http://www.informatik.uni-trier.de/~ley/db/conf/psb/psb2006.html
PSB 2006
http://psb.stanford.edu/psb-online/proceedings/psb06/zhang_x.pdf	31	A New Approach for Alignment of Multiple Proteins Xu Zhang and Tamer Kahveci Pacific Symposium on Biocomputing 11:339-350(2006)	academy accuracy accurate acid acids across advances algorithm algorithms align alignment alignments aligns altschul america amino analysis ancestral annealing annual applicable applied approach assessed based batzoglou berger bioinformatics biology bonnie bradley brudno bryant ceedings chen choice clustal clustalderived coffee comparison complexity comprehensive computation computational computer conference congress consistency correct current deterministic dialign discovery divergent diverse doolittle dress eddy edgar efficiency efficient evolution evolutionary fast feng finding fogel forany formulation fourier frech gary general genetic gibrat gibson given gotoh graphs grasso gupta hein heringa hidden higgins high highly homologous huang ieee improvement improving intel international ismb iterative janies jiang journal katoh kececioglu krink kuma lasters ligent linear lipman local luonan madej mafft markov mathematics matrix method miller misawa miyata models molecular morgenstern multiple muscle national needleman notredame novel nucleic number opinion order page pages pairs partial paths patterns penalties peter phil phillips phylogenetic phylogenetics phylogeny plewniak pnas poch polynomial position practical prediction prerequisite probabilistic probcons proceedings programs progressive protein proteins rapid recomb reconstructs reference references refinement rene research saga schaffer sciences search secondary sensitivity september sequence sequences sharlow shortest significant similarities similarity simossis simultaneously size society solvable space specific states structural structure surprising systems that thiemo thompson thomsen through throughput time tool transform trees trilogy trim united using volume walle wang weight weighting werner wheeler when with wunsch wyns yang
http://psb.stanford.edu/psb-online/proceedings/psb06/chu.pdf	22	Pacific Symposium on Biocomputing 11:231-242(2006)	acad acids across also alvarez amongst analysis analyzing applications applied architecture article artifacts assignment assignments assumptions automated avoided bader bait barabasi bars better beyer binding biocomputing bioinformatics biological biology biotechnol bork bosche buffet bushnell butland cagney cannot casein cerevisiae characterization chiba coli college comparisons complexes composition comprehensive confirmation consensus conserved containing contaminants core cramer cristianini current data database definition determined dezso different diffusion discrete entropy escherichia essential exosome experimental experimentally experts explore fashion feature figure finding frishman from functional further gavin gcnu genetics genome genomes gentleman ghahramani giot graphs griffiths gruhler guldener hattori heilbut here heuristic high hogue hollunder hybrid icml identification identified identify identifying implications improvement improvements independent indian indicate individual inferred infinite interaction interactions interactome interpretation into introduce kernel kernels kinase kondor krause krogan kumar lafferty large latent learning left little london macromolecular making mass maximizing mechnism membership mering method methods mewes mining mips mirny models modules molecular more most mrna must natl nature necessary network networks noble noted nucleic obtained obviously oltvai organization other over ozawa pacific pattern peng peregrin performed polymerase predicting previous probability proc proceedings process processing processome protein proteinprotein proteins proteome proteomics reference references relies report ribosomal right rnap saccharomyces sakaki sampled scale scholtens science screens sense september sequences sets shawe should similar size snrnp snyder some sources sparse specific spectrometry spirin standardized statistical structures subcomplexes such suppl symposium systematic take taylor technical that there these throughput transcription trim tsuda uetz university used utpa well when whole wilhelm with without works would yeast yoshida
http://psb.stanford.edu/psb-online/proceedings/psb06/kushida.pdf	15	Event Ontology: A Pathway-Centric Ontology for Biological Processes Tatsuya Kushida, Toshihisa Takagi, and Ken Ichiro Fukuda Pacific Symposium on Biocomputing 11:152-163(2006)	acids acknowledgments agency amin antezana arnaud asanuma atalay ayaz babur baliga bind biocarta bioinformatics biology biopax bird birney bitterman bono cabo cetin ceusters clark cohen comparative conklin consortium couche dahlquist database demir deville dogrusoz edit eustachio fays fukuda functional gene geneontology genet genome genomics gillespie gopinath gorospe goto gulesir gursoy hekking howitz http ideker immunology inoh intact janky japan jassal joshi kanehisa karp kessler klagges kohler krieger kumar lawlor lemer lewis lomax markiel matthews miller mueller mungall nature neuhaus niiro nisanci nucleic ontology ozier paley pick projects ramage rector references research reviews richelle rosse salomonis santolaria schmidt schwikowski science shannon shtml sinclair slims smith sourceforge stein supported takagi technology this tope ucla vastrik vranizan wall wang website wodak work yamamoto zhang
http://psb.stanford.edu/psb-online/proceedings/psb06/debakker.pdf	44	Transferability of Tag SNPs to Capture Common Genetic Variation in DNA Repair Genes Across Multiple Populations Paul I.W. De Bakker, Robert R. Graham, David Altshuler, Brian E. Henderson, and Christopher A. Haiman Pacific Symposium on Biocomputing 11:478-486(2006)	acknowledge acknowledgments actual address addressed ahmadi also altman altmuller among amount analyses analysis analytical angeles another assistance association bakker barrett based baseline berg between bioinformatics biol blocks calibration cancer carlson casagrande channel characteristics chinese choosing cohort common comparative complex components considered consortium contribution data david designed detect development diploid disease diseases disequilibrium drug efficiency elsewhere epidemiol estimation european evaluation evol example excoffier find finding food frasco frequencies frequency from gene genes genet genetic genome genomewide genotype genotyping hankin haplotype haplotypes haploview hapmap hard have hawaii health hered high hinds human identification implications informative international intertwined issues john johnson juan kolonel laboratory laurence like likelihood linkage linkagedisequilibrium lohmueller mapping maps marchand markers maximally maximum melissa meng meta metabolism mimi molecular mueller multiethnic nature nejentsev neuronal nucleotide nutr particular patterns perform polymorphism polymorphisms population populations power preliminary press principal pritchard project providing quantitative questionnaire receptor references reich required resolution ronald ross sample samples scans science selecting selection sheng should singapore single singlenucleotide slatkin snps sodium statistical stram strategy studies study subjects support supports susceptibility tagging tagsnp technical thank these they this three tradeoff transferability transport true under unit unphased unrelated using variants variation visualization vitamin weale well were which whole with would yuan
http://psb.stanford.edu/psb-online/proceedings/psb06/motsinger.pdf	54	Risk Factor Interactions and Genetic Effects Associated with Post-Operative Atrial Fibrillation Alison A. Motsinger, Brian S. Donahue, Nancy J. Brown, Dan M. Roden, and Marylyn D. Ritchie Pacific Symposium on Biocomputing 11:584-595(2006)	adaptive after allelic almassi american among amyloid analysis analytical angiotensin apolipoprotein application applied aranki arrhythmias arterioscler artery associated association associations atrial auricular available aviles based basel bastone bellman between biochem bioinformatics biol biophys breast brown brugada bypass cancer card cardiac cardiol cardiology cardiomyopathy cardiothoracic cardiovasc cardiovascular care chen chinese chromosome chung circulation clin clinical coding coffey coll collaboration college combinatorial committee common commun comparison complexity complication computational conditional conferences contribute control converting coronary creswell crit crystal current darbar data death deletion detecting determining develop developed diabetes diabetologia diagn didomenico dimensionality discovery discrete discrimination disease diseases disorder donahue drug ecological eichner electrophysiol electrophysiology elements elevation ellinor endpoints engl england environment enzyme epidemiol epistasis error estrogen european event evidence executive expert factor factors familial familiar family fibrillation force frequencies friedman from function fuster gain gaudino gene genegene genes genet genetic genetically genetics genome genotypephenotype genotypes genotyping genoype george grafting guidelines hahn hastie hazards heart hered heterogeneity heterogeneous high hosmer hospital hravnak huge human hypertens hypertension hypertensive ideal identification identifies identifying impact importance index infarction inflammation inflammatory influences insertion insights interaction interactions interleukin intern interventions invest ischaemic isolated jama john journal kcne kcnq lack learning left lemeshow levels linkage locus logistic lone macleod maisel major management maps massad mathew mechanisms medicine mellitus metabolism methods missing model modifier moore morbid morbidity mortality multicenter multifactor multilocus multiple murphy mutation myocardial nature neonatal north novel oberti offspring ommen open operative order pacing parental patients persistence perticone pharmacogenetics pharmacogenomics pharmacol pharmacologic phenocopy policy polymorphism polymorphisms polyneuropathy population portuguese post postoperative power practice predictors presence press prevention princeton processes prophylactic prospective protein randomized rates reactive reduction references regression reif relative remodeling renin report resources retooling reveals review reviews risk ritchie roden rotterdam sayed scan science scottish series shows silico sing single soares society software sons sporadic springer statistical statistics stengard strategies stroke study sudden summary suppl surg surgery susceptibility system tabatabaei task that ther thorac thornton thromb tibshirani transthyretin trends trial tsai type ubiquitous underlies university update using validation variable variations vasc ventricular verlag wang wells wide wiley wilke williams with wolff yamashita yang york
http://psb.stanford.edu/psb-online/proceedings/psb06/imoto.pdf	52	Computational Strategy for Discovering Druggable Gene Networks from Genome-Wide RNA Expression Profiles Seiya Imoto, Yoshinori Tamada, Hiromitsu Araki, Kaori Yasuda, Cristin G. Print, Stephen D. Charnock-Jones, Deborah Sanders, Christopher J. Savoie, Kousuke Tashiro, Satoru Kuhara, and Satoru Miyano Pacific Symposium on Biocomputing 11:559-571(2006)	acids acknowledge acknowledgements acta activate activated affara akutsu analysis another array arterioscler assistance basso bernard bernardo between biochem biochim biocomput bioinform biol biological biophys biosystems cabrero carbohydrate cell cells center chen common commun comp computation computer control culture curr details discussed down drug dunmore encode endothelial evidences expressed factors faseb fatty fibrates friedman further gene genes genet genome glucose goya hartemink hayashida heckerman heterodimerize human humphries imoto inflamm inflammatory informatics institute islam kersten learning lergy ligand ligands machine many marton medical metabolism muna naturally occurring once other paper parent pharmacogenomics pharmacol ppar ppars proteins provided receptor references regulate relation responses retinoid sally savoie science several shipley someren such super symp synthetic system tamada target targets that their these they thromb time tokyo tomiyasu transcription types university vasc waxman will wish with yuki
http://psb.stanford.edu/psb-online/proceedings/psb06/intro-proteomics.pdf	20	Computational Proteomics: Session Introduction Bobbie-Jo Webb-Robertson, William Cannon, Joshua Adkins, and Deborah Gracio Pacific Symposium on Biocomputing 11:212-218(2006)	academic acknowledgments also anal anderson anonymous authors bader bartels biemann bioinformatics biol biomed biotech biotechnol butland cannon cell chem comm comput dancik deep diego enzymology excellent express fenn gavin genome giot gratitude gygi handful heredia hours input johnson langner like link make mann mass mccloskey mccormack meng methods nature only organizers papers pasa pevner presented press proteome proteomics provide rapid referees references regret release ross science september session spectrom submissions successful taylor thank that this together tolic uncountable volunteered would yates
http://psb.stanford.edu/psb-online/proceedings/psb06/lin.pdf	53	A Bivariate Functional Mapping Model for Identifying Haplotypes that Control Drug Response for Systolic and Diastolic Blood Pressures Min Lin, Rongling Wu, and Julie Johnson Pacific Symposium on Biocomputing 11:572-583(2006)	adapt also among approach aquilante article based biologically biometrics botstein cancer candidate casella churchill composed computer consortium contribute curves designing detect detected diggle dobutamine doerge dosages drugs effect effects endrenyi engl evans exert exist explanation from gene genetic genetics giraldo gong guidance haplotype haplotypebased haplotypes hapmap have heagerty heart hypertension impact indicates indicator individual individualized inotropic inter international invest jects johnson kalow lander liang magnitudes makeup mcleod mead medication nabel nature nelder oxford patient patients pharmaceutical pharmacogenetic pharmacogenetics pharmacogenomics pharmacolog pleiotropic possible press previous profiles provide rate references regulate relling respectively response resulting results risk scientific significant sinauer study such suggest sunderland tang terra that there therefore this trends university used variability variants variation wang weir whether within zeger zhao
http://psb.stanford.edu/psb-online/proceedings/psb06/arnold.pdf	21	Pacific Symposium on Biocomputing 11:219-230(2006)	acad acids acknowledgements adjusting aebersold ahead also anal analysis anderson angew annotated annu application applications applied apply applying approach approaches apweiler available awarded baczek bairoch balanced barbacci based been bern better between biemann biocomputing bioinformatics biol biomed biomol biophys biotechnol bond both braun breci bucinski cause certainly challenging charged chem choice class classifiers cleavage cociorva commonly compared comput conf consistent control coon correlate cottrell creasy cybenko data dataset datasets decaestecker decision depending derived determination dongre doubly easily eddes effects electronic electrophoresis elias empirical encouraging engl enhance enhanced environ experience extend fact faculty features febs focus fraction fragment fragmentation from full funded future gibbons goldberg good grant gygi hair hand have however hunt hunter identification ieee imbalanced including indiana insight instrument instruments intend intensities internat into investigations ions itself ivanov jones kaliszan kapp kaufmann kelleher king large latinne learn learning lett local long maccoss machine maldi martin mass mateo math mccormack mcdonald mclafferty mcss mechanism method methods minor mobile models modes modifications moore more morgan moritz natl negative networks neural neurobiol noble nucleic observations office only order other outputs overprediction pacific paper pappin partially patterns payan peak peptide peptides performance perkins photodissociation platform positive potential precursors predicting prediction predictor preliminary president previous print priors problem proc programs proline protein proteome proteomics protons provides publication qian quinlan references regarding regression reid reilly related relative representative required research resing resolved restricted result results riedmiller roth rules russell sadygov saerens samples scheme schieltz schroeder schutz schwikowski scoring sejnowski separability shabanowitz showed shown side signals significant simpson since smith somogyi specialized spectra spectrom spectrometry speed stress struct structure structures study subtle such suggest support svms syka symposium syst tabb techniques terminal tests that this thompson through towards trained training trees triply tryptophan tsaprailis understanding university used useful using versus vice well were will with work wysocki yates young zhang zubarev
http://psb.stanford.edu/psb-online/proceedings/psb06/magi.pdf	49	The Whole Genome TagSNP Selection and Transferability Among HapMap Populations Reedik Magi, Lauris Kaplinski, and Maido Remm Pacific Symposium on Biocomputing 11:535-543(2006)	acknowledgments across adequately african ahmadi also among analyses applied association block blocks both calculations carlson ceph chromosomes common cover current data demand demographic describe disease disequilibrium distinct does drug dunning education english enterprise epidemiol estonia estonian european extent findings found four from gabriel genes genet genome genotyped gerst grammar grant halldorsson haplotype hapmap help hered higher histories history however human informative international istrail japanese jody judson katre kruglyak large linkage lower many mapping maps markers maximally memory metabolism ministry mueller nature nigerian novakoski nucleotide number numerous only optimal pair palm pattern patterns percentage pharmacogenomics polymorphism polymorphisms poorly population populations possible project prospects reaper recombination references reflect require required research salisbury same sawyer schneider science selecting selection sets show significant single singlenucleotide snps somewhat speed stephens structure structures studies study substantially supported tagging tagsnp talas than thank thanks that their they this three transferability transport tsnp tsnps ulvi underlying unnecessary using valuable variation vary vega versa vice which whole wide windemuth with work
http://psb.stanford.edu/psb-online/proceedings/psb06/terribilini.pdf	38	Identifying Interaction Sites in "Recalcitrant" Proteins: Predicted Protein and RNA Binding Sites in Rev Proteins of HIV-1 and EIAV Agree with Experimental Data Michael Terribilini, Jae-Hyung Lee, Changhui Yan, Robert L. Jernigan, Susan Carpenter, Vasant Honavar, and Drena Dobbs Pacific Symposium on Biocomputing 11:415-426(2006)	acad accuracy achieved acids acknowledgments allers andersen animal annu another arch assistance available baldi based battiste been belshan berman bhat binding biochem bioinformatics biol biophys both bourne brunak carpenter cell cells center chakrabarti chauvin chem chung clercq cochrane coffin cold comments comparison complicated computational contribute cook could critical cullen curr daly data decrease demonstrates derse design developing different dillon diseases disord dobbs drug dunbrack eiav endocr enhanced even expedite experimental experimentally experiments explore fact feng fisk formula frank frankel fridell from function functional funds further genes genetic genomics gilliland gontarek grant grants green hakata harbor harris hauber have here high honavar hope hughes identify identifying immune implementations implications infectious information integrated interact interest janin java jeffrey jernigan kaufmann known laboratory learning level life little mabuchi machine malim mancuso metabol methods microbiol mining moore morgan muhandiram murphy nair nalin natl needed nielsen nucleic obtain obtained obvious ofran olsen other parslow part partin phillips plainview pollard possible practical precisely predicting prediction predictions presented press proc protein proteins recalcitrant recognize references regulatory research residues resolution retroviruses rosen rost rusche sander science sequence sequences shamoo shida shindyalov shoemaker significant significantly sijun similarity sites species spring stevenson structural structure submitted suggests summers suppl supported targets technical terribilini thank that their therapies they this time tools turner understanding usda useful using usman varmus very virol wang wannemuehler weissig westbrook when which will williamson with witten wrzeszczynski yamada zapp
http://psb.stanford.edu/psb-online/proceedings/psb06/ye.pdf	40	Modeling and Analyzing Three-Dimensional Structures of Human Disease Proteins Yuzhen Ye, Zhanwen Li, and Adam Godzik Pacific Symposium on Biocomputing 11:439-450(2006)	acad acids acknowledgments acta activating additional aflalo alber algorithms aloy alpha also alternative altman altshuler another arakaki ardlie available bairoch ball because become bertin between binding bioinformatics biol blundell bork bottom boussard brown building cagney cargill cavallo chung code complex complexes conover cornell crystallogr cuff curr current daley data database davis dekker determined diekhans diemand disease diseases distribution docking domain domains eisenstein electron emili eswar evaluate example experimentally extend facchiano famiglietti fields figure filling fitting fleming friedberg friedland friesem from functions further gasteiger gattiker genet genetics genome gerstein giot godwin godzik gramm grant graph graphs grzechnik gtpase guidance hainaut harrison haussler help hemolysin henikoff hernandez highlighted honig huge hypothesis important initio interaction interactions involved ireland jaroszewski johnston judson jurisica kalbfleisch kalyanaraman karchin katchalski katzir kelly knight korkin krause lander lane large limited lipshutz lockshon lukasz luscombe mansfield marcel martin mechanism mering method methods microscopy minieka model modeling models mooney moult mutat mutations narayan natl nature necessary nemesh network networks nucleic number oliver olivier only ophid opin optimization ostrander other patil pawlowski pawson peptide pichaud pieper plan play pochart possibility potential potter predict proc process project protein proteins qureshi ramensky ramirez rasgap references related relatively resolution resource resulting richards role rolfe rothberg russell rychlewski sali scale scheib schwarzenbacher science search shariv shaw shown sites sklar skolnick small snel snps srinivasan stick struct structure structures study studying such suggested suggests sunyaev supported tail template thank that this thomas thornton topf transforming trends tyrkc uetz uniform using vakser vidal vijayadamodar wang warrington ways when will with would xiang yang york ziaugra
http://psb.stanford.edu/psb-online/proceedings/psb06/castellana.pdf	42	Pacific Symposium on Biocomputing 11:454-466(2006)	acad adeyemo akey altschuler bafna barret barrett berno bioinform biol biology biotech blelloch blumenstiel calabrese carnegie carr chapman chemistry chen clark clayton comp computational conf consortium coop cordell cordero crowell daly defelice deng dhamdhere doshi dudbrigde eaves encode faggart fodor frazer furey gabriel genet genetics genome genova gough hacker halld hapmap haussler heward higgens hinds hudson hughes ieee international istrail jacob ject jensen johnson kautzer kidd koivisto lander lect lochner marjoribanks mcdonough mellon merck moore nachman natl nature nguyen nordb norris notes nutland osito patil payne payseur proc program rannala rastas ravi references report rioux roskin rotimi rsson schaffner schwartz science seaman sheehan sheffi shen smith sridhar stern stevens stokowski tavar tech thesis thomas tishkoff todd trends trulson tuomilehto twells ueda ukkonen university vyas ward waterman wijsman wolf xiong yang zhang
http://psb.stanford.edu/psb-online/proceedings/psb06/chen_j.pdf	34	Pacific Symposium on Biocomputing 11:367-378(2006)	about accumulated acknowledgments also alvarez alzheimer analysis applying areas baltimore barbato began being bethesda better beyond biochem biocomputing bioinformatics biol biological biology biotechnology bossy brain brown burks carry catenin cell center chem chen collaborations combined computational computer conduct confidence context currently data database developing disease down essays evidence ewens excellence experimental expressions from fuentealba functions further generate genet genetic going grant hardy have helped helps high highly hopkins http human hutton hypotheses ieee incorporated indiana industrial information inputs institute interaction interactions introduction investigations johns jurisica kowalska library like limited lipton magazine maintaining many mckusick meanwhile medicine method methods microsystems nathans national nature ncbi necessarily network neurobiol neurons neurosci nishimura obtained omim oracle other pacific part partners pattern perez pharmacol povey process protein proteins quintanilla ranked references related relationship relevance reliable resulted results revealed robust schwarzenbacher scope score scoring selkoe server sets showed sivachenko springer statistical stephanie studies study submitted successfully suppl supported symposium systems targets thank that these this through trends university wetzel which with work would york
http://psb.stanford.edu/psb-online/proceedings/psb06/richter.pdf	55	Learning a Predictive Model for Growth Inhibition from the NCI DTP Human Tumor Cell Line Screening Data: Does Gene Expression Make a Difference? Lothar Richter, Ulrich Ruckert, and Stefan Kramer Pacific Symposium on Biocomputing 11:596-607(2006)	activity andrews angelo appl approval bioinf biologies blower botstein boyd brown cancer chem clinical coller comp comput covell cubist development diploma discovery drug eisen ellman fang fligner genetics golub html http humana info iyer jeffrey kohn kramer lander lashkari lazy mesirov munchen myers nature park paul pergamenschikov perou pharmacogenomics pnas pommier preclinical press proc rees references reinhold relationships research richman rijn ross ruckert rulequest sausville schalon scherf screening scudiero shao shoemaker slonim smith sommer staunton structure symp tamayo tanab teicher thesis trial verducci wallqvist waltham wang weinstein yang zhang
http://psb.stanford.edu/psb-online/proceedings/psb06/singh.pdf	37	Struct2Net: Integrating Structure into Protein-Protein Interaction Prediction Rohit Singh, Jinbo Xu, and Bonnie Berger Pacific Symposium on Biocomputing 11:403-414(2006)	about acad additive alzheimer approach assessment bayesian bioinformatics biol biophysical biosynthesis borchelt breiman breitkreutz brenner chapman chen chothia classification clusters comp comparative complexed contain correlated cyst data database datasets deng describing development disease disorders domain dong drug elidan extraction forest forests friedman from gene general generalized genome genomic gerstein grid haas hall hastie hubbard inferring information integrated integration interaction interactions intestinal jagopala jaimovich jansen jarroll joseph journal king klein large learning linear machine maps margalit mehta mering models multiple murzin mutations natl nature network networks optimal orfeomes pairs pazos potential potentials predicting prediction price prion proc proceedings programming protein proteinprotein proteins proteomic protozoa random raptor recomb references repository research resist roth scale science scop seetharaman sener sets similarity sisodia skolnick stark statistical structural targets threading tibshirani towards tyers uetz unified update using viruses wall wong yamanishi zhang zhao
http://psb.stanford.edu/psb-online/proceedings/psb06/wang_h.pdf	28	An SVM Scorer for More Sensitive and Reliable Peptide Identification via Tandem Mass Spectrometry Haipeng Wang, Yan Fu, Ruixiang Sun, Simin He, Rong Zeng, and Wen Gao Pacific Symposium on Biocomputing 11:303-314(2006)	achieve acknowledgments acta aebersold algorithm algorithms also anal anderson andrew applying available baczek bafna based beavis between biochem biochim bioinformatics biol biology biophys biosilico biotechnol both cell chang characteristics chem chen chih cjlin classifier cociorva colinge commun compared comparing comprehensive comput confidence coupled criteria csie dataset datasets demonstrate discov discussions distinguishing dongr drug edwards electrophoresis elias experimental exploiting features feny field first flexible fragmentation frank from function future given haddad have havilio helpful high higher http identification identifications identified improved includes independent informative institute instrument jiang john kaufmann keerthi keller known learning library libsvm like link loss maccoss machine machines mann mass match mateo matthews mccormack measuring methods models module more morgan much named national nature nesvizhskii neural novel obtained omics other pandey peng pepreap peptide perkins pevzner picking popular precision preliminary prerequisite presented programs promising proteome proteomics providing publishers quinlan rapid razumovskaya references results sadygov saraf schwikowski scoring sensitivity sequences sequest significant simple smilansky software sons sophisticated spectra spectrom spectrum statistical steen such support systems tabb taiwan testing thank that then theory threshold today training trans university used uses validation vapnik vector washburn wiley wilm with without wolters work would yate yates york zhang
http://psb.stanford.edu/psb-online/proceedings/psb06/yan.pdf	30	A Point-Process Model for Rapid Identification of Post-Translational Modifications Bo Yan, Tong Zhou, Peng Wang, Zhijie Liu, Vincent A. Emanuele II, Victor Olman, and Ying Xu Pacific Symposium on Biocomputing 11:327-338(2006)	acknowledgement addition aebersold anal bafna bairoch baker barton binz bioinformatics biol biotechnol both bruce burlingame cancer carbon carlson case chait charge chem choi clauser clinicians coalition commun comput computational computer connelly consecutive consider considering contaminants cottrell could creasy curr dancik dasari daughter david davison deal department developed discov discrete distinguished doegenomestolife does doherty drug edition editors elaborative electrophoresis energy explicitly features fenyo foundation frank from frontiers functional further future gasteiger generally genome genomes genomics georgia gooley hall have hendrie herbert hettich hierarchical hochstrasser however http hurst ieee improve incorporates increase intensities ions jensen johnson journal kirby lajoie larimer liang life ling loss losses machines mann marcotte mass match mccormack miller model modeling molecular molloy more mulyukov mumby nagalla national nesvizhskii neutral note number olman opin oppenheim packer pappin part pattern patterns peak peaks pelletier performance perkins pevzner point prentice prince proceedings processes processing program project proteome random rapid rate reddy references research same sanchez saraf schafer science sciences scientists scoring searle sequestration should signal simple since snyder solution sophisticated space spectra spectrom springer state states strader success supported synechococcus system systems tabb tang tangled tanner taylor technol that these this time today together tsur turner under unsuitable utilize verberkmoes verlag wang well which wilkins williams wilm wilmarth with work yang yates zandi zeng zhang
http://psb.stanford.edu/psb-online/proceedings/psb06/lussier.pdf	7	PhenoGO: Assigning Phenotypic Context to Gene Ontology Annotations with Natural Language Processing Yves Lussier, Tara Borlawsky, Daniel Rappaport, Yang Liu, and Carol Friedman Pacific Symposium on Biocomputing 11:64-75(2006)	acids acknowledgments across altman amia annotations aronson ashburner assoc authors bard barell barrell biocomp biocomput bioinform bioinformatics biol biological biomed biomedlee blaschke bodenreider bork brandt brief bull camon cantor cell cellular chang chappey chen cohen completion complex consortium contexts contribution corradi could database development different differential differentiation dimmer dudley eppig example expected experiments expression friedman gene genes genet genome goldsmith grants hayamizu headings hersh high hirschman hripcsak immunol inform investigate iratxeta jamia jianrong kelso king koike krauthammer lash libr lindberg lussier lyudmila magrane mangan mary medical medinfo nadkarni nenadic niwa nucleic ontology organisms organs part perez phenogo phenos phenotypic powell proc provide raychaudhuri references resources respective rhee rogers role sarkar shagina silico simpson smith study subject suppl supported sutphin symp systems takagi thank their this throughput tiffin tool types upon used using valencia valuable wheeler with
http://psb.stanford.edu/psb-online/proceedings/psb06/troncale.pdf	39	Modeling and Simulation with Hybrid Functional Petri Nets of the Role of Interleukin-6 in Human Early Haematopoiesis Sylvie Troncale, Fariza Tahi, David Campard, Jean-Pierre Vannier, and Janine Guespin Pacific Symposium on Biocomputing 11:427-438(2006)	acad actual adpm agreement alla also applied automation bail biochem bioinformatics biology brien campard cells cheshier computer conditions conference considering constitute control could david dependability determining developing does drath enables epigenetic estimated european experimental factor factors fate faure finally formal from functional functionalities future gerhartz grafte grenoble growth haematol heamtology heinrich hfpn hscs hybrid informal interested interesting international ipds level ling literature litz loop maintains manner manolagas mathematical matsuno maximum measured mixed model modification more muller nagasaki natl nets nevertheless only other parameters performance petri plan population positive practical present press primitive proc proceeding proceedings processes production provides pulse quiescent rake references result results silico simulations state stem submitted such suggests symposium system tested that therefore this thomas those transforming useful validate validation values vary verification viswanathan vitro were whatever which whose wolter work would zisowsky
http://psb.stanford.edu/psb-online/proceedings/psb06/delavega.pdf	45	A Tool for Selecting SNPs for Association Studies Based on Observed Linkage Disequilibrium Patterns Francisco M. De La Vega, Hadar I. Isaac, and Charles R. Scafe Pacific Symposium on Biocomputing 11:487-498(2006)	acad access acknowledge acknowledgments additional advantages algorithms also andrew assay assays association automate available bafna becoming beginning best biol biotechniques bjarni block blumenstiel brzoska calculation cannot challenges clark code collins common complete completeness comput considering consortium conversion correspond curlee cycles dailey data datasets defelice dennis derek describing designing detail detailed discussed ease easily enabling ennis eugene experimental extensive face facilities faggart features feedback fenton fiona free from gabriel gene genome genomic genotype gilbert gordon grateful halld halldorsson haplotype hapmap hartshorne help hered hewett higgins human hyland identifying include includes including information informative interaction interest intuitive isaac istrail joanna katherine kejariwal koehler laig lazaruk ldmap leila length leveraging limitations lippert lochner madden main major maniatis manuscript many mccarthy michael moore morton most mutat natl nature need nguyen obtaining online phasing pipeline pius platform potential power press proc project provided providing rapid reference references region reliable researchers rhodes rogers ross rsson scafe schaffner schwartz science searches selection smith snpbrowser snps software solves spier studies suppl support swift tagging tapper tarbox terms that their this thomas those through toinette trevor valuable vega very visualization visualizing wang webster wenz when williams wizards woodage workflows ziegle
http://psb.stanford.edu/psb-online/proceedings/psb06/intro-nlp.pdf	1	Linking Biomedical Information Through Text Mining: Session Introduction K. Bretonnel Cohen, Olivier Bodenreider, and Lynette Hirschman Pacific Symposium on Biocomputing 11:1-3(2006)	assessment biocreative bioinformatics biomedical blaschke colosimo conjuction effectively evaluation extract from gene growing hirschman integrate knowledge krallinger leon lists literature maturity mining morgan normalized often other overall overview papers references reflect session sources suppl task text that this tool tools used valencia with
http://psb.stanford.edu/psb-online/proceedings/psb06/borgwardt.pdf	51	Pacific Symposium on Biocomputing 11:547-558(2006)	ability acad academy accommo acids acknowledgments additional alberts alexander algorithm aliferis analysis analyzing anders approach ares australia australian automatica awad backing ball baranzini barrett based been bfam biocomputing bioinformatics biol biological biology bmbf botstein bridge brown bruce caillier cancer cell central cerevisiae certain cesses chiuso classification cluster comabella combine comparison comprehensive computational computer conditions council cristianini cycle data database dates demeter derive detect diagnosis dimensional doretto drug dunlea dynamic dynamical dynamics edgar edition education eisen environmental evaluation exposed expression extreme eynon finite formats fourth from fujibuchi functional funded furey furthermore futcher garland gene genes genome genomes german ghaoui gollub government grant greller grundy hardin haussler heat hebert hernandezboussard hybridization identification ifac ifnbeta infected initiative interest interesting international invariant issue iyer jarnagin ject johnson joseph journal julian keith kernels knowledge kohane lanckriet large lash learning ledoux leroy levy lewis linear machines mammalian martin matese metho methods microarray millions mining ministry molecular montalban mousavi multicategory multiple namely national natl natsoulis ncbi network networks ngau ngfn nitzberg nucleic oksenberg pacific part pathogen pearson person peter platforms players plos point predict prediction press proc proceedings profiles raff ramoni references regulated regulatory research response roberts rudnev saccharomyces scholkopf science sebastiani series sherlo signatures smola soatto somogyi spellman stanford statnikov stillman stress submitted such sugnet supervised support supported suzek symposium system systems technology textures that this through time tolley topics transcription troup tsamardinos tugendreich types under using vector vidal villoslada vishwanathan vision walter which wilhite will willems with within work wyatt wymore yeast york zachariah zhang
http://psb.stanford.edu/psb-online/proceedings/psb06/maguitman.pdf	8	Large-Scale Testing of Bibliome Informatics Using Pfam Protein Families Ana G. Maguitman, Andreas Rechtsteiner, Karin Verspoor, Charlie E. Strauss, and Luis M. Rocha Pacific Symposium on Biocomputing 11:76-87(2006)	abstract abstracts access acknowledgements additional agreement alamos algorithms alignments also altherr amia among analysis annotation annotations application apweiler assessment automated avidd baeza barrell based becker berry bhupatiraju bibliome binns biocreative bioinformatics biology biomedical biotechniques blaschke boston brettin bright brown build california camon capable categorization causes challacombe cheadle classification classify clustering clusters cohn collaborative colombe colosimo compiegne comprehensive computational computing conclude conduct conference contain contract corbeil corley correct critical currents cytomegalovirus data database dennis department details digiacomo dimmer domain duda dumais durbin eddy edition education elements energy engel enhancing entailed especially evaluation exploiting expression extend extending extraction fair families family feldman fink forthcoming france from functional funded future fuzziness gene generalized genes genet genomic genomics george given gottardo grant grateful gribskov hart have heinrich hersh hierarchies high hirschman homayouni hosack host hovig http human hunter ieee improves includes indexing infection informatics information intelligence intend interannotator international internet interpret investigate jenssen joslyn journal keyterms keyword klacansky klir knowledge komorowski laboratory laegreid lanl latent lempicki linux literature lower luce lynn magrane maslen masys measures medinfo medline medminer mesh meshmap methodology methods metric mining missing mniszewski model modern molecular more morgan motivation multiplex multivariate mylibrary national nature neto network networks observed only ontology other overview pages part particularly pattern patterns pearson performance pfam physica physiological polysemy portland prediction preliminary preparation proc proceedings produce profiling prot protein proteins proximity pubmatrix pubmed ranked rechtsteiner recomb recommender references representing research resources response results retrieval ribiero rocha scherf seed semantic semantics semi september service services sets shatkay shenk show simas similarity simms simple size smith soft sonnhammer space specific srinivasan state steve stork strauss studies study suggest suppl support supported swiss swissprot symp synonymy table tanabe task technical term terms terwilliger testing tests text than thank that theory these thesis this throughput tool tools track transcriptional trec trim turner uncertainty under uniprot university used using valencia validation vector verlag verspoor weinstein well welsh what when which wierman wiley will with word words work working yates york
http://psb.stanford.edu/psb-online/proceedings/psb06/johnson.pdf	4	Evaluation of Lexical Methods for Detecting Relationships Between Concepts from Multiple Ontologies Helen L. Johnson, K. Bretonnel Cohen, William A. Baumgartner Jr., Zhiyong Lu, Michael Bada, Todd Kester, Hyunmin Kim, and Lawrence Hunter Pacific Symposium on Biocomputing 11:28-39(2006)	aaai acquaah action additionally algorithm alignment allow also ambiguous among analysis annotation annotations application applications approaches apweiler ashburner assessment associative aubry automated automatic bada bard barrell based benjamins binns biocreative bioinformatics biological biology biomedical biomedicine bioontologies blake blaschke bodenreider borgelt brenda brief building burgun burstein camon cantor carp categorization cell chebi chemical chimaera cohen combining community comp comparative computerm concepts cone conf conference cream critical curation daml database dates degtyarenko description developments dictionaries dimmer disambiguation doan domain endence english enter entities environment enzyme erability erlein etitive etween evaluation extension external extraction false fikes filter finding france from functional gelman gene general generifs genetics genome genomics goat goble gosp groups gruninger guide halevy hartel hatcher helps high highlights hill hirschman hunter identifiable identify identifying implications importance info information informationminder integrating integration intelligence interop invariants ismb isomorphic jackson john joslyn knowledge konrad krallinger kumar lambrix language leon lesk lexical likely lingpip linking lists logic lucene lussier machine magrane manning maslen matches mcdermott mcentire mcguinness meaning meeting mensah merging methodology might migrate mining morie moulinier mungall musen names natural nature nimes nist notebook odneti ogren ones online ontologies ontology ositional ositionality other overview participant phrasal pine points positions positive predict preprocessing proc processing produce product prompt publication queries rates readable reasoning recognize record references relations relationships research resources results retrieval rhee rice richardson ringwald roth sarkar schomburg search seeks semantic sense services sigdoc sigir sigmod smith source special specific steinbach stemmers stenzhorn stevens structure such suppl survey system task techniques tell terms text that these thirteenth this through tigr tions tool tools towards translation trec turi type umls unification usage used using valencia versp vocabularies volume which wilder with words workshop wroe xtramind
http://psb.stanford.edu/psb-online/proceedings/psb06/bandyopadhyay.pdf	33	Pacific Symposium on Biocomputing 11:354-366(2006)	about acad acids activated activation activator adhesion aids alberts analysis annu apoptosis apoptotic arendt ariumi arsenic ashburner assess assessment astrocytes august basal beliefs beta between bilayered bingo biochem biochemical biocomput biocomputing bioinformatics biol biological biology biophys blankson blockade blood brooks cancer casein categories caveolin cell cells cellular challenge characterization chem chen circuits clin clustering coding combination commun comparative complex components consortium controls cook coyle cross cultural cytoscape data database depletion depolymerizes diaz differentially directed discovering discovery domain during effective effector effects embo enhances eradication even expressed expression extracellular febs finzi focal form from functional ganju garland gene genes genet genome glioblastoma glucocorticoid hanisch haugen henderson heymans high host human ideker immunity immunodeficiency immunol impact induce infect infected infection inhibits instruments integrating interaction interactions issue jenssen kaposi kinase kinases krishnan kuiper kurhekar large latency latent lett levy lifelong lines literature littman llano lymphocytes maere main master matrix mcmillan measure mechanism mediated meggio mering mewes microtubules mitogen modulates modules molecular mononuclear natl nature ncbi network networks nfatc nielsen normal nucleic nurs obstacles ohtsuki ontology overrepresentation pacific pagings pathway patients peri peripheral persaud persistence perspective phenotypic phosphatidylinositol phosphorylation plugin pomerantz potent potentiate proc process producing product profiles proliferating promoted protein proteins proteomics provides reactivation receptor recruitment refaeli reference references regulated regulatory relating relative reservoirs resource response retroviruses reviews rings rink sarcoma scale science sets signaling signalling siliciano stable substrate subunit suppl symp symposium talk target targeting targets tatdependent taylor terminal tgfbeta that therapy through throughput tool tornow transactivator transcription type unification upon using vahey various viral virol virology virus visualization vitro watts weiner wide with wout yang york zeichner
http://psb.stanford.edu/psb-online/proceedings/psb06/neumann.pdf	17	Biodash: A Semantic Web Dashboard for Drug Development Eric K. Neumann and Dennis Quan Pacific Symposium on Biocomputing 11:176-187(2006)	acids american annu association berners bioinform bioinformatics biomol birney bono boulos brass brief carson chem clark cline cohen computing conference contributions coronado discov discovery drug eric eustachio gillespie goble goebel goedert gopinath haber hendler hommeaux inform informatics international internet jassal joanne john joshi kamel karger kashyap lassila leitner lewis liefeld like lord luciano machinery march martin matthews medical medinfo melissa murray neumann nucleic oinn pfeiffer pmid press proc proceedings project prud quan references report review roudsari rust rzepa schmidt science senger sioutos stein stephens stevens stke suppl susie symp tassabehji thank their this tipney today tope tuttle tyrrell vastrik wheeler wide wilbanks world would wright wroe zhang
http://psb.stanford.edu/psb-online/proceedings/psb06/wang_p.pdf	29	Normalization Regarding Non-Random Missing Values in High-Throughput Mass Spectrometry Data Pei Wang, Hua Tang, Heidi Zhang, Jeffrey Whiteaker, Amanda G. Paulovich, and Martin Mcintosh Pacific Symposium on Biocomputing 11:315-326(2006)	acknowledgments address aebersold allen also anal analysis anderle andrea approximate approximation avoid baggerly becker between biases bioinformatics canary cancer carefully centered chem comments conclusion contract control controlled coombes corresponds data density dependent detter developed distance distribution effects emili estimate estimates events example exists experiments family fitting fitzpatrick foundation from fund funded genet gensips given gold hastie have ignoring implemented improved informatics institute intensities intensity iteration john keck kolmogorov lampe like listgarten listwin lular manuscript mean missing mitchell model molecular morris naik national nature nearest need negative neighbor nihca normal normalization number observed over paper partially paul peptide philanthropy pothem probability problem proceedings proteomics quackenbush quality rate referees references remove result sample sauve scaled scheme schemes severe shown smirnov speed supported synthetic thank that this three tibshirani used value values wagner wang were when which with work would xiao yasui zhou
http://psb.stanford.edu/psb-online/proceedings/psb06/intro-sem.pdf	11	Semantic Webs for Life Sciences: Session Introduction Roberts Stevens, Olivier Bodenreider, and Yves A. Lussier Pacific Symposium on Biocomputing 11:112-115(2006)	american berners bioinformatics biological biology biotechnology briefings case change cheung clark comparative consortium creating data describing design discov distributed domain drug experiments framework from functional gene genetics genomics globally gorlitsky hendler identification integrating knowledgebases liefeld life luciano mged mind nation nature object omic ontology parkinson pathway references researchers sciences scientific semantic standards stein stoeckert technologies today tool unification wang will yeasthub
http://psb.stanford.edu/psb-online/proceedings/psb06/good.pdf	13	Fast, Cheap and Out of Control: A Zero Curation Model for Ontology Development Benjamin M. Good, Erin M. Tranfield, Poh C. Tan, Marlene Shehata, Gurpreet K. Singhera, John Gosselink, Elena B. Okon, and Mark D. Wilkinson Pacific Symposium on Biocomputing 11:128-139(2006)	aaai about acquire acquiring acquisition aitr american analogy ananiadou artificial ashburner automatic bases berners bioinformatics biological biology biomoby briefings building capture case chklovski cimiano clustering collaboration collection common commonsense computer concept conference contributors designing distributed domingos editors ernst evaluation everyday exemplar formal frantzi from gene general genetics guided haase handbook hendler heterogeneous hierarchies hotho human information integrates intelligence intelligent interfaces international knowledge laboratory language large lassila learner learning lecture links maedche managing mass method mind mueller multi nature niles notes objects ontologies ontology open pease perkins physol planet plant proceedings proposal public recognition references report resources richardson schoof science scientific second semantic sense services singh source spring staab standard studer successfully symposium system systems technical terms text thesis tool towards tsujii unification upper user using value volunteer volunteers wilkinson word
http://psb.stanford.edu/psb-online/proceedings/psb06/zhang_s.pdf	19	Experience in Reasoning with the Foundational Model of Anatomy in OWL DL Songmao Zhang, Olivier Bodenreider, and Christine Golbreich Pacific Symposium on Biocomputing 11:200-211(2006)	aaai agent algorithm alignment amia analysis anatomical anatomist anatomy annu antoniou applications ashburner assessing assoc automated base based beck biocomput biology biomed biomedical bodenreider borgida brinkley broad cancer case ceur challenges clarification compliance computers conference converting cornet coronado coverage dameron daml darmoni data debugging description digital directions editors eighth electronic enforcing engineering envelope environment european experience experiences expressive february fensel formal foundational fragoso frame from galway gangemi gene goble golbeck golbreich guide haarslev haber hahn handbook hanna harmelen hartel heidelberg hendler hinshaw http human inform informatics institute integrate international into ireland iswc jakobovits journal kashyap knowledge language link ller logic logics mcguinness medicine medinfo mejino merging mesh methathesaurus methodology migrate migrating migration modayur model modeling motivation musen mylopoulos national network november oberthaler ontological ontologies ontology order organizational parsia perspectives pinpointing pisanelli press principles proc proceedings products prompt prot pushing racer reasoning recommendation reference references remodeling representation representing research results rosse rubin schlobach schulz sciencebased second semantic semantics semanticweb semiautomatic services sioutos smith soualmia springer staab steve stevens studer study support sycara symbolic symp systems terminology thesaurus tool towards tuttle umls usability using verlag websemanticsjournal welty what with workshop wright wroe zhang
http://psb.stanford.edu/psb-online/proceedings/psb06/kazic.pdf	14	Putting Semantics into the Semantic Web: How Well Can It Capture Biology? Toni Kazic Pacific Symposium on Biocomputing 11:140-151(2006)	abstract academic acknowledgments adachi addison alamitos also annual applications applied armani asanuma ashburner assoc atshuhiro automated ball ballantine beautifully beckett behaviour berners betsy betweeen biochemical biocheminfo biochemistry bioinformatics biology biomoby blake blameless bloomington bodenreiter bono book books botstein brickley bringing builds butler carroll carsten cases check chem chemistry cherry chilukuri circle clues coli college come comments commission committee company compare completeness computer computers conceptual conference connection connotations considerably contextual daml daniel database dave david davis dean deborah definitions demonstrated department description designissues device different dolinski donald dwight each edition editor editors effort egoshi encouraged english enzyme eppig escherichia example excuse field francisco frank freeman from fujibuchi full function garey gave gene genet genome gerald goto grammar grant grateful guha guide guus harmelen harris have hawaii hayes health heterogeneous hidden hidemasa hill hiroko hiromi hiroyuki hodder home horrocks html http humphreys hunter idea ideally ideas ieee important improved inappropriate incisive indiana information instance institutes intermediary international interoperability intractability introduction ishida issel iubmb iupac jane japan ject jeremy john johnson joint jonathan kamiya kana kanehisa kasarskis kate katrurada kazic kazushige kegg king knowledge kyoto language larry lawrence lewis libr limb lindberg logics london lutz machine make making many march markup mary matese matsumoto mayuko mcgrawhill mcshane meant metabolism michael mike milutinovic mind minoru missouri mistakes moby molecular moss mudge nakatani national nature need nishioka nomenclature noriko ogata okada olivier olken ontology page pages paper parser particular patel patrick people person peter phani philosophy phosphorylase present press proceedings processing project prompted publishing pure queen reading reasoning recommendations reference references report repository representation resource reviewers revised richardson ringwald road robert rubin rules rumiko saeko sanae sato schema schneider schreiber sciences second self semantic semantics semiotes semiotics september sequence sharing sherlock since sixth size slightly society somehow sowa specification stevens stored stoughton structures such supported susumu suzanna syntax system systems takaaki tannen tarver technical terms test that theory they this thymidine tomomi toni tool toshi toyoko trevor trim twenty umberto umls unification union univeristy university usage useful users validating valvo veljko vocabulary volume walks wataru watching wesley westfield what wide with work worthy would york
http://psb.stanford.edu/psb-online/proceedings/psb06/vlachos.pdf	10	Bootstrapping the Recognition and Anaphoric Linking of Named Entities in Drosophila Articles Andreas Vlachos, Caroline Gasperin, Ian Lewin, Ted Briscoe Pacific Symposium on Biocomputing 11:100-111(2006)	alexander anaphora approach august author based biocreative biomedical blaschke cambridge castano christian cluster computer coreference disambiguate editors entity geneva granada hirschman international laboratory literature lynette march master ning proceedings pustejovsky reference references resolution switzerland symposium thesis trails university using workshop yang zhang zhou
http://psb.stanford.edu/psb-online/proceedings/psb06/hoglund.pdf	3	Significantly Improved Prediction of Subcellular Localization by Integrating Text and Protein Sequence Data Annette Hoglund, Torsten Blum, Scott Brady, Pierre Donnes, John San Miguel, Matthew Rocheford, Oliver Kohlbacher, and Hagit Shatkay Pacific Symposium on Biocomputing 11:16-27(2006)	acid acids acta adolph advances agichtein algorithm amino analysis application apweiler automated bacteria bairoch bannai base based better biochem biochim biocomputing bioinformatics biol biology biophys blum botany brunak bucher budding burns carter cells cellular cerevisiae chang chlorop chloroplast choi chou class classification classifier cleavage clin cokol combining commun comparison compartmentation composition compositions conf conference coupling csie database detection development developments discover disruption donnes dunkley dupree emanuelsson embo eskin estimates eukaryotic experimental expert expression extensive feature fechner finberg finding from function functional future gardy gate gene genes genetics genomics german geting gram griffin grimwade hanson heijne hoglund horton http hypotheses imaging improves improving inferring information intelligent investi ismb isotope journal kanehisa kaufmann kelley knowledge kohlbacher kohler large learning lexical library libsvm lilley linand localization localizations location lopit lysozyme macdonald machine machines martin maruyama matthews method methodology mimicking mining miyano molecular morgan motifs multi myers nair nakai nearest negative neighbors network neural nielsen nlsdb nuclear nucleic observed organelle pacific pairs pairwise park past peptides phage plants porter porterstemmer predicted predicting prediction present probabilistic probability proc proceedings prosite prot protein proteins proteomics psbhoeglundshatkay psort readings recent references regions reprint research retrieval ross rost saccharomyces sample scale schneider science secondary september sequence sequences signals sites size sorting spencer stapley sternberg stripping structure subcellular suffix supplement support swiss symposium system systems tagging tamada targeting tartarus terminal tests text their through transit trembl trim using vector walpole wang watson weng with yeast
http://psb.stanford.edu/psb-online/proceedings/psb06/chen_l.pdf	43	Pacific Symposium on Biocomputing 11:467-477(2006)	acknowledge acknowledgments adeyemo adiconis akanuma alcoser allen altshuler anaya andersen andres andrew arch atherosclerosis auwerx avila awata barker barrett beamer beck beilby beiswenger biochem biocomputing bioinformatics biol biological biophys biotechnology blangero blumenstiel borch boyle brodbaek browne busing buttron cambien care chapman charpentier chatterjee cheskin chew chung clement clin clinical colantuoni cole collins commun comuzzie cooper cordero corella council cruz cumming daly deeb defelice deninger despres devlin diabetes diabetologia diaz distler doney echwald ehrmann elahi elbein endocrinol endocrinology engeli eriksson faggart fajas febs feldman fenger fernandez fischer flavell forsen franks frederiksen frew froguel from fruchart fujimoto funding gabriel galan genet genomics gonzalez gotoda grand greten hagura haist halsall hamann hanafusa hansen hara harding haring hasstedt hebebrand hercberg hern hernandez higgins hinney hirose hixson hsueh hung ikegami inoue iovine iwamoto iwasaki jacobson johnsen jorgensen kadowaki karjalainen kasuga katakura kawaguchi kimura koch kuusisto laakso lander larrad lazcano lett lewontin like lindi lipid lochner luan maccluer madsbad maeda maerker maller mancini martinez masulli matsutani mayer mcquillan metab metabolism miettinen mitchell miyashita montgomery moore mori morris motoyama muller munzberg mykkanen nanjo ndez nemoto nguyen nicaud nielsen nishikai obes okada ordovas osmond pacific palmer passinge pedersen perez perusse pihlajamaki pineda poirier poland ponce popul poulsen price professor qaadir rahilly references renn research rett riccardi ringel rios risch rissanen rivellese robitaille roth rotimi rowland ruffa sabatino saito sanchez sanke saruta schaffner schaid science sciences seino serrano sharma shuldiner siegfried sivenius sorensen stumvoll swarbrick symposium takeda taniyama teng theor thompson tines tiret tobe tomita tufano urenberg urhammer uusitupa vaag vaccaro vaisse valdez valve varroud vial vohl volk volund ward wareham world would yamada yamagata yamamoto yasuda yazaki yokoi
http://psb.stanford.edu/psb-online/proceedings/psb06/lu.pdf	6	Finding GeneRIFs via Gene Ontology Annotations Zhiyong Lu, K. Bretonnel Cohen, and Lawrence Hunter Pacific Symposium on Biocomputing 11:52-63(2006)	abstract acknowledgments adding after amia analysis annotations approaches approximately ashburner attributes automatic automatically based bayes benjamins bhalotia biolink biology biomedical biotext candidates characterization classification company concept conference continuously corresponding coverage covered curation current currently data database detroit each estimated example expansion from future gene generate generif generifs genes genet genomics grant have hersh high http implemented improve included indexing informatics information institute jelier john kaufmann know learning least ledge linking literature machine mani mcgraw mgif michigan mining mitchell more morgan national nature nist ontology overview practical predicted previous proceedings processed produce publishing qualitatively quality query quite references reflect remains report represented results retrieval searching shatkay show significantly species standards such summarization supported symposium system techniques technology terms text than that their these this three title tool tools track trec twelfth unification useful utility when which witten work year years
http://psb.stanford.edu/psb-online/proceedings/psb06/page.pdf	25	Experimental Design of Time Series Data for Learning from Dynamic Bayesian Networks David Page and Irene M. Ong Pacific Symposium on Biocomputing 11:267-278(2006)	akutsu algs analysis arkin bacteria based bayesian bernard bioinformatics biomed biomol biophy cambridge causal cell circuits coli comm complexity computational computing concepts constraints control curr dasgupta data derived discrete disruptions distribution dougherty dynamic ecificity ectrometry efficient eriments expression fixed formulae free friedman from games gene genetic glasner harja hartemink hdesm husmeier identification inferring informative interactions intracellular introduction joint kearns kuhara lauffenburger learnability learnable learning maruyama mass mcadams microarray microbio miyano model modelling models modules motifs multiparameter multiple nachman natural network networks nolan numb oolean overexpressions page pages pappin pathways patterns perez phosphorylatiopn pitt press primer priors probabilistic proc proceedings profiles prokaryotic prospect prot protein quantitative receptor references regev regulatory resolved reveals ross rule rush sachs sample schapire science sensitivity september series seungchan shmulevich siam signaling simulation single sites size small stke strategic structure symp systems theory time trim tyrosine uncertainty under valiant vazirani white with wolf yadlin yakhini zhang
http://psb.stanford.edu/psb-online/proceedings/psb06/ling.pdf	5	Automatically Generating Gene Summaries from Biomedical Literature Xu Ling, Jing Jiang, Xin He, Qiaozhu Mei, Chengxiang Zhai, and Bruce Schatz Pacific Symposium on Biocomputing 11:40-51(2006)	above abstracting abstracts accomplishments acids across actual address applicability approach automatic average based because beginning believe bias biocreative bioinformatics biological biology biomedical build centroid challenges clustering colosimo computational concept consortium crosby data databases dependence different discovery document documents domain domains drysdale effective employed encyclopedia enright entire entrez even eventually experts explore extend extracting extraction feldman flybase framework from future gene general generic generif genes genetic genomic goal help heuristic high hirschman hope iliopoulos including incorporate independent indicate information insects issue jing library limitation lists literature longterm mainly manage many marcu medline methods mining mixture model models molecular more morgan most multiple next normailized nucleic obvious organisms other ouzounis overview park precision primarily probabilistic problem process produce promising proposed quality radev realized reduce references researchers resources results same science selection sentence sentences shatkay some specific strategy such suitable summarization summarizing suppl system task test tested testing textquest that this though tool training tsujii uated unclear used using very which will with wong work would
http://psb.stanford.edu/psb-online/proceedings/psb06/robinson.pdf	36	Improving Computational Predictions of Cis- Regulatory Binding Sites Mark Robinson, Yi Sun, Rene Te Boekhorst, Paul Kaye, Rod Adams, Neil Davey, and Alistair G. Rust Pacific Symposium on Biocomputing 11:391-402(2006)	academic acids analysis annealing apostolico application applied approaches artificial assessing associated automation background bailey binding bioinformatics biol biomed biopolymers biotechnol blanchette body boosting brown bussemaker cerevisiae chawla cisregulatory class classification comput computational computer conf conference correlation databases datasets davidson decision delosme design designed detection development diego discover discovery drosophila early efficient element elements elkan embryo evolution expectation expression factor fitting focusing footprinter footprinting freund from functionally generalization genes genet genomic gibbs groups higher hughes icml identification ieee imbalanced imbalances improves inform integrating intell intelligence isse japkowicz journal knowledge learning line linear lnai machine maximization methods minority mixture model modules motifs networks nucleic order over patterning performance phylogenetic predictions press proc proceedings program promoter protein radivojac rajewsky references regulatory related research right saccharomyces sampling schapire schedule sciences sheffield siggia site sites smote synthetic syst systems technique theoretic thijs tompa tools transcription unusual using washington with words workshop
http://psb.stanford.edu/psb-online/proceedings/psb06/lange.pdf	23	High-Accuracy Peak Picking of Proteomics Data Using Wavelet Techniques Eva Lange, Clemens Gropl, Knut Reinert, Oliver Kohlbacher, and Andreas Hildebrandt Pacific Symposium on Biocomputing 11:243-254(2006)	access acknowledgements adam addition algorithm algorithms analytical applications available based berlin biomed biotechnol breen brown bruker cambridge cdal chemistry chemometrics christian communications compares computing cottrell creasy dahl daltonics data databases decker direct discussions early ectrometry electroanalytical electrophoreses electrophoresis enms favorably feng fingerprinting flannery formats framework free genetics germany gobom helpful hopwood http huber identification implementation institute involved jects jens johan john journal kempka kerber kohlbacher lehrach library like louis maass mass mclerran michael molecular mueller nordhoff numerical open openms pappin particular perkins planck press probability prof protein proteomics providing query rapid recip references reinert rodriguez roeraade saarbrucken saarland schuerenb scientific searching sequence shotgun smith sons source sourceforge spectrometers strittmatter supplied support teykolsky thank theiss theory thornquist university using vendor version very wang wavelets wiley wilkins williams winget with would yasui zhen
http://psb.stanford.edu/psb-online/proceedings/psb06/mukherjea.pdf	16	Discovering Biomedical Relations Utilizing the World-Wide Web Sougata Mukherjea and Saurav Sahay Pacific Symposium on Biocomputing 11:164-175(2006)	acquisition annotating apis application artificial august automatic batra bidirectional biocomputing biological biomedical cafarella carnivores castano categorial chain cimiano cochran collier combinatory computational conference corpora description downey etzioni evaluation extracting extraction food format fourteenth france from fukuda gene geneontology genes germany google grammar handschuh hawaii hearst hidden http hyponyms identification identifying incremental information inhibit intel interaction international july kamesam kankar know knowitall kotecki kothari large ledge ligence linguistics literature lousiana management markov methodology model moving mukherjea names nantes national nobata ontology oregon orleans over pacific pages papers park parsing pathway pies popescu portland proceedings products protein pustejovski rdfschema references relational relations resource robust saarbrucken scale schema self shaked soderland softbots srivastava staab subramaniam symposium syntaxns system takagi tamura text thirteenth toward towards tsujii tsunoda umls umlsks weld wide with wong world yates york zhang
http://psb.stanford.edu/psb-online/proceedings/psb06/yip.pdf	18	SemBiosphere: A Semantic Web Approach to Recommending Microarray Clustering Services Kevin Y. Yip, Peishen Qi, Martin Schultz, David W. Cheung, and Kei-Hoi Cheung Pacific Symposium on Biocomputing 11:188-199(2006)	acad aggarwal algorithm algorithms analysis applications applied asia biclustering bioconductor bioinformatics biology biomedical biomoby botstein brown categorical cheng cheung choreography church cluster clustering clusters comparisons conference data datta description dimensional discovery display eisen epclust expression fast features finding first from gene generalized genome groups hartigan high html http huang identifying informatics intel inter international interoperating introduction jected journal kaufman knikker know kwan language large ledge ligent long management markup means mged mgedontology microarray mining mixed model molecular mygrid natl numeric ontologies ontology overview pacific park part patterns pmml predictive primer proc proceedings procopiuc profiles references rousseeuw scenario science semantic services sets sigmod soap sourceforge spaces spellman statistical statistics submission systems techniques transformation validation values version wide wiley with wolf wong wsdl xslt
http://psb.stanford.edu/psb-online/proceedings/psb06/stoica.pdf	9	Predicting Gene Functions from Text Using a Cross-Species Approach Emilia Stoica and Marti Hearst Pacific Symposium on Biocomputing 11:88-99(2006)	acad according achieves acids acknowledgements addition algorithm alignment also altman analysis annonymous annotating annotation annotations applying approach approaches apweiler asignment assessment associating automated automatic barrell based between bhalotia bhuptiraju biocreative bioinformatics biological biology biomediacal biomedical biotext blake blaschke boguski botsein brown brunak brutlag bult camron categories categorization categorizer chalmel chang chiang cluster codes cohen cohn collections combine computational computed consistently consortium correlations coutinho couto craven critical current data database decide decker dimmer discovering display dwight effective ehler eils eisen eliminate entropy eppig evaluation experiment experimental explore expression extracting extraction fibroblasts figo finding foulger foundations from fulmer function functional functions future gene genentech genes genet genome genomic genomics gift glatting goanno gofigure grant grebinski groth group gupta hearst heaton hennig hersh higher hirschman hudson human hybrid illogical improve information integrated investigate iyer jensen joslyn kadin khan king knowledgebase koenig koike kraemer krallinger language lardenois large learning lehrach leon levine like literature lveillard machine machines made manning maximum measure meke members microbiology mining mintz mniszewski models molecular moore moormann mouse muller multiple nakov natl natural nature nenadic niwa novik nucleic ontology opinion orthologous other overview pages patterns performance plan poch possibility predicting prediction predictions preliminary press proc proceedings processing products program protein proteins protrin raychaudhuri recall references report research resource response results rice richardson ross roth ruch sahel scale scheme schmidt schubert schuler schutze schwartz science search sentence september sequence sequences serum shoshan show silva similar situ size solutions spellman staerfeldt stapley statistical staudt stoica suhai support supported sutphin system takagi target task team term terms test text than that this thompson three through tool track transcriptional trec trent trim unification uniprot unstructured using valencia vector verspoor vinayagam volume voting wasserman well white wide with workshop
http://psb.stanford.edu/psb-online/proceedings/psb06/pratapa.pdf	26	Finding Diagnostic Biomarkers in Proteomic Spectra Pallavi N. Pratapa, Edward F. Patz, Jr., Alexander J. Hartemink Pacific Symposium on Biocomputing 11:279-290(2006)	about across addition advances algorithm algorithms alignment aligns also although amink analysis anderson applied approach available baggerly balasubramanian based because better bioinformatics biomedical biostatistics both cambridge campa cancer caprioli carin cellular center charged chemically combines computer coombes could department diagn different doubly duke dynamic emili even example expert features figueiredo figures finally fitzgerald found framework from harmonic hartemink hastiey heights help hierarchical howard http hyunjin identical identification ieee ignore ignores incorporate incorporation informatics information input instead intelligence into isotope jain kobayashi koomen koong krishnapuram larger leading learning less listgarten locations machine markey mass mathematics methods model molecular molecule more morris multiple neal near neural next only output overexpressed pattern patz peak peaks piped possible possibly predominant presence press problem processing prone proposed protein proteomics provide quantification recognition redundant references registration report research result results reyzer roweis same samples schwartz seem selects sequence sequential sequentially shapes share signals similar singly sister smlr soltys sort spectra spectrom speech step steps strategy systems technical than that their these this tibshirani time tipping tissue transactions tumor unified used values variants versions vision volume wang warping were which widths with would wright
http://psb.stanford.edu/psb-online/proceedings/psb06/dudek.pdf	46	Data Simulation Software for Whole-Genome Association and Other Studies in Human Genetics Scott M. Dudek, Alison A. Motsinger, Digna R. Velez, Scott M. Williams, and Marylyn D. Ritchie Pacific Symposium on Biocomputing 11:499-510(2006)	american among analysis appl applications approach arrhythmia arterioscler association balloux barrett bass biocomput bioinformatics biol boehnke breast cancer cardiovascular coalescent common complex computer data detecting determining dimensionality disease diseases divergence drosophila easypop environment epidemiol epistasis error estimating estrogen forward gene general generation genes genet genetic genetics genotyping grants hahn haplotype haploview health hered heterogeneity high human institutes interactions journal kimmel kingman lathrop linkage maps metabolism methods migration missing moore multifactor multilocus national nature network nielsen order part pedigree peng persimilis pharmacogenetics pharmacogenomics phenocopy ploughman population power practical presence processes program proposed pseudoobscura rates reduction references research reveals ritchie simulation simulations simupop sing site sizes slink software sporadic stochastic study supported susceptibility symp therapy this thromb time trait ubiquitous vasc version visualization weeks with work
http://psb.stanford.edu/psb-online/proceedings/psb06/cohen-boulakia.pdf	12	Pacific Symposium on Biocomputing 11:116-127(2006)	abstract according alexaki angeles anyanwu appear argos associations banks barillot bioinformatics biologic biology biomediator biomedical bizer boulakia brockenbrough broekstra browser buneman carroll characterization christophides clark cohen comparison concepts conf conference data database databases declarative derose description design donelson draft eccb ective efficient enabling endent enzymol erhart eswc etzold europ explore framework fresnel froidevaux from goble graph graphs graziani greenwood gutierrez haase hommeaux hornoch html http icdt indep info information integrating integration interaction international ismb iswc karvounarakis khanna klyne lacroix lair language languages life methods molecular mork orne path paths persp pietriga plexousakis preferences presentation proc proceedings provenance prud quan queries query querying radvanyi rank raschid representing resource retrieval scholl science sciences seab second selecting selector semantic seth shaker sources sparql stevens stransky styling syntax system tarczy techniques technologies theory tool ulyanov user using version vidal vldb vocabulary volz where wide with working workshop world wroe xpath zhao
http://psb.stanford.edu/psb-online/proceedings/psb06/kraft.pdf	48	Efficient Two-Stage Genome-Wide Association Designs Based on False Positive Report Probabilities Peter Kraft Pacific Symposium on Biocomputing 11:523-534(2006)	acad acknowledgments altshuler author balmain barratt begg biom biomarkers biometrics botstein bulletin cancer caporaso carlson chanock clayton clin closas consortium daly david discussion elston endocrinol epidemiol exper freedman freimer garcia genet genetics ghormli gilles grants gray hapmap helpful hered hinds hirschhorn hunter inst international jean konig merikangas metab natl nature offit oord pharoah ponder prev proc province references risch rothman sabatti satagopan schork science service stephen storey sullivan suppl supported thanks thiel this thomas tibshirani todd venkatraman verbel wacholder wang witte work ziegler zool
http://psb.stanford.edu/psb-online/proceedings/psb06/gopalakrishnan.pdf	47	TagSNP Selection Based on Pairwise LD Criteria and Power Analysis in Association Studies Shyam Gopalakrishnan and Zhaohui S. Qin Pacific Symposium on Biocomputing 11:511-522(2006)	abecasis acad affected algorithm algorithms altman altshuler analyses analysis applications approach association associations bafna bakker barratt barrett based berno biocomputing bioinformatics biometrics block blocks broad calabrese capture cardon carlo carlson ceedings chapman chen choosing chromosome circumventing clark class clayton cohort common comparison complex components comprehensive considerations consortium containing cooper cordell cormen criteria data delvin deng design designs detecting detection determinants disease disequilibrium diversity doshi doubling dudbridge dynamic eaves eberle efficient entropy epidemiol esposito example festa finding finescale fisher free from generating genes genet genetic genetically genome genomewide genomics genotype genotypes genova gopalakrishnan group hacker haiman halldorsson hampe haploblockfinder haplotype haplotypes hapmap henderson hered heward high hinds hirschhorn http hudson human humans identification informative international introduction istrail itzhak ject jects johnson kaplan kautzer kohane kolonel krawczak kruglyak lazarus leiserson limited linkage lippert locus lunkel manuscript mapping marjoribanks markers martin maximally mcdonough mcgrawhil mcintyre measures meng million minimal minimum model models monte multiethnic multilocus multiple natl nature neutral nickerson nordborg nucleotide olson optimal pairs partitioning patil paul pike polymorphisms power preliminary principal pritchard proc programming przeworski publications references relative resolution revealed rieder risch rivest romani sachidanandam sample samples sasieni scanning schreiber schwartz science screening search sebastiani selecting selection selective september sequence simonsen single size smith snps statistical stram strategies structure studies study subsets symp tagger tagging tags tagsnp testing tests todd traits trim ueda umich under unphased unpublished unrelated using variation vega wagner waterman weiss wijsman with working wright zaykin zhang
http://psb.stanford.edu/psb-online/proceedings/psb06/chun.pdf	2	Pacific Symposium on Biocomputing 11:4-15(2006)	abbreviation abbreviations achieved address ambiguity andrade annotated annotation association based beam bioinformatics biol biomedical biomedicine boosting bork candidate cause conducted considered containing corpus correct could creating data database depends dictionary difficulty discovery disease diseases domain efficacy encompass enju enriching entries evaluating example experiments extraction filtering fish future gathering gaudan gene genes genet genetic genetically genia health hpsg hristovski html http humphrey hybrid improving incorporate increasing index inform information inherited integration interactions international into intro iratxeta ismb knowledge language large libraries linking literature medline medstract mining mitchell miyao name names natural ninomiya number occurrences parsing part perez performance perspect peterlin polysemous postagger pragmatic precision probabilistic problem proc proceedings processing proposed protein proux public purpose pustejovsky rather raynaud recall recognition references regard relation relations resolution resolving safely scale scheme senses servers sets should show size small solution speech strategy stud such support svms swanson syndrome system tagger techniques technol technologies terms testing their this thresholding tokyo topics training tsujii tsuruoka undiscovered unification using utokyo were which with work workshop would