Accepted Papers

Long Presentations

1. A Semi-Supervised Learning Approach to Integrated Salient Risk Features for Bone Diseases, Hui Li, Xiaoyi Li, Murali Ramanathan and Aidong Zhang;
2. PERGA: A Paired-End Read Guided De Novo Assembler for Extending Contigs Using SVM Approach, Xiao Zhu, Henry Leung, Francis Chin, S.M. Yiu, Guangri Quan, Bo Liu and Yadong Wang;
3. An Ensemble Topic Model for Sharing Healthcare Data and Predicting Disease Risk, Andrew Rider and Nitesh Chawla;
4. MRFy: Remote Homology Detection for Beta-Structural Proteins Using Markov Random Fields and Stochastic Search, Noah Daniels, Andrew Gallant, Norman Ramsey and Lenore Cowen;
5. Improving discrimination of essential genes by modeling local insertion frequencies in transposon mutagenesis data, Michael Dejesus and Thomas Ioerger;
6. GLProbs: Aligning multiple sequences adaptively, Yongtao Ye, David Cheung, Yadong Wang, S.M. Yiu, Qing Zhan, Tak-Wah Lam and Hingfung Ting;
7. The TREC Medical Records Track, Ellen M. Voorhees;
8. Temporal Relation Identification and Classification in Clinical Notes, Jennifer D'Souza and Vincent Ng;
9. Global Network Alignment In The Context Of Aging, Tijana Milenkovic, Han Zhao and Fazle Faisal;
10. Binary Response Models for Recognition of Antimicrobial Peptides, Elena Randou, Daniel Veltri and Amarda Shehu;
11. Simultaneous determination of subunit and complex structures of symmetric homo-oligomers from ambiguous NMR data, Himanshu Chandola, Bruce Donald and Chris Bailey-Kellogg;
12. Text Mining of Protein Phosphorylation Information Using a Generalizable Rule-Based Approach, Manabu Torii, Cecilia Arighi, Qinghua Wang, Cathy Wu and K. Vijay-Shanker;
13. Evaluation of Label Dependency for the Prediction of HLA Genes, Vanja Paunic, Michael Steinbach, Abeer Madbouly and Vipin Kumar;
14. Masher: Mapping Long(er) Reads with Hash-based Genome Indexing on GPUs, Anas Abu-Doleh, Erik Saule, Kamer Kaya and Umit Catalyurek;
15. Suffix-Tree Based Error Correction of NGS Reads Using Multiple Manifestations of an Error, Daniel Savel, Thomas Laframboise, Ananth Grama and Mehmet Koyuturk;
16. Genomic Sequence Fragment Identification using Quasi-Alignment, Anurag Nagar and Michael Hahsler;
17. Identification of gene clusters with phenotype-dependent expression with application to normal and premature ageing, Kun Wang, Avinash Das, Zheng-Mei Xiong, Kan Cao and Sridhar Hannenhalli;
18. MarkovBin: An Algorithm to Cluster Metagenomic Reads Using a Mixture Modeling of Hierarchical Distributions, Tin Nguyen and Dongxiao Zhu;
19. PReach: Reachability in Probabilistic Signaling Networks, Haitham Gabr, Andrei Todor, Helia Zandi, Alin Dobra and Tamer Kahveci;
20. A Study of Temporal Action Sequencing During Consumption of a Meal, Raul Ramos-Garcia and Adam Hoover;
21. Reconstructing transcriptional regulatory networks by probabilistic network component analysis, Jinghua Gu, Jianhua Xuan, Xiao Wang, Ayesha N. Shajahan, Leena Hilakivi-Clarke and Robert Clarke;
22. PathCase-MAW: An Online Metabolic Network Analysis Workbench, A. Ercument Cicek, Xinjian Qi, Ali Cakmak, Stephan R Johnson, Xu Han, Sami Alshalwi and Gultekin Ozsoyoglu;
23. Classifying Proteins by Amino Acid Variations of Sequential Patterns, En-Shiun Annie Lee and Andrew K.C. Wong;
24. Improving phosphopeptide identification in shotgun proteomics by supervised filtering of peptide-spectrum matches, Sujun Li, Randy Arnold, Haixu Tang and Predrag Radivojac;
25. Measuring Relatedness Between Scientific Entities in Annotation Datasets, Guillermo Palma, Maria-Esther Vidal, Eric Haag, Louiqa Raschid and Andreas Thor;
26. MoTeX: A word-based HPC tool for MoTif eXtraction, Solon Pissis, Alexandros Stamatakis and Pavlos Pavlidis;
27. Haplotype-based prediction of gene alleles using pedigrees and SNP genotypes, Yuri Pirola, Gianluca Della Vedova, Paola Bonizzoni, Alessandra Stella and Filippo Biscarini;
28. Color distribution can accelerate network alignment, Md Mahmudul Hasan and Tamer Kahveci;
29. TCGA Toolbox: an Open Web App Framework for Distributing Big Data Analysis Pipelines for Cancer Genomics, David Robbins, Alexander Grüneberg, Helena Deus, Murat Tanik and Jonas Almeida;
30. Greedy Randomized Search Procedure to Sort Genomes using Symmetric, Almost-Symmetric and Unitary Inversions, Ulisses Dias, Christian Baudet and Zanoni Dias;
31. A generalized sparse regression model with adjustment of pedigree structure for variant detection from next generation sequencing data, Shaolong Cao, Huaizhen Qin, Yu-Ping Wang and Hong-Wen Deng;
32. Classifying Immunophenotypes wtih Templates from Flow Cytometry, Ariful Azad, Arif Khan, Bartek Rajwa, Saumyadipta Pyne and Alex Pothen;
33. PRASE: PageRank-based Active Subnetwork Extraction, Ayat Hatem, Kamer Kaya and Umit Catalyurek;
34. Topological properties of chromosome conformation graphs reflect spatial proximities within chromatin, Hao Wang, Geet Duggal, Rob Patro, Michelle Girvan, Sridhar Hannenhalli and Carl Kingsford;
35. Meta-analysis of Genomic and Proteomic Features to Predict Synthetic Lethality of Yeast and Human Cancer, Min Wu, Xuejuan Li, Fan Zhang, Xiaoli Li, Chee-Keong Kwoh and Jie Zheng;
36. Quantitative Early Detection of Diabetic Foot, Viktor Chekh, Shuang Luan, Mark Burge, Cesar Carranza, Peter Soliz, Elizabeth McGrew and Simon Barriga;
37. Protein Structure Refinement by Iterative Fragment Exchange, Debswapna Bhattacharya and Jianlin Cheng;
38. Detecting differential splicing events with revealing mechanisms using RNA-Seq, Nan Deng and Dongxiao Zhu;
39. Decomposing Biochemical Networks Into Elementary Flux Modes Using Graph Traversal, Soha Hassoun, Ehsan Ullah, Shuchin Aeron and Calvin Hopkins;
40. Flexible RNA design under structure and sequence constraints using formal languages, Yu Zhou, Yann Ponty, Stéphane Vialette, Jerome Waldispuhl, Yi Zhang and Alain Denise;
41. SpliceGrapherXT: From Splice Graphs to Transcripts Using RNA-Seq, Mark Rogers, Christina Boucher and Asa Ben-Hur;
42. An Ensemble Model for Mobile Device based Arrhythmia Detection, Kang Li, Suxin Guo and Jing Gao;
43. Performance Model Selection for Learning-based Biological Image Analysis on a Cluster, Jie Zhou, Anthony Brunson, John Winans, Kirk Duffin and Nicholas Karonis;

Short Presentations

1. Designing Autocorrelated Genes, Rukhsana Yeasmin, Jesmin Jahan Tithi, Jeffrey Chen and Steven Skiena;
2. Fine-Scale Recombination Mapping of High-Throughput Sequence Data, Catherine Welsh, Fernando Pardo-Manuel de Villena and Leonard McMillan;
3. A Framework for Identifying Affinity Classes of Inorganic Materials Binding Peptide Sequences, Nan Du, Marc R. Knecht, Paras N. Prasad, Mark T. Swihart and Tiffany Walsh;
4. Clustering Coefficients in Protein Interaction Hypernetworks, Suzanne Gallagher and Debra Goldberg;
5. Transforming Genomes Using MOD Files with Applications, Shunping Huang, Chia-Yu Kao, Leonard McMillan and Wei Wang;
6. Read Annotation Pipeline for High-Throughput Sequencing Data, Shunping Huang, James Holt, Leonard McMillan and Wei Wang;
7. Identifying protein complexes in AP-MS data with negative evidence via soft Markov clustering, Yu-Keng Shih and Srinivasan Parthasarathy;
8. Stable Feature Selection with Minimal Independent Dominating Sets, Le Shu, Tianyang Ma and Longin Latecki;
9. Visual Analytics to Optimize Patient-Population Evidence Delivery for Personalized Care, Ketan Mane, Phillips Owen, Charles Schmitt, Kirk Wilhelmsen, Kenneth Gersing, Ricardo Pietrobon and Igor Akushevich;
10. GPU-Optimized Hybrid Neighbor/Cell List Algorithm for Coarse-Grained MD Simulations of Protein and RNA Folding and Assembly, Andrew Proctor, Cody Stevens and Samuel Cho;
11. Gene Set Cultural Algorithm: A Cultural Algorithm Approach to Reconstruct Networks from Gene Sets, Thair Judeh, Lipi Acharya and Dongxiao Zhu;
12. GapsMis: flexible sequence alignment with a bounded number of gaps, Carl Barton, Tomas Flouri, Costas Iliopoulos and Solon Pissis;
13. An Island-Based Approach for Differential Expression Analysis, Abdallah Eteleeb, Robert Flight, Benjamin Harrison, Jeffrey Petruska and Eric Rouchka;
14. Cloud4SNP: Distributed Analysis of SNP Microarray Data on the Cloud, Giuseppe Agapito, Mario Cannataro, Pietro Hiram Guzzi, Fabrizio Marozzo, Domenico Talia and Paolo Trunfio;
15. glu-RNA: aliGn highLy strUctured ncRNAs using only sequence similarity, Prapaporn Techa-Angkoon and Yanni Sun;
16. Classification of Alzheimer Diagnosis from ADNI Plasma Biomarker Data, Jue Mo, Stuart Maudsley, Bronwen Martin, Sana Siddiqui, Huey Cheung and Calvin Johnson;
17. The Forward Stem Matrix: An Efficient Data Structure for Finding Hairpins in RNA Secondary Structures, Richard Beal and Donald Adjeroh;
18. Simulating Anti-adhesive and Antibacterial Bifunctional Polymers for Surface Coating using BioScape, Vishakha Sharma, Adriana Compagnoni, Matthew Libera, Agnieszka K. Muszanska, Henk J. Busscher and Henny C. van der Mei;
19. Systematic Assessment of RNA-Seq Quantification Tools Using Simulated Sequence Data, Raghu Chandramohan, Po-Yen Wu, John H. Phan and May D. Wang;
20. Application of a MAX-CUT Heuristic to the Contig Orientation Problem in Genome Assembly, Paul Bodily, Mark Clement, Jared Price, Nozomu Okuda, Stanley Fujimoto, Quinn Snell and Cole Lyman;
21. A Confidence Measure for Model Fitting with X-Ray Crystallography Data, Ramgopal Mettu and Yang Lei;
22. Predictive model of the treatment effect for patients with major depressive disorder, Igor Akushevich, Julia Kravchenko, Ken Gersing and Ketan Mane;
23. ChainKnot: a comparative H-type pseudoknot prediction tool using multiple ab initio folding tool, Jikai Lei, Prapaporn Techa-Angkoon, Yanni Sun and Rujira Achawanantakun;
24. A Privacy Preserving Markov Model for Sequence Classification, Suxin Guo and Sheng Zhong;
25. An Image-Text Approach for Extracting Experimental Evidence of Protein-Protein Interactions in the Biomedical Literature, Luis Lopez, Jingyi Yu, Cecilia Arighi, Manabu Torii, Vijay Shanker, Hongzhan Huang and Cathy Wu;
26. Multi-Objective Stochastic Search for Sampling Local Minima in the Protein Energy Surface, Brian Olson and Amarda Shehu;
27. Heuristics for the Sorting by Length-Weighted Inversion Problem, Thiago Da Silva Arruda, Ulisses Dias and Zanoni Dias;
28. Towards Independent Particle Reconstruction from Cryogenic Transmission Electron Microscopy, W. Lewis Collier, Jean-Yves Herve' and Lenore Martin;

Accepted Highlights Talks

1. Combinatorial clustering of residue position subsets predicts inhibitor affinity across the human kinome, Drew Bryant, Mark Moll, Paul Finn and Lydia Kavraki;
2. YOABS: Yet Other Aligner of Biological Sequences - the first O(n) alternative to Smith-Waterman alignment of gapped sequences, Vitaly Galinsky;
3. Large scale signaling network reconstruction, Seyedsasan Hashemikhabir, Eyup Serdar Ayaz, Yusuf Kavurucu, Tolga Can and Tamer Kahveci;
4. DiffSplice: the Genome-Wide Detection of Differential Splicing Events with RNA-seq, Yin Hu, Jan Prins and Jinze Liu;
5. Algorithms and Systems for Interactive Online Drug Discovery, David Koes and Carlos Camacho;
6. Maximizing the Information Content of Experiments in Systems Biology, Juliane Liepe, Sarah Filippi, Michal Komorowski and Michael Ph Stumpf;
7. Top-Down Network Analysis to Drive Bottom-Up Modeling of Physiological Processes, Christopher Poirel, Richard Rodrigues, Katherine Chen, John Tyson and T. M. Murali;
8. Optimal timepoint sampling in high-throughput gene expression experiments, Bruce Rosa, Ji Zhang, Ian Major, Wensheng Qin and Jin Chen;
9. Construction of Protein Phosphorylation Networks by Data Mining, Text Mining, and Ontology Integration: Analysis of the Spindle Checkpoint, Karen Ross, Cecilia Arighi, Jia Ren, Hongzhan Huang, Darren Natale and Cathy Wu;
10. Spatial Genome Conformation and Gene-Gene Interaction Networks of Human Cells, Zheng Wang, Renzhi Cao, Kristen Taylor, Aaron Briley, Charles Caldwell and Cheng Jianlin;
11. SPARCS: a method to analyze (un)structured regions in coding RNA sequences, Yang Zhang, Yann Ponty, Mathieu Blanchette, Eric Lécuyer and Jerome Waldispuhl.