Submission 160: mahmoud elhefnawi, Mohamed Ahmed and Jon Garibaldi.
MysiRNA-Designer: A workflow for Efficient siRNA Design Considering splice-variants, Multi-score filtration, Target Accessibility and both perfect and seed-matching off-targets
Submission 172: Kiyeol Kim and In-Ho Cha.
Significance of molecular markers in survival prediction of oral squamous cell carcinoma
Submission 182: Franziska
Hufsky, Kerstin
Scheubert, Florian
Rasche and Sebastian
Böcker.
Fragmentation Trees from MSn Data
Submission 214: Meng-Ru Ho, Kuo-Wang Tsai and Wen-Chang Lin.
Pseudo? Regulation of Young Duplicated Genes in Human
Submission 215: Vindyashree C.
Sequence and conformational analysis of AgrD peptides. Implications: bacterial studies in Staphylococcus aureus
Submission 216: Ahmad Mahmoody-Ghaidary, Cedric Chauve and Ladislav Stacho.
Theoretical advances on multichromosomal median computation
Submission 217: Bruno Zeitouni, Valentina Boeva, Andrei Zinovyev, Kevin Bleakley, Isabelle Janoueix-Lerosey, Sophie Loeillet, Patricia Legoix-Ne, Alain Nicolas, Olivier Delattre and Emmanuel Barillot.
SVDetect - FREEC: two complementary tools for the detection of genomic structural variants from deep sequencing data
Submission 219: Magdalena Stock,
Antje Burse and Wilhelm Boland.
Annotation
of Phaedon cochleariae's transcriptme and
establishment of BLAST servers and genome
browser
Submission 220: Sudeep Srivastava and Liang Chen.
A two parameter generalized Poisson model to improve the analysis of RNA-seq data
Submission 221: John Reid and Lorenz Wernisch.
STEME: Efficient EM for motif search using suffix trees
Submission 222: Xiaolin Hao, Rui Jiang and Ting Chen.
CROP: Clustering 16S rRNA for OTU Prediction
Submission 223: Florian Schatz, Sascha Möller and Manfred Schimmler.
Smarti - A fast short read alignment algorithm
Submission 224: Matthew D. Whiteside, Matthew R. Laird and Fiona S. L. Brinkman.
Ortholuge: a tool for precise, high-throughput prediction of orthologs
Submission 225: Daron Standley, Taeho Kim, Takashi Mino, Alexis Vandenbon, Yutaka Suzuki and Osamu Takeuchi.
An Integrated Approach to RNA Regulatory Motif Discovery
Submission 226: Ho-Lin Chen, Anne Condon and Hosna Jabbari.
An $O(n^5)$ Algorithm for MFE Prediction of Kissing Hairpins and 4-Chains in Nucleic Acids
Submission 227: Samart Wanchana, Sarah Covshoff, Rowan Sage, Gane Wong, Julian Hibberd and Richard Bruskiewich.
Cloud-Based High-Throughput Comparative Analysis of Plant Species Genomes
Submission 228: Dennis Wang, Augusto Rendon and Lorenz Wernisch.
Cis-regulatory binding predicts gene expression across human tissues.
Submission 229: Shatavia Morrison, Aurora Cain and Cynthia Gibas.
Genosets: Pangenomic view of Vibrio vulnificus Biotype 1 E-genotypes strains through use of next gen sequencing
Submission 230: Christian Frech and Nansheng Chen.
Computational comparison of six Plasmodium genomes identifies putative human virulence genes
Submission 231: Yaron Butterfield, Olena Morozova, Alexandra Maslova, Michael Blough, Suganthi Chittaranjan, Jennifer Chan, Nina Thiessen, Richard Varhol, Yongjun Zhao, Martin Hirst, Richard Corbett, Stephen Yip, Gregory Cairncross and Marco Marra.
Integrative genomic and transcriptome analysis of oligodendroglioma using next generation sequencing technology
Submission 232: Uri Weingart, Erez Persi and David Horn.
Specific Peptides Facilitate Metagenomic Analysis
Submission 233: Leonid Zaslavsky, Boris Fedorov, Azat Badretdin, Yiming Bao, James Brister, Stacy Ciufo, William Klimke, Kathleen O'Neill, Alexandre Souvorov and Tatiana Tatusova.
Visualizing Multiscale Complexity and Features of Biological Sequence Datasets
Submission 235: Sandra Smieszek, Paul Devlin and Alberto Paccana.
Towards a programming code of circadian clock in plants
Submission 236: Murray Patterson.
The Gapped Consecutive-Ones Property
Submission 237: Jung Eun Shim and Insuk Lee.
Network-guided prediction of function-driven domains
Submission 238: Annika Kreuchwig, Gunnar Kleinau, Franziska Kreuchwig, Catherine L. Worth and Gerd Krause.
Interactive online toolbox for sequence-structure-function analysis based on comprehensive mutation data
Submission 239: Kevin Silverstein, Kenneth Beckman, Matthew Bower, Kari Bunjer, Matthew Schomaker, Teresa Kemmer, Lisa Schimmenti, Sophia Yohe, Randolph Peterson, Amy Karger, Monika Roychowdhury and Bharat Thyagarajan.
Optimization of Bait Selection for Sequence Capture Arrays
Submission 240: Ting Gong, Nicole Hartmann, Isaac Kohane, Volker Brinkmann, Bolan Linghu, Frank Staedtler, Martin Letzkus and Joseph Szustakowski.
Computational Deconvolution of Complex Transcriptomics Data from Clinical Trials
Submission 241: Shailesh Tripathi and Frank Emmert-Streib.
Comparing the influence of the sample size on the differential expression of pathways on univariate and multivariate methods
Submission 242: Francesca Cordero, Daniele Manini, Andras Horvath and Gianfranco Balbo.
Simplification of a complex signal transduction model by the application of invariants and flow equivalent server
Submission 243: Elena Rivas and Sean Eddy.
Probabilistic modeling improves RNA secondary structure prediction
Submission 244: Ying Zhang, Mark Romanish and Dixie Mager.
Finding Transposon-Sensitive Zones in Mammalian Introns
Submission 245: Amin Emad, Wei Dai and Olgica Milenkovic.
Protein-protein interaction prediction using non-linear matrix completion methods
Submission 246: Jaeyoung Kim, Miyoung Shin, Munpyo Hong and Erkhembayar Jadamba.
A SNP Ranking Method Using Gene Relation Network Derived from Literature for Genome-Wide Association Study
Submission 247: Jianlin Cheng, Zheng Wang and Jesse Eickholt.
Designing and Benchmarking the MULTICOM Protein Structure Prediction System
Submission 248: Jea Woon Ryu, Byeol Na Park, Sung Jin Cho, Jun Ho Park, Jae Soo Yoo and Hak Yong Kim.
Identification of putative domains that suppress cancer cell growth from cancer target proteins
Submission 249: Tobias
Petri, Robert
Küffner and Ralf
Zimmer.
Experiment Specific Expression Patterns
Submission 250: Byeol Na Park, Sung Jin Cho, Jun Ho Park, Jae Soo Yoo and Hak Yong Kim.
Transcriptional regulation of cancer-related target proteins based on microRNAs
Submission 251: Jurgen F. Nijkamp, Marcel A. Van Den Broek, Marcel J.T. Reinders, Jean-Marc Daran and Dick De Ridder.
Whole genome sequencing, assembly and annotation of the Saccharomyces cerevisiae strain CEN.PK 113-7D
Submission 252: Louella Vasquez and Sach Mukherjee.
Exploring early drivers of stem-cell reprogramming by an integrative statistical approach
Submission 253: Ratna Prabha, Dhananjaya Pratap Singh, Alok Srivastava and Dilip Arora.
Codon selection pattern in Thermosynechococcus elongatus genome
Submission 254: Yves Gagnon, Mathieu Blanchette and Nadia El-Mabrouk.
Evolution by Whole Genome Duplication
Submission 255: Babak Alipanahi Ramandi, Nathan Krislock, Ali Ghodsi, Henry Wolkowicz, Logan Donaldson and Ming Li.
SPROS: An SDP-Based Protein Structure Determination from NMR Data
Submission 256: Florian Hahne, Remi Terranova, Jonathan Moggs, Olivier Grenet and David Heard.
Locus-specific DNA methylation analysis via amplicon deep sequencing
Submission 257: Andrew Parker, Karl Griswold and Chris Bailey-Kellogg.
Functional deimmunization of therapeutic proteins by IP^2 (Integer Programming for Immunogenic Proteins)
Submission 258: Ole Schulz-Trieglaff, Matthew Hims, Niall Gormley, Geoffrey Smith and Dirk Evers.
Assembling whole genomes using Illumina mate pair reads
Submission 259: Patrick Schmid, Nathan Palmer, Isaac Kohane and Bonnie Berger.
Building Large-Scale Gene Expression Classification Databases Using Active Learning
Submission 260: Alex Pankov, Raymond Cavalcante, Daniel Dewoskin, Rob Scharein, Catherine Park, Mariel Vazquez and Javier Arsuaga.
Using Computational Algebraic Topology to Characterize Chromosomal Instability in Cancer
Submission 261: Meromit Singer, Alexander Engstroem, Alexander Schoenhuth and Lior Pachter.
Determining coding CpG islands by identifying regions significant for pattern statistics on Markov chains
Submission 262: Richard Varhol, Tina Wong, Irene Li, Margret Asgeirsdottir, Yaron Butterfield, Richard Corbett, Anthony Fejes, Greg Stazyk, Inanc Birol and Steven Jones.
An Integrated Database And Viewer For Tracking Illumina and SOLiD Sequencing and Analysis
Submission 263: Saman Vaisipour, Russell Greiner, David Wishart, Meysam Bastani and Chun-Nam Yu.
Learning Predictors by Integrating Multiple Microarray Datasets
Submission 264: Heesun Shin, Mandeep Takhar, Zsuzsanna Hollander, Janet Wilson-Mcmanus, Raymond Ng, Robert Balshaw, Paul Keown, Robert Mcmaster, Bruce Mcmanus and Scott Tebbutt.
Exploratory multivariate analysis of peripheral whole blood gene expression data in organ transplantation
Submission 265: Jesse Gillis and Paul Pavlidis.
Multifunctionality drives gene characterization: A re-evaluation of hubs and promiscuity in gene function prediction
Submission 266: Elena Peterson, Jeffrey Jensen, Hyunjoo Walker, Alexandra Schrimpe-Rutledge, Lee Ann Mccue, Samuel Payne, Joshua Adkins and Bobbie-Jo Webb-Robertson.
A Visualization and Evaluation Platform to Facilitate Prokaryotic Proteogenomic data analysis - VESPA
Submission 267: Warren Cheung, Francis Ouellette and Wyeth Wasserman.
MeSHOPs: Medical Subject Heading Overrepresentation Profiles
Submission 268: Eugene Bolotin, Karthikeyani Chelappa, Wendy Hwang-Verslues, Chuhu Yang and Frances Sladek.
HNF4A Transcription Factor Binding Sequences are Widespread in Alu Repeats
Submission 269: Leon French and Paul Pavlidis.
Relationships between gene expression and brain wiring in the adult rodent brain
Submission 270: Jason Wong, Luke Hesson, Mathew Sloane, John Pimanda, Michael Bourke, Nicholas Hawkins and Robyn Ward.
Computational identification of universal alterations in DNA methylation and nucleosome positioning in a matched normal/tumor sample
Submission 271: Samuel Handelman, Js Verducci, Jj Kwiek, Sb Kumar and Da Janies.
GENPHEN: Genotype/Phenotype Association with Reference to Phylogeny
Submission 272: Sharon Bruckner, Tim Conrad and Christof Schuette.
Understanding biological networks with the random walker's perspective
Submission 273: Yasuhito Inoue.
Proteome-wide classification and identification of transmembrane protein sequences in plant genomes
Submission 274: Jocelyne Bruand,
Theodore Alexandrov, Srinivas Sistla, Maxence
Wisztorski, Céline Meriaux, Michael Becker,
Michel Salzet, Isabelle Fournier, Eduardo
Macagno and Vineet Bafna.
Exploring
MS Imaging Data in a semi-supervised and interactive
manner.
Submission 275: Raheleh Salari and Teresa M Przytycka.
The effect of SNPs on Boltzmann distribution for RNA secondary structure
Submission 276: Mark Seligman and Chris Fraley.
Model-averaged L1-penalized regression for biological data sets
Submission 277: Raymond Lim and Paul Pavlidis.
Wide-scale Comparison of Transcriptome Data
Submission 279: Armando Solis.
Optimal Use of Protein Structural Data for Knowledge-Based Potentials
Submission 280: Andrew Roth, Samuel Aparicio and Sohrab Shah.
Detecting Somatic Mutation In Tumour/Normal Paired Sample Sequence Data
Submission 282: Richard Jang, Xin Gao and Ming Li.
A Graph-based Peak Walking Algorithm for the Chemical Shift Mapping of Peaks in Serially Titrated 15N-HSQC NMR Spectra
Submission 284: Tiffany J. Chen, Matthew R. Clutter, Nikesh Kotecha, Garry P. Nolan and Serafim Batzoglou.
Automatically Finding Leukemic Cells that React Differently to Chemotherapeutics
Submission 285: Seokjong Yu, Junho Park, Jihee Lee, Jongtae Lim, Weiwei Bao, Mikyoung Kim, Hyunju Kim, Mirim Jo, Jeawoon Ryu, Hakyong Kim and Jaesoo Yoo.
ezBioNet: a Modeling and Simulation System for Biological Reaction Networks
Submission 286: Kana Shimizu and Koji Tsuda.
SlideSort: A fast and exact tool for finding all similar pairs from next-generation sequencing data
Submission 287: Seokjong Yu, Junho Park, Jihee Lee, Jongtae Lim, Weiwei Bao, Mikyoung Kim, Hyunju Kim, Mirim Jo and Jaesoo Yoo.
A Simulation for the G-Protein Coupled Receptor Signaling Model
Submission 288: Junho Park, Seokjong Yu, Jihee Lee, Jongtae Lim, Weiwei Bao, Mikyoung Kim, Hyunju Kim, Mirim Jo, Jeawoon Ryu, Hakyong Kim and Jaesoo Yoo.
Design and Implementation of a Protein and Disease Retrieval Services System Based on Integrated Databases
Submission 289: Chen Li, Masao Nagasaki, Chuan Hock Koh and Satoru Miyano.
Parameter estimation of a neuronal fate decision simulation model in C. elegans using online model checker: a high-level Petri net approach
Submission 290: Yilong Li, Eevi Kaasinen, Miika Mehine, Taru Koski and Lauri A. Aaltonen.
Genetic changes associated with uterine leiomyoma
Submission 291: Nitendra Sahu and Dv Kohli.
Pharmacophore modeling and 3D-QSAR of novel chalcone derivatives as Plasmodium falciparum growth inhibitors
Submission 292: Slim Fourati, Carolyn Nessim, Michael Hallett and Sylvie Mader.
Gene-expression signatures predicting therapeutic response of breast tumors to tamoxifen
Submission 293: Vicky Choi, Chunfang Zheng and David Sankoff.
Maximal Strip Recovery based on Interval Graphs
Submission 294: Markus Bauer, Anthony Cox and Dirk Evers.
Comparison of BWT Construction Algorithms for Very Large Read Collections
Submission 295: Aurora Cain, Adam Price, Shatavia Morrison, Robert Kosara and Cynthia Gibas.
Visualization-Driven Analytical System for Comparative Microbial Genomics
Submission 296: Charlotte Ng, Susanna Cooke, Kevin Howe, Scott Newman and James Brenton.
Genomic instability and evolution in high-grade serous ovarian cancers
Submission 297: Xianlong Wang, Dongqing Huang, Chenwei Lin, Brian Piening, Amanda Paulovich and Pei Wang.
A DNA Copy Number Co-deletion Network Identifies Genetic Interactions
Submission 298: Jonas Paulsen and Eivind Hovig.
Computational aspects of three-dimensional genomics
Submission 299:
Joseph Herman, Ádám Novák,
Rune Lyngsø and Jotun Hein.
Efficient
calculation of a representative multiple sequence
alignment from posterior samples
Submission 300: Adam Sardar and Julian Gough.
Horizontal Gene Transfer of Protein Domain Architectures
Submission 301: Damian Wójtowicz, Fedor Kouzine, Arito Yamane, Craig J. Benham, Rafael Casellas, David Levens and Teresa M. Przytycka.
Genome-wide mapping and computational analysis of non-B DNA structures in vivo
Submission 302: Matt Oates, Julian Gough and Alistair Hetherington.
An Exhaustive Search for the Inositol 1,4,5-triphosphate Receptor Protein in Plants
Submission 303: Mahboubeh Ghoryshi.
Elastin Polymorphism Associated With Increased Risk Thoracic Aortic Aneurysm and Dissection
Submission 304: Oksana Korol and Marcel Turcotte.
Module Inducer - a tool to automatically extract knowledge from biological sequences
Submission 305: Steve Goldstein and David Schwartz.
De Bruijn graph assembly for optical maps
Submission 306: Stale Nygard, Trond Reitan, Trevor Clancy, Vegard Nygaard, Johannes Bjørnstad, Biljana Skrbic, Theis Tønnessen, Geir Christensen and Eivind Hovig.
Identifying pathogenic signaling and regulatory networks by integrating microarray data with prior knowledge
Submission 307: Allen Chen, Christopher Lin, Janet Luo, Jack Chen, Joy Chen, Eleanor Wong, Javier Arsuaga, Mariel Vazquez, Caoan Wang and Rainer Sachs.
Neanderthal sharing haplotypes and gene flow in modern humans
Submission 308: Erin E. Gill, Geoff L. Winsor, Matthew R. Laird, Karin Breuer, Shannan J. Ho Sui, Nancy Y. Yu, Raymond Lo, Robert E. Hancock, David J. Lynn and Fiona S. L. Brinkman.
Computational Approaches and Tools for Infectious Disease Bioinformatics
Submission 309: Bonnie Kirkpatrick and Kristian Stevens.
Efficiently Constructing Phylogenies from Partial Characters
Submission 310: Jin Zhang and Yufeng Wu.
Finding Deletions with Exact Break Points from Noisy Low Coverage Paired-end Short Sequence Reads
Submission 311: Andrew T. Kwon, David J. Arenillas, Rebecca Hunt Newbury and Wyeth W. Wasserman.
Evolutionarily Conserved Regulatory Programs
Submission 312: Nitin Udpa, Dan Zhou, Gabriel Haddad and Vineet Bafna.
Exploring Tests of Selection in Pooled Data
Submission 313: Rebecca Hunt Newbury, David J. Arenillas, Andrew T. Kwon and Wyeth W. Wasserman.
Beware of genomic nucleotide composition while hunting transcription factor binding sites in ChIP-based experiments
Submission 314: Fong Chun Chan, Sanja Rogic and Randy Gascoyne.
Detection of Differential Splicing Between Two Groups Using Gene Expression Arrays
Submission 315: Sandhya Balasubramanian, Dinnanath Sulakhe, Eduardo Berrocal, Conrad Gilliam and Natalia Maltsev.
Analysis of complex disorders from the systems biology perspective.
Submission 316: Andrew Mcpherson, Chunxiao Wu, Iman Hajirasouliha, Fereydoun Hormozdiari, Faraz Hach, Anna Lapuk, Stanislav Volik, Sohrab Shah, Colin Collins and S. Cenk Sahinalp.
Comrad: a novel algorithmic framework for the integrated analysis of RNA-Seq and WGSS data
Submission 317: Mahdi Belcaid, Guylaine Poisson, David Schanzenbach and Kyungim Baek.
Inferring Hierarchical Population Structure through a Consensus of Significant Evolutionary Events
Submission 319: Jiayin Wang, Li Wei and Yufeng Wu.
A Graph Synchronization Model for Identifying SNP Interactions in Disease Association Studies
Submission 320: Yaron Butterfield, Richard Corbett, Steven J.M. Jones and Inanc Birol.
Post analysis of SNV calls: Annotating, filtering and quality assessment
Submission 321: Elizabeth Permina, Julia Medvedeva and Vsevolod Makeev.
Modulon Identification for Stress and Housekeeping Regulons Using Bacterial Gene Expression Array Data
Submission 322: Christine Lo, Nitin Udpa and Vineet Bafna.
Haplotype Phasing with Single Genome Amplification
Submission 323: Bhavjinder K. Dhillon, Shannan J. Ho Sui, Jennifer L. Gardy, Robert C. Brunham, Patrick Tang and Fiona S.L. Brinkman.
Bioinformatics Approaches for Analyzing Short-Read Illumina Sequences of Whole Mycobacterium tuberculosis Genomes from an Outbreak
Submission 325: Matthew Ruffalo, Mehmet Koyuturk and Thomas Laframboise.
Comparative analysis of algorithms for next-generation sequencing read alignment
Submission 326: Li Wei and Shaojie Jiao.
Identifying SNP Interactions with Multiple Phenotypes using Fish-Agent Logic Regression
Submission 327: Virginie Bernard, David J. Arenillas, Dimas Yusus and Wyeth W. Wasserman.
Exome and genome analyses: Prioritizing the variant calling
Submission 328: Chen Yanover and Philip Bradley.
Large-scale characterization of binding landscapes using structural simulations: application to C2H2 zinc-finger transcription factors and MHC proteins
Submission 329: Chris Fjell, Jennifer Tan, Matt Mayer and Robert Hancock.
MetaGEX: a systems biology meta-analysis toolkit and data repository with web server interface
Submission 331: Dariusz Przybylski, Iain Maccallum, Sante Gnerre, Filipe J. Ribeiro, Joshua N. Burton, Bruce J. Walker, Ted Sharpe, Giles Hall, Terrance P. Shea, Sean Sykes, Aaron M. Berlin, Daniel Aird, Maura Costello, Riza Daza, Louise Williams, Robert Nicol, Andreas Gnirke, Chad Nusbaum, Eric S. Lander and David B. Jaffe.
High-quality draft assemblies of large and small genomes from massively parallel DNA sequence data
Submission 332: Shengsheng Zhang, Shib Basu, Mikyong Lee, David Acland, Judith Bowler, Kathryn Brocklehurst, Steve Elvidge, Philip Green, Peter Kilby, Elaine Mackay, Jo Mattocks, John Ray and Ravi Tailor.
Protein Modeling and Engineering Increased Pepsin Susceptibility into a Heat-Tolerant Variant of Escherichia coli Phytase
Submission 333: Hang He and Huangdong Meng.
A Novel Data Mining Approach for Detecting the Mutated Peptides
Submission 334: Christopher Bun and Catherine Putonti.
Performing Phylogenomic Analysis on Unassembled Short-Read Genome Sequences
Submission 335: Lin He, Xi Han and Bin Ma.
An Efficient De Novo Sequencing Algorithm for the Identification of Modified Peptides from MS/MS spectra
Submission 336: Layla Oesper, Sarah Aerni, Ryan Drebin and Benjamin J. Raphael.
Reconstructing Cancer Genome Organization from Paired End Sequencing
Submission 337: Mai Hamdalla, David Grant, Sanguthevar Rajasekaran, Reda Ammar and Dennis Hill.
Efficient Prediction of Biological Structures from Molecular Formulas
Submission 338: Richard Morgan, Yvette Luyten and Geoffrey Wilson.
RATIONAL ALTERATION OF DNA RECOGNITION: SIMPLE MUTATIONS THAT CHANGE TYPE IIG RESTRICTION ENZYME SPECIFICITY
Submission 339: Lucas Swanson, Inanc Birol, S Cenk Sahinalp, Gordon Robertson, Karen Mungall, Readman Chiu, Shaun Jackman, Jenny Qian, Sam Lee, Deniz Yorukoglu, Rong She, Yongjun Zhao, Richard Moore, Marco Marra, Steven Jm Jones, Aly Karsan and Pamela Hoodless.
Detecting Chimeric Transcripts in RNA-seq Data
Submission 342: Leila Rahnama and Stephane Aris-Brosou.
Dating the adaptation of H1N1 and H3N2 subtypes of Influenza A viruses in different hosts
