18th Annual International Conference on Research in Computational Molecular Biology
Pittsburgh, Pennsylvania
April 2-5, 2014

Poster Sessions

ISCB Poster Session NSF Poster Session

ISCB Poster Session
Thursday, April 3
2:10pm-2:30pm, Ballroom, William Pitt Union

1 Progressive promoter element combinations classify conserved orthogonal plant circadian gene expression modules
Sandra Smieszek and Bart Przychodzen

3 Folding Prediction of Bi-dimensional (2D) Structure of Proteins using an Ant Colony Optimization Algorithm (ACOA)
John Fredy Gómez Rojas, Álvaro Andrés Obregón Carreñno, Dario José Delgado Quintero and Rodrigo Torres

5 Exploring distance between fusion genes in human genetic interaction network
Nanfang Xu

7 Identification of Gene Biomarkers for Anti-Cancer Drugs Using Parallel PLS-Based Models
Iraj Hosseini, R. Joseph Bender and Feilim Mac Gabhann

9 eFINDSITEPPI: Structure Based Prediction of Protein-Protein Interactions
Surabhi Maheshwari and Michal Brylinski

11 Source-target connectivity in networks of uncertain topology
Andrei Todor, Haitham Gabr, Alin Dobra and Tamer Kahveci

13 Validated methods for predictive genetics
Michael R. Brent, Ezekial Maier, Brian Haynes and Tamara Doering

15 Terrace aware phylogenomic inference
Olga Chernomor, Bui Quang Minh and Arndt von Haeseler

17 Deciphering the chromatin-related signaling from histone modification and chromatin modifier data
Juliane Perner, Julia Lasserre, Martin Vingron and Ho-Ryun Chung

19 Computational analysis of protein-ligand interactions of enzyme genes involved in sulphate reduction
Paul Leyva-Miranda, Fernando Bastida-Gonzalez, Gemma Ramirez-Salinas, Jose Correa-Basurto, Paola Zarate-Segura and Claudia Guerrero-Barajas

21 Identification of Conserved RNA Structural Motifs using A Subgraph Random Sampling Approach
Jiajie Huang, Kejie Li and Michael Gribskov

23 A Global Profiling of Alternative Splicing Exon Expression Patterns across Multiple Human Tissues with RNA-Seq Data
Zhiyi Qin, Yi Xing and Xuegong Zhang

25 The Prediction of Protein-Protein Interactions between Myoglobin and Haptoglobin Through Computational Modeling and Confirmation of Binding through Mass Spectrometry
Ololade Fatunmbi, Rinat Abzalimov, Anne Gershenson and Igor Kaltashov

27 Finding Differential Splice Junctions as Biomarkers in Prostate Cancer from Next Generation Sequencing Data
Iman Rezaeian, Ahmad Tavakoli, Dora Cavallo-Medved, Lisa Porter and Luis Rueda

29 Using a Hierarchical Classification Model for Predicting Ten Breast Cancer Subtypes
Forough Firoozbakht, Iman Rezaeian, Alioune Ngom, Lisa Porter and Luis Rueda

31 An optimal experimental design scheme for learning Boolean network models
Nir Atias, Michal Gershenzon, Katia Labazin and Roded Sharan

33 A differential co-expression networks approach to uncovering mechanisms underlying skeletal muscle pathophysiology
Kavitha Mukund and Shankar Subramaniam

35 Rewiring of airway gene expression-based networks by bronchial dysplasia and lung cancer
Anna Tassinari, Bin Zhang, Duncan Whitney, Kate Porta, Stephen Lam, Marc Lenburg, Avrum Spira and Jennifer Beane

37 Finding network motifs using MCMC sampling
Tanay Kumar Saha and Mohammad Al Hasan

39 Improvements in protein function prediction using confidence in protein interactions
Kathryn Doroschak, Thomas Schaffner and Lenore Cowen

41 BisKit: A pipeline for large-scale bisulfite sequencing analysis
Jawon Song, Nathan M Springer and Matthew W Vaughn

43 A novel method for identifying OR relationship in eQTL mapping
Zhiyong Wang, Jinbo Xu and Xinghua Shi

45 Higher-order chromatin domains link eQTLs with the expression of far-away genes
Geet Duggal, Hao Wang and Carl Kingsford

47 Dissecting Germ Cell Metabolism through Network Modeling
Leanne Whitmore and Ping Ye

49 Hybrid Approach Using SVM and MM2 in Splice Site Junction Identification
Srabanti Bhunia and Deepak Garg

51 Biomedical Data Fusion by Simultaneous Matrix Tri-factorization
Marinka Zitnik and Blaz Zupan

53 High-throughput genome scaffolding from in vivo DNA interaction frequency
Noam Kaplan and Job Dekker

55 Sex-specific expression of hepatic lincRNAs: potential role in growth hormone (GH) regulation of liver epigenetic states.
Tisha Melia and David Waxman

57 Algorithms and complexity results for genome mapping problems
Cedric Chauve, Jan Manuch, Ashok Rajaraman and Joao Paulo Pereira Zanetti

59 Privacy Preserving Calculation of Fisher Criterion Score for Informative Gene Selection
Suxin Guo, Sheng Zhong and Aidong Zhang

61 Efficient Alignment and Variant Calling at Scale Using the Cloud
Frank A Nothaft, Matt Massie, Ameet Talwalkar, Bill Bolosky, Jeremy Elson and David Patterson

63 Computational Analysis of Domain Interactions Between Components of the SCF Ligase
Mina Maleki, Mohammad Haj Dezfulian, William Crosby and Luis Rueda

65 Reconstructing dynamic microRNA-regulated interaction networks
Marcel Schulz, Kusum Pandit, Christian Lacks Lino Cardenas, Namasivayam Ambalavanan, Naftali Kaminski and Ziv Bar-Joseph

67 Active Learning Based Matrix Completion for Predicting Drug-Target Interactions
Maja Temerinac-Ott, Armaghan W. Naik and Robert F. Murphy

69 Assessing Collective Disease Association of Multiple Genomic Loci
Marzieh Ayati, Pamela L. Clark, Mark R. Chance and Mehmet Koyuturk

71 A Combinatorial Perspective of the Protein Inference Problem
Chao Yang, Zengyou He and Weichuan Yu

73 Computational modeling of miRNA biogenesis: an insight into transcription and processing
Annalisa Marsico, Thomas Conrad, Martin Vingron and Ulf Ørom

75 Identification of Gene Biomarkers for Anti-Cancer Drugs Using Parallel PLS-Based Models
Iraj Hosseini, R. Joseph Bender and Feilim Mac Gabhann

77 Generative models of the spatial organization of neurons
Rebecca Elyanow, Xuexia Jiang, Devin Sullivan and Robert F. Murphy

79 A combinatorial approach for analyzing intra-tumor heterogeneity from high-throughput sequencing data
Iman Hajirasouliha, Ahmad Mahmoody and Ben Raphael

81 Transfer learning for reconstructing dynamic signaling and regulatory networks
Siddhartha Jain and Ziv Bar-Joseph

83 Fast Lossless Compression via Cascading Bloom Filters
Roye Rozov, Ron Shamir and Eran Halperin

85 Loads-To-Nodes: A Framework for Managing Biological Databases on Massively Parallel Environments
Dana Silverbush and Roded Sharan

87 Network orientation via shortest paths
Ahmad Salah and Li Kenli

89 Molecular function profile meta-analysis deciphers common molecular and pathological signatures of leukemia stem cells
Xinan Yang, Aurelie Desgardin, Jianjun Chen, Jill de Jong and John Cunningham

91 microRNAs located in the Hox gene clusters are implicated in Huntington.s disease pathogenesis
Vinay Kartha, Andrew Hoss, Xianjun Dong, Jeanne Latourelle, Alexandra Dumitriu, Tiffany Hadzi, Marcy MacDonald, James Gusella, Schahram Akbarian, Jiang-Fan Chen, Zhiping Weng and Richard Myers

93 A Neutrophil Phenotype Model for Extracorporeal Treatment of Sepsis
Robert Sheehan, Alex Malkin, Shibin Mathew, Heinz Redl and Gilles Clermont

95 TEAM: TE Annotation from Methylation
Gregory Zynda

97 Discovering conserved secondary structures in lncRNAs
Ardalan Naseri and Shaojie Zhang

99 MRFalign: Protein Homology Detection through Alignment of Markov Random Fields
Jianzhu Ma, Sheng Wang, Zhiyong Wang and Jinbo Xu

NSF Poster Session
Friday, April 4
5:30pm-7:00pm, Ballroom, William Pitt Union

2 SynDeC: High-throughput synapse detection and characterization in electron microscopy images
Kelvin Liu, Saket Navlakha, Santosh Chandrasekaran, Alison L. Barth and Ziv Bar-Joseph

4 TACO: a general-purpose tool for predicting cell-type.specific transcription factor dimers
Aleksander Jankowski, Shyam Prabhakar and Jerzy Tiuryn

6 Speeding Up Sequence Alignment for MetaGenomic Clustering Using Early Stopping
Louis Oliphant, Nicola Pedretti and Matthew Pozderac

8 Efficient Modeling and Active Learning of Biological Responses: Learning without Prior Knowledge
Armaghan Naik, Joshua Kangas, Devin Sullivan, Christopher Langmead and Robert F. Murphy

10 Convex Risk Minimization To Infer Networks From Probabilistic Diffusion Data At Multiple Scales
Emre Sefer and Carl Kingsford

12 Effects of Geometry on Computational Kinetics Models of Early Endosomes
Rohan Arepally, Devin Sullivan and Robert F. Murphy

14 omiRas: a Web server for differential expression analysis of miRNAs derived from small RNA-Seq data
Soeren Mueller, Lukas Rycak, Peter Winter, GüKahl and BjöRotter

16 Variant detection model with improved robustness and accuracy for low-depth targeted next-generation sequencing data
Patrick Flaherty and Fan Zhang

18 A new method for gene-fusion detection: Fusion-Detection by Assembly (FDA)
Nanfang Xu

20 Algorithms for inferring evolutionary models of tumor progression from single-cell heterogeneity data
Salim Akhter Chowdhury, Alejandro Schaffer, Stanley Shackney, Darawalee Wangsa, Kerstin Heselmeyer-Haddad, Thomas Ried and Russell Schwartz

22 Identification of Binding Site Enrichment of Ikaros in Leukemia with a new data analysis pipeline
Xiaokang Pan, Chunhua Song, Sadie Steffens and Sinisa Dovat

24 An Image-derived 3D Generative Model for the Spatial Dependence of Multiple Protein Patterns Reveals Differences between Plant Protoplasts in Different Drug Conditions
Pingshan Zhang, Gregory Johnson, Joshua Kangas, Alexander Dovzhenko, Klaus Palme and Robert F. Murphy

26 Mathematical modeling of Ras/MAPK signaling network kinetics provides insights into mechanisms of FGF2-induced cell cycle arrest in the K-Ras-driven mouse Y1 adrenocortical tumor cells
Marcelo S. Reis, Matheus H.S. Dias, Fáo Nakano, Junior Barrera and Hugo A. Armelin

28 Epistatic interactions during somatic evolution in cancer
Navodit Misra

30 CeTICSdb: a platform for interdisciplinary research that allows quantitative and qualitative -omics analyses and mathematical modeling of signaling networks
Marcelo S. Reis, Milton Y. Nishiyama-Jr, Daniel F. Silva, Ináo L.M. Junqueira-De-Azevedo, Julia P.C. Da Cunha, Junior Barrera, Leo K. Iwai, Solange M.T. Serrano and Hugo A. Armelin

32 IQ-TREE: A simple and efficient stochastic search algorithm for estimating maximum-likelihood phylogenies
Lam Tung Nguyen, Heiko Schmidt, Arndt von Haeseler and Bui Quang Minh

34 Computing Free Energies With PyBrella
Charles Yuan and David Koes

36 Accelerating systems biology computation: Rapid estimation of equilibrium and kinetic quantities via weighted ensemble sampling
Rory Donovan, Daniel Zuckerman, James Faeder, Andrew Sedgewick, Jun Ma and Markus Dittrich

38 Kraken: ultrafast metagenomic sequence classification using exact alignments
Derrick Wood and Steven Salzberg

40 Cloud Computing Chemogenomics Knowledgebases and Cheminformatics Tools for Polypharmacology Networks
Haibin Liu, Lirong Wang and Xiang-Qun Xie

42 Ligand Affinity Prediction with Grid Inhomogeneous Solvation Theory and smina
James Castiglione and David Koes

44 Probabilistic Method for Detecting Copy Number Variation in a Fetal Genome using Maternal Plasma Sequencing
Ladislav Rampasek, Aryan Arbabi and Michael Brudno

46 ENNET: A Method for Gene Regulatory Network Inference
Janusz Slawek and Tomasz Arodz

48 MASSIVELY PARALLEL PARE PREDICTION TOOL (MPPP): High-performance identification of plant sRNA targets at genome level
Atul Kakrana, Reza Hammond, Parth Patel, Mayumi Nakano and Blake Meyers

50 Pluribus - Using Multiple Manifestations of a Sequencing Error in a Suffix-Tree to Improve Correction
Daniel Savel, Thomas Laframboise, Ananth Grama and Mehmet Koyuturk

52 Identification of Alternative Topological Domains in Chromatin
Darya Filippova, Rob Patro, Geet Duggal and Carl Kingsford

54 Benchmarking of base pair interaction predictions from RNA 3D structures
Shahidul Islam and Shaojie Zhang

56 Identification of Cohesive and Reproducible Patterns of Epistasis in Psoriasis
Pam Clark, Mark R. Chance and Mehmet Koyuturk

58 Comparative Assembly Hubs: Web Accessible Browsers for Comparative Genomics
Ngan Nguyen, Glenn Hickey, Brian Raney, Joel Armstrong, Hiram Clawson, Ann Zweig, Jim Kent, David Haussler and Benedict Paten

60 Effects of EPHB6 Expression in Human Breast Tumours on Metastasis and Survival
Matthew Shannon, Andrew Freywald and Anthony Kusalik

62 Novel transcriptional signatures of host immune response can distinguish viral hemorrhagic fever infection from respiratory virus infection
Sara Garamszegi

64 Examination of Stability of HMMs When Applied to CpG Island Prediction
Daniel Hogan and Anthony Kusalik

66 Construction of a Metabolic Interactome for Insight into Microbial Ecosystems
Brian Granger

68 GLAD: A mixed-membership model for heterogeneous tumor subtype classification
Patrick Flaherty, Jon McAuliffe and Hachem Saddiki

70 Integration of Disparate Mapping Algorithms for Improved Alignment of Short Sequencing Reads
Matthew Ruffalo, Thomas Laframboise and Mehmet Koyuturk

72 Reference-free Inference of Tumor Phylogenies from Single-Cell Sequencing Data
Ayshwarya Subramanian and Russell Schwartz

74 Predictive Models for Head and Neck Cancer Stage from Genomic and Proteomic Data
Chanchala D. Kaddi and May D. Wang

76 Estimating insertion, deletion, and recombination rates of Insertion Sequence (IS) elements in the genome of Escherichia coli
Heewook Lee, Ellen Popodi, Patricia Foster and Haixu Tang

78 Tumor heterogeneity in Chronic Lymphocytic Leukemia
Luis Zapata and Stephan Ossowski

80 Pareto-optimality and Consensus Support in Duplication-Transfer-Loss Reconciliation
Ran Libeskind-Hadas, Yi-Chieh Wu and Mukul Bansal

82 BlindCall: ultra-fast base-calling of high-throughput sequencing data by blind deconvolution
Chengxi Ye, Chiaowen Hsiao and Hector Corrada Bravo

84 Benchmark Analysis of Algorithms for Reconstructing Full Splice Forms from RNA-Seq
Katharina Hayer, Angel Pizarro, John Hogenesch and Gregory Grant

86 A method for predicting protein-protein interaction types
Yael Silberberg, Martin Kupiec and Roded Sharan

88 Extensive Cross-regulation in Post-transcriptional Regulatory Network in Drosophilia
Marcus Stoiber, Gemma May, Michael Duff, Robert Obar, Spyros Artavanis-Tsakonas, Ben Brown, Brenton Graveley and Susan Celniker

90 De novo discovery of transcription factor footprints from high-resolution sequencing data
Alessandro Mammana and Ho-Ryun Chung

92 DREISS: Decomposition of gene Regulatory network into External and Internal components based on State Space models
Daifeng Wang, Fei He, Sergei Maslov and Mark Gerstein

94 ReconModels.org: An Online Database of Reconstructed Metabolic Networks
A. Ercument Cicek, Bryan Marty, Xinjian Qi and Gultekin Ozsoyoglu

96 Discovering conserved secondary structures in lncRNAs
Ardalan Naseri and Shaojie Zhang

98 RVD2: An ultra-sensitive variant detection model for low-depth targeted next-generation sequencing data
Patrick Flaherty and Yuting He