Automated prediction of gene ontology functional annotations with confidence scores using protein sequence data." Proteins. 2009;74(3):566-82. "
De novo fragment assembly with short mate-paired reads: Does the read length matter?" Genome Res.. 2009;19(2):336-46. "
PMC
Reconstruction of biochemical networks in microorganisms." Nat. Rev. Microbiol.. 2009;7(2):129-43. "
PMC
Identification of potential pathway mediation targets in Toll-like receptor signaling." PLoS Comput. Biol.. 2009;5(2):e1000292. "
PMC
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
Dereplication and de novo sequencing of nonribosomal peptides." Nat. Methods. 2009;6(8):596-9. "
PMC
Metabolic network analysis integrated with transcript verification for sequenced genomes." Nat. Methods. 2009;6(8):589-92. "
PMC
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. "
Decomposing complex reaction networks using random sampling, principal component analysis and basis rotation." BMC Syst Biol. 2009;3:30. "
PMC
Connecting extracellular metabolomic measurements to intracellular flux states in yeast." BMC Syst Biol. 2009;3:37. "
PMC
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
A dynamic network of transcription in LPS-treated human subjects." BMC Syst Biol. 2009;3:78. "
PMC
Structural analysis of polarizing indels: an emerging consensus on the root of the tree of life." Biol. Direct. 2009;4:30. "
PMC
A noisy paracrine signal determines the cellular NF-kappaB response to lipopolysaccharide." Sci Signal. 2009;2(93):ra65. "
PMC
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. "
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
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. "
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. "
Integrating metabolic, transcriptional regulatory and signal transduction models in Escherichia coli." Bioinformatics. 2008;24(18):2044-50. "
QNet: a tool for querying protein interaction networks." J. Comput. Biol.. 2008;15(7):913-25. "
Network-based prediction of human tissue-specific metabolism." Nat. Biotechnol.. 2008;26(9):1003-10. "
Global analysis of host-pathogen interactions that regulate early-stage HIV-1 replication." Cell. 2008;135(1):49-60. "
PMC
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
Conservation and rewiring of functional modules revealed by an epistasis map in fission yeast." Science. 2008;322(5900):405-10. "
PMC
A consensus yeast metabolic network reconstruction obtained from a community approach to systems biology." Nat. Biotechnol.. 2008;26(10):1155-60. "
PMC
ChromaSig: a probabilistic approach to finding common chromatin signatures in the human genome." PLoS Comput. Biol.. 2008;4(10):e1000201. "
PMC
Thrombin receptor and RhoA mediate cell proliferation through integrins and cysteine-rich protein 61." FASEB J.. 2008;22(11):4011-21. "
PMC
Protein networks markedly improve prediction of subcellular localization in multiple eukaryotic species." Nucleic Acids Res.. 2008;36(20):e136. "
PMC
Inferring pathway activity toward precise disease classification." PLoS Comput. Biol.. 2008;4(11):e1000217. "
PMC
Epigenetic control: slow and global, nimble and local." Genes Dev.. 2008;22(9):1110-4. "
PMC
Rethinking proteasome evolution: two novel bacterial proteasomes." J. Mol. Evol.. 2008;66(5):494-504. "
PMC
Efficient control of population structure in model organism association mapping." Genetics. 2008;178(3):1709-23. "
PMC
Tauopathy with paired helical filaments in an aged chimpanzee." J. Comp. Neurol.. 2008;509(3):259-70. "
PMC
A multidimensional chromatography technology for in-depth phosphoproteome analysis." Mol. Cell Proteomics. 2008;7(7):1389-96. "
PMC
Comparative proteogenomics: combining mass spectrometry and comparative genomics to analyze multiple genomes." Genome Res.. 2008;18(7):1133-42. "
PMC
Common genetic variants in the chromogranin A promoter alter autonomic activity and blood pressure." Kidney Int.. 2008;74(1):115-25. "
PMC
Impact of individual mutations on increased fitness in adaptively evolved strains of Escherichia coli." J. Bacteriol.. 2008;190(14):5087-94. "
PMC
Correcting for gene-specific dye bias in DNA microarrays using the method of maximum likelihood." Bioinformatics. 2008;24(1):71-7. "
PMC
Accurate annotation of peptide modifications through unrestrictive database search." J. Proteome Res.. 2008;7(1):170-81. "
Genome-wide mapping and analysis of active promoters in mouse embryonic stem cells and adult organs." Genome Res.. 2008;18(1):46-59. "
PMC
Clustering millions of tandem mass spectra." J. Proteome Res.. 2008;7(1):113-22. "
PMC
Does trypsin cut before proline?" J. Proteome Res.. 2008;7(1):300-5. "
Algorithm for identification of fusion proteins via mass spectrometry." J. Proteome Res.. 2008;7(1):89-95. "
Short read fragment assembly of bacterial genomes." Genome Res.. 2008;18(2):324-30. "
PMC
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
Discovery and revision of Arabidopsis genes by proteogenomics." Proc. Natl. Acad. Sci. U.S.A.. 2008;105(52):21034-8. "
PMC
Aerobic fermentation of D-glucose by an evolved cytochrome oxidase-deficient Escherichia coli strain." Appl. Environ. Microbiol.. 2008;74(24):7561-9. "
PMC
Adrenergic polymorphism and the human stress response." Ann. N. Y. Acad. Sci.. 2008;1148:282-96. "
PMC
Bivariate microarray analysis: statistical interpretation of two-channel functional genomics data." Syst Synth Biol. 2008;2(3-4):95-104. "
PMC
Comment on "Protein sequences from mastodon and Tyrannosaurus rex revealed by mass spectrometry"." Science. 2008;321(5892):1040; author reply 1040. "
Empirical entropic contributions in computational docking: evaluation in APS reductase complexes." J Comput Chem. 2008;29(11):1753-61. "
PMC
Phosphorylation-specific MS/MS scoring for rapid and accurate phosphoproteome analysis." J. Proteome Res.. 2008;7(8):3373-81. "
PMC
Spectral probabilities and generating functions of tandem mass spectra: a strike against decoy databases." J. Proteome Res.. 2008;7(8):3354-63. "
PMC
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
Retroviruses and opportunistic infections - 15th annual conference." IDrugs. 2008;11(4):233-5. "
Evaluation of paired-end sequencing strategies for detection of genome rearrangements in cancer." PLoS Comput. Biol.. 2008;4(4):e1000051. "
PMC
Functional maps of protein complexes from quantitative genetic interaction data." PLoS Comput. Biol.. 2008;4(4):e1000065. "
PMC
In silico discovery of transcription regulatory elements in Plasmodium falciparum." BMC Genomics. 2008;9:70. "
PMC
Analysis of the human kinome using methods including fold recognition reveals two novel kinases." PLoS ONE. 2008;3(2):e1597. "
PMC
eQED: an efficient method for interpreting eQTL associations using protein networks." Mol. Syst. Biol.. 2008;4:162. "
PMC
A sequence-based survey of the complex structural organization of tumor genomes." Genome Biol.. 2008;9(3):R59. "
PMC
Predicting gene essentiality using genome-scale in silico models." Methods Mol. Biol.. 2008;416:433-57. "
Genomic mid-range inhomogeneity correlates with an abundance of RNA secondary structures." BMC Genomics. 2008;9:284. "
PMC
The Alternative Splicing Mutation Database: a hub for investigations of alternative splicing using mutational evidence." BMC Res Notes. 2008;1:3. "
PMC
Calculation of splicing potential from the Alternative Splicing Mutation Database." BMC Res Notes. 2008;1:4. "
PMC
Molecular Simulation of HER2/neu Degradation by HSP90 Inhibitors." Journal of the Chinese Chemical Society. 2008;55:297-302. "
Publisher
2007
Comparative genomics of small RNAs in bacterial genomes." OMICS. 2007;11(1):58-73. "
Whole proteome analysis of post-translational modifications: applications of mass-spectrometry for proteogenomic annotation." Genome Res.. 2007;17(9):1362-77. "
PMC
Integrating physical and genetic maps: from genomes to interaction networks." Nat. Rev. Genet.. 2007;8(9):699-710. "
PMC
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
ChIP-chip: data, model, and analysis." Biometrics. 2007;63(3):787-96. "
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
Optimization of primer design for the detection of variable genomic lesions in cancer." Bioinformatics. 2007;23(21):2807-15. "
Systematic condition-dependent annotation of metabolic genes." Genome Res.. 2007;17(11):1626-33. "
PMC
In silico elucidation of the molecular mechanism defining the adverse effect of selective estrogen receptor modulators." PLoS Comput. Biol.. 2007;3(11):e217. "
PMC
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. "
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
Distinct and predictive chromatin signatures of transcriptional promoters and enhancers in the human genome." Nat. Genet.. 2007;39(3):311-8. "
Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project." Nature. 2007;447(7146):799-816. "
PMC
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
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
Developmentally regulated activation of a SINE B2 repeat as a domain boundary in organogenesis." Science. 2007;317(5835):248-51. "
Metabolic characterization of Escherichia coli strains adapted to growth on lactate." Appl. Environ. Microbiol.. 2007;73(14):4639-47. "
PMC
ChIP-chip for genome-wide analysis of protein binding in mammalian cells." Curr Protoc Mol Biol. 2007;Chapter 21:Unit 21.13. "
Correcting base-assignment errors in repeat regions of shotgun assembly." IEEE/ACM Trans Comput Biol Bioinform. 2007;4(1):54-64. "
Discovering tightly regulated and differentially expressed gene sets in whole genome expression data." Bioinformatics. 2007;23(2):e84-90. "
Mass spectrometric detection of tissue proteins in plasma." Mol. Cell Proteomics. 2007;6(1):64-71. "
Population-based sample reveals gene-gender interactions in blood pressure in White Americans." Hypertension. 2007;49(1):96-106. "
Histone methylation-dependent mechanisms impose ligand dependency for gene activation by nuclear receptors." Cell. 2007;128(3):505-18. "
PMC
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
Evidence for large inversion polymorphisms in the human genome from HapMap data." Genome Res.. 2007;17(2):219-30. "
PMC
Improving gene annotation using peptide mass spectrometry." Genome Res.. 2007;17(2):231-9. "
PMC
Selective modulation of promoter recruitment and transcriptional activity of PPARgamma." Biochem. Biophys. Res. Commun.. 2007;364(3):515-21. "
PMC
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. "
Microbial regulatory and metabolic networks." Curr. Opin. Biotechnol.. 2007;18(4):360-4. "
Leveraging the HapMap correlation structure in association studies." Am. J. Hum. Genet.. 2007;80(4):683-91. "
PMC
Toward whole cell modeling and simulation: comprehensive functional genomics through the constraint-based approach." Prog Drug Res. 2007;64:265, 267-309. "
Quantitative prediction of cellular metabolism with constraint-based models: the COBRA Toolbox." Nat Protoc. 2007;2(3):727-38. "
A homeostatic model of IkappaB metabolism to control constitutive NF-kappaB activity." Mol. Syst. Biol.. 2007;3:111. "
PMC
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
A proteome-wide protein interaction map for Campylobacter jejuni." Genome Biol.. 2007;8(7):R130. "
PMC
Systems biology of macrophages." Adv. Exp. Med. Biol.. 2007;598:62-79. "
Estimation of the number of extreme pathways for metabolic networks." BMC Bioinformatics. 2007;8(1):363. "
PMC
Network-based classification of breast cancer metastasis." Mol. Syst. Biol.. 2007;3:140. "
PMC
Integration of biological networks and gene expression data using Cytoscape." Nat Protoc. 2007;2(10):2366-82. "
PMC
Identifying statistical dependence in genomic sequences via mutual information estimates." EURASIP J Bioinform Syst Biol. 2007:14741. "
PMC
2006
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
Systems approach to refining genome annotation." Proc. Natl. Acad. Sci. U.S.A.. 2006;103(46):17480-4. "
PMC
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. "
Kdo2-Lipid A of Escherichia coli, a defined endotoxin that activates macrophages via TLR-4." J. Lipid Res.. 2006;47(5):1097-111. "
Integrated analysis of regulatory and metabolic networks reveals novel regulatory mechanisms in Saccharomyces cerevisiae." Genome Res.. 2006;16(5):627-35. "
PMC
Systems analyses characterize integrated functions of biochemical networks." Trends Biochem. Sci.. 2006;31(5):284-91. "
The model organism as a system: integrating 'omics' data sets." Nat. Rev. Mol. Cell Biol.. 2006;7(3):198-210. "
Systematic identification of functional orthologs based on protein network comparison." Genome Res.. 2006;16(3):428-35. "
PMC
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
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. "
Enhanced automated function prediction using distantly related sequences and contextual association by PFP." Protein Sci.. 2006;15(6):1550-6. "
PMC
Identification of genome-scale metabolic network models using experimentally measured flux profiles." PLoS Comput. Biol.. 2006;2(7):e72. "
PMC
DyNAVacS: an integrative tool for optimized DNA vaccine design." Nucleic Acids Res.. 2006;34(Web Server issue):W264-6. "
PMC
AliWABA: alignment on the web through an A-Bruijn approach." Nucleic Acids Res.. 2006;34(Web Server issue):W613-6. "
PMC
cis-Acting site controlling bidirectional transcription at the growth-differentiation transition in Dictyostelium discoideum." Eukaryotic Cell. 2006;5(7):1104-10. "
PMC
Identification of highly specific localized sequence motifs in human ribosomal protein gene promoters." Gene. 2006;365:48-56. "
Long-range periodic patterns in microbial genomes indicate significant multi-scale chromosomal organization." PLoS Comput. Biol.. 2006;2(1):e2. "
PMC
Towards multidimensional genome annotation." Nat. Rev. Genet.. 2006;7(2):130-41. "
Retention and loss of amino acid biosynthetic pathways based on analysis of whole-genome sequences." Eukaryotic Cell. 2006;5(2):272-6. "
PMC
Metabolic analysis of adaptive evolution for in silico-designed lactate-producing strains." Biotechnol. Bioeng.. 2006;95(5):992-1002. "
Microinversions in mammalian evolution." Proc. Natl. Acad. Sci. U.S.A.. 2006;103(52):19824-9. "
PMC
Experimental and computational assessment of conditionally essential genes in Escherichia coli." J. Bacteriol.. 2006;188(23):8259-71. "
PMC
Comparative genome sequencing of Escherichia coli allows observation of bacterial evolution on a laboratory timescale." Nat. Genet.. 2006;38(12):1406-12. "
Matrix formalism to describe functional states of transcriptional regulatory systems." PLoS Comput. Biol.. 2006;2(8):e101. "
PMC
Identifying repeat domains in large genomes." Genome Biol.. 2006;7(1):R7. "
PMC
Comprehensive curation and analysis of global interaction networks in Saccharomyces cerevisiae." J. Biol.. 2006;5(4):11. "
PMC
A direct comparison of protein interaction confidence assignment schemes." BMC Bioinformatics. 2006;7:360. "
PMC
UniPep--a database for human N-linked glycosites: a resource for biomarker discovery." Genome Biol.. 2006;7(8):R73. "
PMC
Representing and comparing protein structures as paths in three-dimensional space." BMC Bioinformatics. 2006;7:460. "
PMC
Discovering regulated networks during HIV-1 latency and reactivation." Pac Symp Biocomput. 2006:354-66. "
Publisher
Unrestrictive identification of post-translational modifications through peptide mass spectrometry." Nat Protoc. 2006;1(1):67-72. "
2005
Molecular determinants of crosstalk between nuclear receptors and toll-like receptors." Cell. 2005;122(5):707-21. "
PMC
Achieving stability of lipopolysaccharide-induced NF-kappaB activation." Science. 2005;309(5742):1854-7. "
Stimulus specificity of gene expression programs determined by temporal control of IKK activity." Science. 2005;309(5742):1857-61. "
The econometrics of evolution." Nat. Chem. Biol.. 2005;1(4):191-2. "
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
The Plasmodium protein network diverges from those of other eukaryotes." Nature. 2005;438(7064):108-12. "
PMC
ChemDB: a public database of small molecules and related chemoinformatics resources." Bioinformatics. 2005;21(22):4133-9. "
Inference and analysis of haplotypes from combined genotyping studies deposited in dbSNP." Genome Res.. 2005;15(11):1594-600. "
PMC
Systematic interpretation of genetic interactions using protein networks." Nat. Biotechnol.. 2005;23(5):561-6. "
PMC
Candidate metabolic network states in human mitochondria. Impact of diabetes, ischemia, and diet." J. Biol. Chem.. 2005;280(12):11683-95. "
k-Cone analysis: determining all candidate values for kinetic parameters on a network scale." Biophys. J.. 2005;88(3):1616-25. "
PMC
Chemoselective covalent coupling of oligonucleotide probes to self-assembled monolayers." J. Am. Chem. Soc.. 2005;127(24):8600-1. "
PMC
Direct isolation and identification of promoters in the human genome." Genome Res.. 2005;15(6):830-9. "
PMC
Kernels for small molecules and the prediction of mutagenicity, toxicity and anti-cancer activity." Bioinformatics. 2005;21 Suppl 1:i359-68. "
Peptide sequence tags for fast database search in mass-spectrometry." J. Proteome Res.. 2005;4(4):1287-95. "
InsPecT: identification of posttranslationally modified peptides from tandem mass spectra." Anal. Chem.. 2005;77(14):4626-39. "
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
Orthologous repeats and mammalian phylogenetic inference." Genome Res.. 2005;15(7):998-1006. "
PMC
Assessing computational tools for the discovery of transcription factor binding sites." Nat. Biotechnol.. 2005;23(1):137-44. "
Conserved patterns of protein interaction in multiple species." Proc. Natl. Acad. Sci. U.S.A.. 2005;102(6):1974-9. "
PMC
Reconstruction of cellular signalling networks and analysis of their properties." Nat. Rev. Mol. Cell Biol.. 2005;6(2):99-111. "
Identification of post-translational modifications by blind search of mass spectra." Nat. Biotechnol.. 2005;23(12):1562-7. "
A high-resolution map of active promoters in the human genome." Nature. 2005;436(7052):876-80. "
PMC
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
Comment on "Oscillations in NF-kappaB signaling control the dynamics of gene expression"." Science. 2005;308(5718):52; author reply 52. "
PMC
Untangling the web of functional and physical interactions in yeast." J. Biol.. 2005;4(2):5. "
PMC
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
Identification of post-translational modifications via blind search of mass-spectra." Proc IEEE Comput Syst Bioinform Conf. 2005:157-66. "
An optimal DNA segmentation based on the MDL principle." Int J Bioinform Res Appl. 2005;1(1):3-17. "
Publisher
Metabolic pathways." In: Loomis WF, Kuspa A, eds. Dictyostelium Genomics, pp. 41-57. Far Hills, N.J.: Horizon Press; 2005. "
Publisher
Amazon
2004
Fragment assembly with short reads." Bioinformatics. 2004;20(13):2067-74. "
Uniform sampling of steady-state flux spaces: means to design experiments and to interpret enzymopathies." Biophys. J.. 2004;87(4):2172-86. "
PMC
Variance-modeled posterior inference of microarray data: detecting gene-expression changes in 3T3-L1 adipocytes." Bioinformatics. 2004;20(17):3108-27. "
A novel method for multiple alignment of sequences with repeated and shuffled elements." Genome Res.. 2004;14(11):2336-46. "
PMC
Integrating high-throughput and computational data elucidates bacterial networks." Nature. 2004;429(6987):92-6. "
Topological analysis of mass-balanced signaling networks: a framework to obtain network properties including crosstalk." J. Theor. Biol.. 2004;227(2):283-97. "
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. "
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
Flagellar biosynthesis in silico: building quantitative models of regulatory networks." Cell. 2004;117(6):689-90. "
WebLogo: a sequence logo generator." Genome Res.. 2004;14(6):1188-90. "
PMC
Reconstruction and validation of Saccharomyces cerevisiae iND750, a fully compartmentalized genome-scale metabolic model." Genome Res.. 2004;14(7):1298-309. "
PMC
The JAK-STAT signaling network in the human B-cell: an extreme signaling pathway analysis." Biophys. J.. 2004;87(1):37-46. "
PMC
The ASTRAL Compendium in 2004." Nucleic Acids Res.. 2004;32(Database issue):D189-92. "
PMC
Evolutionary and functional relationships within the DJ1 superfamily." BMC Evol. Biol.. 2004;4:6. "
PMC
Reconstruction of microbial transcriptional regulatory networks." Curr. Opin. Biotechnol.. 2004;15(1):70-7. "
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. "
Hierarchical thinking in network biology: the unbiased modularization of biochemical networks." Trends Biochem. Sci.. 2004;29(12):641-7. "
Comparison of network-based pathway analysis methods." Trends Biotechnol.. 2004;22(8):400-5. "
Leveraging two-way probe-level block design for identifying differential gene expression with high-density oligonucleotide arrays." BMC Bioinformatics. 2004;5:42. "
PMC
Integrating phenotypic and expression profiles to map arsenic-response networks." Genome Biol.. 2004;5(12):R95. "
PMC
2003
Large-scale evaluation of in silico gene deletions in Saccharomyces cerevisiae." OMICS. 2003;7(2):193-202. "
Systemic metabolic reactions are obtained by singular value decomposition of genome-scale stoichiometric matrices." J. Theor. Biol.. 2003;224(1):87-96. "
Network-based analysis of metabolic regulation in the human red blood cell." J. Theor. Biol.. 2003;225(2):185-94. "
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
Reconciling gene expression data with known genome-scale regulatory network structures." Genome Res.. 2003;13(11):2423-34. "
PMC
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
Development of network-based pathway definitions: the need to analyze real metabolic networks." Trends Biotechnol.. 2003;21(5):195-8. "
Metabolic pathways in the post-genome era." Trends Biochem. Sci.. 2003;28(5):250-8. "
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
Analysis of metabolic capabilities using singular value decomposition of extreme pathway matrices." Biophys. J.. 2003;84(2 Pt 1):794-804. "
PMC
Genome-scale reconstruction of the Saccharomyces cerevisiae metabolic network." Genome Res.. 2003;13(2):244-53. "
PMC
Identifying constraints that govern cell behavior: a key to converting conceptual to computational models in biology?" Biotechnol. Bioeng.. 2003;84(7):763-72. "
Constraints-based models: regulation of gene expression reduces the steady-state solution space." J. Theor. Biol.. 2003;221(3):309-25. "
Genome-scale microbial in silico models: the constraints-based approach." Trends Biotechnol.. 2003;21(4):162-9. "
2002
Extreme pathways and Kirchhoff's second law." Biophys. J.. 2002;83(5):2879-82. "
PMC
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
The genome-scale metabolic extreme pathway structure in Haemophilus influenzae shows significant network redundancy." J. Theor. Biol.. 2002;215(1):67-82. "
Metabolic modelling of microbes: the flux-balance approach." Environ. Microbiol.. 2002;4(3):133-40. "
Extreme pathway lengths and reaction participation in genome-scale metabolic networks." Genome Res.. 2002;12(12):1889-900. "
PMC
Transcriptional regulation in constraints-based metabolic models of Escherichia coli." J. Biol. Chem.. 2002;277(31):28058-64. "
Genome-scale metabolic model of Helicobacter pylori 26695." J. Bacteriol.. 2002;184(16):4582-93. "
PMC
2001
Regulation of gene expression in flux balance models of metabolism." J. Theor. Biol.. 2001;213(1):73-88. "
Metabolic modeling of microbial strains in silico." Trends Biochem. Sci.. 2001;26(3):179-86. "