PSB 2012 Abstract Book PACIFIC SYMPOSIUM ON BIOCOMPUTING 2012 ABSTRACT BOOK Papers are organized by session then last name of first author. Presenting authors’ names are underlined. 1 PSB 2012 Abstract Book ACCEPTED PROCEEDINGS PAPERS WITH ORAL PRESENTATIONS .................................... 10 IDENTIFICATION OF ABERRANT PATHWAY AND NETWORK ACTIVITY FROM HIGH- THROUGHPUT DATA ......................................................................................................................... 11 SSLPRED: PREDICTING SYNTHETIC SICKNESS LETHALITY ................................................. 12 NirmAlyA BandyopAdHyAy, SanJay RanKa and Tamer KAHveci Predicting tHe Effects of Copy-Number Variation in Double and Triple Mutant Combinations ...................................................................................................................................... 13 Gregory W. CArter, MicHelle HAys, Song Li, TimotHy GAlitsKi INTEGRATIVE NETWORK ANALYSIS TO IDENTIFY ABERRANT PATHWAY NETWORKS IN OVARIAN CANCER ......................................................................................................................... 14 Li CHen, JiAnHuA XuAn, JingHua Gu, Yue Wang, ZHen ZHang, TiAn-Li Wang, Ie-Ming SHiH Role of SyntHetic Genetic InterActions in UnderstAnding FunctionAl InterActions Among PAtHwAys ................................................................................................................................ 15 ShAHin MoHammadi, Giorgos KolliAs, And Ananth GrAmA Discovery of MutAted SubnetworKs AssociAted witH ClinicAl DAtA in CAncer ............... 16 Fabio Vandin, PAtricK ClAy, Eli Upfal, Benjamin J. Raphael INTRINSICALLY DISORDERED PROTEINS: ANALYSIS, PREDICTION AND SIMULATION .................................................................................................................................................................. 17 QuAsi-AnHArmonic AnAlysis reveAls intermediAte stAtes in tHe nucleAr co-activator receptor binding domAin ensemble ............................................................................................ 18 VirginiA M. Burger, Arvind RamAnAtHAn, AndreJ J. SAvol, CHristopHer B. StAnley, PrAtul K. AgArwal and ChakrA S. ChennubhotlA EFFICIENT CONSTRUCTION OF DISORDERED PROTEIN ENSEMBLES IN A BAYESIAN FRAMEWORK WITH OPTIMAL SELECTION OF CONFORMATIONS ..................................... 19 Charles K. Fisher, Orly UllmAn, Collin M. Stultz INTRINSIC PROTEIN DISORDER AND PROTEIN-PROTEIN INTERACTIONS ..................... 20 Wei-Lun Hsu, CHristopHer Oldfield, Jingwei Meng, Fei HuAng, Bin Xue#, VlAdimir N. UversKy, Pedro Romero, And A. KeitH Dunker SUBCLASSIFYING DISORDERED PROTEINS BY THE CH-CDF PLOT METHOD ................. 21 Fei Huang, CHristopHer Oldfield, Jingwei Meng, Wei-Lun Hsu, Bin Xue, Vladimir N. UversKy, Pedro Romero And A. KeitH DunKer FUNCTIONAL ANNOTATION OF INTRINSICALLY DISORDERED DOMAINS BY THEIR AMINO ACID CONTENT USING IDD NAVIGATOR ...................................................................... 22 AsHwini PAtil, SHunsuKe TerAgucHi, Huy DinH, KentA NAKAi, Daron M StAndley MODULATING PROTEIN–DNA INTERACTIONS BY POST-TRANSLATIONAL MODIFICATIONS AT DISORDERED REGIONS ............................................................................ 23 DanA VuzmAn, Yonit HoffmAn, YaAKov Levy MICROBIOME STUDIES: ANALYTICAL TOOLS AND TECHNIQUES ...................................... 24 EstimAting populAtion diversity witH unreliAble low frequency counts ........................ 25 JoHn Bunge, DAnKmAr BoHning, HeAtHer K. Allen, JAmes A. Foster 2 PSB 2012 Abstract Book COMPARISONS OF DISTANCE METHODS FOR COMBINING COVARIATES AND ABUNDANCES IN MICROBIOME STUDIES ................................................................................... 26 Julia FuKuyAmA, PAul J. McMurdie, Les DetHlefsen, DAvid A. RelmAn, SusAn Holmes SEPP: SATe ́ -EnAbled PHylogenetic PlAcement ........................................................................ 27 S. Mirarab, N. Nguyen, T. WArnow ARTIFICIAL FUNCTIONAL DIFFERENCE BETWEEN MICROBIAL COMMUNITIES CAUSED BY LENGTH DIFFERENCE OF SEQUENCING READS .................................................................. 28 QuAn ZHAng, THomAs G. DoAK, YuzHen Ye MetaDomain: a profile HMM-bAsed protein domAin clAssificAtion tool for short sequences ............................................................................................................................................. 29 YuAn ZHAng, Yanni Sun MODELING HOST-PATHOGEN INTERACTIONS ......................................................................... 30 STRUCTURAL MODELS FOR HOST-PATHOGEN PROTEIN-PROTEIN INTERACTIONS: ASSESSING COVERAGE AND BIAS .................................................................................................. 31 Eric A. FranzosA, Yu XiA IDENTIFICATION OF CELL CYCLE-REGULATED, PUTATIVE HYPHAL GENES IN CANDIDA ALBICANS .......................................................................................................................... 32 RalucA GordAn, SAumyAdiptA Pyne, MArtHA L. BulyK Determining confidence of predicted interActions between HIV-1 and human proteins using conformAl metHod ................................................................................................ 33 Ilia Nouretdinov, Alex GAmmermAn, YAnjun Qi, JuditH Klein-SeetHaraman PERSONALIZED MEDICINE .............................................................................................................. 34 Interpretome: A Freely AvAilAble, ModulAr, And Secure PersonAl Genome InterpretAtion Engine ....................................................................................................................... 35 KonrAd J. KarczewsKi, Robert P. Tirrell, PAblo Cordero, NicHolAs P. TAtonetti, Joel T. Dudley, KeyAn SAlAri, MicHAel Snyder, Russ B. AltmAn, StuArt K. Kim A KinAse inHibition mAp ApproAcH for tumor sensitivity prediction And combinAtion tHerApy design for tArgeted drugs ............................................................................................... 36 RanAdip PAl and NoAH Berlow MIXTURE MODEL FOR SUB-PHENOTYPING IN GWAS ............................................................ 37 David WArde-Farley, MichAel Brudno, QuAid Morris, AnnA Goldenberg TEXT AND KNOWLEDGE MINING FOR PHARMACOGENOMICS ............................................ 38 THe ExtrAction of PHArmAcogenetic And PHArmAcogenomic RelAtions – A CAse Study Using PHArmGKB ................................................................................................................................ 39 Ekaterina BuyKo, Elena Beisswanger and Udo Hahn LINKING PHARMGKB TO PHENOTYPE STUDIES AND ANIMAL MODELS OF DISEASE FOR DRUG REPURPOSING ............................................................................................................... 40 Robert HoeHndorf, AniKA OellricH, DietricH RebHolz-ScHuHmann, Paul N. Schofield, Georgios V. Gkoutos IntegrAting VA’s NDF-RT drug terminology witH PHArmGKB: PreliminAry Results .... 41 JyotisHmAn PAtHAK, LAurA C. Weiss, MAttHew J. DursKi, QiAn ZHu, Robert R. FreimutH, Christopher G. Chute 3 PSB 2012 Abstract Book Discovery And ExplAnAtion of Drug-Drug InterActions viA Text Mining ......................... 42 BetHAny PercHA, YAel GArten, Russ B. AltmAn RANKING GENE-DRUG RELATIONSHIPS IN BIOMEDICAL LITERATURE USING LATENT DIRICHLET ALLOCATION ................................................................................................................. 43 YongHui Wu, Mei Liu, W. Jim ZHeng, ZHongming ZHAo, HuA Xu ACCEPTED PROCEEDINGS PAPERS WITH POSTER PRESENTATIONS ............................... 44 INTRINSICALLY DISORDERED PROTEINS: ANALYSIS, PREDICTION AND SIMULATION .................................................................................................................................................................. 45 CORRELATION BETWEEN POSTTRANSLATIONAL MODIFICATION AND INTRINSIC DISORDER IN PROTEIN .................................................................................................................... 46 Jianjiong GAo and Dong Xu Intrinsic disorder witHin And flAnKing tHe DNA-binding domAins of HumAn trAnscription fActors ......................................................................................................................... 47 Xin Guo, MArtHA L. BulyK, and Alexander J. HarteminK Coevolved residues And tHe functionAl AssociAtion for intrinsicAlly disordered proteins ................................................................................................................................................. 48 Chan-SeoK Jeong and Dongsup Kim CRYPTIC DISORDER: AN ORDER-DISORDER TRANSFORMATION REGULATES THE FUNCTION OF NUCLEOPHOSMIN ................................................................................................... 49 DiAnA M MitreA And RicHArd W KriwAcKi ON THE COMPLEMENTARITY OF THE CONSENSUS-BASED DISORDER PREDICTION .. 50 Zhenling Peng and LuKasz Kurgan MICROBIOME STUDIES: ANALYTICAL TOOLS AND TECHNIQUES ...................................... 51 PROTEOTYPING OF MICROBIAL COMMUNITIES BY OPTIMIZATION OF TANDEM MASS SPECTROMETRY DATA INTERPRETATION ................................................................................ 52 Alys Hugo, DouglAs J. BAxter, WilliAm R. CAnnon, AnAntH KAlyAnArAmAn, GAurAv KulKArni, StepHen J. Callister pHyloseq: A Bioconductor pAcKAge for HAndling And AnAlysis of High-tHroughput pHylogenetic sequence dAtA ..........................................................................................................