http://psb.stanford.edu/psb-online/proceedings/psb09/ PSB 2009 http://psb.stanford.edu/psb-online/proceedings/psb09/mitrofanova.pdf 21 September 22, 2008 acad acids across adai against algorithm approach approaches assign bader based between biogrid bioinformatics bosche brohee candidates capable chen clustering clusters colt compared complex complexes computationally conclusions confidence conservation constitute continuous database datasets date define diffusion direction disc discrete distance dongen each efficient enright expensive experimental explore flake focs functional future gavin gomory gruhler hard hartuv have heilbut helden high hirsh hogue however http ibaraki ideker identified identifying implementation interaction internet jansen jurisica karp kelley king krause large lerman manipulation maps marcotte maslov material math matula measure meila method mipd mips mirny modules nagamochi natl nature network newman nucl other ouzounis phys plan pnas possible predictions presented proc producing promising protein proteins przulj quality rates recomb references reliable research robust scale science score shakhnovich shamir sharan shown siam sneppen species spectral spirin strong tarjan thebiogrid this through tree trees tsioutsiouliklis very when with would yang yuan http://psb.stanford.edu/psb-online/proceedings/psb09/dudley.pdf 4 IDENTIFICATION OF DISCRIMINATING BIOMARKERS FOR HUMAN DISEASE USING INTEGRATIVE NETWORK BIOLOGY abreu acad acids acknowledgements adachi aging alex alterovitz america amia anderson annu approach associated authors bachner baker barrett based baumgart begins behavioural bell benjamini biochem biocomput biofluid biofluids biol biomarker biomarkers biotechnology bodenreider borovecki bottom bowel brain british broad butte caby cancer candidate candidates carding cell chen children clin combinatorial compliments comprised computing condition contributions dennis dial discern discerning discovery discriminately disease diseases dudley embo encumbered endeavor engl establishes establishing etzioni expression febs foundation framework from full further gastroenterology gene general genetics genome genomics grants haagsman health howard hughes human identify immunol importance incorporate inflammatory institute integrative inter interest johnson journal kaushik lamb lamparski lancet lebrand life like liotta lucile maes manufacturers markers mass medical medicine mendrick methods might model models molecular more muller nascimento national natl nature neonatology nephrol nephrology nesatyy network neurobiol niel novel nucleic offer olsen omenn packard papadakis paves pharmaceutical pharoah pisitkun potti proc profiles prospective protein proteomes proteomics provides quickly radich ramaswamy reducing references refine relationships research reviews rioux sciences segal sinai skrenchuk smith space sparrow spectrometry start support supported suter symp thank that this thongboonkerd topdown toxicology traditional transplant tusher vast wetering while wide williams with work would york zhang http://psb.stanford.edu/psb-online/proceedings/psb09/zhang-m.pdf 14 September 22, 2008 adam algorithm algorithms algs arndt attie bergeron berlin bioinformatics blanchette block branch breakp caprara chapman chloroplast cocoon combinatorics comparative comput computer computing conf data decomp distance downie doyle editors efficient erform erimental ermutations evolutionary exact finding focs foundations friedb from gene genome genomic genomics graphs hall halving hannenhalli ieee interchange into inversion lecture median medians method mice mixtacki molecular moret multichromosomal multiple notes numb oint oints olynomial optimal order ositions oulos ound outp pages palmer pevzner phylogeny plant practical problem problems proc rapid rearrangements reconstructing reconstruction references results reversal sankoff science siep soltis solution solutions sorting springer stoye symp syst systematics tang tannier tesler transforming translocation unifying verlag view volume wabi with workshop yancop zhang zheng http://psb.stanford.edu/psb-online/proceedings/psb09/kuchaiev.pdf 5 September 16, 2008 acad acids also applications applied approach arising available avoid barab barabasi bastuck bauch bauer becomes bioinformatics biology bishop bork bosche boucher bouwmeester boyle breitkreutz chapman chiba clark collins complexus computational conference copley corneil crucial cruciat data dickson different distribution drewes eccb edelmann encer erti european flamminia from furga gavin generate genet geometric gnau grandi graphs greenblatt heurtier higham hofert holstege hudak huhse human ieee information interface jenovic journal jski jurisica kemmeren klein krause krogan kuhara kuster learning leutwein london machine maritana marzioch math merino metric michon milenkovi model modeling models modern mohan mooney multidimensional muta natl nature network networks neubauer nishizawa noise nucleic oltvai once only other oxford ozawa pattern peng penrose peters physics points press proc proceedings properties proteins proteomics prulj publ quality querfurth quez radivo raida random real recognition references reguly remor research reviews rick royal rudi ruffner rybin sakaki scaling schelder schultz science seraphin should since society space species specific springler stark structural such tashiro that theory this thus train tyers university used vespignani weissman with workshop world yamamoto zhao http://psb.stanford.edu/psb-online/proceedings/psb09/sachse.pdf 31 September 22, 2008 abstracts acad academic accumulation acid activation activity agglutinin aktouf algorithm algorithmen allen amsellem analysis anatomical anatomy annual applications architecture article atrial axial balke based basis bayesian berlin bernard bers bertrand bhavanandan biocomp biol biophys bolte bootman brickmann bridge burton calcium canine cannell cardiac cardiol cardiology cardiomyocyte cardiomytes cardiovasc cells cellular changes channel channels chem chen cheng circ circulation cleft cline closing clusters colocalization comp computational computer concentration concise conf confocal conklin construction contractile contraction contractions coomb cordeiro cordelieres coronado coupling crossman cullen datena delorme density depletion description diad diadic digital dihydropyridine dimensional discrete diseased disorganization distinct distribution dordrecht dreidimensionaler during dystrophin editors electron electrophysiology ershler erti ertrophied examination excitation fabiato faces failing failure features felder foell following force frank from fruhauf galimb gating generierung geom germ gilb giles goetze goldhab graphics guided guinea haworth heart hearts heidelb heiden higazi high hole human ieee imag image imageprocessing images imaging implicated induced infarction initiation inoue interaction into isofl iterative kamp kaprielian katlic kluwer laake langer lecture lederer light living llewelyn local localization location longuet lorensen louch mammalian manzanera marching martina mccallister mcculle mechanics medial meeting mendaten method microsc microscopic microscopy modeling models moore mork movement movements murine muscle myocardial myocardium myocyte myocytes natl neonate netherlands normal notes novel numerical ojeda organization orphaned ossible page pages patterns perroton peskoff phenomenon photon physiol preteux proc proceedings proteins publishers purkinje quantification quantitative rabang rabbit receptor receptors reconstruction reconstructions reduced reduction references release resolution restoration reticulum revealed richardson roderick role rothery ryanodine sachse sarcolemma sarcoplasmic savio schnellen science scriven sedarat september severs sexton sialic sialoglycoproteins signalling simulation single site size sjaastad skinned sobie soeller song souchier space sparks spitzer springer stern stevenson stromme submicrometer surface symp synchrony system tachycardia techniques theory thinning three thyroxinstimulated tibbits tour transients transverse transversetubular triggered trim tubular tubule tubules using ventricles ventricular vision visualisierung volu volume ward wheat with wolff wong workshop york http://psb.stanford.edu/psb-online/proceedings/psb09/jin.pdf 20 September 23, 2008 aach ability acad academy acids acknowledgments activities activity addressing aebersold affects ajitha aldridge alexander algorithm algorithms aligning alternative among analyses analysis andreas andrew application applied approach ashton assessment associates associations assume auspices avila babu bacterioplankton based berend berger between biochemical biogrid bioinformatics biol biological biotechnol bobby bork bottani boucher bourgine breitkreutz brunak budding buhler bumgarner campillo causal causality cell cellular centromere chain changes chau chayant checkpoint chen chris christian christine christmas christos chromosoma chromosome church class coexpression coli collado combination community comparative complex complexes connecting consequently conserved contract contrast control cornell cortex cortical cycle cytoplasmic data database datasets david debojyoti demonstrated derived desikan detangle diagrams dimitrov direct dongbo during dutta dynamic dynamics dynein embedded emphasize environmental escherichia event events evolving example explorations expression facilitates factors faloutsos farkasovsky fell fengzhu fields filamentous finding form formation framework francois free from fuhrman function functional functionally functions funded galitski gene general genet genome genomic gerstein global goodlett grants graph graphs graphscope growth guelzim guldener guojie haiyuan hans haraguchi have hiraoka homogenous hong hongchao hood however huerta hutchins ideker identification identify iliana implicated implication important importantly incapable inference information integrated integration interaction interactions interacts intermediate issue jaideep jensen jessica jimeng jingfen joshua juhl karp kempe kepes kinesin kinetochore kinetochores koujin krassen krause kuntzel large lars ldrd leonid level lichtenberg limitations limited ling link links llnl local lorrie lunjiang luscombe madadhain madan marine mark martin matthias measurement mering metabolic metabolism method mewes michael microarray microtubular microtubules mike mining mips mirny modular module modules molecular more mother motor mpact munsterkotter nabetani nabil national natl nature network networks nicholas nucleic oesterheld oliver ordering organization ouzounis padhraic pagel pages papadimitriou paper parameter paul peer perez performed perturbed peter phase philip philipp place point prasanna prediction present prinz proc proceedings project properties protein proteomic provide provides quansong questions ranish ranking references regulation regulatory reguly repository resource results reveals rives roland ruan rueda ruepp runsheng samuele sarah scale schwalbach science sciences segregation september sequential series serve sets shiwei siegel sigkdd similarity simultaneously size small smyth snel snyder social soren sorger species specific spindle spirin spiros srinivasan srivastava stanley stark starting static steele stephen structure study stumpflen such supported susanne systematically systems taking tantipathananandh tanya teichmann temporal temporally teresa that their theory thieffry this thorsson thus time timothy tools topological traditional transcriptional trim tsutsumi tyers type tytell ules ulrich ulrik uncovers under unique victor vides volker wagner want warping webkdd werner while wide wiring with wolf work world xiaopeng yeast zhang zhao http://psb.stanford.edu/psb-online/proceedings/psb09/intro-knowledge.pdf 33 September 22, 2008 acids across address alignments amia analysis annu approaches ashburner aspects backer ball barclay based bayesian beginning biol biology biomarkers biomed biomedical blake bodenreider both botstein bush buskirk butler cherry choice colleagues combinations combinatoric comparing conf continue data davis demonstrate detection dhaval difficult disease distance diverse dolinski domains driven dudek dwight early eppig ever explosion exponentially expression focus focusing framework genes genet gordillo greater grow guide gwas halevy harris hill hornoch ieee importance improved include inform insight insights integrate integration into issel kamal kasarskis knowledge learning leverage lewis linked linking literature local looking louie machine martin matese metabolomic methods metric modifying molecular mork nguyen nucleic papers pathogens pathways phylogenic prior problems proc profiles proteomic provide references refine regions related reliable rely reported resources richardson ringwald ritchie robertson rubin sanchez sciences session shaker sherlock should show snps solved species stolba study such support symp tarczy tarver that these this tjoa tools under vector very webb when while will http://psb.stanford.edu/psb-online/proceedings/psb09/bush.pdf 35 BIOFILTER: A KNOWLEDGE-INTEGRATION SYSTEM FOR THE MULTI-LOCUS ANALYSIS OF GENOME-WIDE ASSOCIATION STUDIES* accurate acids acknowledgments afraid aggregate algorithms analysis another application applied applying araki assess assessing association barnes base based bateson because becker between bias biases biocomput bioessays biofilter biol biologic biological biology borecki breakdown bridges bright cambridge candidate carlson cell cellular ceric certainly coggill color colour common complex computing conceptual contains correction correlation could creation croft culverhouse data database defined delivery dependent determining discovery disease diseases displaying diversity divide drosophila duan dust each eberle eddy edinburgh effect egmont eisenberg environment eosin epistasis established estimated eustachio experimental eyes factors families finn fisher fokkens forslund franke frankel functional gathering gene genes genet genetic genome genomes genomic gillespie given gold gopinath goto grants hahn hattori have health hered heredity higney hirakawa hotz http human hypotheses impact implication improve improving inclusion independent index influence inheritance institutes interacting interactions interdependencies introduce itoh jassal jong joshi just kanehisa katayama kawashima kegg knowledge kramer kruglyak lange largest level lewis life likely limits linking list literature lloyd loci lysosomal main many mapping melanogaster mendel mendelian methods mistry model models modern modifiers moore more mutations national nature nearly netpath network networks nickerson notably nucleic number okuda other overall overlap pairs pathways perspective petersen pfam phenotype positional possible power press pretty principles prior prioritized prioritizing processes promotion protein proteins provide provides province ramaswami ranked ranking reactome reconstruction referenced references reich relation relatives reporting represented research ritchie routine royal salwinski sammut scans schmidt schork separately shows small society soft some sonnhammer source sources specific statistical statistically strategy studies studying suarez subset subsets such support supported supporting supposition susceptibility symp synthesis systematic systems tate test that there these this thornton though tokimatsu tool tope transactions traversing trends ubiquitous university unknown using value vastrik wang watanabe when where white whole wide wijmenga williams with work xenarios zoology http://psb.stanford.edu/psb-online/proceedings/psb09/workshop-post.pdf 51 Post-transcriptional gene regulation: RNA-protein interactions, RNA processing, mRNA stability and localization accessibility accurate acids acting adenosines affinity algorithm alignment allain also alternative alternatively among analysis anantharaman annotating anton appropriate aravind area aspects association auweter available bacteriophage bartel based bases bateman because been bejerano beyond bibliography binding biogenesis bioinformatics biol black blatter blencowe boring both bound brain brown burge calif capture carmona cell cells characterization characterize chip classification clear clery clip cmfinder coat code coding collections combinatorial community comparative compensatory complete complexes components comput computational conserved constraints context contextfree continue coordination covariance curr cytotopically darnell data database deep describing despite detect determinants develop developments diego different differential difficult discovered discuss domains durbin easily eddy edwards effort either emerging emphasis encoded engele epstein even events evolution example exon experiment experimental exploring extensive extensively extracts faced families family farh features febs finding fitting flanked focus focused free frey friedersdorf from function functionally garrett gaul gene generative genes genet genome genomes genomics gerber global goal gold gorostiaga grammars griffiths grimson grun gunsalus guruceaga haussler heavily herschlag high however hughey human identification identifies identify identifying improved include increase indicates inferring interaction introduce investigating involved iovino isoforms isolation issue jensen jiang johnston jones kapur keene kent kertesz khanna known komisarow koonin krek lander large last learned level levels lewis ligands lindblad living macmenamin mads mammals marshall matches mechanism mele metabolism method methods mian microarray microarrays microrna micrornas miller mirna mirnas model modeling models montano montuenga more morris most motif motifs moxon mrna mrnas much mutations ncrna ncrnas near needed networks nova nucleic oberstrass often open opin paired pairing particular pascual pedersen piedade plos post posttranscriptional predict predictions predictor predictors preference preferences preliminary present primary problems procedures protein proteins protoc quantify questions quite recent recently recognition regan region regulated regulation regulators regulatory regulons related rely remain representations rfam ribonucleoprotein rnas role rosenberg rosenbloom rubio ruggiu ruzzo saez sakakibara scale schneider science secondary secondarystructure seed segal segura selection selex sequence sequences sequencing shai shen should siepel signals single site sites sjolander smaller solutions some space specific specificity spliced splicing still stochastic stoffel stoilov stranded strategies struct structure structures studied subject substantial such summary target targeting targets tend than that their there these this though thousands tiling trans transcriptional trna tuerk understanding underwood unique unnerstall until using valverde variety vitro vivo weinberg were which wider will with wolf wong work workshop xing years yeast http://psb.stanford.edu/psb-online/proceedings/psb09/qutub.pdf 30 INTEGRATION OF ANGIOGENESIS MODULES AT MULTIPLE SCALES: FROM MOLECULAR TO TISSUE* acad acknowledgments activation adams adaptation advances alitalo also angiogenesis aoto appl basilyan become begin bethesda bioessays biol biomed blood boland cancer capillary carmen cell cellular chem chen circ coetzee combine combining component comprehensive conn contributions covassin cultivate daly david design develop development discussions dominguez dynamic each emmanouil existing experimental factor faseb feilim filion florence flow format from gabhann gahbann gale generate goldman growth heart holash holderfield hughes hypotheses initiative integration jacob james karagiannis kejing knowledge koller koskimaki laboratory large lawson level levels lobov maintain marianne mechanistic members michael microcirculation mikhail modeling models modules molecular movement multiscale murphy nakatsu natl nature noguera noren offers organ organism oxygen papadopoulos physiol physiology platform popel press proc process produce proliferation quantitative qutub references renard represent research revision rigorous sainson scale semenza siekmann signaling simulation software stefanini submitted systematic test thank that their theor therapeutic these this thurston tissue tools transport troise tsoukias used valenzuela validation vempati visualization wiegand will work yancopoulos yang http://psb.stanford.edu/psb-online/proceedings/psb09/wang.pdf 25 DISSECTING THE INTERFACE BETWEEN SIGNALING AND TRANSCRIPTIONAL REGULATION IN HUMAN B CELLS acids acting action activity algorithm analysis analyzing approach approaching aracne ashburner automated bader based basso betel bichsel bind bioinformatics biological biology biomolecular bussemaker cell cells cellular chemical circuitry compound computer condition context cover cycle dahlquist data database development developments discovery dynamic engineering enrichment epidermal essential exploring expression factor factors family febs foat from gardner gene genet genetic genmapp genome genomics global gough growth hemmings hermjakob hogue human humans identification identifying inferring initial intact interacting interaction interactions interpreting issue kanehisa kegg kinases knowledge lecture lett linding lymphocytes mammalian mapk margolin mass matrix microarray mode modelling modulators modules molecular morphogenesis multiple network networks notes nucl nucleic nucleotide ontology open pathways peri phosphorylation platform pnas post profiles profiling protein proteins proteomics receptor reconstruction reference references regulators regulatory research resolved resource revealed reveals reverse roberts science sequence signal signaling sites source specific specificity spectrometry steffen studying submitted subramanian suppl systematic systems tamaskovic targets tepper therapeutics time tool trans transcription transcriptional transduction transfactomedb translational tyrosine unification viewing vivo wang wide xenarios zhang http://psb.stanford.edu/psb-online/proceedings/psb09/phan.pdf 40 IMPROVING THE EFFICIENCY OF BIOMARKER IDENTIFICATION USING BIOLOGICAL KNOWLEDGE acknowledgments actions active aerts although american analysis annals applications approach array artifact association assumes assurance augment award based been behavior bellazzi benefits beta between bigh biochem bioinformatics biol biological biomarker biomarkers biomedical biophys biotechnol biotechnology bootstrap braga breast british cacorrect cancer carcinoma cell cells change chip choose chuaqui class classification clear clin clinical coalition combinatorial commonly commun comput contexts control correction correlates correlation cross cxcl cxcr data dataset derive diagn differentially discoveries discovery distinguished dolah dougherty easily effectiveness efficiency efron encompass engineering existing expandable experiments expert expressed expression factor factors false feature filter fold follow forseberg from functional fundel funding furthermore fusion gene general genes genetics genome genomic genomics georgia golub grants growth have health hope however human identification identifying igfbp impact improve improvements improves including increases independent indicate influencing informatics institutes integrated integrating integration intelligently inter international intraplatform ivanov jones journal kidney knowledge kong kuffner laboratory limited literature maqc measurements metastasis method methods metric metrics microarray microarrays microsoft mining molecular monitoring morey mukherjee multivariate national nature neto novel number observations oligonucleotide online only optimal other outcome overall park points post practices prediction predicts prioritization proced process profiling progression project proposed prostate proteomics quality rank ranking real reduces references regulated renal reproducibility required research resulting results roberts rosendahl ryna scholar schrader schuetz science selection shown shows signalling signatures simulations singh smallsample specific statistical stokes study such supported system targets test tests tgfbi that theoretical this through tibshirani time towards transactivator transforming true tumors used using valid validation variety veer well whether wide will without wrapper zimmer zupan http://psb.stanford.edu/psb-online/proceedings/psb09/nakamura.pdf 22 September 23, 2008 adachi alch algorithm allo amer assoc available binary biocomput bioinformatics biol biology bottani brunel calzone cation chen circadian computational control cross csikasz deal decreasing doucet filtered freitas friedman fujarewicz fujii fujita genetic genome gordon graphical hashimoto hata hayashi higuchi http ieee ieice iino imoto increasing inform inoue interactions journal jsbi kaufmann kimmel kitagawa larger lipniacki mallet mammals matsuno mazurie mechanism ment miyano morgan much murakami nachman nagano nagasaki nagy nakahama nature novak number okitsu only order oyama pacheco paral particles perrin peter prediction proceedings programming proportional quach ralaivola references regev regulatory replace requires resampling salmond samples search searching shigeyoshi silico simulations smith springer stat sugano suggested suzuki swierniak symp syst takasugi tamada tasaki teong that their thiagara transaction tras tyson ueda ueno verlag wakamatsu weights with yamaguchi yamane yamasaki yields yoshida yoshimori http://psb.stanford.edu/psb-online/proceedings/psb09/gibson.pdf 19 September 24, 2008 acad accompanied acknowledgments acterization advances after against altocumulus amoutzias analysis ancestral ancient annotation assessing assessment barab based batada bauer berenbrink bertin between biol biological biology biotechnol birren born bornberg bzip case ceedings cell cellular cerevisiae chara comparative comparison complementary complex complexes complexus comprehensive comput computation contains curation cusick data date degenerative derived distinction duplicate duplication duplications dupuy dynamics effect elowitz emerge equal evidence evol evolution evolutionary evolves experimentally explore factors flammini force foundation free friedman from functional funding fungi further gavin gene genes genetics genome genomes gibson global goldberg grant graph history homomeric hormozdiari hybrid ideker increasingly interaction interactions interactome interologs kamp kaufmann kellis kepler kishony krogan lander landscape large largee leal lessons levy lond machinery mads maritan material mering model modeling modularity modules mutations national natl natural nature neofunctionalization network networks novel ohno oltvai organization origins party pastor pereira pfeffer philos pinney plos predictions preservation presser principles proc prolonged proof protein proteins proteome proteomics prulj questioning rapid rapidly rattray reconstruction redundant references regev regulogs reguly reveals revision robertson role roth saccharomyces sahinalp sampling satorras scale scalez science seed september sets sharan size small smith specificities springer stepwise still stratus study subfunctionalization substantial supported survey systematic systems tarassov teichmann this through topological topology trans transcription transfer trim ubiquity uetz under upon valuable veron vespignani vidal vivo wagner wapinski whole work world yeast yook york zhang zquez http://psb.stanford.edu/psb-online/proceedings/psb09/tari.pdf 9 QUERYING PARSE TREE DATABASE OF MEDLINE TEXT TO SYNTHESIZE USER-SPECIFIC BIOMOLECULAR NETWORKS acids acknowledge acknowledgement advances algorithm alibaba also altman analysis annotation appreciate architecture assessment assoc ataxias authors automatic babur banner baral base betts biocomputing biocreative bioinformatics biological biology biomedical biomolecular bradley bruijn bull cabig cagney cell cellular cerevisiae challenge chang characterizing chemogenomic coexpression collaborative comments comprehensive connected construction cytoscape dasgupta data database degeneration demir dependency disorders dogrusoz donaldson drug embo entity environment executable explained extracting extraction fast febs flaherty formulation free frishman froidevaux from functional functionally fundel furious gene generalized genes genet genome genomes genomic genoquery gerstein getting giaever giot global gonzalez grammars grant graph grinberg guldener hard helpful hermjakob hewett hoffmann human huynen identifying ieee inform inherited intact integrated integration interaction interactions jean knowledge krallinger kuffner labedan lafferty language leaman leitner lemoine leser lett lewington like link literature machine markiel martin mary method mewes mining mips model models module molecular molecules montecchi named nature navigating network networks noort nucleic number oliver open ozier pacific palazzi pankalla paper parse parsing pathways patika pharmacogenetics pharmgkb plake pnas prebind principles proceedings profiling properties protein proteinprotein proteomics provided pubmed purkinje qpath query querying recognition references related relation relationships relex reviewers robust rubin ruppin russell scale schiemann second segal semantic semcdi sequences sfaz shannon shironoshita shlomi simple sleator small snel snyder software source suppl supplement support survery symposium tari task text textomy this through tree trees uetz understanding using valencia vector visual warehouse whole workshop world would yeast zimmer http://psb.stanford.edu/psb-online/proceedings/psb09/webb-robertson.pdf 42 A BAYESIAN INTEGRATION MODEL OF HIGHTHROUGHPUT PROTEOMICS AND METABOLOMICS DATA FOR IMPROVED EARLY DETECTION OF MICROBIAL INFECTIONS agaton anal analyt anderson bernard bernardo biocomput bioinformatics biol biomed chem chemom chen chrom commun comput daly deng devijver duxbury electrophoresis expert friedman genome hajjar hall hartemink hober hwang ildiko immun infect intell jarman jebara kittler lanckriet lewis life longnecker martens mass monroe moore naes noble pnas pounds prentice proteome proteomics rapid references reif smith spectrom strittmatter suppl symp tech technometrics troyanskaya uhlen white wiley http://psb.stanford.edu/psb-online/proceedings/psb09/kanabar.pdf 45 September 22, 2008 accelerate acknowledgments alfred ambesi application approaches artificial bacteriol bansal bateson belcastro bernard between beyhan bilecen bioinformatics biology booth cambridge case casper causality computational conference connell demsar development dimensional disease driessche eaton eleventh elidan epistasis fellowship fong foundation franco friedman from further general genes genetics genotype grant hartemink here heredity heydorn high hill hold http huang immun impiombato incorporate infect inference intel interaction international into investigations jarvis jects johnson journal juvan knockoutnets koller kuspa lauffenburger leon levy ligence lindley linial markowetz mendel metzger microbiology models molecular more morris murphy nachman nature nolan ordering pathways pearl perez phenotype phenotypes predicted presented press princeton principles proceedings processes promise reasoning references regev related sachs salama schoolnik science segal shaulsky simons sloan smith sozhamannan spang statistics sternberg supported sysbio systems than thus ucsc understanding university using variety various vpsr vpst wang which wide wormbook yelensky yildiz zupan http://psb.stanford.edu/psb-online/proceedings/psb09/carey.pdf 36 September 19, 2008 acknowledged architectures biology chan chudin clayton computational cowley create done efforts experiments expression extensible forrest from fundamental genet genetics genevar genome hered humgen interpretation interpreting knowledge leung molony much nica observed play plos references relationships remains representing results role sanger schadt stranger that these trans transparent well will williams work http://psb.stanford.edu/psb-online/proceedings/psb09/tastan.pdf 48 PREDICTION OF INTERACTIONS BETWEEN HIV-1 AND HUMAN PROTEINS BY INFORMATION INTEGRATION acad accelerate acids acknowledgments addison aids aloy annu ashburner assisting baeza bauer berger between bieniasz biochem biocomput bioinformatics biol biological biotechnol brass breiman calderwood career cell chen comput computational curr dandekar data database datasets davis define department derived dyer effective efforts endocrinol england enright epidemic experimental exploiting extends faulon features forests foundation framework frankel fraser freeman from functional genes genet genome genomic gomez grants grossmann harlow health here hivinteractions hope hosts http human hypotheses identify identifying independent inform information inspected institutes integrated interacting interaction interactions interactome jansen jeong joseph kato klein knowledge learning liang machine mangelsdorf marcotte margalit martin mathivanan matsubara methods microbiol modern most multiple murali national natl nature ncbi neto network nevado niaid nieto noble nucleic opin organism pairs panchenko paper park part pathog pathogens pazos plos predicting predictions press proc promising protein proteins providing puntervoll random references refseq reliable retrieval russell rzhetsky science seetharaman shoemaker singh single skolnick sobral sociometry sources sprinzak steroid strogatz supervised suppl supported symp testable that these this trends trkola unaids update valencia very virol watts were wesley will with within work yates york young zhao http://psb.stanford.edu/psb-online/proceedings/psb09/hart.pdf 38 UNISON: AN INTEGRATED PLATFORM FOR COMPUTATIONAL BIOLOGY DISCOVERY acids acknowledgments addison additional addresses alignments analyses analysis andreeva annotation announcement approved apweiler ashburner ashkenazi automatically available ball baratin barrett based bateman being benson berman beyond bhat bioinformatics biol biological birney blake bork botstein bourne brauer brazma brenner bruford bryant burgoon butler cambridge canese cell chaffron chandonia chapter cherry chetvernin chothia church ckler classification colleagues combinations comments common communication comprehensive computing concise connection considered consortium content contributions corrections curated curr currency cutoff data database databases date dave davis death department deployment depth dicuccio differ direct discerned distributed diverse documentation doerks dolinski dowell durbin durinck dwight easily eddy edgar eimon enables engineering eppig excels exceptional expert expression facilitate family feature features federhen feedback feng filtering finn forthcoming free freely from geer gene geneseq genet genome gilliland goldenpath gough griffiths hansrai harris hart hgdownload hill hler hollich howorth http huang hubbard huber identifying immediate immunol improvements included including installation integrative interface interpro into introduction investigated issel jensen jokerst jones josh kaminker kapustin kasarskis kasprzyk kejariwal khanna khovayko kratz krogh kuhn landsman lassmann learning level lewis license ling lipman list load local lush machine madden made madera maglott manuscript many marshall match matese matthew mering methods miller mining mistry mitchison models moor moreau moxon mukhyala mulder murzin necessitates nucleic numerous online open ostell other ouellette package pathways pharma philippi possible povey practical precomputed prediction predictions press probabilistic problem progress projects protein proteins protoc pruitt queries readily references released releases report richardson ringwald rubin schuler schuster scientific score searching sequeira sequence sequences server several shah sherlock sherry shindyalov shortcomings significant simran sirotkin sites sneddon snel solution sonnhammer source sourcetm souvorov speculative stajich starchenko status stein stern stored strasser such support system systems tarver tatusov tatusova text thanks that thomas thomsonreuters those through tomasello tools trusted types ucsc ugolini under understood uniprot unison unit university updated users using vivier vogel wagner walzer weissig wesley westbrook wheeler wilson windgassen with wright yaschenko yuen zacharewski zhang http://psb.stanford.edu/psb-online/proceedings/psb09/shen-orr.pdf 41 TOWARDS A CYTOKINE-CELL INTERACTION KNOWLEDGEBASE OF THE ADAPTIVE IMMUNE SYSTEM ability able above absence abstract abstracts abundance acad accepted accumulate accuracy acknowledgments activation added additional address advocate affected ages agreement ailun alex algorithm alizadeh allows alon also altman always analysis analyze analyzed analyzing annotation another antibody appear appearance approach architecture areas array asked assay assayed assays assemble assembled assess assessed assign associated associations auto automatic automatically available average away axis background based become been being better between binary bind binding binds bioinformatics biol biological biology biomed biomolecular biostatistics bipartite black blockers blood body both brown building butte byproduct cannot capture captured cell cells cellular challenge check checking chemotherapeutic chen children cohen color come communicating communication compared comparing comparison compendium complexity complicated components comprehensive computable computer concepts conditions conducting confidence confirm connected connecting considerable considered consist consolidated context contrasted cope core correctly correctness correlation corresponding costimulate costimulatory could covered criteria critical ctls curated currently cutoff cytokine cytokines cytometry cytoscape dark data database databases dataset datasets date decrease decreases deduced defines degree delta dendritic denote denotes dense density derived despite details detect detected diehn different difficult dilutions direct directional directionality directionless directly discards discoveries discovering discovery discussion done dots downstream drawn driven drop drops each easier easily edge edges effector effectors either electronic element ellison employing encode encyclopaedia encyclopedia enriching entrez environment establish estimate evaluate even evidence evident examination example exclusively expanding expansion expected experimental experimentally experiments expert experts exploration express expressed expresses expressing expression extension extent extract extracted extracting extraction extracts facilitates false family females field figure filtering find findings fine first flow follow form format formatted foundation foxp framework frankenstein free frequency from full function functional functionality funding further furthermore future gamma garten geared gene genes genetic geneways genome genomics given golub grant gray grey grow hand have health hedco helper here high higher himc hours however human humans hypothesis hypothesized hypothetical ibelgaufts identification identified identify ifng ignoring immune immunexpresso immunol immunological immunology incorrect increase increased incubation indicative individual individuals induced infer inflammation inflammatory inform information inhibition integrate integrated integrating integration inter interacting interaction interactions interestingly interpretable interpretation into intracellular invest irizarry jeffrey keeping kenny kits knowledge knowledgebase known kohane lack language larger largest last least length leukocytes level lexicon lgals library lifted light likely limit link literature lucile luminex lysates lysed machine majority males manual manually many marker match matches matching measured mediated medicine membrane methods mice microarray microenvironment millipore mines mining misleading model models molecular monitoring more most mount muller multi multiple multiplex must namely national natl natural nature necessarily negative network networks nigms node nodes normalization note novel novo number observe observed obtained occurrence occurring ocklenburg often oligonucleotide online only ontologies ontologybased oppenheim order organisms other output outside overall packard pairs palmer panomics parsing participate particular partner path pathfinder paths pathway pathways pearson perfect performed peripheral perspective pharmacogenetics pharmacogenomic pharmgkb pharmspresso phosphatase plex plos positive positives possible potential power predefined predominantly presence present previous primary principle prioritization prioritize probe proc procarta processing produce producer producing production products profiles proof protein proteinprotein proteome provide publically publicly published quality question rantes rare rarely rate rates reached reality reannotating recent receptor receptors reference references reflects regulate regulated regulation regulatory relationship relationships relevance relevant relying remaining remarkably reported reporting reports representation represented representing represents requirements requires requiring research researches resource resources respectively response responses result resultant results retrieval reverse risk roberts rong rual russell rzhetsky same scale search searches second secrete secretion semantic sensitive sentences separate serum shannon should showed showing shows signatures similar similarly simplified single size skrenchuk slonim smaller social software solely some sources spanning specializing specific specifically spleen spleens staining stands stanford steps sternberg stimulated stimulation stress strong studies subset subsets such suggest suggests summaries support supported supporting surface susceptibility system systems take tamayo targets test testable tested text textpresso than thank that their them then theoretical theoretically theory there therefore these this those three threshold through throughput thus time times tissue tissues tool tools total towards traced training treg tregulatory true tune twelve type types under understanding undetermined undirected unified unique university unlike unprecedented used uses using usually utility utilization utilized validate validation validity value variables various varying verified verify version very visualizing warranted ways websites week well were when which while white width will with within work would http://psb.stanford.edu/psb-online/proceedings/psb09/kasson.pdf 46 COMBINING MUTUAL INFORMATION WITH STRUCTURAL ANALYSIS TO SCREEN FOR FUNCTIONALLY IMPORTANT RESIDUES IN INFLUENZA HEMAGGLUTININ acad accounts accuracy acid acids acknowledgments affinity alignment alone amino among amsterdam analogs analysis antibody antigenic apparent assist association atchley auewarakul authors avian bahar barrere based basic berry bestebroer better between bhlh binding binds biochemistry bioinformatics biol biotechnology bizebard blackburne bolotov bosecke boston both bound bourne bovin brandman branson brown bull carbohydrate casari cases catalysis cell cells center changes changing chem chunsutthiwat closely clustering clusters cohen combined common comparing complex complexed conclusions confirmed context correlated correlations covariation crowther crystallography cumulative curr daniels data defines dependent dernovoy development diat discussions domains dress dunn during edgar effect effects eggs either embryonated enable enables evol evolution evolutionary evolving existing experiments extensive eyal facilitates families feldmann fellowship fitch fleury fouchier foundation frank from functional fusion future gambarian gambaryan gamblin generation genetic gigant glick global globular gloor glycosylation goldstein grown haemagglutinin haire hanson have head health helpful hemagglutinin hemagglutinins high hiramatsu hist hoffman horimoto host human hypotheses hypothesize identified immune important influenza informatic information inhibitors interpretation isolates jampangern johnson jones jong kaufman kawaoka kiryutin kiso klenk knossow kongchanagul lapedes learning lerdsamran lichtarge ligand linked lipman losing louisirirotchanakul machine magnetic mapping marinina martin matrosovich mdck membrane method metric mining moiety molecule morgan mortality mosk mueller multiple muramoto murata muscle mutagenesis mutations mutual national natl nature near network neutralizing nidom novel nuclear nucleic number ohuchi opin organization ostell osterhaus outside pandemic park particularly pathog phenotype pittayawonganon plos pooruk positions potentially practical predict pressure proc properties protease protein proteins proton puthavathana range rasmussen readily receptor receptorbinding receptors references regard region regulation residues resonance resource response responsible rigolet rimmelzwaan robust roles rudneva russell sakaitagaw sander sangma sauter sawada schiffer science search searching selective sequence shilov shinya sialic sinitsyn site sites skehel small smith spanish specificity spectral spectroscopy stevens struct structural structure structures subtypes such suggest supported suptawiwat surface surfaces surveillance suzuki swanstrom swine targets tatusova techniques terhalle thank that theoretic theory these this thitithanyanont thornton throughput thus tools trace troyanskaya tuzikov type understand understanding ungchusak updating useful using usui valencia virol virology virus viruses visualization wahl wharton while wiley will wish with witten wollenberg work world yamada zaslavsky http://psb.stanford.edu/psb-online/proceedings/psb09/kahn.pdf 13 September 23, 2008 adams aerni alekseyev also analysis annual antonescu architecture arvestad bailey based bashir berglund bertrand bioinformatics biol biology blanchette bonet brown cancer cardone chen cheng clark clusters collins comp complex comput computational conference costello delcher deletions display distances duplications eichler eighth elemento evol evolution evolutionary extend gascuel gene genet genetics genome genomic gray green haussler history huang human ieee infer insertions integrated interesting international jiang joie jong jsarowicz kahn kobayashi kurtz lagergren lefranc linardopoulou lonardi lupski mabrouk marques marron methods miller mills model molecular moret mutat myers nash nature nefedov occur orthology padilla paris pevzner phillippy pienta proceedings raphael recomb reconstructing reconstruction references reinert research ried salzberg samonte sankoff schwartz science sennblad sequence shivaranjani shumway siam siepel smoot song stankiewicz suppl swenson syst tang that trans trask tree trends under ventura vinar volik wahl waldman windle would york zhang zheng zhong http://psb.stanford.edu/psb-online/proceedings/psb09/cheng-y.pdf 27 September 21, 2008 above acad according active addressed agmon algorithm allison allow although anal apbs appl area areas avoid bajaj baker bartol based been begin below berry binding biological biomolecular biomolecules biophys biopoly biopolymers blackburn boles boltzmann bond briggs brownian calculate calculated carlo cellular chem cheng chengpsb chern close coalson collins combining comp comput computational concentration conclusion conditions consistent constants context continuum currently data davis densities density describe develop diffusion domain doniach drug during dynamics eastman edelstein eisenberg elcock electrostatic electrostatics element energy entropy equations ermak error experimentalists experiments finally finite first free from gabdoulline gamblin generator genest geom goal gradient graf haire have holst implement improvement included instead interaction iteratively krissinel kurnikova large ligand limitations limited local luty macmillan macromolecules madura main makes mapping martin matter mccammon mccmmon mcell medina mers mesh meshes method methods microphysiology modeling molecular monte must nadler natl nature neuraminidase neuroscience nitzan node nonlin northrup noted noyola olson only other package phys poisson potential preparing present press previous proc proceedings process proteins qualitatively quite radic rate read realistic references regularized researchers results reyna reynolds russell same sanner saxton scalable schuss schutter science second september shen simple simulating singles site size skehel smart smol smoluchowski soft software solution solver solving song specifically spehner stable stat state steady stevens stiles still study studying substantial suen symp synaptic systems tara taylor tetrahedral that theories third this together tools trim ultimate under using value wade walker wang while will with wlodek work yeomans york zhang zhou http://psb.stanford.edu/psb-online/proceedings/psb09/zhang-x.pdf 49 September 22, 2008 according accuracy adult akey algorithm algorithms alpha also american among analysis applications approache artificial associated association bailey begins benefit between biallelic biology biostatistics blocking bonney bound breast brute cancer candidates cardon carlson case ceedings chase childhood church classification combinatorial common comparison complex components computation conference confronting correction corrections criteria curtis daly data decreasing deluna derive described detect dimensionality discussed disease disequilibrium dramatically dupont duxbury each easily eberle effective efficient eliminating encoded epidemiol epidemiology epistasis error estrogen evans even events examined exhaustive expression fallin family fast fastanova fastchi ferrell find finding first focus following force functional future gauvreau gene genes genet genetic genetics genome genomewide genotype genotypes genotypic given goal grove hahn halperin haplotype have herbert heterogeneity heterozygous highorder http human idea identified identify important incorporated infarction inferring initially intel interaction interactions international invariant investigate involving ismb journal kardia kimmel kishony kohane kruglyak kunkel laboratory large larger largest lazarus ligent linkage loci locus lymphotoxin main mainly mapping marchini marker maximizing mcmillan metabolism method methods mice minimal missing models modified modular molecular moore more morris much multifactor multilocus multiple myocardial nature nearest neighbor nelson network networks neural nickerson nicodemus north nucleotide number nyholt obesity oped other over oxford ozaki pacific pagano pair pairs panels paper parameter parker parl partitioning partitions performed permutation plos pnas polymorphism polymorphisms predict prediction press principal principle principles procedure proceedings procs province prune pruning quantitative ramoni reduction redundant references remaining represent research respectively retrieval reveals ritchie roberts roodi roses rusyn same science search searches sebastiani second segr select selected selection september sham shamir shannon sherriff similar simple sing single size sliding snps some space speed sporadic square stage statistical step storey studies study subsequent subset supp suppl susceptibility systems tagging task test testing tests than that then this thomas threadgill threshold track trait trees trim tsai twolocus type units univeristy upper used using value variant variation versus wade wang weiss when where whole wide will windows wise with work yeast zhang http://psb.stanford.edu/psb-online/proceedings/psb09/intro-biomole.pdf 1 BIOMOLECULAR NETWORKS: FROM ANALYSIS TO SYNTHESIS acknowledgments allowing alterovitz approach arnold artech authors based basu bayesian bioinformatics biological biomarkers biotechnol boston case collins contributed cyclic dwyer engineering expertise extend gerchman graciously house identify isaacs london methodology modeled nature network often pathways peer process publishers ramoni references relationships review reviewers sachs session submitted system systems thank their this time used weiss work http://psb.stanford.edu/psb-online/proceedings/psb09/costello.pdf 3 September 19, 2008 acknowledgments adai altman amin anders annotation bader baliga beason biocomput bioinformatics biol biology botstein brauer brouwer brown butte cagney cantor carmel center chaudhuri chiba chiriac comments computer consortium crombie database date derisi dolinski eads edition eisen elledge fraser gasch gene genet genome genomics giot godwin haber harel hastie hattori hibbs hogue huang ideker iyer john judson kohane kuang lehner lesk mansfield marcotte markiel metzner microbiol molecular mulholland myers nature nirenburg ontological ontology owen oxford ozawa ozier paques parts plos pnas practice press principles radivo ramage raskin references research robson saldanha schwikowski science semantics shannon sherlock simons sons spellman study support symp tang thank theesfeld tibshirani troyanskaya uetz university vitols wang wible wiley wong yoshida zhang http://psb.stanford.edu/psb-online/proceedings/psb09/lim.pdf 47 MASTER REGULATORS USED AS BREAST CANCER METASTASIS CLASSIFIER* acad after alizadeh also armitage aster atkins atsma average barnes bartelink based basso bernards berns between bioinformatics biol bloomfield boldrick botstein brown byrd califano caligiuri chan chinnaiyan classifier classify coller consistently cross dalla dataset datasets davis delahaye dhanasekaran difference directed domany downing ebert edges eisen encodes engl especially explicitly favera ferrando finally findings five foekens fold friend from gaasenbeek gelder generate genet getz gillette givol glas golub good greiner grever hart have hill huard hudson hypotheses independent inferred jatkoe kela kerkhoven klein klijn kooy koscielny kuefer kustagi lancet lander large leading learning lefebvre levy lewis linsley logic look lossos mani margolin marti marton master mehra meijer mesirov michiels model models montie moore mootha mukherjee natl nature neil nemenman network neuberg odom oncogenic only other outperformed overlap palomero parrish paulovich perner peterse phenotypic pienta pomeroy poor powell previously proc processes prognosis prognostic protocols published rational real references regulation regulators rhodes roberts rodenhuis rosenwald rubin rutgers sabet same samples schreiber science shah sherlock shown sieuwerts sigaux signature signatures since slonim soulier springer statistical staudt stolovitzky subramanian subsampling substantially sulis suppl syst talantov tamayo tchinda testable testing tests that theory these they this tibshirani timmermans tomlins tran understanding used using validation vapnik varambally veer velde vijver visible voskuil wang warnke weisenburger weng were when which while wilson witteveen yang young zhang http://psb.stanford.edu/psb-online/proceedings/psb09/daemen.pdf 44 September 16, 2008 acad academic acids acta albertson anal baiocchi belgian bhaskar biochim bioframe bioinformatics biol biology biopattern biophys bioptrain blegen breast bruford buday cambridge cancer cantor cawley chem chen chin comput conference consortium cristianini current curtis downward encode endometriosis ernsi federal fridlyand garnis genet genetics genomics gestel holstege hoyle international iota iuap ject johnson joint klijn kluwer kretschmer kuraya lkopf lockwood lohi michl miranda moepert moka natl nature networks neural nnstedt north nucleic office oncogene opinion park parvin pathol pinkel policy press proc proceedings ramjaun ranka references reinders reinholz research rubin schmidt schraml scie science scientific shah shawe silicos sinica snijders speed starita statist strep strokemap subramanian suppl suykens tamayo taylor treat troyanskaya tsuda tumours university vapnik vries wain wang wiley will world xiao xuan yang http://psb.stanford.edu/psb-online/proceedings/psb09/sachs.pdf 7 September 20, 2008 annual artificial biochem biocomput bioinformatics biol biophys calder carlson causation chem comm comput computation computational conference cooper daheron dahleh daley discovery donis dynamics fifteenth fitzgerald friedman gibbons gifford gilbert glymour grantcharova harms hartemink heckerman intel itani jaakkola jakkola kauffman koller kudla kumar lauffenburger ligence ligent linial meek modeling moelling morgan murphy nachman nielsen nips nodelman nolan ohannessian orton pace pearl perez preparation press probabilistic proceedings prudhomme reasoning references richardson russell sachs schoeberl science second shelton signaling sorger stke submitted symp systems through uncertainty understanding verma volume vyshemirsky west wille woolf young http://psb.stanford.edu/psb-online/proceedings/psb09/tian.pdf 10 Pacific Symposium on Biocomputing 14: (2009) acad accurate acids alignment amid analysis annotation arnold ashburner automatic bacteria bafna ball based batzoglou berger biocomput biocomputing bioinformatics biol biological biology biotechnol blake botstein butler calculation carlo cellular cherry clustering comparison comparisons complexes comput conserved consortium curtis data database davis dolinski down dwight empirical encyclopedia eppig fast flannick frishman from ftpnetworks garrels gene general genes genet genome genomes global gotermfinder goto graemlin grama guldener harris hill http ideker identification interaction interactions interologs issel issue kalaev kanehisa karp karpinets kasarskis kegg kelley koyuturk kuhn kyoto large learning lewis machinery mannhaupt matese matthews mcadams mccuine mewes mips modeling monte multiple munsterkotter natl nets network networks north note novak nucleic ontology orthologs pacific pagel pairwise paralogs parameter park pathways patterns potential princeton proc procedures protein proteins pull reboul recomb references relevance remm revealed richardson ringwald robust root rubin ruepp samatova searches sequence sham sharan sherlock singh sittler sndb sonnhammer species srinivasan stanford stockwell storm strack stumpflen subramaniam suthram symp symposium szpankowski tarver through tool topkara ucla uetz unification using vaglio values vidal vincent warfsmann whole with within yeast zhang http://psb.stanford.edu/psb-online/proceedings/psb09/pan.pdf 39 September 22, 2008 14:48 Proceedings Trim Size: 9in x 6in agarwala akey algorithms analysis ancestral applied arteriosclerosis association baca balding based beane bell besenbacher bioinformatics biology both candidate carefully cholesterol churchill clustering coalescent coasim comparative complex computational computations conduct cormen data designed ding direct disease disequilibrium durbin effective efficiently environment epidemiology evaluating events evolutionary experimental explores fast fect fernandez fine fixed flexible gain gene genealogies genes genet genetic genetics genome genotype graph graphs groupings haplotype haplotypes history hudson hutchins ieee implied improving imputed incompatibilities inference inferred inferring intermediate introduction jiang journal kaplan laboratory larribea leiserson lessarda linkage local loci mailund mammalian mapping marker maximally mcclurg methods miller minichiello mining model modeling more morris mouse multiple nature number ollikainen onkamo order origin paigen pattern perfect phylogenies pletcher population possible power previous pritchard properties provide qhpm quantitative real recombination references regulating resolutions resource results reused rivest sample samples scale schierup schork sensible sequences sets sevon shattered show simulated simulating simultaneous single slutzki space springer statistical stein studies subspecific szatkiewicz tests than that theoretical thrombosis toivonen trait traits transactions tree treedt treeqa trees under using vascular vasko verlag villena waldron wang what whittaker whole wiltshire xiong yang york zollner http://psb.stanford.edu/psb-online/proceedings/psb09/zhang-q.pdf 15 INFERRING GENOME-WIDE MOSAIC STRUCTURE alcohol algorithm algorithms allows analysis ancestral bafna beane bioinfomatics bioinformatics biol biological bounds chen churchill clark close compatible comput computation compute computer constrained constructing dehydrogenase deng ding drosophila dynamic efficiency efficient erties events evolution finding founder from genetics genome genomes genomewide genotyp graphs griffiths gusfield halldorson haplotyp hein history http hudson hutchins improved imputed imputedsnpdata imputedsnps inference inferring international intervals istrail journal june kaplan kreitman lower mamm manuel mcmillan melanogaster minimal minimum mosaic mouse myers nature networks novel nucleotide numb olymorphism optimal oratory ounds pardo parisimonious partitioning perfect phylogenetic pnas proceedings programming prop proposed recombinaiton recombinants recombination recombinations reconstruction references resource robustness sample schwartz sciences sequence sequences song statistical structure structured system szatkiewicz tech their third threadgill ukkonen unknown villena wabi wang waterman wide with workshop zhang http://psb.stanford.edu/psb-online/proceedings/psb09/bidaut.pdf 34 September 22, 2008 acad acids andersson barrett benson bidaut bioinformatics biol biotechnol brestelli brown bruno bryant bunting campb cancer canese chetvernin church clifton comments curr darlington dean diabetes dicale dicuccio dimos dufour edgar endocrinol erger federhen feolo fondation fujimoto funded gasbarrini geer genomics gherraby ghislain gordon grant greer hackney hawley helmb hematol hoffman hong inca initially institut invest ivanova jotte kaestner kapustin kawase khan khovayko kishimoto korbutt lakey landsman lemischka lipman madden maglott manuscript marchand matsuzaki mazzarelli mcweeney melton metab miller mills molofsky moore morrison mulligan murray naka nakagawa national natl nayar nomura nucleic ochs ochsner opin ostell oudes ouyang pardal permutt petersen pharm physiol pinney piscaglia pizarro pour proc pruitt ramalho recherche references santos scearce schaniel schuh schuler science seeb sequeira serada shapiro sherry shumway shup sirotkin sorensen souvorov stapp starchenko stem stoeckert strick sutherland tanaka tatusov tatusova their this trends true turnley uchida valuable venable wagner wahiba walashek weiss wheeler wilde work yaschenko yoon http://psb.stanford.edu/psb-online/proceedings/psb09/tamada.pdf 24 September 22, 2008 acad acids acknowledgments acta affara arterioscler bernardo bind biochem biochemistry biochim biocomput biogrid biol biophys biosystems biotechnol blanquart blood bonsai borlak burns center chem circ clin commun computation computer eisenb endocrinol genet genome genomenetwork gervois glass graeb gray gupta hayashida heuvel hprd html http human immunol imoto index information institute intact invest isbra janes kleemann kodama lapp lefebvre lnbi lond medical mint morgan natl nilsson nucleic oncogene online philos physiol proc provided references science straus super suppl supplementary symp system tamada thebiogrid thromb thum time tokyo trans trends tusher uniroma university vanden vasc yaffe http://psb.stanford.edu/psb-online/proceedings/psb09/voelz.pdf 32 September 17, 2008 academy accessible across addaa alphab annual arendall auerbach ayton bakker bartel bashan biochemical biology biophysics biotechnology bouzida bowman carlo chain chains chem chembiochem chemical chemistry clark close coarse computational conformation cruz current cutout davis debenedetti derived each energy ensemble ensign erformed european exceptionally exit found freeborn from function generalized genetics gerstein gong grained green guarnieri hansen huang izvekov jagopal journal karplus kcal kollman kremer krishna kumar laaksonen landau lengths lovell lucent lyubartsev mankin martsinovski mers model molecular monte moore msfp muto nakamura nakatogawa nascent national nature nissen noid opinion osomal pande pangiotopoulos park petrone phys physical physics pmfs potential praprotnik presence press prisant proceedings proteins references residue review reviews ribosome richardson rosenberg sampled sampling sanbonmatsu scaringe schmeing science sciences seila september sequence sequences shell shevkunov shkurko simulation site size snow soukup squires stable steitz step strobel structural structure swendsen tozzini trace trends trim tung tunnel type used using vera view voelzrevised volume vorontsovvelyaminov voss voth wang wiseman word wspc yanofsky yonath http://psb.stanford.edu/psb-online/proceedings/psb09/eswaran.pdf 28 MULTI-SCALE MODELING OF THE HUMAN VERTEBRAL BODY: COMPARISON OF MICRO-CT BASED HIGHRESOLUTION AND CONTINUUM-LEVEL MODELS acknowledgments adams also amount analyses analysis anatomic applied architecture assessment bayraktar benefit better between bevill billion biomech biomechanics body bone both buckley cann center centrum changes company comparison compressive computational computed computer computing conditions continuum correlated cortical crawford datastar deformation degrees density depend diagnostics diego directly disc distribution during effect element engineering estimates eswaran extend failure faulkner femur financial finite flexion former forward fraction fracture freedom from funding further grant grimm gupta half hasegawa hayes health here high highly homminga huiskes human ieee implicit including influence initial institute interest journal keaveny kopperdahl large level liebschner load loading loads locations lumbar mechanical mechanics mechanisms method methods micro microlevel micromechanics miner modeling models modulus more morgan national networking nonlinear npaci observed orthopaedic osteoporosis over patient patterns performance performed physiological power predicts preparation proceedings properties proximal quantitative radiology recommended references regions relationships remains removal reported research resources results rice rietbergen risk scanning sections sharing shell silva site solid specific specimen spine strength studies supercomputer than these this thoracolumbar through tissue tomography tomographybased trabecular transfer type ultrascalable university using verhulp vertebrae vertebral vitro volume voxel whole with within without work yang http://psb.stanford.edu/psb-online/proceedings/psb09/sen.pdf 8 CONTEXT-SPECIFIC GENE REGULATIONS IN CANCER GENE EXPRESSION DATA* absent addition advantage advantages algorithm algorithms analysis annotated annotation approach archives asserts available barry bayesian bioinformatics biological biology biosystems burton caarray cabig cancer capture captures cell cellular chen clinical cluster clustering clusters compared comparison components comput computational conditioning conf connected context contexts conventional currently data demonstrated densely disease dougherty edges eisen enrichment exhibit expo fifth found friedman gene genes graph gskdata hahn have home http https identification ieee immunology incorporation information inter interesting international intgen intl intra jack jung laboratory larger learning line mapping meaningful medicine mining multivariate network networks noted occurrence oldford olga pages pathology patient pmid pnas prediction proc processing produced properties purposes rarely references regulatory related relationships relevant research results rivas samples sets signal silico specific statistics study subset such sungwon syst tcbb techniques tembe that these this through transactions tumor type uncertainty used using weinberg when which while with working workshop yidong zeeberg http://psb.stanford.edu/psb-online/proceedings/psb09/cheng-b.pdf 2 September 24, 2008 10:32 Proceedings Trim Size: 9in x 6in abdel accelerated adaptive adipocytes advances aided allows also analysis annual antifolate antifolates applications applying approximate arkin automatic automation avoiding bacterial berkeley bifurcation binding biochemical biochemistry biological biology biospice biosynthesis bition braaten brower bruck burnett cell cells channels characterization characterize chem chemical chemically chemistry cheng circuits cofactor cofactors coli college computation computational computer computera conclusions conference coupled currently depletion design developmental digital dihydrofolate dimacs direct diversity drive dynamics effect effects efficient electronics engi epigenetic escherichia evolution ewing exact experimental explicit exploring expression feedback feidler fett flexibility fluctuations gate gene genetics gibson gillespie glucose goldman hearne hernday homsy illustrates implementation implicit incorporating infected information infrastructure inhi input integrative interconversion into intricate journal kinetic kinetics knight kumar leaping lentiviral loop many mathematics mcadams medicine memorandum method methylenetetrahydrofolate midwest mikulecky modeling modules nagel negative network networks omics only output pages pathway petzold phage phenotypic phys physical populations positive preceding princeton problems proceedings program provides purine pyrimidine rape rathinam reacting reactions references research response review riedel role ross scenarios schaffer section seither selection semiconductor september simulate simulation site size sort species spice stepsize stiffness stochastic stochasticity such suppression switch symposium synthase synthesizing synthetic system systems temporal tetrahydrofolate that thymidylate toettcher tools toward transient trent trim utilization variety versus vivo weinberger weiss with working workings workshop zohdy http://psb.stanford.edu/psb-online/proceedings/psb09/neal.pdf 29 ADVANCES IN SEMANTIC REPRESENTATION FOR MULTISCALE BIOSIMULATION: adaptation amia anatomy annotation approach arts based bhalla biochemical biocomput bioinformatics biol biological biology biomedical biosimulation biotechnol borg bovendeerd bridging campagne cardiovascular carlson cell cellml circ circadapt circulation collado computer cook crubezy delhaas determines development environment eriksson evolution ferguson finney foundational from gennari grosso heart hemodynamics home html http hucka human hunter index informatics information integration interaction interactive journal jsim kirn knowledge light load lumens mapping mechanical mechanics mejino merging minimum miriam model modeling models multi multiscale musen neal novere ontologies ontology organs page physics physiol physiome press prinzen project prompt properties protege proteins reference references requested rosse sarcomere scale semantics shape studies suite symp system systems tools ventricular verbeek vides weight http://psb.stanford.edu/psb-online/proceedings/psb09/han.pdf 12 IDENTIFYING PARENT-DAUGHTER RELATIONSHIPS AMONG DUPLICATED GENES1 academy accelerated america analogous analysis ancestral annual assignment asymmetric bailey based berlin betran between bioinformatics biology biomedical cannon cauldron chromosomal chromosome classification comparative computational conference conserved consortium cores crucibles data deletion demuth derived disease distinguishing divergence diversity drosophila duplication duplications eichler emerson evolution evolutionary extensive ferretti first fitch from gain gene genes genet genetics genome genomes hahn high histone homologous human identification insights integrating international jiang journal kent koonin lengths lessons loci long loss macaque mammalian mexico modifications molecular mouse msoar nadeau national ohno original ortholog orthologs orthology orthoparamap paralog paralogs paralogy pevzner phylogenies primate primates proceedings proposed proteins punctuated rate rearrangement rearrangements reconstruction references retroposed reveals rhesus sankoff santa science sciences segment segmental segments sequencing since sonnhammer springer states subtypes system systematic taylor tesler thornton throughput traffic trends united verlag young zheng zoology http://psb.stanford.edu/psb-online/proceedings/psb09/palmisano.pdf 23 September 18, 2008 acknowledgments annual approach arkin bioconcur bioinformatics biol biology biotechnology briefings bright cardelli chemical chemistry ciliberto ciocchetta cmsb computational computer concur controls conversations cosbi cross csikasz cycle danos deling dematt developmental discussions entcs erdi fbtc fisher ghomi gillespie goldbeter gonze halloy henzinger hillston inform journal krivine laneve lecca lett lncs mathematical methods models mura nagy nature novak nurse palmisano panina phys physical physics priami proc process reactions references regev review romanel sabouri science shapiro sible silverman springer steuer tech thank theor theoretical toth tyson http://psb.stanford.edu/psb-online/proceedings/psb09/workshop-opensci.pdf 50 OPEN SCIENCE: TOOLS, APPROACHES, AND IMPLICATIONS * acknowledging actualize additional addressed adopting also archive articulating aspirations benefit benefits best biology celebrate change clearly commons community concerted course develop effect effort eisen equally examples find forward from fully gathering goals good http identify institute involved january learnt momentum open openscience organize paper perimeter pirsa plos pointing points possible practice practices principles provide readingroom recorded references resources right risks science sciencecommons seminar sensitively seriously smolin specific standards starting stock supported take targets that them these thing time times towards useful vickers what widely will work york http://psb.stanford.edu/psb-online/proceedings/psb09/colak.pdf 18 September 22, 2008 above abundant acid alon baskerville berenbrink bioinformatics biological biology bipartite bowie cannot chklovskii circuits colak coli complete complexity computational computations computer confirm corneil database deduced design eisenberg ester experiments finding fraser from generate graphlets grgm grochow hajirasouliha higham hormozdiari however introduction ismb issue itzkovski jurisica karp kashtan kellis matter middendrof miller milo moser network networks newman nonlin nucleic paczuski pettit phys physical plenum plos pnas press principles proc proceedings przulj rafiey rasajski recomb references report research review sahinalp salwinski science seen shen simith simon soft stat strogatz systems table tech that theorem theoretical there this university watts wiggins yeast http://psb.stanford.edu/psb-online/proceedings/psb09/zhang-y.pdf 16 September 20, 2008 acad access alignment alignments amores analysis another anticipate appear appearance approach approaches associated automatically available baertsch before berlin bertrand biol biologist birney bonet cardone carlo cause chen chuzhanova clamp clusters comparative comput computed computing considered consortium conversion cooper currently developed differing donley duplication durbin eichler elemento environmental event events evol evolution explored ferec force free gascuel gene generated genet genetics genewise genome genomewise green groups hardison haussler have health here higher hoffman however hurdle hurle identifying identity instance inversions jiang joie keeney kent lefranc long lynch mabrouk macaque marques means method miller monte nadeau natl nature nisc ohno orthologs other patrinos percent perspectives pevzner pickett postlethwait present presented problems proc proceedings program promising quality raney ratan recomb references reliable remains reviews rhesus schwartz science scientific sequencing several siepel smit song springer strategies swanson tang taylor tesler than that totally ventura vinar wang what which will with work york zhang zones http://psb.stanford.edu/psb-online/proceedings/psb09/fox.pdf 37 September 23, 2008 acids aravind ausiello babu bader barabasi batada berriz bertin bioinformatics biol biotechnol blanchette botstein boucher brasch breitkreutz brown cambridge chiang church comp comput computing curr cusick davis dupuy eisen evol febs felman ferdig flannery fraser gandhi garrels genome gentleman gerstein goldberg haeseleer hart hartemink hartley helmercitterich hermjakob hirsh hogue hosack huber hurst jarvis jeong jordan jurisica kerrien koonin letters lewington luscombe marcotte mason mathivanan matthews mika montecci mudali nature nucleic numerical oltvai opin palazzi plos pnas press quondam ramani reboul recipes references reguly remm rost roth sarkar scharfe scholtens science scientific sherman smith sonnhammer 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previously proc processes quiescent quinones references response rounthwaite science scott segal share significantly similarities smith specific spellman sporulation starvation structure study subgraphs such suggest suggests summary suppl syst tech that their theory there these thomas three underannotated understanding university wang washburne werner which wileyinterscience with yeast york