http://www.informatik.uni-trier.de/~ley/db/conf/psb/psb2005.html
PSB 2005
http://helix-web.stanford.edu/psb05/webb-robertson.pdf	40	A Bayesian Framework for SNP Identification B.M. Webb-Robertson, S.L. Havre, and D.A. Payne Pacific Symposium on Biocomputing 10:421-432(2005)	academic acids altschul analysis atlas beroud biol biometrics buckley cunningham dayhoff delong detection eagen evol gene genet genome genomics goldman hardison hasegawa hemoglobin henikoff huisman human kimura knight linblad lipman majewski mutat nielsen nucleic orcutt pnas press references schwartz signal smith soussi suchard syllabus tamura theory variants waterman webb yang york
http://helix-web.stanford.edu/psb05/gennari.pdf	12	Integrating Genomic Knowledge Sources Through an Anatomy Ontology J.H. Gennari, A. Silberfein, and J.C. Wiley Pacific Symposium on Biocomputing 10:115-126(2005)	aberrantly accumulates acids aitken aligning american amia anatomical anatomist anatomy annual antonio apoptotic applied approach arnold ashburner association baldock barclay bard bartek bartkova base based between biocomputing bioinformatics biomedical blake bodenreider bono brinkley bult cancer carcinoma carcinomas cardiff cdna cell colorectal computer cooperates correlation creating crubezy cyclin daml data database databases death description design development digital directional driven embo entry environment eppig eriksson essential evolution expression fall fergerson foundational gene geneontologyconsortium generation genes genetic gennari genome glasgow goble grosso grzeschiczek halevy heterogeneous hinshaw hornoch human hyperplasia implementation informatics integration interactive international ismb jakobovits journal kadin kasukawa knowledge kowalski kranenburg kremer lees lexical list logic lovec lukas lymphoma mammary mapping mediated mediator medical mejino merging methodology methods mice microarrays migrate mmtv modayur model mork moroy motivation mouse musen nature neuronal nucleic oncogene online ontology organizational pacific prad principles proceedings product profiling prompt prot queries reference references remapping representation representations research resource result richardson riken rosse rule sael schema schmidt schulze scotland sets shaker shapiro smith sofg sources species stevens strauss structural studies subset suite symbolic symposium system systematic systems tarczy through tools transcriptome transgenic translation travillian using wang washington williams with wroe yagi zantema zhang zukerberg
http://helix-web.stanford.edu/psb05/karklin.pdf	2	Classification of Non-Coding RNA Using Graph Representations of Secondary Structure Y. Karklin, R.F. Meraz, and S.R. Holbrook Pacific Symposium on Biocomputing 10:4-15(2005)	aaai ability accuracy accurate acid acids acknowledgments algorithms also andersen anonymous another application applications applied approach areas assessing automated baldi bateman because believe benedetti between bioinformatics biol biophys biopolymers brunak burges bustamante calculating carter case ceedings chauvin chem class classification classifiers coding coli combining comments comparative complete composition computational computationally conceptually conclusion conference conjunction considerations context could csgf curr data database defense defined department design differentiate dinucleotide discovery discriminative distinguish distribution dowell dubchak eddy efficient energies energy evaluation evidence exists expanding explorations exploring extending families family fawcett fellowship filters finding folded folding folds fontana free from functional gartner gave genes genet genomic genomics graduate grammars grant graph graphs great griffiths group have heuristic hofacker holbrook identical identification identify implications include inokuchi insightful interest international jones journal karklin kashima kernels khanna klautau klein know krogh labeled laboratories learning ledge lightweight lower machine machines macke many marginalized marshall method methods mining molecules morosetti motifs mrnas ncrna nhgri nielsen noncoding notes novel nucleic nucleotide objects opin other overview pages parameters particularly pasquali pattern potential practical prediction presented press problems produced promising random range recognition references relatively repertoire report representations requires research researchers results reviewers rfam rifkin rivas rnas same schlick schuster science secondary september sequences several showed similarity simple size some special specific stability stochastic storz struct structure structured structures suboptimal suggest suited support supported survey technical techniques than thank that their theory there this tinoco topological train trim trna tsuda tsui tuning tutorial uncharacterized universe uses using vector volume which wide with work workman would wuchty zuker
http://helix-web.stanford.edu/psb05/yamakawa.pdf	22	Multi-Aspect Gene Relation Analysis H. Yamakawa, K. Maruhashi, and Y.Nakao Pacific Symposium on Biocomputing 10:233-244(2005)	about acad acquisition analysis analyzing annual applied apply ashburner aspect aspects aware been biocomputing bioinformatics biokdd biological biology card changes characteristics classification clustering cognitive concept conceptual conducted conf consist consisted conventional could criterion currently data decomposition detailed develop development different during each etmic examining example experiment explaining exploring expression extract extracted extracting extracts fairly find fqspl from fujitsu function functions future garland gene genes genesphere genet global help helpful helping http identified information interesting issues japan japanese kennedy kidney knowledge larger life limited list lord many matchability maturation measures meetings method methods microarray might mine mining molecular more multiple natl nature neural ontology overall pacific pakdd patterns point preliminary previously proc process processing producing profiling proposing quickly range realized reasoning references regard relatively researchers robertson science semantic similarity simple situation society software some structure stuart studies successfully suggested suggests summarizing symposium task tend terms that these this thousand tool tools trying type unification user using viewpoints wagatsuma well which with workshop xminer yamakawa
http://helix-web.stanford.edu/psb05/frey.pdf	47	GenRate: A Generative Model That Finds and Scores New Genes and Exons in Genomic Microarray Data B. Frey, Q. Morris, W. Zhang, N. Mohammad, and T. Hughes Pacific Symposium on Biocomputing 10:495-506(2005)	able above accounts active activity adjacent algorithm alignment alternative analysis annotation applied applying approach arabidopsis arranged arrangement arrays audio august axis based bases bias bibliography bioinformatics biol biotechnol blast blat calibration cdna cdnas chromosome chromosomes columns combines compared compatible consortium constructed containing content correctly curve curves dashed data databases demonstrate dempster developing differential directed directions discovery dominates drosophila each empirical epub estimate even event example exon exons expect expected experimental exploration expressed expression extending extension fabricated factor false fantom february find first found fraction frames frequently frey from full functional future gene generative genes genet genome genomic genrate graphical graphs group high hild huber hughes human identifies ieee images incomplete indeed infor integrated kapranov kent knowing known kschischang labeled landscape large length levels like likelihood many maskless maximum measurements microarray microarrays mining model models modules mouse musculus nature nuwaysir obtained obviously occur occurs october okazaki oligonucleotide open order original ostendorf other over overlapping particular patterns permuted phase photolithography placed plot pool pools positive positives predicted preparation probability probes proc produced product profiles profiling proportion purpose putative quantification random rate reading reasonable removal represented research results review riken rinn royal scale science segal sequence sequences several shai shoemaker should shows significance since single sites solid spatial speech splicing stabilization stat statistical structures such summarizes summary synthesizer team technology test that then theory there these they this thousands tiling tissue tool toronto towards trans transcription transcriptional transcriptionally transcriptome under undirected unify univ unpermuted using variance varying verify version very viewed where which whole wide with without yamada zhang
http://helix-web.stanford.edu/psb05/badea.pdf	43	Sparse Factorizations of Gene Expression Guided by Binding Data L. Badea and D. Tilivea Pacific Symposium on Biocomputing 10:447-458(2005)	abiotic activated activator activity advances agglutinin algorithm algorithms alpha analysis anchor annex annotations application barkai bergmann biclustering binding biol biology botstein brown brunet cassette cell cellular cerevisiae chemical cheng church cluster clustering coding communication compendium conditional conjugation consortium controlling coregulation coupled data desensitization development differentiation dimensionality discovery display domany during efficient eisen exploring expression external factor factorization functional fungi fusion fuzzy gasch gene genes genet genome getz golub growth heat hematopoietic hoyer hughes identification ihmels induction information interpreting involved ismb iterations iterative karyogamy kinase largescale learning levine linked maps martigny mating matrix means mesirov metagenes methods microarray mitogen molecular nature negative networks neural nips objects ontology organizing parameters parts pathway pattern patterns pheromone physical pnas polarized press proc process processing profiles protein putative questionable receptor reduction references regulatory reproduction required response review saccharomyces science self sensu serine seung sexual shmoo shock signal signaling signature significant similarity site sparse spellman stimulus strong substance subsystem subunit surface switzerland tamayo targets them threonine threshold through tidor tool transcription transcriptional transducer transduction transporter unification using values wide with yeast
http://helix-web.stanford.edu/psb05/singh.pdf	6	ChainTweak: Sampling from the Neighbourhood of a Protein Conformation R. Singh and B. Berger Pacific Symposium on Biocomputing 10:52-63(2005)	accurate acids algo algorithms aloupsis altman analysis analytical anatomy angle apaydin approach automated babbitt bank basch berman biedl bioinformatics biol biophys biopolymers branden cahill chains chem chivian closure communication comp conformational connectivity construction contact continuum coutsias data decoys depristo development diamond dihedral discrete discriminate disordered dudek dunker dynamics edelsbrunner efficient energy exact flat folding from functions garland geom gerlt gerstein grpa guntert huang hydrophobic initio intl intrinsical introduction jorgensen keasar kinematic kolodny krishnamoorthy levitt libraries ligand linkages locked lotan macromolecules maintenace manocha measure michael mobile modeling mooney motion novel nucl park personal phys polygonal polypeptide ponder prediction preferences proc prot protein proteins ring samudrala scheraga siam smal state structure structures studying symp symposium that tooze torsion tropsha ulmschneider under unlocked using view wedemeyer with wriggle
http://helix-web.stanford.edu/psb05/yampolsky.pdf	41	Untangling the Effects of Codon Mutation and Amino Acid Exchangeability L.Y. Yampolsky and A. Stoltzfus Pacific Symposium on Biocomputing 10:433-444(2005)	acad acids biol biology burgess cary church clark cooper crow ebersberger evol fitch fredman genet genetics genome gojobori goldman grantham graphis guide hasegawa henikoff ikemura institute introduction journal kimura krawczak maglott metzler minneapolis miyata miyazawa mutat nakamura natl nielsen nucleic paabo population proc pruitt publ references review sander schwarz science sneath statistics stenson stoltzfus theoretical theory vitkup yampolsky yang yasunaga
http://helix-web.stanford.edu/psb05/wang.pdf	7	Coarse and Reliable Geometric Alignment for Protein Docking Y. Wang, P.K.Agarwal, P.Brown, H. Edelsbrunner, and J. Rudolph Pacific Symposium on Biocomputing 10:64-75(2005)	about acad accurate acid acids acknowledgement adapt aflalo agarwal aimed albl algorithm algorithms alignments allowing alone along always analysis analytic another appear appl approach association authors bank based belongs below benchmark berman bespamyatnikh between bhat biased biochemical bioinform bioinformatics biol biomolecular biopolymers body bound bourne brief calculation camacho candidate candidates cavities cell chen cheng choi class classify clustering comparison complementarity complementary complexes comput computational conclude configuration configurations conformational conformations connolly correlation cost created crystallogr curr dalke data densely density descriptors despite detecting determination different differs discrete discussion docked docking drugs duke durham dynamic dynamics edelsbrunner eisenstein electrostatics elevation engin estimating evidence experiments extra extreme fast features feng find finding fischer flexibility friesen from funct further gabb gatchell generate generated generates genet genomes geom geometric geometry gilliland globin goldman graphics harer hashing hemo heuristic high hits humphrey implying improve improved improvement improvements information initial instead interactions interface intl into ithin jackson janin katchalski katzir kimura least lengauer lenhof less lessel level ligands like likely local locally lower manifold manner manuscript marking matches matching mechanism metabolism method methods minimum mintseris modeling modelling molecular moont more most motions moves multiple native natl nature near neither nucleic nussinov often opin ores pairs paper pathways point points possible predict prediction prior problem proc proceedings processes produced promising protein proteins protrusions provide qsdock quadratic ranking ranks reasonably recognition reduce references refined refinement rely remark resolution results rigid rmsd rudolph running sample samples sandak scale schomburg schulten scores scoring search second select september shape shariv shinkdyalov significantly similar size skin small smith smooth software solution some sort space sparser stage sternberg still struct structural structures subunit suite sullivan surface sympos techniques thank that their there these they this time today trapped triangulation trim typically unbound uniformly univ used useful using vajda vakser vicky visual wang ways weissig weng westbrook which wiley wipke with within wolfson work workable workshop would yield zdock
http://helix-web.stanford.edu/psb05/sirohi.pdf	29	Study of Effect of Drug Lexicons on Medication Extraction from Electronic Medical Records E. Sirohi and P. Peissig Pacific Symposium on Biocomputing 10:308-318(2005)	aaps achour acquisition ambiguity ambiguous american assoc association automatic based bieling biocomputing bioinformatics biolink biological biomedical biomedicine blake boosting care chemistry chen clinical computing conceptual conference cooper cronic databases decision development dictionary disposition documentation dojat drug drugs edgar effects evans extraction family firstdatabank friedman from gene genes healthcare http hunter inform johnson knowledge koike landc language learning lepage lexical life linking literature machine mancinelli mcleod medicine naacl name names natural nddf nomenclatures ontologies pacific patient personalized pharmacogenetics pharmacogenomics pharmsci plustm precision proceedings processing promise protein recall recognition references relations resolution rieux rindflesch rule sadee sciences side source support symposium system tagging takagi tanabe targets terms tessi text tool tsujii tsuruoka tuason umls weinstein what wilbur workshop
http://helix-web.stanford.edu/psb05/tang.pdf	35	Discovering Sequence-Structure Motifs from Protein Segments and Two Applications T. Tang, J. Xu, and M. Li Pacific Symposium on Biocomputing 10:370-381(2005)	academic achieve acids acta altschul analysis anderbert annotation another applications argos assignments baker barton beginning beta between biochim biol biophys biopolymers biotechnol blast both brevern burges bystroff capture capturing cluster clusters coil coils comp conclusion condition confidence conformational consequently contributing could cuff curr current currently data detection discovery discretization does domain edition effective employment etchebest everitt excluding fidelis fold funct functional future generated genom going guibas halsted have hazout helpful hobohom hunter improvement include incorrect inter interactions into investigate jbcb jones kabach kind knowledge koehl kolodny lesk levitt local long longer made mapping mark matthews mining most mostly motif motifs motivated nevertheless nucleic obtained only opin partition potential prediction press producing profiles profound promising protein proteins provide range recognition references regions repeat residue results rost sander scharf schneider secondary segments sequence shao sheet short sibbald space structure study subramaniam substantial success suppl tertiary their these they this underway unreliable using values venclovas very were which wide work york yuan zemla
http://helix-web.stanford.edu/psb05/reif.pdf	28	Exploratory Visual Analysis of Pharmacogenomic Results D.M. Reif, S.M. Dudek, C.M. Shaffer, J. Wang, and J.H. Moore Pacific Symposium on Biocomputing 10:296-307(2005)	academic acids acknowledgments across additionally address ageing allow also alternative american analyses analysis anscombe applications applied authors available bauer bioinf biol biotechnology botstein brown center cheok cheshire combine command comp contact cost data dennis devel developed development diaz directions display distribution dopazo draghici engines extended foundation from funds future generous genet genetic genome genomic gentleman goto grants graph graphics harris hattori health helen homology hood ihaka including incorporate independence independent information inheritance institute institutes integrate interface issues java kanehisa kawashima kirov kleberg learning library line machine maglott marchler mckusick mech mechanism medicine mendelian methods model multiple multivariate nathans national naturally nucl okuno ongoing online organisms other output permutation plans platform press process programmable proteomic provide pruitt publicly quantitative references results robert schmoyer sequence shahrour snoddy sources stat statistical statistician strategies studies such supported testing tests that there this those tool tools tufte uriarte users version visual while will with work zeeberg zhang zhong
http://helix-web.stanford.edu/psb05/karchin.pdf	38	Improving Functional Annotation of Non-Synonomous SNPs with Information Theory R. Karchin, L.Kelly, and A. Sali Pacific Symposium on Biocomputing 10:397-408(2005)	acad acids adams alber annu baker battiti bell biochem biochemistry bioinformatics biol biophys biopolymers bowie browser build cambridge cargill cell chasman chem choi cline conference cover cristianini dean dumais engelman enzymol evans fiser genet genome grantham henikoff http ieee ijcnn information international john kabsch klein knowledge krishnan kwak laskowski leabman management markiewicz matthews mckusick methods moult mutat natl ncbi networks neural nucleic omim pharmacogenomics phys pieper press proc prog proteins references relling rennell rost sali sander saunders science shenkin sons springer stat suckow sunyaev tourassi trans trends ucsc university vapnik verlag wang weaver westhead wiley wolpert york zamyatin
http://helix-web.stanford.edu/psb05/bechhofer.pdf	9	Ontology Driven Dynamic Linking of Biology Resources S.K. Bechhofer, R.D. Stevens, and P.W. Lord Pacific Symposium on Biocomputing 10:79-90(2005)	access acknowledgments anniversary annotated applications artificiale association associazione authors based bates bechhofer bioinformatics biology bontchev browser carole carr chris cohse collaboration community comparative computational conceptual conference consortium cunningham database delivering describing developed development digital distributed domain eighth environment epsrc examples expasy experiments factors features flag found framework functional gate gene genetics genomics goble graphical grid hall harmelen helen hendler hill hong http human hypermedia hypertext indexing intel international internet italiana jasis john jonathan journal july kimball kong language libraries ligenza like linguistics link linking lord march marcia maynard mcguinness mechanisms medline meeting mged nature notizie ontology open original osterbye overview page pages parkinson periodico permission persistence phil philadelphia pilot proceedings prot protein proxy published publishers readers recommendation references robust roure science sean semantic sequence service services sloth southampton stability stoeckert structuring support supported swiss system systems tablan taxonomy tenth terminological thank tool tools understanding unification university upon urls webvise wide wiil with world would wren
http://helix-web.stanford.edu/psb05/bodenreider.pdf	10	Non-Lexical Approaches to Identifying Associative Relations in the Gene Ontology O. Bodenreider, M Aubry, and A. Burgun Pacific Symposium on Biocomputing 10:91-102(2005)	acids acknowledgments acquaah across addison address agrawal agresti analysis annotation annotations applications architecture ashburner aspects association associations aubry authors bada baeza based bean between beyond biocomput biol biomedical bodenreider borgelt bretagne burgun categorical coefficients cohen common comparison compositional computational computerm computing conseil contribution daml data database databases dependence description directions duarte eberlein england environment expect experimental formal functional funded future gene genet germany gional goat goble guide harlow http hunter imielinski include information integrating interesting international interpretation introduction issue issues items kelly kumar language large leipzig logic many marc markers mcentire medical melo mensah methodology migrate mining model modern mosser near neto nucleic ogren ontology paper part preliminary press proceedings product provided pubs rapd reasoning record redundancy references relations relationships results retrieval ribeiro rules santos scope sets sigmod similarity smith space species stevens structure study support swami symp system technical terminology terms thank this those tigr turi umls unified using vector wesley which wiley with workshop wroe yates york zeng
http://helix-web.stanford.edu/psb05/bernard.pdf	44	Informative Structure Priors: Joint Learning of Dynamic Regulatory Networks from Multiple Types of Data A. Bernard and A.J. Hartemink Pacific Symposium on Biocomputing 10:459-470(2005)	academic acknowledge acknowledgments added also amenable amink anonymous appear approaches authors available award barash based berkeley bioinformatics biol biotechnology california career cell chaos complexes connection critically cycle data developed developing directions duke dynamic editor edwards elucidating expressed expression foundation framework friedman from fruitful further generalization gifford glasner glass goto graphical gratefully greater hartemink have heckerman higuchi http hughes husmeier ieee imoto improvements incorporate interaction into jaakkola jarvis joint jordan joseph kluwer koller learning like linial manuscript material merge method methods mian might miyano models module most murphy nachman nariai national nature networks number other page preparation principled proc program protein publishers range recomb references regulators remain reviewers russell science segal sequence simon smith smulders sophisticated sources spellman straightforwardly suggestions supplemental support tashiro thank that their under university wang when which widely wider with would yelensky young
http://helix-web.stanford.edu/psb05/rogozin.pdf	39	From Context-Dependence of Mutations to Molecular Mechanisms of Mutagenesis I.B. Rogozin, B.A. Malyarchuk, Y.I. Pavlov, and L. Milanesi Pacific Symposium on Biocomputing 10:409-420(2005)	acad acta adams adelman akad aksenova ames anderson annu babenko bacteriol bankier barrell bebenek benzer berikov betz biochim biofizika bioinform bioinformatics biol biophys bishop boerwinkle bouchonnet boulikas bozek brief bruijn carcinogenesis cariello cell charlesworth chem choi chromatin clavel cold computational consequences cooper coulson craig crow curr damage derenko dokl domains drake drouin ellegren emrich environ eperon essigmann evol evolutionary fems firb fowler fuchs gaddis galkin genet genetics genome glazko glickman golding gordenin grid hackett hanaoka hanawalt hance harb harpending harris haussler hawkes health immunol inouye italian jurka kage kazazi kepler klonowski klotz kolchanov kunkel lecossier lilley loeb mahrt malim malyarchuk martin matsuda michaels microbiol milanesi miller milstein mullins mutat natl nature nauk neuberger newton nierlich nonrandom okada oller opin organizations pannell pavlov perspect petersen piegorsch platforms pozdniakov proc projects quant rada references repair resnick ripley roberts rogozin rose sanger saul scalable schaaper schreier science sharp sheehy siepel skopek smith solovyev spring staden stoneking storb streisinger symp terzaghi theor through tsugita veaute vigilant virtual watt webster wilson wolfe young youssoufian zavolan zhang zhao
http://helix-web.stanford.edu/psb05/hoffman.pdf	14	The Clinical Bioinformatics Ontology: A Curated Semantic Network Utilizing RefSeq Information M. Hoffman, C. Arnoldi, and I. Chuang Pacific Symposium on Biocomputing 10:139-150(2005)	account acids alleles amberger amia analysis andreas anonymousan antigens antonarakis artic assoc audience ball basis baskin baxevanis bffo bioinformatics biomedical biotechnology birth blood bocchini california cancer cantor center centered cgibin church clark claustres clinical codes committee communication complex computational cruz curated cystic cytogenetic data database dbsnp defects describe desgeorges development different discovery discussion disease disorders dunnen edgar existing exons extensions factors fibrosis flanking flegel framework france furey gassner gene geneclinics generic genes genet genetests genetic genome genomics goyette group growing guide hamosh harris hgmd hgtext hornoch http huff human identifier inform informatics information inheritance integration integrative international into introducing ireland iscn issue john katz kholodov knowledge knowledgebase laussel locuslink logical loinc lussier maglott mamm march marsh mcdonald mckusick mendelian metcalfe methylenetetrahydrofolate milos model molecular mort mouse mthfr muller mutant mutat mutation mutations names national ncbi nomenclature nucleic observation omim online ontology orig ouwehand pagon personal phenotypes platelet practical practice proc proteins pruitt putting recommendations reductase references refseq regions relationships report resource resources rocha sang santa sarkar schonitzer schunter science scott sherry sicotte silico sons sources southern standing stenson structure suggestions symp system tarczy terminologies terry testing tissue trends ucsc university update using valle variation vocabulary wagner ward watkins weak wheeler wiley working
http://helix-web.stanford.edu/psb05/russel.pdf	5	Exploring Protein Folding Trajectories Using Geometric Spanners D. Russel and L. Guibas Pacific Symposium on Biocomputing 10:40-51(2005)	academy acknowledgments addition against algorithm alignment annual another applications apply approach arya aspects authors barrier based been better between biochemical biology capture captures cargo chunks common comparative comparing complicating computational computing compututational conformation consortium constructing could curves daad data deformable descriptor determinants dimensional ding discrete distances dividing dokholyan easier easy edelsbrunner electrophoresis energy environment eppstein euclidean eugene expasy explorer fast feng find first fold folding gaps geometry grant grants guex guibas handbook have heffernan history however http incorporating into issues jayachandran ject jectories journal june kolodny lanky letscher lewyn like lindahl location macromolecular many martz matched matching measuring mechanism microbio might model modeling molecular motif mount much narasimhan national need nguyen nikolay number optimally pages pande parts paths pdbviewer peitsch persistence plan point powerful press problem problems proceedings protein proteinexplorer proteins provides providing quickly rachel rasmol references regarding relevant resolved result rhee role salowe savers science sciences screen searching segmentation seventh shakhnovich shirts short sidechain significant simple simplification simulations single sippl small smid sorin space spanner spanners spanning sparse spdbv stanford strip structure structures such suggesting suggestions supported suspect swiss symposium techniques than thank that theory there thin this three through topolical topological trees trends trying twenty umass understanding unfolding unite valuable vijay visualization volume water well which will with without work world would zomorodian
http://helix-web.stanford.edu/psb05/hayete.pdf	13	GOTrees: Predicting GO Associations from Protein Domain Composition Using Decision Trees B. Hayete and J.R. Bienkowska Pacific Symposium on Biocomputing 10:127-138(2005)	acad acids alignment analysis annotation annual anonymous application approach apweiler arabidopsis artificial ashburner assemblies associating automated bairoch ball based bateman bayesian berger berlin biocomput bioinformatics biol biological biology biomedical birney boeckmann breiman brucei buell camon cerevisiae chang chiang christie chromosome classification codes coiled coils coli combining comp comparative complete conference consortium correlations cross data database davis decision delcher description direct discovering diskin dolinski domains drosophila effects entropy enzymol escherichia expression expressions families flybase foulger framework friedman from function functions gene genes genet genome genomes genomics germany ghedin gofigure groth group haas haft harris hennig heterogeneous hidden hill hvidsten implementation improving induction intelligence interaction international interpro issel joardar journal karp kasif khan king knowledgebase komorowski krishnan krogh laegreid lagreid large larsson learning letovsky literature machine magrane mammalian markov maximal maximum meke metacyc methods microb mixture model models mulder multifun multifunctional murthy natl nucleic nucleotide oblique ontologies ontology pairwise pathogen patterns pfam physiol plant polymorphisms predict predicting prediction press probabilistic proc proceedings process prodom products profiles program project projects prot protein proteins pseudomonas raychaudhuri references regression research residue riley rule saccharomyces sayed scale scheme schug selengut sentence sequence serres single situ sources species strategies study suppl supplement swiss syed symp syringae system systems tarver temporal through tigrfams time tomato tool topology transcript transmembrane trees trembl troyanskaya trypanosoma unification uniprot universal using wadsworth wasserman westhead wilson with wormbase wortman yona
http://helix-web.stanford.edu/psb05/debie.pdf	46	Discovering Transcriptional Modules from Motif, Chip-Chip and Microarray Data T. De Bie, P. Monsieurs, K. Engelen, B. De Moor, N. Cristianini, and K. Marchal Pacific Symposium on Biocomputing 10:483-494(2005)	access acids advance agrawal biocomputing bioinformatics biology biotechnology cell computational conference costanzo data database debie friedman genetics genome hartemink international issue joseph journal kanehisa kellis lanckriet lapidot management marchal mewes molecular narai nature nucleic pacific pilpel proceedings references research revised science scientific segal sigmod spellman submitted suppl symposium tavazoie thijs vert world
http://helix-web.stanford.edu/psb05/tari.pdf	20	Understanding the Global Properties of Functionally-Related Gene Networks Using the Gene Ontology L. Tari, C. Baral, and P. Dasgupta Pacific Symposium on Biocomputing 10:209-220(2005)	acad academic agrawal albert alon american architecture ashburner assessing bacterial ball barab barabasi barkai biological biology biotechnology blake bollobas bornholdt botstein cell centrality chemotaxis codes coexpression collective constructed contains data definitions defs degrees derived diameter draghici duplicate dynamics embo emergence evidence evol evolves experimentally explained expression extreme fell free from functional gene geneontology genes genetics genome genomic genomics global goldberg gominer graphs handbook hartwell hopfield html http huynen interaction interactions interconnection internet interpretation jeong journal khatri krawetz large leibler lethality lett london magazine martins mason metabolic metabolism model modular molecular murray nature nets network networks noort oltva oltvai ontology organization ostermeier ottvai oxford phenomenon phys press princeton proc profiling protein proteomic random rapidly redundant references reports resource reviews robustness roth scale scaling schuster science sciences self simple small snel sociology strogatz supplement surette tombor tool understanding unification university wagner watts wide wired world worlds yeast zeeberg
http://helix-web.stanford.edu/psb05/anantharaman.pdf	37	Fast and Cheap Genome Wide Haplotype Construction via Optical Mapping T.S. Anantharaman, V. Mysore, and B. Mishra Pacific Symposium on Biocomputing 10:385-396(2005)	algorithms alignment analysis anantharaman applied britten cheap closely comp construction contiging discrete divergence errors etween false fast fixed from genome genomic genomics halperin handling haplotyp haplotype haplotyping html http hybridization indels individual into ismb jority lancia lncs long mapping maps mathematics mishra molecule multiple mysore optical ordered parameter parida partitioning pnas populations positives practical probabilistic problem recomb reconstruction references related reports research restriction samples schwartz sequencing single targets tech technical tractability validation variations wabi waterman wide
http://helix-web.stanford.edu/psb05/marshall.pdf	16	Linking Ontological Resources Using Aggregatable Substance Identifiers to Organize Extracted Relations B. Marshall, H. Su, D. McDonald, and H. Chen Pacific Symposium on Biocomputing 10:162-173(2005)	acids ambiguity analysis analyze analyzing application arizona articles assoc based bioinformatics biological biology biomedical biotechnology capture center cerevisiae chen christie closedclass comp computational data database documents domain drugs edgar efficient extracting extraction forthcoming friedman from fukuda full function fusion gaizauskas game gene genes genew geneways genies genome grammar hanisch human hybrid identification identify identifying informatics information inhibit integrating journal july kernel knowledge lanckriet language leroy lexical ling literature marshall martinez mcdonald methods model molecular name names national natural networks nomenclature nomenclatures nucleic organisms other over palakal papers parser parsing pasta pathway pathways playing prediction processing protein provides pustejovsky references regulatory related relation relational relations relationships resources rindflesch robust rzhetsky saccharomyces scientific sequences shallow simulation source structures submitted system tagging tanabe text texts tools toward tuason update updates using visualizing wain wheeler wilbur words world yeast
http://helix-web.stanford.edu/psb05/makita.pdf	48	Bayesian Joint Prediction of Associated Transcription Factors in Bacillus subtilis Y. Makita, M.J.L. De Hoon, N. Ogasawara, S. Miyano, and K. Nakai Pacific Symposium on Biocomputing 10:507-518(2005)	acids analysis approach babu bacil bateman binding bioinformatics biol biological biology bulyk cambridge cells chapman church cisregulatory closest coin coli comparative computational conf context contribution data database dbtbs density dependent determinants discovery discriminative distance durbin eddy escherichia estimation expression factor factorbinding factors families finn from functional gene genes genetics genome genomics griffiths hill hoch hollich holme hoon http identifying imoto information inter intergene issue jones khanna kobayashi krogh length london losick makita marshall masuda mcguire metabolic microbiol mitchison miyano model models modules molecular motif moxon nakai nakao novel nucleic occurrence ogasawara operon overrepresentation pfam physiological possible predicting prediction press probabilistic proc protein proteins recomb references regulation reitzer relatives research schneider segal sequence sharan sigma silverman sinha sites sonenshein sonnhammer sparial statistical statistics structure stud subtilis suppl teichmann themes tompa transcription transcriptional trends university using washington wide yeats
http://helix-web.stanford.edu/psb05/brown.pdf	31	Subfamily HMMS in Functional Genomics D. Brown, N. Krishnamurthy, J.M. Dale, W. Christopher, and K. Sjölander Pacific Symposium on Biocomputing 10:322-333(2005)	acids acknowledgements against ailey algorithm algorithms alignment also alternate appl assessed attwood authors bateman between bioinformatics biol biosci brenner builds chothia classification comments comput conf construction conte curr detection directly does edgar eisen felsenstein foundation fraser from galperin gaulton genet genome gough grant green health here homolog hubbard hughey ieee increased information insightful institutes intell investigated issues koehl koonin lander levitt method modeling murzin national nucleic opin park performance pharmacol proc provide references regard report reviewers science sequence sequences several share shmm shmms should silico simply single software subfamilies subfamily such supported syst system tech thank that their this trends ucsc under used venter weighting wish with work
http://helix-web.stanford.edu/psb05/pegg.pdf	34	Representing Structure-Function Relationships in Mechanistically Diverse Enzyme Superfamilies S.C.-H. Pegg, S. Brown, S. Ojha, C.C. Huang, T.E. Ferrin, and P.C. Babbitt Pacific Symposium on Biocomputing 10:358-369(2005)	abascal academic acids annu ashburner babbitt benson biochem biochemistry bioinformatics biol biology boeckmann bohlmann bonner bork brenner brien chem classification cohn committee comp comput copley crock croteau curr database dodevski eddy enzyme enzymes genet genetics genome gerlt gibson green henschen herschlag higgins horn international issue iubmb jansonius jensen karp kirschner koonin life lottspeich microbiol miller molecular niermann nomenclature nucleic opin osterman overbeek palmer palsson paul pegg pettersen press priestle proteins raines recommendations reed references reviews schilling schmidt stasiowski steele szadkowski thompson trends union unpublished valencia watson webb weininger wilmanns yanofsky york
http://helix-web.stanford.edu/psb05/leaver-fay.pdf	3	An Adaptive Dynamic Programming Algorithm for the Side Chain Placement Problem A. Leaver-Fay, B. Kuhlman, and J. Snoeyink Pacific Symposium on Biocomputing 10:16-27(2005)	acad acknowledgements adaptation adaptive alenex algorithm allow allowed also annealing approximations away baker base baserotamers being bellman better biol bounds chem collision complexity computations could curr dahiyat dantas decrease degree delarue designs desjarlais desmet dictated dunbrack dynamic eliminate eliminated elofsson energies energy eriksson even expect fixes from funded future gains gordon grant group handel have hazes heirarchically hellinga high holm hopefully incorporate interaction into ireton itself kloks koehl kuhlman lasters leaver like looger lovell lower maeyer make mayo modeled moreover natl nature only opin optimal partial partially performance phys preserving press princeton problem proc produce programming prot proteins range reached reduce redundant references research residue resolution resolutions resolved richardson rotamer rotamers same sander saven science simulated snoeyink some spatial springer states stiffly stoddard struct structure that their theoretical these this tighter treat treewidth univ varani varying vertex vertices wabi want were while will with wolynes word work would zhou
http://helix-web.stanford.edu/psb05/nguyen.pdf	33	Two-Stage Multi-Class Support Vector Machines to Protein Secondary Structure Prediction M.N. Nguyen and J.C. Rajapakse Pacific Symposium on Biocomputing 10:346-357(2005)	advances analysis argos backofen baldi barton based bioinformatics biology biopolymers cambridge chichester clote cold computational crammer cristianini cuff data dependences empirical enzymol estimation frishman function garnier genetics genome gibrat harbor ieee information introduction jones journal kabsch king krogh laboratory learing machines methods molecular mount networks neural ouali platt press proc processing protein proteins references riis rost salamov sander science sequence shawe singer solovyev sons spring springer sternberget structure support systems taylor theory transactions university vapnik vector verlag wiley york zemla zvelebil
http://helix-web.stanford.edu/psb05/gui.pdf	26	Threshold Gradient Descent Method for Censored Data Regression with Applications in Pharmacogenomics J. Gui and H. Li Pacific Symposium on Biocomputing 10:272-283(2005)	achieved addition adjusting also among annals another applied approaches based biocomputing bioinformatics biological biometrics both building care certain chan clinical closely correlated correlations cross davis department descent deserve determining developed dimensional does done effect efron england event expect expression extensions friedman further gene genes genetic genomic give goal golub good gradient hastie heagerty high highly however identify important include including indicator interact interactions interesting investigation johnston journal lasso levels luan lumley medicine mentioning method methods model more numerically observed only optimal outcome pacific parsimonious pathways patients penalization pepe performance pharmacogenomics popescu possible practice precisely prediction predictive problem procedure profile profiles proposed references regression regularization related relevant report risk robust rosenwald royal same science select selected series sharing should since slonim society some stable stanford statistical statistics study such summary survival symposium tamayo technical that their them then therefore these this threshold tibshirani treatment type university used useful using validation value variable variables very want which with worth wright
http://helix-web.stanford.edu/psb05/preface.pdf	0	Pacific Symposium on Biocomputing 10:v-xx(2005)	abbreviation able abstracts accept acknowledge addition addresses after again aided alex alexa alexander algebra algorithm algorithmic alignment aloha also alternative altman among analysis analyzing anonymous another apologize appear application applications applied approaches architectures archival areas array arti ashburner assembling association attention automated automatic available babbitt based because been before being below between biochemical biocomput biocomputing bioethics biogeometry bioinformatics bioinformation biological biology biomedical biomolecular biomolecules biopolymer biopolymers biosystems biotechnology bodenreider bourne bring brought building burkard bustamante busy calculus carlos carrillo carroll case cell center chain chairs challenges cheminformatics chemistry chosen christos citation citations cited citeseer citing classical classification clear clinical cluster collection colorado combinatorial come common commonly comparative competitive complete completed complex complexity components computation computational computer computing concepts conference consider contains continues control controlling convincing coordinated course coverage covered critical cross daml data databases date david decade dedicated department description design dimmic discounts discovering discovery discussing disease disequilibrium disorder disordered distributed does drug duke dunker duplication each edelsbrunner education educational efforts eisenberg eker emerging encourage energy engineering enters environment eran eskin even evolution evolutionary exceptions exciting exists expanding experiments expertly expression extracted extracting extraction fact factor feature fiction field first five flexibility folks formal forward four fraction free frequency frequently from fuhrman fukuda function further future gauge gene general genetic genetics genome genomes genomic genomics genotypes geometry getting gifford glycobiology goble going good grants graphical grass greater group haplotype haplotypes hartemink have having health hein herbert high highwire histogram hmms hormone however http human hunter hybrid identification identifying impact inadvertently include included includes index indexed indexing indiana individual inference inferring informally informatics information infrastructure institutes intelligent interaction interactions interactive interests international internet iscb issue issues jaakkola james jensen joint jotun journal journals joyce jung keith kernel keynote keyword kinase klein knapp knight knowledge known laderoute language large larry last lawrence learning left leif leslie less liang library like limited lincoln linkage linking list listing literature locus logic look machines mainstream major make managed mankind manuscripts many mapping maps marco mark markers marks marylyn mass matsuno matt mccray measure mechanical medicine meeting members meseguer meta metabolic methodology methods michael michelle microarray migrate milward mining mitchell miyano modeling modelling models moderate modern modulation molecular molecules months mooney more most multi multiple must muster nagasaki names national natural network networks noble nonetheless noticed number october offer ofran often olivier online only ontologies ontology opportunity organization organized organizers organizing other others ouzounis over overall pacific pain papers parentheses partial participants particular particularly pathway pathways patrick patsy performance perspectives petri pharmacogenomics pharmacology phenotypes philip phylogenetic phylogenetics phylogenies physiology place pleased plotted population populations post precision predicting prediction preface presented press pride principal principally proceedings process processes processing program promoter proposals proposed proposing protein proteins proteomics provide provided provides publication publications published pubmed pulman punta quality quantum rate ratings raychaudhuri recall references referring regev regions registration regulation regulatory related relationship relationships relevant remain representation requires resources response result retrieved reveal reverse review reviewed ritchie roots rost russ russell sample scale schauser schedule school science sciences scientific scientists sean search second segal selected sequence sequences series service services session sessions shamil shapiro shared sharing showing shows side signaling silverman simulation since sizes society solicit solution some somogyi sonmez spectrum splicing sponsor sporulation stable stanford statistically stephen stevens stochastic straightforward string structural structure structures stuart studies studying submitted submitting successful summarize sunyaev support symbolic symp symposium system systems takagi take tamura targets task tasks teaching team temporal tenth teri terms text than thank that their them theme then theoretic theory there these they this thomas thomson those three throughput tiffany tight time times timothy tissue together tools topic topics toward tracks trait travel tropsha true tsunoda tutorial tutorials types ucla unable understand understanding unique university useful using validate values variation vector venue very visualization ways what where which wide wilke will wished with work working would wroe yanay year years young your
http://helix-web.stanford.edu/psb05/chen-yu.pdf	45	Genome-Scale Protein Function Prediction in Yeast Saccharomyces cerevisiae Through Integrating Multiple Sources of High-Throughput Data Y. Chen and D. Xu Pacific Symposium on Biocomputing 10:471-482(2005)	acad acids ackley acknowledgments across adams addition address alexandrov also alternative altman among analysis annealing annotation applied ares assign asthana automated bader barrell bartel based bauer bayesian becker bennett better binary bioinformatics biol biological biology biotechnol biotechnology boltzmann bosche botstein boutilier brown bussey cagney cambridge carbon carmel cell challenge chen chiba chien chung clare cognitive combining complexes computational computer conditional conference consortium contrast cristianini cruciat current data davis decision deng department dependencies develop developed different discussion discussions distributions doegenomestolife dolinski dujon eccb eisen elaborate emili energy entire estimation exactly exploring expression fashion feldmann fields fifth first flammini foundation frishman from function functional funded furey furthermore future galibert gasch gavin gene genetics genome genomes genomic gibbons giot global goffeau grandi greenbaum gruhler grundy guldener haerdle harel hausser haussler heilbut helpful hierarchical high highthroughput hinton hishigaki holt http icml ieee includes including inference information integrated integrations interaction international introduction jansen jeffery joshi journal judson kasif king kluger knight krause krogan kuhara lafferty learning letovsky life like likelihood lockshon loren machine machines major mannhaupt mansfield maritan marzioch maximum mayer mccallum mehta method methods mewes michon microarray millar model modeling models mokrejs molecular moore more muta nakai narayan nation natl nature network nishizawa nonparametirc nucleic obtain obtained omics ontology optimization over owen ozawa parameters part partially pavlidis peptide pereira pochart points post posterior prediction press problem proc proceedings process program project propagating protein provides published qiang random randomly recomb references regression represents research result rick rinehart robust roth sakaki same schemes schultz schwikowski science sejnowski selected sequestration sets shown simulated society solve spellman srinivasan starting statistical sternglanz stochastic storz such sugnet supervised suppl supplement supported synechococcus systematic table takagi tanigami tashiro taylor technique thank this throughput together troyanskaya uetz under using vazquez vespignani weston will winkler winston with work would yamamoto yeast ying zhang zhao
http://helix-web.stanford.edu/psb05/intro-sg.pdf	30	Inferring Function from Structural Genomics Targets: Session Introduction P.C. Babbitt, P. Bourne, and S.D. Mooney Pacific Symposium on Biocomputing 10:319-321(2005)	acids berman bhat bourne feng funct genomics gilliland laskowski nucleic references research shindyalov struct watson weissig westbrook
http://helix-web.stanford.edu/psb05/philippakis.pdf	49	ModuleFinder: A Tool for Computational Discovery of Cis Regulatory Modules A.A. Philippakis, F.S. He, and M.L. Bulyk Pacific Symposium on Biocomputing 10:519-530(2005)	acad acids alkema altschul andr athin authors award berger berman bertrand biocomput bioinformatics biol birren blan blanchette boffelli bulyk cervera chem chette chiang church cliften cognia comput computing critical defense department discussion eisen endrizzi engineering fellowship fickett foundation frith from fund funded gaul genet genome gish glasgow grad graduate grant halfon hansen helpful http huber hughes informatics irvin jason johan kellis krivan lagergren lander lawrence levine lipman love mahdavi manuscript mark markstein martinos mcguire michelson mike miller milton moses myers national natl nature nhgri nimwegen nucleic omas oula palumbo part patterson phrma posakony prakash proc rajewsky reading rebeiz reeves references reinert report research roman schbath schwikowski science siggia sinha spouge sson starter stormo suppl supported symp technical thank this thompson tompa ucsc umbarger university vergassola warner wasserman waterman weng william work yelensky
http://helix-web.stanford.edu/psb05/ogren.pdf	17	Implications of Compositionality in the Gene Ontology for Its Curation and Usage P.V. Ogren, K.B. Cohen, and L. Hunter Pacific Symposium on Biocomputing 10:174-185(2005)	academic acquaah acquisition altman analysis annotation annual application ashburner bada bard binary biocomputing bioinformatics biological biology capable categorization categorizer cell checking clinical codes cohen cohn compositional concurrency consistency consortium control corrected correcting creating cybernetics daml deletions description design eberlein edition environment fulmer gene genome glasgow goat goble hall hands hard heaton http hunter implementation information insertions joslyn jurafsky karp kluwer knowledge language levenshtein lexical linguistics logic martin mathematical mcentire medicine meeting mensah methodology methods meulen migrate mniszewski mungall natural nature networks notebook obol ogren ontologies ontology open pacific papcun partee participant prentice press proceedings processing protein proximity publishers rechtsteiner rector references research resource reversals rocha science search semantic sigir simas source sourceforge speech stevens structure submission symposium term terminology terms text theory tool type unification using verspoor wall word workshop wroe
http://helix-web.stanford.edu/psb05/peccoud.pdf	27	Parameterization of a Nonlinear Genotype to Phenotype Map Using Molecular Networks J. Peccoud and K. Vander Velden Pacific Symposium on Biocomputing 10:284-295(2005)	able acad acknowledgements akesson algorithm alleles alon along analysis analyze analyzing animating annu anonymous applications arthur associating assumed assumes atkinson bard bates been better between bickel biocomput biol biomed biotechnol blake breeder breeding build building cantor capture cell century challenge chapman chris cliffs collect collected collins comments complex conditions considered contribute contributing controlling cooper copies copy covert curr current customize data david dean deciphering define dennis described determinants developing development diploid dominance dynamical each effective elowitz engl englewood environmental epistatic equations ermentrout evans expected expression falconer febs find four gardner gene generalization genes genet genetic geneticist geneticists genetics genome genotype genotypes grateful group guet guide hall hammer handle harlow hasty have help here herrgard heterozygous homologous homozygous hope hsing human individuals inspired interactions introduce introducing isaacs john just kaern knight kramer lane leibler lett level like line longman mackay macroscopic manipulate maps mark markers mathematical mayo mcleod mcmillen mechanisms medication merrill methods model models molecular more multiple multiplicity myers natl nature needed networks next nielsen ninfa nonlinear numerical only opin optimization organisms other oudenaarden ozbudak palsson paper parameter pathology patient patients patil peccoud pharmacogeneticists phenotype phenotypes phenotypic plant podlich possible predicting prentice proc quantitative reed references regression relationship relling remain require requires researchers response reviewers ronen rosenberg same savageau schnabel science setty several shraiman siam silico simulating sons sources strategies students stupak such suggestions support surette symp systems tchuraev than that thattai their these they thieffry this thomas those total trait traits transgene treatment tropynina unchanged unconstrained understand using valuable variation variations watts ways weatherall which wiley winkler with without work working would xppaut york
http://helix-web.stanford.edu/psb05/cantor.pdf	11	GenesTrace: Phenomic Knowledge Discovery via Structured Terminology M.N. Cantor, I.N. Sarkar, O. Bodenreider, and Y.A. Lussier Pacific Symposium on Biocomputing 10:103-114(2005)	acids acknowledgements across advanced amia analysis annotation april ashburner associating association authors automated bases behind between bimc bioinformatics biological biology biomedical blois bodenreider both buried camon circular clinical codes complex complications computing convergence data database department development diagnosis disease diseases distinct elucidate encoded entropy envisage epub etiology examining explicit expression following from gene genedisease genes genestrace genetic genetically genetics genome genomics goals grants hamosh help hierarchical high holds human hypotheses implementation implicit inderpal information inheritance inherited integrating interface intermediating interpro iratxeta jenssen jianrong journal keyword knowledge kohli language levels like links literature manifestations many mappings maximum medical medicine mendelian mining multiple mutation nature network niaid nucleic occurrences online ontology part pathophysiologic pathways perez phenomena phenomic prevention principal proc project prot proteome proteomic raychaudhuri references relationships represented research respectively scientific similarly studies supported swiss symp system systems terminology testable thank that these throughput together tool traces tracing treatment trembl umls understanding unification unified using were with
http://helix-web.stanford.edu/psb05/chen-b.pdf	32	Algorithms for Structural Comparison and Statistical Analysis of 3D Protein Motifs B.Y. Chen, V.Y. Fofanov, D.M. Kristensen, M. Kimmel, O. Lichtarge, and L.E. Kavraki Pacific Symposium on Biocomputing 10:334-345(2005)	abell accurate acid acids acknowledged acknowledgements active activity additional akutsu algorithm alignment allowing altschul amer amino analysis approach artymuik assoc automated bachar bandwidth bank barker based bending berman binding bioinf bioinformatics biol biomedical birnbaum blast blundell bourne brief brutlag ceedings chains chapman chem coast cohen common comp comparison comparisons computer confidence confirmation congruity consortia constraint contours coordinate critical crystallography curr data database databases defines density derivation design detection determining dimensions dimes disc discovery distance distribution domain drug effector engineering entropy equipment estimation evolution evolutionary experiments families family fast fellowship fellowships foundation from func funct function functional functions funded gapped generation genet geometric grant graph gratefully gulf hall hashing high higher hinge holm hulo hybrid identification identify identifying ieee importance improvements independent interactions interactive isaac jhoti jones kernel laing laskowski lead lichtarge liebowitz local london macromolecular manning march marron matching math matrices method methods mihalek model molecular motif multiple national nevill nucl nussinov opin orengo overview patterns point prediction predictions probabilistic probability proc programs prosite prot protein proteins ranking recent references regulation reliable residues rigoutsos rosen russell sander scalable science scoring search searches searching selection selections sensitive sept september sequence sets shape sheather side sided significance silverman similarities similarity site sites size sloan sowa stark stat statistical statistics struct structural structure structures substructural sunyaev support supported surfaces survey symp taylor technique template templates theoretic this thornton throughput tingey tool trace training trim using verbitsky vigre vision visualizing wallace webfeature were whitaker wolfson work
http://helix-web.stanford.edu/psb05/spasic.pdf	19	A Flexible Measure of Contextual Similarity for Biomedical Terms I. Spasic and S. Ananiadou Pacific Symposium on Biocomputing 10:197-208(2005)	adding addressing alignment ambiguity amia ananiadou angeles annual apostolico applications apply approach approximate aronson artificial automatic baeza based believe biology biomedical biomedicine block boosting canada classification coling collection colton compression computer conf content contexts contextual corpora correction creating cruces dagan data developed dictionary dimacs directly disambiguation discovery effective eijk estimation evaluate exploration extract extracting extraction facilitated farach fischer flexibility french from gene giancarlo grefenstette human identifying improve indexes indirectly information intel interactions interest interested inventory inverted japan jelier know kors kyoto language learning ledge lexical ligence locuslink machine management mapping marcus markovitch matching mathematical measure medline meeting metamap metathesaurus methodology methods mining molecular mons montreal moura mulligen name navarro nenadi neubert obtained ones other palmer particular plan powell precision problem program protein recall recognition references resnik retrieval rulebased rules salford sapporo schijvenaars schulman selection semantic semantics sequence silva similar similarities similarity similarly sold sparse spasi special speech stone string support symbols symposium system tasks taxonomy term terminology test text that thesaurus thesis through tsujii tsuruoka umls university using verb wagner weeber which while word workshop yates year ziviani
http://helix-web.stanford.edu/psb05/qi.pdf	50	Random Forest Similarity for Protein-Protein Interaction Prediction from Multiple Sources Y. Qi, J. Klein-Seetharaman, and Z. Bar-Joseph Pacific Symposium on Biocomputing 10:531-542(2005)	acad acids analysis analyzing application approach assessment associates available bader based bayesian bioinformatics biol biology biotechnol biotechnology breiman budding cell cerevisiae clustering combining comparative complete complexed complexes comprehensive computational consortium data database datasets deng different discovery distance domain elion enright events explore expression forests framework from functional fusion gavin gene genet genetic genome genomes genomic ghaemmaghami gilchrist global hogue html http hybrid identification inferring information integration interacting interaction interactions interactome interpreting jansen joseph kinases large learning localization machine mapping maps mass meeting mering metric modules natl nature network networks nips nucleic obtained ontology organization pairs paper place predicting proc protein proteinprotein proteins proteome proteomic random references regulatory saccharomyces scale science sets side sources spectrometry statistical supplementary supporting systematic their this tong tool transcriptional trends uetz unification update using with xenarios xing yeast zhang
http://helix-web.stanford.edu/psb05/ferrin.pdf	25	Enhancing Data Sharing in Collaborative Research Projects with DASH T.E. Ferrin, C.C. Huang, D.M. Greenblatt, D. Stryke, K.M. Giacomini, and J.H. Morris Pacific Symposium on Biocomputing 10:260-271(2005)	ability acad acids acknowledgments across active activity additional address addresses administrative allow allows already also among analysis anderson applications area areas available base based batch becomes becon benefit between biocomputing bioinformatics boundaries bounded broader carzaniga catalyzing client code collaborating comes communication complex components composition computer computing conference constraints cost course create cross cugola dash decentralized deligiannidis design develop development different digital directly discover discovery display distributed document documented enabling enactment endpoint engineering environment environments evaluation event events evolutionary exploiting export extension first flexible focusing form foster framework from fuggetta functional further future gane general genes globus goble grant graphically grid groups hall hewett houston http human ieee implementation implementations information infrastructure initiatives instances integration intent interaction interface interfaces international jacob joint journal kaiser kesselman knowledge language leabman level leverage libraries lightweight lotus make manipulate manuscript mechanisms membrane metacomputing metis model modeling models modify monitor more morrison multiple mygrid natl natural nihroadmap nitto notification nucleic object often oinn ongoing openpbs oracle organizational other pacific paradigm personalised pharmacogenetics pharmgkb pipeline pipelines platform portable prentice present presentation print proc process processing products project provides realization references related relationships requirement requirements requires research researchers restrictions reveals roadmap robinson rosenblum running sarson science scientific second security service services sessioniv shaul software some source specification sponsored status stevens structured stryke supercomputer suppl support supported symposia symposium system systems taverna team techniques technologies texas that there these this through tochi tool toolkit tools transactions transporter transporters ucsf used user variation view vivtek weblogic well wftk wide will wimp wolf work workflow workflows world zerhouni
http://helix-web.stanford.edu/psb05/orchard.pdf	18	The Use of Common Ontologies and Controlled Vocabularies to Enable Data Exchange and Deposition for Complex Proteomic Experiments S. Orchard, L. Montecchi-Palazzi, H. Hermjakob, and R. Apweiler Pacific Symposium on Biocomputing 10:186-196(2005)	aach acids aebersold amanchy amid ansorge apweiler arkin armstrong arnold ashburner ausiello bader bairoch balakrishnan ball barker barrell berardini berriman betel bioinformatics biotechnol blake boeckmann bolouri bork bornstein botstein bowden brass bray brazma brown brun bult camon cash causton ceol cesareni chandran chandrika cherry chisholm choudhury christie citterich clark cornish costanzo cruz cuellar deery deshpande deutsch dimmer dolan dolinski donovan doyle drabkin dronov duan dunkley dwight eilbeck eisenberg engel eppig expert febs feierbach ferro finney fisk foulger gaasterland gandhi garavelli garcia garwood gaskell gasteiger gaudet genet ghosh gilles ginkel glenisson goryanin grant gwinn hannick harris harsha hedley helmer hermjakob higney hill hingamp hirschman hodgman hofmeyr hogue holstege hong howard http huang hubbard hucka hunter husi hybrigenics ireland jacq jaiswal jonnalagadda julian jung juty kasberger kavitha kell kerrien kersey kibbe kirby kishore kitano kremling kristiansen kumar kummer lappe legrain lett letts lewington lewis lilley loew lomax lopez lucio magrane margalit markowitz marshall martin matese mendes menezes mering mersch mewes minch mjolsness mohammed mohan montecchi moore mudali mundodi mungall muthusamy nakayama nash natale nature navarro nelson nielsen nikolski niranjan novere nucleic oliver orchard padma palazzi pandey parkinson paton peri poux prasad press proteomics quackenbush quondam ramya rana rashmi redaschi references review rhee riba richter ringwald robinson roechert roepstorff rubin sakurada salwinski sander saravana sarkans sauro schaff schulzekremer schwarz seigfried selig selway sethuraman shanker shapiro sherlock sherman shimizu shivashankar sinha spellman spence stead steipe stelling sternberg stewart stoeckert surendranath suresh takahashi talreja taylor theesfeld tomita tonellato valencia vidal vilo vingron vrushabendra wagner walker wang weimin white whitfield wojcik wood wortman xenarios yates yatish zanzoni zeng
http://helix-web.stanford.edu/psb05/lu.pdf	15	GO Molecular Function Terms Are Predictive of Subcellular Localization Z. Lu and L. Hunter Pacific Symposium on Biocomputing 10:151-161(2005)	acid acids amino analysis application approach apweiler ashburner automated bacteria bairoch ball base based biochem bioinformatics biology biophys blake blatter boeckmann bork botstein brinkman brunak butler cells cellular cherry chou cokol commun complete davis defays dolinski donovan dwight eisenhaber emanuelsson embo eppig ester estreicher eukaryotic finding gardy gasteiger gene genet genomes genomics gram harris heijne hidden hill hubbard hybrid improving incorporating inferring issel journal kanehisa kasarskis knowledge knowledgebase krogh lambert larsson learning lewis lexical localization location machine markov martin matese mcgraw michoud mitchell model molecular nair nakai nature negative networks neural nielsen nuclear nucleic ontology phan pilbout predict predicting prediction prot protein proteins psort references reinhardt research richardson ringwald rost rubin schneider sequence sherlock signals simon sites sonnhammer spencer subcellular supplement support swiss tarver terminal their through tool topology transmembrane trembl trends tusn unification using vector wang wanted with
http://helix-web.stanford.edu/psb05/draghici.pdf	24	Identification of Genomic Signatures for the Design of Assays for the Detection and Monitoring of Anthrax Threats S. Draghici, P. Khatri, Y. Liu, K.J. Chase, E.A. Bode, D.A. Kulesh, L.P. Wasieloski, D.A. Norwood, and J. Reifman Pacific Symposium on Biocomputing 10:248-259(2005)	able acad academy acid acids acknowledgements across addition against agency agron ahmed akopyants algorithm algorithms alignment alignments allow also altschul always amino among amplified analysis andersen anim anthracis anthrax antibiotics antigenic antonescu apathogenic appel appl applicable application applied approach area army associated authors automata avid bacil bacillus bacteria bacterial bacteriol badger bandyopadhyay based batzoglu baum bell benson berger between beutin bioinformatic bioinformatics biol biology bioshield biotechnology bishara blankespoor blast blum bogush bomb bray briggsae cabios call cambridge campylobacter capripoxvirus carlos carlton catalog caugant cawthraw cereus chandler characterization check chin chissoe choice cholera chromosomal chromosome classification clin clinical close closely clustalw cockerill codon coli colonization command common comparative comparing comparison comparisons completely comprehensive computational computer conservation construction content contrast conversion coordinate crickmore cross crystal cycle daly database david davies dean defence defense delcher delvecchio describe design destruction detection determined development diatchenko differences different differentiation directorates dissemination dissimilarities distinguish diversity dobrindt drghici drobniewski drug dubchak duggleby dunham dwyer economical efficient elegans elements ellerbrok emphasis encoding environ environmental escherichia eukaryotes evolution existing exon fast feitelson fems filamentous find finding fingerprinting fingerprints finnie first fleischmann fluorescent fradkov fragment frazer frequency from fujiyama fund gamez gapped gautier genbank gene general generation genes genet genetic genome genomes genomic genomicfingerprinting genomics gibson global goat gouy grantham gusfield hacker hadfield hardison hattori health helgason helicobacter hidden higgins hill hohl horizontally hosamani http human hutson hybridization hypothesis ichiba identification identify ieee ikemura improving inactivation infections informatics information interleukins introns isolates jackson janke january jects jejuni jones journal kanaya karsch kasif kearney keim kent kingsley kinouchi kitching known kolsto kozuki kramer kudo kurtz laker lamonica lander large lebedev length lereclus lett letters levels lewandowski liang light limited linear lipman localization locksley long looking loots lysogenic macht madden manning mapping marker mass matching materiel matrix mccready mccreight medc medical melling mercier mesirov method meyer microarray microarrays microbial microbiol microbiology miller mizrachi mlsc molecular mondal mori mouse multiple multivariate nakamura national natl nattermann nature ncbi needleman neta neural newell nishi nonamer norwegian novel nucleic nucleotide oehler oeltjen ohlebusch okazaki oligonucleotide olsen only open opulation organism organisms organizing ostel other ozel pachter pages paper passive pathogenic pathovars patra pattern patterns pauli pave penalties periodontitis pesticidal pestis peterson phage phillippy polymorphism population position potentials potter poxviruses predicting prediction press probes proc proceedings prod production program programme programs progressive prokaryotic protection protein proteins pylori quinn radnedge random rapid rasool real realtime reason redkar reduction references regulation regulator regulatory related relationship relative requires research resistance results reveal revealed reviews rflp risk rose rpob rubin salmonel salzberg scale schaffer schnepf schumacher science sciences search self sensitive sensitivity sept september sequence sequences sheep shimuzu shumway signatures silent similarities similarity singh size skowronski smith smoot software soil space species specific strain strains strategy straub strings structure subsequences subset subtractive suffix suppl supported suppressive surveys sutils sutractive switching symp synteny taxik taxplot taylor tembhurne that then theory these this thompson threat through thuringiensis ticknor time tonks tools toxin transferred tree trees trim trop truly turnbull typhimurium unfeasible unique university unveiling update uropathogenic usage used using utilization vaccine velikodvorskaya versatile virus viruses waldor wang ward wassenaar watanabe waterman weapon webb weight weighting weiner were wheeler which white whole williams with work works worsham wunsch wunschel xanthomonas yamada yersinia york zahler zeigler zhang