Published in J Comput Biol on January 01, 2001
Spectral probabilities and generating functions of tandem mass spectra: a strike against decoy databases. J Proteome Res (2008) 3.84
Protein identification by spectral networks analysis. Proc Natl Acad Sci U S A (2007) 2.81
De novo peptide sequencing and identification with precision mass spectrometry. J Proteome Res (2007) 1.95
Advances in structure elucidation of small molecules using mass spectrometry. Bioanal Rev (2010) 1.76
Spectral dictionaries: Integrating de novo peptide sequencing with database search of tandem mass spectra. Mol Cell Proteomics (2008) 1.60
Accurate mass measurements in proteomics. Chem Rev (2007) 1.36
De novo sequencing and homology searching. Mol Cell Proteomics (2011) 1.21
De novo peptide identification via tandem mass spectrometry and integer linear optimization. Anal Chem (2007) 1.12
Automated interpretation of MS/MS spectra of oligosaccharides. Bioinformatics (2005) 1.12
MODi: a powerful and convenient web server for identifying multiple post-translational peptide modifications from tandem mass spectra. Nucleic Acids Res (2006) 1.08
ProLuCID: An improved SEQUEST-like algorithm with enhanced sensitivity and specificity. J Proteomics (2015) 1.07
Multi-spectra peptide sequencing and its applications to multistage mass spectrometry. Bioinformatics (2008) 1.04
Computational mass spectrometry for small molecules. J Cheminform (2013) 1.01
A high-throughput de novo sequencing approach for shotgun proteomics using high-resolution tandem mass spectrometry. BMC Bioinformatics (2010) 0.99
Better score function for peptide identification with ETD MS/MS spectra. BMC Bioinformatics (2010) 0.96
Constrained de novo sequencing of conotoxins. J Proteome Res (2012) 0.95
UniNovo: a universal tool for de novo peptide sequencing. Bioinformatics (2013) 0.94
Introduction to computational proteomics. PLoS Comput Biol (2007) 0.94
A Mixed-Integer Optimization Framework for De Novo Peptide Identification. AIChE J (2007) 0.88
A novel scoring schema for peptide identification by searching protein sequence databases using tandem mass spectrometry data. BMC Bioinformatics (2006) 0.87
DeNovoID: a web-based tool for identifying peptides from sequence and mass tags deduced from de novo peptide sequencing by mass spectroscopy. Nucleic Acids Res (2005) 0.87
Applications of graph theory in protein structure identification. Proteome Sci (2011) 0.79
Proteomics for systems toxicology. Comput Struct Biotechnol J (2014) 0.79
Proteomics and the analysis of proteomic data: 2013 overview of current protein-profiling technologies. Curr Protoc Bioinformatics (2013) 0.79
New Approaches to Comparative and Animal Stress Biology Research in the Post-genomic Era: A Contextual Overview. Comput Struct Biotechnol J (2014) 0.77
Algorithms and design strategies towards automated glycoproteomics analysis. Mass Spectrom Rev (2016) 0.77
A new parameterized algorithm for rapid peptide sequencing. PLoS One (2014) 0.75
ProbPS: a new model for peak selection based on quantifying the dependence of the existence of derivative peaks on primary ion intensity. BMC Bioinformatics (2011) 0.75
Peptide Peak Detection for Low Resolution MALDI-TOF Mass Spectrometry. Mass Spectrom (Tokyo) (2014) 0.75
Peptide de novo sequencing of mixture tandem mass spectra. Proteomics (2016) 0.75
De novo peptide sequencing by deep learning. Proc Natl Acad Sci U S A (2017) 0.75
A better scoring model for de novo peptide sequencing: the symmetric difference between explained and measured masses. Algorithms Mol Biol (2017) 0.75
Genomic sequencing. Proc Natl Acad Sci U S A (1984) 92.36
Systematic determination of genetic network architecture. Nat Genet (1999) 25.45
Computational identification of cis-regulatory elements associated with groups of functionally related genes in Saccharomyces cerevisiae. J Mol Biol (2000) 14.30
Finding DNA regulatory motifs within unaligned noncoding sequences clustered by whole-genome mRNA quantitation. Nat Biotechnol (1998) 13.99
Methods for generating precise deletions and insertions in the genome of wild-type Escherichia coli: application to open reading frame characterization. J Bacteriol (1997) 12.41
B lineage--specific interactions of an immunoglobulin enhancer with cellular factors in vivo. Science (1985) 9.73
A computational analysis of whole-genome expression data reveals chromosomal domains of gene expression. Nat Genet (2000) 9.47
A comprehensive library of DNA-binding site matrices for 55 proteins applied to the complete Escherichia coli K-12 genome. J Mol Biol (1998) 7.75
Identifying regulatory networks by combinatorial analysis of promoter elements. Nat Genet (2001) 7.74
Correlation between transcriptome and interactome mapping data from Saccharomyces cerevisiae. Nat Genet (2001) 7.16
Comparing the predicted and observed properties of proteins encoded in the genome of Escherichia coli K-12. Electrophoresis (1997) 6.82
RNA expression analysis using a 30 base pair resolution Escherichia coli genome array. Nat Biotechnol (2000) 6.36
The personal genome project. Mol Syst Biol (2005) 5.47
Exploring the DNA-binding specificities of zinc fingers with DNA microarrays. Proc Natl Acad Sci U S A (2001) 5.08
Conservation of DNA regulatory motifs and discovery of new motifs in microbial genomes. Genome Res (2000) 4.34
Regulatory networks revealed by transcriptional profiling of damaged Saccharomyces cerevisiae cells: Rpn4 links base excision repair with proteasomes. Mol Cell Biol (2000) 4.15
Biclustering of expression data. Proc Int Conf Intell Syst Mol Biol (2000) 3.97
Cell-type-specific contacts to immunoglobulin enhancers in nuclei. Nature (1985) 3.94
Quantifying DNA-protein interactions by double-stranded DNA arrays. Nat Biotechnol (1999) 3.87
Characterization of the cobalamin (vitamin B12) biosynthetic genes of Salmonella typhimurium. J Bacteriol (1993) 3.42
Crystal structure of yeast phenylalanine transfer RNA. I. Crystallographic refinement. J Mol Biol (1978) 3.19
The Isw2 chromatin remodeling complex represses early meiotic genes upon recruitment by Ume6p. Cell (2000) 2.95
Modeling gene expression with differential equations. Pac Symp Biocomput (1999) 2.85
Systematic management and analysis of yeast gene expression data. Genome Res (2000) 2.83
Aligning gene expression time series with time warping algorithms. Bioinformatics (2001) 2.82
Selection analyses of insertional mutants using subgenic-resolution arrays. Nat Biotechnol (2001) 2.80
RNA-ligant interactions. (I) Magnesium binding sites in yeast tRNAPhe. Nucleic Acids Res (1977) 2.79
The cleavage site of the restriction endonuclease Ava II. Nucleic Acids Res (1978) 2.60
Primary structure of T4 DNA polymerase. Evolutionary relatedness to eucaryotic and other procaryotic DNA polymerases. J Biol Chem (1988) 2.52
In situ localized amplification and contact replication of many individual DNA molecules. Nucleic Acids Res (1999) 2.52
Microarray analysis of the transcriptional network controlled by the photoreceptor homeobox gene Crx. Curr Biol (2000) 2.36
Alignment and structure prediction of divergent protein families: periplasmic and outer membrane proteins of bacterial efflux pumps. J Mol Biol (1999) 2.08
Sequence variability and candidate gene analysis in complex disease: association of mu opioid receptor gene variation with substance dependence. Hum Mol Genet (2000) 2.05
Fast assignment of protein structures to sequences using the intermediate sequence library PDB-ISL. Bioinformatics (2000) 2.04
Dynamic simulation of the human red blood cell metabolic network. Bioinformatics (2001) 1.92
A controlled trial comparing foscarnet with vidarabine for acyclovir-resistant mucocutaneous herpes simplex in the acquired immunodeficiency syndrome. The AIDS Clinical Trials Group. N Engl J Med (1991) 1.89
Predicting regulons and their cis-regulatory motifs by comparative genomics. Nucleic Acids Res (2000) 1.88
Research technologies: fulfilling the promise. FASEB J (1999) 1.85
Thyroid hormone regulates the mouse thyrotropin beta-subunit gene promoter in transfected primary thyrotropes. J Biol Chem (1989) 1.84
Orally administered 4-aminopyridine improves clinical signs in multiple sclerosis. Ann Neurol (1990) 1.70
Observations on the induction of bone in soft tissues. J Bone Joint Surg Br (1975) 1.68
Diadenosine phosphates and the physiological control of blood pressure. Nature (1994) 1.53
Pleiotropic mutations within two yeast mitochondrial cytochrome genes block mRNA processing. Cell (1979) 1.51
Correlation between response to acyclovir and foscarnet therapy and in vitro susceptibility result for isolates of herpes simplex virus from human immunodeficiency virus-infected patients. Antimicrob Agents Chemother (1994) 1.50
Genomic analysis of bacteriophages SP6 and K1-5, an estranged subgroup of the T7 supergroup. J Mol Biol (2004) 1.44
Low-density lipoproteins inhibit the Na+/H+ antiport in human platelets. A novel mechanism enhancing platelet activity in hypercholesterolemia. Circulation (1997) 1.43
Quantitative whole-genome analysis of DNA-protein interactions by in vivo methylase protection in E. coli. Nat Biotechnol (1998) 1.41
Identification of oxidized low-density lipoprotein in human serum by NMR spectroscopy. Clin Sci (Lond) (1998) 1.40
Secondary structural complementarity between DNA and proteins. Proc Natl Acad Sci U S A (1977) 1.39
Effect of diadenosine polyphosphates on Ca2+ ATPase activity. J Mol Med (Berl) (1997) 1.37
Lambda red recombineering in Escherichia coli occurs through a fully single-stranded intermediate. Genetics (2010) 1.36
Assessment of the treatment effect of enoxaparin for unstable angina/non-Q-wave myocardial infarction. TIMI 11B-ESSENCE meta-analysis. Circulation (1999) 1.34
Probing the limits of genetic recoding in essential genes. Science (2013) 1.33
Large scale bacterial gene discovery by similarity search. Nat Genet (1994) 1.33
Computational comparison of two draft sequences of the human genome. Nature (2001) 1.32
Complementary recognition in condensed DNA: accelerated DNA renaturation. J Mol Biol (1991) 1.28
Haloperidol, lorazepam, or both for psychotic agitation? A multicenter, prospective, double-blind, emergency department study. Am J Emerg Med (1997) 1.27
Taurine promotes the differentiation of a vertebrate retinal cell type in vitro. Development (1993) 1.21
Purification and characterization of colicin V from Escherichia coli culture supernatants. Biochemistry (1994) 1.20
Dieting and depression reexamined. A critical review of reports of untoward responses during weight reduction for obesity. Ann Intern Med (1974) 1.19
The effect of 3-mercaptopicolinic acid on phosphoenolpyruvate carboxykinase (GTP) in the rat and guinea pig. Arch Biochem Biophys (1975) 1.19
The LPP1 and DPP1 gene products account for most of the isoprenoid phosphate phosphatase activities in Saccharomyces cerevisiae. J Biol Chem (1999) 1.17
The genomic sequencing technique. Prog Clin Biol Res (1985) 1.15
Platelet function in patients with obstructive sleep apnoea syndrome. Eur Respir J (2000) 1.14
A whole genome approach to in vivo DNA-protein interactions in E. coli. Nature (1992) 1.14
DNA sequencing with direct transfer electrophoresis and nonradioactive detection. Methods Enzymol (1993) 1.13
The effects of whirlpools baths in labor: a randomized, controlled trial. Birth (1996) 1.11
Multiplex sequencing of 1.5 Mb of the Mycobacterium leprae genome. Genome Res (1997) 1.05
Design strategies and performance of custom DNA sequencing primers. Biotechniques (1999) 1.04
In vivo phosphorylation site of hexokinase 2 in Saccharomyces cerevisiae. Biochemistry (1994) 1.04
Fulminant disease simulating bacterial sepsis with disseminated intravascular coagulation after a trip to East Africa. Intensive Care Med (2000) 1.03
Postpartum safety and satisfaction following early discharge. Can J Public Health (1996) 1.03
Cloning and expression of T4 DNA polymerase. Proc Natl Acad Sci U S A (1987) 1.03
Regulation of rat mesangial cell growth by diadenosine phosphates. J Clin Invest (1995) 0.99
Predicting ligand-binding function in families of bacterial receptors. Proc Natl Acad Sci U S A (2000) 0.99
Algorithms for identifying protein cross-links via tandem mass spectrometry. J Comput Biol (2001) 0.98
Identification and characterization of diadenosine 5',5"'-P1,P2 -diphosphate and diadenosine 5',5"'-P1,P3-triphosphate in human myocardial tissue. FASEB J (1999) 0.97
Cytosine specific DNA sequencing with hydrogen peroxide. Nucleic Acids Res (1995) 0.97
Morbidity and mortality of patients with AIDS and first-episode Pneumocystis carinii pneumonia unaffected by concomitant pulmonary cytomegalovirus infection. Am Rev Respir Dis (1991) 0.95
Influence of treatment on leptin levels in patients with obstructive sleep apnoea. Eur Respir J (2004) 0.95
Autophosphorylation-inactivation site of hexokinase 2 in Saccharomyces cerevisiae. Biochemistry (1997) 0.95
Manipulating replisome dynamics to enhance lambda Red-mediated multiplex genome engineering. Nucleic Acids Res (2012) 0.94
The logic of intercellular communication in the immune system. Immunol Cell Biol (1998) 0.94
A weight matrix for binding recognition by the redox-response regulator ArcA-P of Escherichia coli. Mol Microbiol (1999) 0.93
More Haemophilus and Mycoplasma genes. Science (1996) 0.92
Increased intracellular generation of reactive oxygen species in mononuclear leukocytes from patients with diabetes mellitus type 2. Exp Clin Endocrinol Diabetes (2000) 0.91
Effect of concurrent anxiety on response to sertraline and imipramine in patients with chronic depression. Depress Anxiety (2001) 0.90
Increased plasma phenylacetic acid in patients with end-stage renal failure inhibits iNOS expression. J Clin Invest (2003) 0.90
The effect of individualized professional support on duration of breastfeeding: a randomized controlled trial. J Hum Lact (2000) 0.90
On the cardiac contractile, biochemical and electrophysiological effects of cantharidin, a phosphatase inhibitor. J Pharmacol Exp Ther (1995) 0.89
HDL3-mediated inhibition of thrombin-induced platelet aggregation and fibrinogen binding occurs via decreased production of phosphoinositide-derived second messengers 1,2-diacylglycerol and inositol 1,4,5-tris-phosphate. Arterioscler Thromb Vasc Biol (1998) 0.88
Dinucleotides as growth-promoting extracellular mediators. Presence of dinucleoside diphosphates Ap2A, Ap2G, and Gp2G in releasable granules of platelets. J Biol Chem (2000) 0.88
Identification and characterization of P(1), P(7)-Di(adenosine-5')-heptaphosphate from human platelets. J Biol Chem (1999) 0.88
Formins: phosphoprotein isoforms encoded by the mouse limb deformity locus. Proc Natl Acad Sci U S A (1993) 0.87
Adenosine(5') oligophospho-(5') guanosines and guanosine(5') oligophospho-(5') guanosines in human platelets. J Clin Invest (1998) 0.87
Solid-phase synthesis of biologically active lipopeptides as analogs for spirochetal lipoproteins. Pept Res (1994) 0.87
Vascular actions of diadenosine phosphates. J Auton Pharmacol (1996) 0.87
Long-term effects of vitamin B(12), folate, and vitamin B(6) supplements in elderly people with normal serum vitamin B(12) concentrations. Gerontology (2001) 0.87
Contrast medium-induced nephropathy: the pathophysiology. Kidney Int Suppl (2006) 0.87