http://www.informatik.uni-trier.de/~ley/db/conf/psb/psb2007.html PSB 2007 http://psb.stanford.edu/psb-online/proceedings/psb07/johnson.pdf 22 Pacific Symposium on Biocomputing 12:233-268(2007) abbreviations above acids acknowledge acknowledgments action addison advances aitken algorithm aligning also alternations altman amia among analyses analysis ananiadou anatomical anatomies anatomy annu annual anonymous applicable applied approach approaches artech ashburner assistance assoc authors automated automatic available awareness bada bard based baumgartner bernstein between binder biocomput biocomputing bioinformatics biol biolink biology biomedical biomedicine bioontologies bodenreider brenda burgun cantor case categories cell challenges chang chem chemical cited cohen colombe colosimo combination combining comments competitive complementary computational concepts cone conf conference consortium constructing coronado cream creating csli customized daml data database databases degtyarenko dependence derived description design detected detecting developments dictionaries dictionary disambiguation discussing discussion documentation ebeling edberg editor editorial editors effective employ entities entity enzyme equally error errors euzenat evaluated evaluation example factors fault folding framework from future gelman gene generic genet genome gibson gospodneti grant gratefully gremse handbook harman hartel hatcher have hayamizu heldt helpful helps hirschman house however huhn human hunter identification identify illustrates implementation improved independently info inform informatics information insightful international introduction issue issues itnl johnson journal kester kinoshita klein knowledge lambrix language leach lesk lexical lexically linguistic linguistics linking logics lucene luger lussier machine malo manc mani manis many mappings matching mccray mcnaught medinfo medline mentioned merging methodology methods mice michael mihalcea mining mitchell mitkov model modelling models molecular morgan mork mouse multiple name natural netter ning normalization nucleic object october oepen ones online ontological ontologies ontology order organism oriented other output oxford pacific pages pairs paper papers patterns pedersen pine porter possible pottinger ppswr precisely present press proc proceedings processing professional program publications quality readable reference references reflected relations relationships reported representations research resource resources reviewers rhee ringwald same sarkar schema schomburg schutze semantics sense series session should shvaiko sigdoc similar smbm software sonia spelling stripping structural suffix suffixing suggest suites suppl supported survey symp symposium system systems tanabe technique techniques tell terminological terms test testing text thank that there these this three todd tool tools tsnlp tutorial types umls unification university updates using very vocabularies webber were wesley with word work york zhang http://psb.stanford.edu/psb-online/proceedings/psb07/lu_z.pdf 25 Pacific Symposium on Biocomputing 12:269-280(2007) abstracting acquaah addisonwesley afantenos amia analysis annotation annotations applications aronson artificial association automatic automatically based baud bayes benjamins bhalotia bhupatiraju binder biocomputing biocreative bioinformatics biology biomedical bionlp biotext categorization characterization classification cohen coling colosimo company computational concept conference congress contrast correction cremmins custom dictionaries disambiguation documents dolbey domain edition electronic entity expansion extracted extraction extracts fang fijk finding folk from geissbuhler gene generating generif generifhelp generifs genomics hall health hearst hersh hirschman html http human humphrey hunter improve indexing information intelligence international introduction jackson january jelier jiang john jurafsky karkaletsis language lexical ling linguistics linking lists literature mani martin matching medical medicine mensah microarray milano mitchell models more morgan mork moulinier mulligen murphy nakov name named names nanba natural ncbi normalization normalized object okumura online ontology oriented overview pacific page pages patient patterns perspective prentice press proceedings processing producing professional projects publishing query readable recognition record references report resources results retrieval review revising rubinstein ruch schatz schijvenaars schwartz schwartzuemie searches searching simon speech spelling springer stamatopoulos summaries summarization suppl survey symposium synonym systems task testing text them tools track trec twelfth using variability verlag ward weeber white with workshop zhai http://psb.stanford.edu/psb-online/proceedings/psb07/markley.pdf 15 Pacific Symposium on Biocomputing 12:157-168(2007) anal annu barabasi beckmann bino bioessays bioinform biol biomol biotechnol boston brandon brief castle chapman chem chemical comput connelly cook curr daouk data discov doreleijers draper drug easton farr fiehn funct genom goodacre griffin guenther hall hardy holmes index jenkins kaddurah kell kopka krause kuhn kyogoku laboratories lane lange lindon ludwig mading maille markley maziuk meeting mendes metabolomics microbiol molec nature newman nicholson nikolau nobeli oliver oltvai opin paton philadelphia phillips plant proceedings prod prog protein rayment references research rhee rochfort roessner rubtsov sadtler saito science scientific seavey shift siuzdak smedsgaard smith society sojourner spadaccini spectr spectra standard steinbeck struct sumner taylor thornton trauger tunali ulrich uritboonthai viant volkman walsh wang want weckwerth westler wurtele zolnai http://psb.stanford.edu/psb-online/proceedings/psb07/gonzalez.pdf 3 Pacific Symposium on Biocomputing 12:28-39(2007) aberrations abstracts acids adams advanced ahmed allow alzheimer america american amount amplifications analysis annotations april apweiler armstrong arterioscler association atherosclerosis attention ausiello available ayoubi bader bairoch baltimore baral based bell betel bethesda bijnens bind biocomputing biocurator biogrid bioinformatics biol biolink biomedical biomolecular biotechnology block boucher breitkreutz british calling cbioc cellular center cesareni chen chettier chidambaram chromosomal circulation cited cohen collaborative committee comparison computer connectivity content critical curation cytokines daemen data database datasets davulcu descriptive detroit development disease diseases donnell driven duan duplicates edition eisenberg english european ewens experiments expression extractor falagas falciparum false febs fields finding flegal focused formula friday from furie future galitski gene general generating generifs genetic genetics genome genomic goff gonzalez gorelick grammar grant grove haase hawaii heart helmercitterich helps hermjakob hesselberth higney hogue hong hopkins horrevoets howard http hughes hugo hunter improvement includes incorporate informatics information inheritance institute intact integrated integration interacting interaction interactions interactome interface international interpretation intex introduction investigated issues johns jones joshi journal kerrien kissela kittner kostoff kuiper kurschner labaer lacount lecture letters lewington link linkages literature lloyd lusis lutgens malaria mallat manolio margalit marler maui measures medical medicine medline meeting meigs members mendelian methodology methods michigan mining mint modular module molecular montecchi mudali mutations nakamura national nature negatives network networks nodes nomenclature normalization notes nucl nucleic omim online ontology open orchard organization originating other pacific palazzi parasite parsing pathogenic pathways pfeil phansalkar physiol plasmodium play pnas pollutes potentially protein proteins proteome proteomic pubgene public publishing quondam record reduce references regulatory reguly relevant report repository research result richardson rivera rives roechert roepstorff roger role rosamond rumsfeld sahasrabudhe salwinski schoenfeld science scientific shen sherman sidney since singh sivachenko sleator smoller society sorlie soteriades source specific springer stark states statistical statistics steinberger stroke studies studying stump subcommittee such suppl symposium syntactic tari technologies tedgui temperley text texts that then third this thom thromb through tool topee transcriptomics tuning tyers uncover unexplored union united university unnecessary update using valencia vasc vignali vingron wasserthiel well weng wide wilson with wolf work workshop world xenarios zanzoni zheng http://psb.stanford.edu/psb-online/proceedings/psb07/sam.pdf 7 Pacific Symposium on Biocomputing 12:76-87(2007) acad accuracy accurate acids across adaie additional agarwal albano albert alfaro also although anaemia analysis anemia annotations applied approach apweilerc armstrong artic ashburner assigning associated associations attachment augments ausiello automatic bader bairoch ballj barabasi barkerb baron barrettes based basis batish bayesian become beemsj benthems berg bertola berwick besides between beyond biocomputing bioinformatics biol biological biosystems biotechnol birth blaked blanco blood boeckmanns bokhoven bono borlawskyc botsteinh bowen breitkreutz brun brunello brunner butlerj cancer carando case cellular certainly cesareni chazellem cherry chinese chung classifying clin cockayne collins colorectal combining community compare comparison complementing complex computation conclusion confirmed consortium contains context core correlate cotran could current currently data database databases dataset datasets date davis defective defects demonstrated dermatol determine developed developmental different dimensions direct discovery discussion disease diseases disorder distinct domains donaldson driel duplications dynamics early edited eisenberg emergence emerging enables encode encyclopedia ercc erythematosus establish eustachio evaluated evidence evol evolution excision exist explore expression expressions extend extracted faces fact factsheets fanconi febs fell ferrero ferro framework free friedman from fujibuchi function functional future gamalielssonb garelli gaspar gene genes genet genetic genome genomes genomic giampietro gielisj gillespie goldbergo gomez goto gotoolbox graph greenbaumy haematol hamster hanawalt headings helmercitterichg help high hodgkin hogue hoogervorst html http human ideker identified identify identifying ifar inheritance inside integrating intend interaction interactions international issue jacq jansen joenje joshi kalyanasundaram kanehisa kegg king klugern knowledge knowledgebase kofman krogans kumart kutler kyoto language large larger lassiga last lett levanon library light limited link literature lubovac lupus lussier lymphoproliferative machinery mahavisnot malformation many mapping maps marcotte martano martin maui mclaren mechanism medical medicine meijer mendelian mesh metabolic method mining model modeling modules molecular montecchi more morton mouren multistrategy nabieva national natl ncbi network networks noise nonetheless nucleic nucleotide number ogata olsson omim oncogene online only ontologies ontology oostromr optimal order orig ouellette pacific pairs palazzi patel pathol pathologic pathway pathways pawsonc pediatr permutation perspective phenogo phenotypes phenotypic phys pinsky plan polythetic predict predicting prediction predictions preferential preprint probabilistic proc processing properties protein proteinprotein proteins proteome provides pubs quality quantity quondam random rapp rappaport reactome references registry regulation related relationship relationships relatively reliable remains remy repair report resampling result results rhodes rice robbins rzhetsky salwinski same satagopan sato scalable scale scales scaling scheffer schmidt science sharan shared sharing sheet shown significant significantly since singh single small smaller smith sorasio spite spivak stage starkm statistical statistically steeler still structure studies study subject subpathways suppl symposium syndrome syndromes system systematically systemic than that their theoretic theoretical therefore thieffryb this thrasher through throughput tomlinss tongz tool tope topological tyers umls underlying unveil used using valid valuable varamballyv variable vastrik venegas vermeulen wagner were which whole with wolting wong world worth would xenarios year yeast zanzoni zenteno zhanga http://psb.stanford.edu/psb-online/proceedings/psb07/zhao.pdf 46 Pacific Symposium on Biocomputing 12:496-507(2007) accuracy accurate acids addition algorithm algorithmic algorithms also altschul analysis annotation aoki appears application approach araki arkin aspects assignment assimilation automata bacillus based because between biocomputing bioinformatics biological biology blast bodlaender bounded branch build castro ceedings chemical chen classes cold coli comparative compensated complete computational computationally computer conclusion conditions conserved considered consistency constrain constraints constructed context contribution coped correctly could critical data database dbtbs decomposition dept developments difference difficult discrete discussion dynamic each effectiveness efficiency efficient efficiently escherichia evaluations expression fail famili families finding formulated from functional further fusion gama gapped gene generation genes genetics genome genomic genomics goto graph graphs green growth hand harbor hattori have hicks high hirakawa however huang human improve improvement including incomplete incorporate incorporating independent inference informatics information informs inherently integer interactions international intractability issue itoh jiang kaiser kanehisa karp katayama kawashima kegg kinoshita kolotoglu koonin koster krummenacker languages larger lecture lipman loquium madden makes makita mapping maximum metabolic method microbes miller minors more mount multidimensional multiple naive nakai nakao nature netherlands network nielsen noise notes novel nucleic ogasawara olman only operations operon operons optimal optimization organization orleans orthologous orthology other pacific palenik palsson pathway pathways peralta perspective phosphorus pnas possible practically predict predicted prediction predictions press price problem proceedings profiles programming programs prokaryotes protein real reed references regulation regulatory regulondb represented rescue research reviews robertson romero salgado scalable scale schffer science search seek september sequence sequenced seymour showed shown similarity simpler simply since size some sophisticated spring springer structural structure structures subtilis such symposium synechococcus target tatusov tech technically techniques template templates them theoretic thiele this tolerate towards transcriptional tree trim trivial trying tutorials university used utilize utilizing utrecht verlag version very wagg well when width with work zhang zhao http://psb.stanford.edu/psb-online/proceedings/psb07/intro-protein.pdf 0 Pacific Symposium on Biocomputing 12:1-3(2007) acknowledgements among best biochemical building capable chairs chalkboard collins excellent future genomics green guttmacher guyer help inferences interactively like making many nature numerous papers pathways references research reviewers roadmap science selecting session submissions thank their used vision visualizing would zerhouni http://psb.stanford.edu/psb-online/proceedings/psb07/kasson.pdf 4 Pacific Symposium on Biocomputing 12:40-50(2007) acta alamethicin analysis annualized approach armstrong aromatic assembly association axelsen berendsen berger between bilayer bilayers biochemistry biochim biocomputing biol biophys blocking bullough bushweller cafiso cause cell chang change chemistry chen cheng cohen computational computing conformation conformational constant cross data dependent dipalmitoylphosphatidylcholine displays domain dushoff dynamics earn edholm editor effect epidemiol evidence fast flexible fluid fluorescence forrest fraternali free from full fusion glycine glycoprotein gray groenhof gromacs haemagglutinin haque hemagglutinin hemifusion herrmann hess huang hughson hydration hydrophobic implications inducing influenza interaction jahnig journal kantchev killian kleinjung koppaka lague lentz lindahl lipid lipids loose mark mechanism melikyan membr membrane membranes micelles mismatch molecular mortality multiple mutant nature nterminal ompf opening orientation pacific pande pandemic pastor peptide peptides phenotype plan plasticity plotkin point pore position pressure properties proteins qiao references regression residues resolution role roux sansom savers science screen secondary self services shirts simonsen simulation simulations skehel specific spoel states straus struct structure structures study suggest symposium systems tamm tatulian temperature their thomas tieleman triggering unite united using vaccaro viboud virol virus wharton white wiley wilson with world http://psb.stanford.edu/psb-online/proceedings/psb07/sautter.pdf 36 Pacific Symposium on Biocomputing 12:391-402(2007) accelerates acknowledgements additional advantage agosti alias also altova apache architecture assp automated automation available backfiles bergen better biodiversity bionlp blackwell both bryan butler catapano characters christie collaborators computer correction current data description detail detection develop difficulties digitized docs eacl ecol editing editor encyclopedia engineering entity equal error evaluation evol existing extracting extraction findit from functionality future gate gazetteers gene general gillingham global gmbh goldengate grover heidorn hidden http idaho ieee include includes informatics instance integration intend interest into introduction issue java journal juang july koning launches level life like lingpipe lucene magazine markov markup mashups mikheev models moens more moritz morphological morris name named names nature neil news opennlp oxygen oxygenxml plan proceedings process project publishing rabiner recognition recognize references results sarkar sautter semi sequence service should shown significantly simplifies solution solutions species states stephenson suggestions support taxongrab taxonomic terry text thank that their this token tools trends ultraedit unikarlsruhe valuable version volume wilson wise without work years york http://psb.stanford.edu/psb-online/proceedings/psb07/karamanis.pdf 23 Pacific Symposium on Biocomputing 12:245-256(2007) active advances alspector anaphora anaphoric application applications articles automatically barclay beyond biocomputing bioinformatics biological biology biomedical bionlp biotechniques boisen bontcheva bootstrapping briefings briscoe carroll ceedings challenge cohen cohn coling colombe colosimo cunningham curation current data database design development domain drosophila editing entities entitiesview environment erbrowser erview evaluating evaluation expression extraction figure framework freeman from gasperin gate gene ghahramani graphical hands hersh hierarchical highlighted hirschman hollingsworth hookah humancomputer hunter hyde identification informatics information interaction internet introduction john jordan karamanisetalpsb kenny learned learning lessons lewin linking literature maynard mccabe medminer meeting mining model models moore morgan mueller name named names navigating neural normalization ontologybased organism pacific plos practice preece prerequisite proceedings processing profiling proformaeditor rasp recognised recognition record references release resolution retrieval retrieving robust rogers scherf science scientific second semi september sharp size smith sons statistical statistics sternberg structure supervised suppl survey symposium system tablan tanabe tesauro text textpresso texts through tidhar tipster tool tools touretzky trim typeset using vlachos watson weinstein weischedel wiley with work workshop http://psb.stanford.edu/psb-online/proceedings/psb07/scholz.pdf 16 Pacific Symposium on Biocomputing 12:169-180(2007) acids avaraham ball barrett beckmann benson bergmuller bernhart bino bioinformatics biol biotechnology birkemeyer bryant canese chervitz chetvernin church comp dicuccio dormann draper edgar fiehn func garwood genome genomics goodacre hall hardy ilic jaiswal jenkins kellogg kopka krueger lect mccouch mclaughlin miller nature notes nucleic plant proc pujar references reiser research sarkans schauer scholz sherlock smith spellman steinhauser stewart taylor trends troup usadel weckwerth wheeler wohlgemuth http://psb.stanford.edu/psb-online/proceedings/psb07/seki.pdf 29 Pacific Symposium on Biocomputing 12:316-327(2007) abstracts acknowledgments addition american andrade annotations annual aronson associated association associations based benchmark berg between bhuptiraju biocomputing bioinformatics biology biomedical bork brass carefully case characteristics cohen compare compared computational conference consideration considerations could created croft data database discovering discovery disease distance distribution domain eijk enhance especially estimates evaluation exploring fawcett findings fish framework from full funded future gene generating genes genetics genomics goble grant graphs having hearst hersh hierarchical hypotheses implicit improved inference informatics information intermediate investigate iratxeta jelier journal keywords klein knowledge kors kraemer laboratories layer learned leveraged like linguistics literature lord measures medical medicine medline meeting mining model models molema mons moreover mostafa mulligen network notes only ontology other over overall overview pacific pages perez perspectives plan potential practical prediction present previous probabilities probability proceedings propagating proposed public publications raynaud realistic references relying report researchers resources retrieval ross schijvenaars schuemie science search semantic separated similarity simply simulate small society specific srinivasan stevens structure study such swanson symposium syndrome system systems technical technology text textual thalidomide that therapeutic those through tool tools track training transactions trec turtle undiscovered untangling uses using weeber were where with wjst work would http://psb.stanford.edu/psb-online/proceedings/psb07/intro-nlp.pdf 19 Pacific Symposium on Biocomputing 12:205-208(2007) aaron access acknowledgments ahlers aims alan alexander alfonso alignment although analysis ananiadou annotating annotation answering aplication approaches area areas arens ariadne aronson artech assessment associating association associations assurance automatic available based been benjamin beween bhupatira bibliome biocomputing biocreative bioinformatics biological biology biomedical biomedicine bionlp blaschke bodenreider boyer bretonnel briscoe building cakmak caroline castano categorization centre chemicals chen chew christian chruszcz citations classifying cognitive cohen collaboration colombe colosimo computational conference coreference corpus creating critical curation currently dale daniel datasets david deeper definitional demner describe different dina discovering discovery diseases documents domain done driven drysdale edward efforts engines enhancing evaluating evaluation explain extracting extraction fault figures fine fiszman flesch flybase four francois freely from full fushman gaps gene generif genes genomics gildea goertzel grant graphical gultekin guodong hearst helen hereditary hersh hirschman hong house human humphrey hunter identifiers ijcnlp images implicit improving increased inderjeet indexing information institute integrating introduction james javed jectives jeffrey jian jianji john johnson journal julia jurafsky karamanis karin kaufman kazuhiro keane kraemer kreulen labeling laboration lang language large laura lawrence levels lewin libraries linguistics linking literature lynette mani mapping marc marcelo marti matching mcnaught medline medstract mention mentioned methodology michel might mining model molecular morgan mostafa multiple murphy national natural nikiforos normalization noun olivier online only ontology ordonez overview ozsoyoglu pacific pages papers participation patents patricia paul pharmacogenomics phoebe phrase physicians posed possibility predications proceedings processing protein publicly publishers pubmed pustejovsky quality question questions rachel ravi references resolution retrieval revision rhodes rinde rindflesch robert roberts roles ross ruth saur scale seal search seki semantic servers session shooshan shortage similarity similarly single situation some sonya sophia sophistication stacked standards stephen strings structure substantial summarization summary supported susanne symposium system systems task technology teja text that them there these this thomas through towards track traditional trec unique user using valencia verspoor watry wellner what will william with within work xiaofeng yang year ying zhang zhenzhen zhiyong zhou http://psb.stanford.edu/psb-online/proceedings/psb07/yu.pdf 30 Pacific Symposium on Biocomputing 12:328-339(2007) aaai access accessibility acknowledgement actions acute address advanced alessandro algazy alper also although american amia among analysis annual anonymous answer answerable answering applying appraise approach articles artificial asked assessing assessment assoc associated assuring babel based behaviors being bell benigeri bergus berkowitz berland best beware beyond bhavnani bichakjian biocomputing biscup bonati booher broder care career case caveant chambliss childs christensen cimino classifying cline clinical clinicians cognitive commentary comments comparisons comprehensive computer conclusions conduct conference consumer consumers contexts controlling could crabtree cross current database databases davis definitional degrees depression depth design diagnostic different difficult diverse doctors domain domains drucker ebell educ education effects efficiency electronic elliott encouraged engine engines english ergonomics erlang evaluated evaluation evidence ewigman expertise eysenbach fact factors familiarity family feasibility female ferguson finally find findings focus follow formative found four france friedman fulfilling future gagliardi gemmell general glennie google griffiths groups handheld have haynes health healthcare heitlinger help hersh hickam hubs human ideal identifying imaging impact implications include incontinence inform information integrated intelligence interaction international internet interviews introduced jacquemart jadad jama jasist johnson joint journal judging kirby knowledge kohler kravitz kreiter larger learning lector levels levy lifelong limited little lueder lundberg marapr mcclung measurement measuring medical medicine medline medqa meeting memex method metrics moore morales more multimedia murray musacchio mylifebits namely narrow navigating need needed needs nineteenth novel number obstacles onelook only oriented osheroff pacific pandolfini participated patient peck pediatricians pediatrics performance performed peterson physicians plante pluye podichetty point poorly portals posed postgrad potential powerful pract precise preferred presents proceedings process professionals promising promot public pubmed purcell qualitative quality question questions qusetion radiography rather rating readability reader reasoning reference references regarding reliability research resources response restricted results retrieval review reviewers rosenbaum sable sacchetti sacherek sample sandvik scatter schwartz science scope search searching sectional seeking select selfdirected shanker shen shortcomings silberg similar society solutions source spanish specific spent state stevermer strategy straus stud study success such suggest survey symposium system systematic systems takeshita taxonomy technol technology terms tests thank that their these this three tice tidmarsh time timely tools topic towards track treatment trec types uptodate urinary urologic urology usability users using validated valuable viewed viewer viewor vinson vision voorhees want washington white whitfield wide with wong work workshop world would wyatt yield zvara zweigenbaum http://psb.stanford.edu/psb-online/proceedings/psb07/ganesan.pdf 12 Pacific Symposium on Biocomputing 12:127-132(2007) above acad address advanced advances alignment allow also analysis approach area areas assemble based begin beginning better beyond biocomputing bioinformatics biomedical biotechniques blast bound branch categorize cell coll complicate comprehensive confusing continues data databases defined described different direction directions directly diverse dynamic ebert endless engine engl enrichment even evolve example expand experimental expression facilitating fast from frustrating future gene generations genes genetic genome genomic gillette golub google great groups grow growth harvester helping however human identify image images importance information inputs integrate interconnected interest interface interfaces interpreting into investigators itself just knowledge lander language like likely living look mass maze mesirov meta metabolite metabonomics might modeling molecule mootha more mukherjee natl needs occur other pacific paulovich pomeroy portals possibilities possible proc processing profiles profiling proliferation protein proteomic pubmed pyramid range rapidly references reports research researcher researchers resources seamlessly search sequence sequerome services similar singleinterface sounds spawn specific spectrometric spread step structure subramanian such surg symposium systems tamayo targets that their they this those thus time tools upload user users versus very want what when while wide will wings would http://psb.stanford.edu/psb-online/proceedings/psb07/sontag.pdf 41 PROBABILISTIC MODELING OF SYSTEMATIC ERRORS IN TWO-HYBRID EXPERIMENTS acids analysis approach ariel assessment bader bayesian best biology biotech boxem cerevisiae christian comparative complexes comprehensive computational computing concepts confidence cygd data database elidan error experiments explore extensibility february framework friedman from gaining genome genomic global guldener hanah high hybrid increasing integrated interaction interactions interactome issue jaimovich jansen january journal krogan landscape large lunn marc margalit markov mering methods mike model modelling nature network networks nevan nucleic october olivier peter pierre pnas predicting protein reconstructing references regulatory relational research saccharomyces scale science sets siming specificity spiegelhalter statistics structure takashi thomas throughput towards transcriptional uetz vidal vidalain winbugs yeast http://psb.stanford.edu/psb-online/proceedings/psb07/ahlers.pdf 20 Pacific Symposium on Biocomputing 12:209-220(2007) abstraction accomplishments acids acknowledgments adapt adaptation administered advanced advances agency aggregating agreement algorithm altman amia analyzing andrade anlp annotations annu annual appl applications apply appointment argument aronson articles artificial asserting assertions assigning assoc association author automatic barnett base based between beyond binding biocomput biocomputing bioinformatics biological biologist biology biomed biomedical biomedicine bionlp bioontology blaschke bodenreider bork borlawsky bretonnel bridging browne bruce brutlag burgun byrd capture care challenges chang changes characterizing chen chiu chodorow chronic chun citations class clinical closed cohen collaboration complexity comput computational conceptual conference content context contribute data department developed developing development diagn diagnosis dictionaries dictionary discovery discuss disease diseases distance domain drug drugs druker dubitzky easton edgar edited education effective efficacy empty energy engl enhanced enhancing etiology existing expert expressing extracting extraction filter first fiszman form francisco friedman from fuller future gene genedrug generated genes genetic genetics genies genomics george glasgow guthrie hakonarson halapi heads health heidom hersh hewett hierarchies hirschman hishiki hltnaacl hristovski http humphreys hunter hypernymic inform informatics information inhibitor institute institutes intelligence intelligent intend inter interaction interactions international interpretation interpreting intramural involved jensen journal kaufman kilicoglu kinase klein knowledge krauthammer lang language large lawrence learning lenauer leroy leukemia lexical libbus library lindberg line linguistic linguistics literature lussier machine major majoros management managing mapping markers martin martinez masseroli mccray medical medicine medinfo medline medpost meeting metamap metathesaurus methods mewes mining modeling modifying molecular morgan myeloid naacl nagata names national natural nature network nucleic oliver ontology output ouzounis pacific parser part participation pathways pereira pharmacogenetics pharmacogenomic pharmacogenomics pharmgkb phenogo phenotypic potential precision predicate predications proc proceedings processing program programs propositions protein provided publishers rajan range rappaport reducing references relations relationships represent research response resta retrieval reviews ridge rindflesch rubin rzhetsky safety saric schneider schoolman science scientific semantic semantics semrep shagina shallow shiba slater smith space specific speech springer srinivasan stanford stipulated structure stuart study summarization suppl support supported symp symposium system systems tagger tagging talpaz tanabe techniques terminologies text that there this through tools traditional tsujii tsuruoka types tyrosine umls unified using valencia variation verlag visualization weinstein wilbur wilks with wong words workshop xing yandell zimmer http://psb.stanford.edu/psb-online/proceedings/psb07/vandeplas.pdf 42 Pacific Symposium on Biocomputing 12:458-469(2007) aebersold anal analysis arlinghaus caprioli carroll chaurand chem component falvo farmer febs gerke hallahan heeren howson joliffe knochenmuss kriegeskotte lett malmberg mann mass mccombie nature nygren principal proteomics references shea spectrom springer staab stoeckli verlag weissman york http://psb.stanford.edu/psb-online/proceedings/psb07/cadag.pdf 32 Pacific Symposium on Biocomputing 12:343-354(2007) about account acids acknowledge acknowledgements adams addition additionally address advantage against alice alignment also alteration altschul american analysis analytic analytical anderson annotate annotation annotations answer april apweiler array ashburner assistance association attwood authors automated automation available bairoch ball bank barberos based basic bateman bauer beyond biocomputing bioconductor bioinformatics biologic biological biology biomediator biomedical biotechnology blast blocks both capabilities cdna celniker center challenge cited clarke classification closest cohesive coin comparative compare conserved consistently controlled corpet couples created curation current data database databases determined determining developing development dhileep disparity diverse documentation domain domains donelson drosophilia dynamically ecology elizabeth engine ensembl erwin evaluate evaluated evaluation evolution expert expertise expression families family figenix framework from functional functions further furuno future gaasterland garrels genbank gene genes genetics genome genomes genomic genomics gish golding gouret gouzy grant growing guide harris have henikoff herzberg heterogeneity hope hornoch html http hulo identification imia important improve include incorporating index inferring informatics information initial integrated integration integrative intelligent international interpretation interpro into iterations janos java jess journal june kasukawa knowledge koski lending length library like local louie magpie manually marchler means medical medicine medinfo melanogaster model molecular more mork must myler myriad national nature ncbi nearest necessity neighbor neuroscience newly nhgri novel nucleic often ongoing online ontology organisms pacific paper parallel parasitic parasitology performance pfam phylogeny pipeline platform post potter powerful presented proceedings prodom projects prosite protein protozoa protozoan queries records references regularly relies requirements research resource results robust rule rules sandia sayed schema science scientists search searching sensen sequence sequenced sequences services shaker sites sivam size software sources such supported symposium system take tarczy tasks technical technique terms test that their this threshold tool training transmembranelocating trends true trypanosomatid unification using valuable variable vitiello vocabulary wang well which while will with work worthey would yeast http://psb.stanford.edu/psb-online/proceedings/psb07/maglia.pdf 34 Pacific Symposium on Biocomputing 12:367-378(2007) aaai accessing across adult alignment allow altig amer amia amphibian amphibians anatomical anatomist anatomy annotation antoniou anura anurans applications automatic baltimore biocomputing biological biologist biology biomedical biotech bombina bombinatoridae boston brinkley canada caragea caudata chandramouli collaborative communication comparative compare concept conference congress consistent construction controlled copeia could cranial cross current data database databases davies defining determine development dexa different digital distributed diverse diversity domain driven duellman ecological edmonton electronic embryologist embryology embryos england enhancing environment evolutionary existing expression facilitate fellbaum fensel fergerson find foster foundational fourth framework fully gauch gene given good groups guides harmelen helping herpetologica heterochrony hierarchical hierarchically hiroshima hoeft honavar hope hopkins ieee images including informatics integrate integration interactive intermedia international internet isei iswc japan john johns king knowledge knublauch krakow language large leopold lexical lexicon library maglia management many matching medical medinfo merged metamorphic mining model morpholgynet morphological morphologist morphology morphologynet musen name nature niles notes novel online ontogeny ontologies ontology open option orders organisms orientalis osteology other pacific paedomorphic patterns pease phylogenetic phylogeny plugin poland potentials powerful practices preferred present press primer principles proc prot provide provides pugener querying realize reecy references reilly related relations representing retrieving role ross rosse search searching semantic semi shapiro significance similar siren sirenidae skeletal smith soldatova sons species speech standardizing structure structures structuring studies study suggested summary sussex symp symposium synonym systematics taxonomic taxonomy term terminological text that third thus tool towards trueb types understand university update upper used users using vocabularies vocabulary west wiley will with within wordnet working workshop world zool http://psb.stanford.edu/psb-online/proceedings/psb07/yang.pdf 17 Pacific Symposium on Biocomputing 12:181-192(2007) acad ahmed ahorn anal anduix anticancer atri axelson bailey baron basse bassilian baverel bergner biochem biocomputing bioenerg bioeng biol biomed biomembr biomol biotechnol bloomfield bluggel boren boros botstein brown bubendorf burgess bussow byerley caligiuri cancer canioni cascante celis cell centelles chem cline coller comin dang dauner delaglio derisi discov dohner dolde downing drug durozard edmond eisen fernandez fjosne gaasenbeek gasser genet golub gopher govil gribbestad grzesiek gupta haberl hein heinzle herrmann herskowitz himmelbauer huard imaging jagannathan jeffrey jensen kallioniemi kamzolova kibbey klose kononen krane krause kvinnsland lander lapidot lauridsen lehrach lepine lewis loda lundgren magn malloy marcus marin martin mehta meister merle mesirov migita mihatsch mirlacher moch mulder mulholland natl newgard nielsen nock orntoft ostergaard pacific papas patel pathol petersen pfeifer phadke pharmacol physiol portais pratap proc rasmussen rastan ratz references reson rosiers sarkar sauer sauter schalkwyk schmidt schoeller schraml schuster science seenu sharma sherry shim shulman sitter slonim spine srivastava storey stuhler symposium szyperski tamayo tang ther today vercoutere villadsen voss vuister wilgenbus wittmann wolf zhao http://psb.stanford.edu/psb-online/proceedings/psb07/borgwardt.pdf 1 Pacific Symposium on Biocomputing 12:4-15(2007) ability acad accuracy acknowledgments across acute addison adme adult akutsu alternatives amato among analysis andreas annual approach arts attributed australia australian authors backing bair baldi based between bfam bhardwa biocomputing bioinformatics bioinforo bmbf books borgwardt breast brors bullinger cambridge cancer center chemical classification clinical coevolution combinatorial communications community completeness computation computational computer computers conf conference convolutional correlation council cross cruz data department discrete dohner dricot ecml editors education efficiency efficient eils eisen engl equation european excellence expression expressivity extene fast first flach fraser freeman frohling function functional functions funded gardiner garey gene genome genomes german government grant graph graphs guide harary hardness hart haussler held hirozane hirsh hlich human identify improves informatics information inokuchi interacting interaction interactions international intractability ject johnson kashima kera kernel kernels kishikawa kriegel laub learning leukemia lkopf machine mammalian marginalized mathematical matics matrix matthias microarray mining ministry molecular moler myeloid national natl nature nels network networks neural ngfn nicta nocedal numerical operations optimization outcome pacific part pascal perret phenotypes pkdd platform pollack prediction predicts preprocessing press proc proceedings profiles profiling prognostic program protein proteinprotein proteins proteome qsar ralaivola ramon reading references regression report research results rtner rual saigo santa scale schlenk schonauer schraudolph science sciences september sequences series siebert siker similarity sions size smola software solution specific springer structures subclasses suppl supported swamidass sylvester symposium tasks technical technology thank theory this through tibshirani towards transactions trees trim tsuda twenty ucsc ueda under veer venkatesan versus vert vijver vishwanathan wall warmuth warnat wegner wesley with within work workshop wright wrobel zell http://psb.stanford.edu/psb-online/proceedings/psb07/yoon.pdf 18 Pacific Symposium on Biocomputing 12:193-204(2007) acid acids acknowledgements algorithm along also amino anal analyze anselm approaches arias availability based betweenness biochem bioinformatics biol biology biotechnol blumer boyer brandes centrality chan chem common complete computer conjugation connections containing could curr cysteine degradation degree department derivatives development discov drug edge effective facilitate fiehn findings formation found from funded gale girvan glycine goto grant griffin help hewitt high immediate implementing influence interact interacts involved involves kanehisa ketoglutarate lancet liberation liver mainly make managing masubuchi math matter medium metab metabolic metabolites module modules moiety newman nicholson nolan nonlin nucleic nutrients nutritional opin other part partners pathobiology phys prabhu profile prospectively reaction reactions references requires schuster science significantly smith soci soft stat state states studies substrate such suggest sulfide sulfur tafazoli taken thank that these this together toxicity toxicol toxicology transamination transformation trethewey tufts turn under university used varying were which with work yoon zeng http://psb.stanford.edu/psb-online/proceedings/psb07/kou.pdf 24 Pacific Symposium on Biocomputing 12:257-268(2007) abbeel abstract accessing acknowledgments advanced advantage agency applying articles between beyond bibe bioinformatics biokdd biology biomedical bionlp bioscience blostein bruijn captions categorization cell chang chen classify cohen commonwealth conditional context darpa data defense department dependency depicting dictionary discriminative entity exploring extracting extraction features fernando field finder fluorescence focus from future gene genome getting grant grants health high hunter icdm idea identifying image images information integrating inter into ipto jects jensen joffe journal journals know koller krallinger ksce language ledge line literature location locations lular martin mentions microscope mining models molecular more murphy name networks neville office online pennsylvania porreca probabilistic proceedings processing protein proteomics publications pubmed rafkind random recal recognition references related relational relevance research retrieval ryan searching sentences services shatkay slif stacked stacking structuring subcel such suppl supported take taskar tasks technology text understanding using valencia velliste wang what will work http://psb.stanford.edu/psb-online/proceedings/psb07/neveol.pdf 27 Pacific Symposium on Biocomputing 12:292-303(2007) amia aronson artif asserting assessment assignment automatic based baud beyond biomed biomedical bodenreider boost categorization chang chapter cikm controlled cycles darmoni descriptors developmentevaluation diseases document documents domain during etiology experiment experiments exploiting fiszman free french from gateway geissb genetic health help hierarchical hler hofmann hole hristovski html http humphrey hypernymic indexer indexing indman inform initiative intel interaction internal interpreting investigation james journal kilicoglu knowledge langlais language lapalme learning libbus library linguistic lnai loranger machine machines manage mapping medical medicine medinfo medline mesh mork national natural nelson networks neural online preliminary proc process processing productivity propositions quality references relation report resources retrieval rindflesch rindflesh rogers rogozan ruch ruiz semantic semantics semgen semrep sigir srinivasan structure suggested support symp synonymy systems technol term terms text thesaural translation translator transtype umls using vector visited vocabularies wilbur with http://psb.stanford.edu/psb-online/proceedings/psb07/fu.pdf 39 Pacific Symposium on Biocomputing 12:421-432(2007) academy acknowledge addona aebersold also anal andrew annual appel bafna basic bern biocomputing bioengineering bioinfo bioinformatics biol biology biotechnol breci carlson cellular chait chem chen china chinese clauser colinge comments commun comp comput computational conference cong cottrell creasy dancik dessingy discussions doherty dongbo early edwards electrophoresis elias fenyo frank frey from gibbons giron goldberg goodlett grant gras gratefully gygi haddad havilio helpful hendrie hernandez ieee institute international jingfen johnson keller king kirby kolker lajoie liang licklider ling magnin mann many marcotte mass masselot mayya mccormack molecular national nature nesvizhskii ninth omics others pacific paper pappin peng perkins pevzner prince prof program proteome proteomics purvine quanhu rapid references research rezaul roth runsheng sadygov saraf schwikowski sciences sheng smilansky smith spectrom stolyar supported symposium systems tabb taylor technologies thank this thoreen valuable vath version wang wilm work wysocki yang yates zeng zhang zhou http://psb.stanford.edu/psb-online/proceedings/psb07/sridhar.pdf 8 Pacific Symposium on Biocomputing 12:88-99(2007) acids active advancing algorithm analysis anatomy annual arita based biocomputing bioinformatics biology blau bowden broder caldwell capabilities catechol chanda cise classical cochrane coli comparators complexity complexus complications computational computers connectivity cornish current damage data database davidov deane decomposition department discovering discovery disease drews drug druggable duke encyclopedia entire enzyme enzymes escherichia essentiality european evolution example expression facilitate falciparum febs florida foundation free from fulfilling function functional gene genes genetic genome genomes genomic global goto graph hatzimanikatis historical hitting hofmeyr identification imielinski imoto important induced information inhibition inhibitors international into investigating jeong journal kahveci kanehisa kegg kyoto lemke letters levodopa living medical medicine metabolic metabolism metabolite methyltransferase millennium mining modeling modules molecule mombach multi mycoplasma nature network networks neurochemistry news nucleic online opinion opmet optimal organisms organizing pacific parkinson pathways pediatrics perspective pharmacology phenylketonuria plasmodium pleiotropic pnas postgenomic prediction proceedings production profiles promise protein proteome ranka rare reaction redundancy references regulation report research reverse review reviews role scale science september sequencing similarities size small smith sniegoski somogyi sridhar stoichiometric strategy structural structure studies surtees symposium systematic systems takenaka target targets technical teichmann theoretical through today toxicology trim uncompetitive understanding university venter versus wide world zero http://psb.stanford.edu/psb-online/proceedings/psb07/liu_l.pdf 45 Pacific Symposium on Biocomputing 12:484-495(2007) acad acids acknowledge acknowledgements acknowledges addition additive among analysis andrew annu aparicio applications approximation archive arndt ashworth austin bader baker bansal base bell benos berger berman biggin billeter biochem biocomputing bioessays bioinformatics biol biomol biomolecular biophys biopolymers bonvin both brandl brenner brooks bruccoleri bulyk burley calculations camb career case ceedings center chandonia charmm cheatham chem chen church community comput computational computer copies copy correlation crooks curr darden defg department developing dickerson duarte edes efficiency ellenb embo endres energy erger error escom estimation experimental fields fink flanagan foundation free fricke from funding furthermore geffers genet genome gerstein gohlke gold goutte grant gunsteren guntert hall hannett harrison harvey havranek hehl heinemann helps honig http improve jennings johnson jona kanin karplus keller king kollman konig kono krull lafontaine lavery leiden liebich ling luginbuhl luscomb matys mcknight merz method methods michael model molecular monnat more morozov mrac mukherjee multi multiple muzzey natl nature ncrr neidle nucleic ohnhauser olafson oliphant olson onufriev opin otting pacific paillard pairs patikoglou phys pittsburgh prentice primer principles proc proteins provides pruss quantify references replacement reviews richmond sarai sauer schacherer schneider schreib schulthess schwab science script selective sengupta september shakked siggers siggia sigler silkov simmerling simon simulation size sklenar snyder starter states stephens stoddard stormo struct structure structures struhl such sunnerhagen supercomputer sussman suzuki swaminathan symposium systems testing theoretical these thiele thornton time trends trim tuerk tung ubbthreads urbach venable vershon vinson volkert wang water weiner westhof which whitaker wilkinson wilson wingender wingreen wolb woods wspc wuthrich wyrick young zeitlinger http://psb.stanford.edu/psb-online/proceedings/psb07/pulim.pdf 6 Pacific Symposium on Biocomputing 12:64-75(2007) about accessibility acid acids acta adamczak advice algorithm alignment aloy amino assessing assessment atomic ball bank berger berman biocomput bioinform bioinformatics biol biophys biopolymers bonded bossen caffrey canutescu capri cell chain chem classification combining complex comput conservation conserved contain correlated correlation crystal crystallogr cytokines data database death degrado describing development dictionary dunbrack effective environment evaluation evol evolution experiment factor family features flexible fold forest from geometrical godzik graph graphs henikoff human hydrogen hymowitz immunol improving information integrating interaction interactions interfaces interferon interferons interprets investigation janin joining joseph kabsch klein kohlbacher krause lenhof levitt like linear matrices meller members method more mouse multiple murzin mutations necrosis neighbor nucleic olmea optimal order partial partners pattern pazos performance pestka phylogenetic porollo potential potentials predicting prediction predictions programming protein proteinprotein proteins przybylski random rapid raptor receptor receptors recognition reconstructing references rest rost russell saitou sander scop secondary seetharaman sequence sequences shelenkov side similarity singh skolnick solvent sources statistical struct structural structure structureinto structures substitution summa surface symp tertiary than their theory threading through trail trees triggering tumor unified using valencia walter with zhang http://psb.stanford.edu/psb-online/proceedings/psb07/kelly.pdf 5 Pacific Symposium on Biocomputing 12:51-63(2007) author chang complex content corresponding full http libusha lipopolysaccharide msba references reyes salilab science sciencemag structure transporter vanadate with http://psb.stanford.edu/psb-online/proceedings/psb07/ng.pdf 35 Pacific Symposium on Biocomputing 12:379-390(2007) about accommodate accommodates acids across acting adaptations added additional advantage after algorithm algorithms allow amazon analysis ancient andre animals annual aoki application applied approach araki armour artificial assessing association available avoids awad ball bard barkai barrett bennett bergmann binding biocomputing bioinformatics biological biology botstein boussard breese broaden brown case ceedings cell chakraburtty chemical cluegene clues cluster clustering clusters code coexpressed coexpression coffey coherent collaborative collected compendium complementary comprehensive computer computing conference conservation conserved consortium correspond could cycle cygd data database dataset datasets defined demeter dense designed developing developments different discovery diverged diversity dujon each edgar either elegans empirical enables entire envision evolutionary evolved example experimental explicit expres expression extend extending facilitate factors fashion filtering finding finetuning focused formats fourteenth friedlander friend from fujibuchi function functional gachotte gaillardin garcia gene generalized generalizing generecommender genes genet genetic genetics genome genomic genomics global gollub goto guldener hattori have having hebert heckerman helden hernandez hirakawa horak huang hughes humans identified identifies identify identifying ieee ihmels indicates information intel internet into issue item itoh iyer jones july kadie kanehisa kaps kastenmuller katayama kawashima kegg kidd king kinoshita known koller large larger lash ledoux lemer lieb ligence linden load mach made make mammals maps martinez marton massive matese members memory method mewes meyer mice michael microarray millions mining modular modules montigny more munsterkotter nature ncbi network networks newly ngau nitzberg node normalize nucleic number online ontology organisms organization ortin other over owen pacific participants pathway pathways pattern patterns perez performance performed period phylogenetic platforms possibly predicted predictive present primary problem proceedings processes profiles program prohibitively promoter protein provide range rather recent recommendations recommended recommender recruited references regulation regulatory relates research result revealed revealing richelles roberts rudnev sarig scafe science score search searched searches segal september sequence sequences several sherlock shoemaker simon sion sites size slade slow slower smith snyder sometime souciet source species specific speed stanford stepaniants stoughton strack stuart study subgraphs such suggests suppl suzek symposium talla than that these this tool tools trans transcription transcriptional tree trim troup types uncertainty undergone unification updated uses using variety villenvue website well when where which wide wilhite will with wodak would wymore yeast york zachariah zhou http://psb.stanford.edu/psb-online/proceedings/psb07/knox.pdf 14 Pacific Symposium on Biocomputing 12:145-156(2007) abola abstracts accuracy accurate acids acta advanced alignment altman altschul amberger analysis angelis annotated annotation application approach apweiler atlas atomic atoms automated automatic bacmap bacterial bairoch bank banks barker barrett base basys batalov bateman beard benson biocomputing bioinformatics biol biological biology biomedical biotechniques biotechnology blast bocchini boeckmann bonds bordoli boyko brooksbank bryant bryson bucher builders cameron canese casp caspi castro center chalifa chanda chem chemical chen church coin compendium complete comprehensive comput concept consumer coordinates cruz cryst data database deciphering dicuccio dimensional discovery disorders docking dohr domselaar dong drug drugbank durbin easton eddy edgar ellison encoding enrichment european evaluation experiences expert exploration expression factors families federhen ferro finn flexible flexx four friesner from frye functional gallin gapped gasteiger gattiker gene genecards generation genes genetic genevaux genome genomes genomic genomics glide goto greiner griffiths grote habibi halgren hamosh hassanali hatfield hattori health heijne helmberg hewett hidden hines hoffmann hollich hrabe huang hulo human hunter identify identifying ihop implementing improvements improving information inheritance institute interactive internet introduction issue jiang jones kanehisa kawashima keeffe kegg kenton khanna khovayko klein knowledge knowledgebase knox kramer krogh labaer lancet langendijk larsson lengauer ligands lipman literature litminer lopez macromolecules madden maglott magrane maier manning markoff markov marshall mcguffin mckusick medminer mendelian miller mining model montgomerie monzavi moxon murphy national navigation nazhad neill novel nucleic okuno oliver omim online opin orth ostell pacific perrone pfam pharm pharmacogenetics pharmgkb picture players pollard pontius predicting prediction prilusky problem profiling programs promise prosite protein proteins proteome proteomic provided pruitt psipred publication quality quantitative query ranjan rapid rarey rebhan recent references reformulation regulation related resource resources richardson ritter rivera rouani rubin rules sadowski saux schaffer scherf schneider schriml schuler schuur scoring scott screening search secondary selzer sequeira server sherry shrivastava sigrist silico sirotkin sites smiles smith sonnhammer space starchenko steinhauer stothard structural structure stuart studholme sundararaj suppl support sussman suzek sykes symposium syst systems szafron tanabe target targets tatusov tatusova text ther therapeutic thornton three tool topology towards transmembrane uniprot universal using vadar valencia wagner weininger weinstein weng werner wheeler wikigene willard wishart with woolsey yaschenko yeats zhang http://psb.stanford.edu/psb-online/proceedings/psb07/rhodes.pdf 28 Pacific Symposium on Biocomputing 12:304-315(2007) algorithm annual approach approximate apps automatic babel barnard base based benefits biocomputing biotechnology brand branddrugs brecher cambridge center chemical cheminformatics christoph commun computer computing conference ctfile curse dalby data dayhtml daylight description design developed dimensionality discovery downloads downs drugs elsevier encoding faqs feature file finger fingerprints flower formats generation grier group gunshurst heller helma hounshell html http humana identifier inchi inchifaq includes indexing indyk information international introduction isis iupac journal know knowledgebase kramer language laufer ledge leland limited mdli measures methodology mining model molecular motwani murray name national ncbi nearest neighbors nimes nomenclature notation nourse open openbabel pacific pages practical prescribed prescription proceedings programs properties pubchem public raedt reallife references removing representation research rhodes rules rust salton science search searching september services seventh several sigkdd similarity size smiles sorry sourceforge space standard state stefan stein string struct structure support symposium system systems tchekhovskoi theory towards trim unique university unofficial used vector weininger willett wong wwmm yang http://psb.stanford.edu/psb-online/proceedings/psb07/intro-proteomics.pdf 37 Pacific Symposium on Biocomputing 12:403-408(2007) addona aebersold american anal analytical anderson auberry bader bartlet baxter bioinformatics biol biological biotechnol bleasby butland camp cannon cell chait chem chemistry clauser comput computing contract dancik development directed electrophoresis environmental fenyo fields frank funds giot hansen heredia jacobs jarman jeffery jones journal kangas keller kolker laboratory langner mann mass mccormack moore mottaz nature nesvizhskii noble oehmen office pappin patterson payan petritis pevzner pnnl proteome proteomics rahman references research robertson schieltz science scientific shen smith society song spectrom spectrometry strittmatter under vath webb well wilm yates young http://psb.stanford.edu/psb-online/proceedings/psb07/alves.pdf 38 Pacific Symposium on Biocomputing 12:409-420(2007) acid aebersold algorithms alves amino anal analyses answer approach arendt arnold aveline baldwin based biochem bioinformatics biological burlingame cambridge carbon carr cell changes chem chen cheung clauser clemmer computational cormen correlate cottrell creasy curr data database databases dbparser detectability dezube does dondeti dongre edit electrophoresis emili epstein expression free friedrichs function geer global goehle going group guidelines hefta human identification identify identifying improving inference integrating interpretation introduction jonscher keller kislinger knight kolker kowalak label leiserson mann markey mass maynard mccormack mcdonald mean mendoza method meyer mixtures model modified nature need nesvizhskii novotny omics opin opiteck pappin peptide peptides perkins picone pierce predicted press probabilitybased problem profiling protein proteins proteome proteomic proteomics publication purvine quantification questions radivojac rappsilber references reilly reproducibility resing rivest russell schieltz searching sensitivity sequence sequences shotgun software source spectra spectrometry standard statistical stein studies tandem tang technologies ther toward trends using wattawa what wolf working yang yates yeast http://psb.stanford.edu/psb-online/proceedings/psb07/cakmak.pdf 21 Pacific Symposium on Biocomputing 12:221-232(2007) aaai abner accuracy acids acknowledgments addison agichtein among analysis annotation answering assessment assigning associating automatic automatically available award biocreative bioinformatics biological biomedical blaschke brin cakmak cambridge case categories characterizing charles classification codeproject codes coling collections compositional concept concepts consortium construct data database determining different disambiguation electronic embo entities entity entrez entropy equipment etzioni eukaryotic evaluation experimentally exploring extended extracting extraction factor fcgi fellbaum fine fleischman foundation from functions future geannextended gene generating genes genome grained grant gravano holland homology hovy http iaai imataka informatics information initiation izumitani kamber kaufmann knowitall koike krallinger large learning leon lexical library literature lovasz mann matching maximum measures methods microsoft mining morgan named names nashua ncbi niwa north noun nucleic ogren olsen ontologies ontology open other paper parameters part pathcase pathways patterns plain press processing proper protein proteins pubmed query question raychaudhuri references regulator relations research resource riloff salton scale scoring semanet semantic semanticsimilaritywordnet settles share similarity snowball sonenberg source specific structure supervised supported synonym tagging takagi task tasks techniques techreports terms text textbased textual that theory this tool translation translational untagged useritems using valencia version wang webdb weight wesley wide with wordnet world yeast york http://psb.stanford.edu/psb-online/proceedings/psb07/hampikian.pdf 33 Pacific Symposium on Biocomputing 12:355-366(2007) acad acid acids against algorithmic amino analysis applied approach approximate assisted availability based between bioinformatics biol biology center charge chem chen code codon common comput computation computational consortium continuous denaturation determined discrete distance distances distribution doerks efficient electron exact exons expected fast field fondufe friedman general generated genes genomes genomic gotoh guanine hampikian heller henderson herpesvirus hill hopping houston human ienaka inman intersite intron introns jones journal july keck learning leung like long machine marsh mcgraw mechanism microscopy missing mitchell mittendorf models molecule moore motif natl nature nicod nicodeme nucleic nucleosome number occurrences otaki over oxidation pattern phage phonon phys polaron poly positioning possible preferences probability proc protection protein proteins proteome proximal rahmann random reis riddle rivals savva schuster science segal selection sequences short solving speed statistics stefanov strings structural test texas texts thastrom time translational transport underrepresentation uniform usage vingron wang wernisch widom words yamamoto york http://psb.stanford.edu/psb-online/proceedings/psb07/chang_d.pdf 11 Pacific Symposium on Biocomputing 12:115-126(2007) aberdam anal analysis analyst antti applications baker balcerowska biomed carlson charuel chem chemistry chemometrics clayton clinical cloarec colquhoun concepts data defernez epstein everett fuciarelli greenshaw greiner halouska hanton harbo holmes intell jarman lefebvre lindon lowry magn magnetic mcgrath mckay megavariate meng mercier multi nature neurosci newton nicholson pharm phytochemistry pounds powers press principles provost querengesser references reson resonance robertson silverstone siuda slupsky systems umetrics walley webb weljie wishart http://psb.stanford.edu/psb-online/proceedings/psb07/cook.pdf 2 Pacific Symposium on Biocomputing 12:16-27(2007) acad acetyltransferase acids active alpha altering alzheimer amyloid analysis analyzing anatomy apoptosis appl archiving aspartic babu babur bace baek basis bennett berezovska beta betaamyloid between biochemical biocomputing biocyc bioeng bioinformatics biol biological biology biomedical biomolecular biopax biotechnol birney bono busse buxbaum carboxyl cell cellml cells cellular chem cleavage coactivator collaborative collection complex complexes constitutes construction converting cook corepressor correction corresponding cytoplasmic cytoscape databases davis demir density dependent deposits describing diagrams disease dogrusoz domain eanes embo enhance environment enzyme evaluation evidence exchange expansion expression factor farley finney foundational from fuchs funahashi functional functions gamma gene generate generated genes genome genomes gerber glenner gopinath graphical gress haploinsufficiency hardy histone http hucka hyman hypothesis implications induces informatics integrated interaction involved jaeger jassal joshi journal kang kappab karp khan kinoshita kitano knowledge knowledgebase kochlacs lambrix language level lewis link links lipoprotein magazine markiel markup matsuoka matthews medinfo medium mejino merriam model modeling models molecular moore multi multiple national natl nature necrosis network networks neuron neurosci nicastrin notch nuclear nucleic ohgi ontologies ontology open ouzounis ozier pacific pathogenesis pathol pathway pathways physiol physiological pietrzik precursor presenilin problems proc process processing production pros protease protein proteins quaranta reactome receptor reference references regulated regulates related representation representations research resource road rose rosse sastre sauro sbml scale schmidt science secretase selkoe sequences shannon shrobe signaling simulation site software sourceforge spring stein steiner steps stochastic stromback strooper sudhof symbolic symposium systems szolovitz tapscott template terminal that their therapeutics therapy tope transcriptionally transcriptively transmembrane tumor using ustachio vassar vastrik visual washington what whelan with without wong yoon http://psb.stanford.edu/psb-online/proceedings/psb07/intro-biodiversity.pdf 31 Pacific Symposium on Biocomputing 12:340-342(2007) abbott across activities adriatic advancements against ager agosti alternat amphibian ancient andersen animal annotated annotation annotations antibiotics application applying approach assist association astolfi atkinson automated automatically avian azevedo baker based basso batel beaty been before behavioral benefit biochem biocomputing biodiversity biol biological biomedical bioscience bisby blackmore both bravo cadag calisher calixto castle cell chemical coccinea communities complement complemented consequences conservation consider considerable context could croatia cruz current data defined delivery demonstrate describe development diagnosis discussion disease diseases diversification dunnum dusek ecological ecology economist embedded emergent encyclopedia entities environment evid evolution evolutionary examine excluding existence existing experimentally experiments exploitation fallon federated fett filho final finally first follow framework from garnham gene generated genes global greater hampikian hantavirus hawaii heterogeneous historical history hits hitting hoped host iiwi incorporate infected informatics information infrastructural inst integrate integrated internet interpreted invertebrates involved knowledge ksiazek laboratory legacy life light literature lizard lizards local lond maglia makler malaria mammals managing mcneil media mediated methodological methods microbial mills models modern molecular mons moreira morphological morphology morrison muller naming natural nature need needed neto newly next nichol ontologies ontology organisms organize oswaldo pacific palma palmer papers parasite parasites parasitol parasitology parmenter part parts pathogenicity pathways pelaez peters peterson pharmacol philos physiological plasmodium popular practical predominant present primary proc products progress propose prospecting prototype pulmonary quiet range reach recent references regards regions registry relevant relictum repeat research resources review revolution ricklefs rovinj salazar sampling santos sautter schall schroder science scientific semi sequence sequencederived session shake significant sileo silva sinden soares soberon source spark species sponges status structures suggest suppl sustainable switching symposium syndrome synergistic system targets taxonomic taxonomists taxonomy techniques temporal that their then there these this three times today tools towards traditional trans treatment tree trends trop tuberculosis types umminger unconventional update uses utility vande vestiaria virulence vitro vivo which wildlife will wilson with within woods yates york young zool http://psb.stanford.edu/psb-online/proceedings/psb07/karakoc.pdf 13 Pacific Symposium on Biocomputing 12:133-144(2007) aguo aided analyticon antibiotics aptula assinex banglore based biocomputing bioinformatics bleda byname cambridge cambridgesoft canada castro cenk chem chemical chemidplus cherkasov collection comp company comput computing conference cplex cronin curr data database dearden design diaz discovery distance drug duffy edition engineering environment fallahi garcia garciamarch gimenez gold group halgren hammond high hmdb html http human icde ieee ilog index indexing india jaen jankovic journal karakoc macker march mathematical merck metabolome model molec molecular molecules montreal moscow murcia nadb netzeva oltra operational ozsoyoglu pacific pareja patel perez performance pharmacy press products programming proximity redpoll references rowe sahinalp salabert salabertsalvador salvador schultz schuurmann search sequence software soler struct symposium tasan theochem tomas ualberta vert villanueva voutzoulidis worth http://psb.stanford.edu/psb-online/proceedings/psb07/morgan.pdf 26 Pacific Symposium on Biocomputing 12:281-291(2007) about acids aclismb after agreement along ambiguity amia anaphoric annotations annu anonymized aronson articles assessment association automated automatic automatically available azure based biocomput biocomputing biocreative bioinform bioinformatics biological biology biomed biomedical bionlp biopython blaschke bootstrapping cohen colosimo comput computational concept conf conjunction contrast criteria data database databases dataset described detroit development dictionaries disambiguation domain drosophila effect elucidated entities entity evaluating evaluation expanding extracted fall fang game gene geneontology genes genew gold hanisch have hirschman homepage http human identification identifiers identifying ieee improving inform information interannotator investigate issue knowledge language learning lexical linguistics linking lists literature made mapping matching mention mentioned methods mining model morgan motivation naacl name named names natural ncbi nomenclature nomenclatures normalization normalized nucleic ontologies ontology organism overview pacific part participants playing podowski preparation proc proceedings processing properties protein proteins publicly quality recognition references resource retrieval scalable scheduled scientific second semantics site some source sourceforge spring standard submissions suggestions summary supervised suppl symp symposium synonym syst system task tentatively term text textual this tsai tuason uniprot unique universal universe updates used using variability variation various vlachos wain weakly website wellner which will with workshop york http://psb.stanford.edu/psb-online/proceedings/psb07/leung.pdf 44 Pacific Symposium on Biocomputing 12:472-483(2007) acad acids altschul american annu appear applications article association atchley bailey bibe biochem biocomputing bioinformatics biology biomol boguski carlstedt chin cleic computer dudoit eisen elkan endocrinol eskin fitch fraenkel function genetics gifford gordan gordon gustafsson hartemink ismb jbcb jiang journal karp keles lann lawrence leung maclsaac molecular mulder narlikar nati natl nekludova neuwald odom ohler pabo pacific pevzner proc proteins recomb references reilly rosenfeld sandelin sauer schreiber science sciences sinha smith statistical struct structure supp symposium system tompa tsang wabi wang wasserman wolfe wootton wright xing young zilliacus http://psb.stanford.edu/psb-online/proceedings/psb07/valdivia-granda.pdf 9 Pacific Symposium on Biocomputing 12:100-111(2007) acad academic acids acknowledgments also andres anuradha approach arun ascher assessment associated atzler azuaje baiker bala bartlett bateman bavari beaudry benson berche berger biocomputing bioinform bioinformatics biol biological blaschke bockler bork boutell breakefield brief brown buller burnett carlisle cell challenge chandrika chatterjee classifying clustering complete comput cortes countermeasures cuenin data deepthi desai deshpande development diagnostics diaz discov disease domains dong dopazo draghici drug durbin eddy efficacy eitzen engl everett explorations exposure expression finn fossum futschik gandhi geisbert gene genes genet granda griffiths gritz gupta haas hanumanthu harsha hauer have health henchal henderson hensley herceg hoffmann hollich host hsiao huggins ideker ilyinskii implications important independent inglesby institutes integrating intramural jackson jacob jahrling jama jensen jones jose kannabiran karathia karsch khanna khatri kluwer kotala krallinger krishnakanth kumar kumaran kuroda lassmann layton leduc letvin lifton like lipman loizou mack mahesh manson marshall martinez mathew mazzara mcdade menon microarray microbiol mishra mistry mizrachi mohan mosk moxon murr nagini national natl nayak neuroscience nucleic oehmig olefsky ostell osterholm owen pacific palumbo palvankar pandey panicali parker perera perl perrizo perry pfam philippon pointed possibility prasad 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