ACM BCB 2012 Program (Tentative)


Sunday, October 7, 2012

Immunoinformatics and Computational Immunology Workshop

Location: San Juan 1


8:30 – 10:30 Session I (Regular Talks)

  1.  "Serum Antibody Repertoire Profiling Using Virtual Antigen Screen", Xinyue Liu, Luke Tallon, Lisa Sadzewicz, Elena Klyushnenkova and Yurij Ionov
  2.  "miHA-Match: Computational Detection of Tissue-specific Minor Histocompatibility Antigens", Magdalena Feldhahn, Pierre Dönnes, Benjamin Schubert, Karin Schilbach, Hans-Georg Rammensee and Oliver Kohlbacher
  3. "Decoding Dendritic Cell Function Through Module and Network Analysis", Gaurav Pandey, Ariella Cohain, Jennifer Miller and Miriam Merad
  4. "Using Quantitative Dose-response Data to Benchmark B-cell Epitope Prediction for Antipeptide Antibodies", Salvador Eugenio Caoili
  5. "Immunoinformatic Analysis of Chinese Hamster Ovary (CHO) Protein Contaminants in Therapeutic Protein Formulations", Kristen Dasilva, Andres Gutierrez, Leonard Moise and Anne De Groot

10:30 – 11:00 Morning Break


11:00 – Noon Session II (Short Talks)

  1. "Human peptide homologues encoded by hepatitis C virus promote the response of regulatory T cells in chronically infected patients", Phyllis T. Losikoff, Loren D. Fast, Martha M. Nevola, Sasmita Mishra, Joe Desrosiers, William Martin, Matt Ardito, Frances Terry, Anne S. De Groot and Stephen H. Gregory 
  2. "Minimal mutations that define lewis y reactive antibodies", Somdutta Saha, Anastas Pashov, Ramachandran Murali and Thomas Kieber-Emmons
  3. "Human immunology project consortium (HIPC) database", Peter Li
  4. "Quasi analysis of the HIV-1 Negative Regulatory Factor (Nef) sequences in the Los Alamos National Laboratory HIV sequence database: pattern and distribution of positive selection sites and their frequencies over years", Elnaz Shadabi Ma Luo, Rupert Capina, Binhua Liang and Francis Plummer
  5. "Immunogenicity scores across the Leishmania major proteome", Sebastian Loli, Andres H. Gutierrez, Mirko Zimic and Annie S. De Groot

Noon - 1:30 Lunch

1:30pm -  3:00 Tutorial Part-I Immunoinformatics Resources

  1. Introduction (15 minutes), Vasant Honavar
  2. Immune Epitope Database (30 minutes), Bjoern Peters
  3. Eukaryotic Pathogen Database Resources (30 minutes), Jessica Kissinger

3:00pm – 3:30 Afternoon Break

3:30pm -  5:30 Tutorial Part-II Immunoinformatics Tools

  1. Predicting long MHC-I binders (30 minutes), Claus Lundegaard
  2. iVAX: Interactive Vaccine Design Toolkit (45 minutes), Anne De Groot
  3. Interactive Screening and Protein Re-engineering Interface (ISPRI) (45 minutes), Anne De Groot

5:30pm – 6:30 Poster Session

Biological Network Analysis and Applications in Translational and Personalized Medicine

Location: Eola Ballroom

10:00am – Noon  Session I (Regular Talks)

  1. "Genome Scale Inference of Transcriptional Regulatory Networks Using Mutual Information on Complex Interactions", Vijender Chaitankar, Preetam Ghosh, Mohamed O. Elasri, Kurt A. Gust and Edward J. Perkins
  2. "Unraveling Multiple miRNA-mRNA Associations through a Graph based Approach", Pietro Hiram Guzzi, Pierangelo Veltri and Mario Cannataro
  3. "A Collective NMF Method for Detecting Protein Functional Module from Multiple Data Sources", Yuan Zhang, Nan Du, Liang Ge, Kebin Jia and Aidong Zhang

1st International Workshop on Parallel and Cloud-based Bioinformatics and Biomedicine

Location: San Juan 2

1:00pm – 3:00pm Session I (Regular Talks)

  1. "An Iterative MapReduce Approach to Frequent Subgraph Mining in Biological Datasets", Steven Hill, Bismita Srichandan and Rajshekhar Sunderraman
  2. "High Performance Phosphorylation Site Assignment Algorithm for Mass Spectrometry Data Using Multicore Systems",Fahad Saeed, Trairak Pisitkun, Jason Hoffert and Mark Knepper
  3. "Parallelization of the Spectral Deconvolution Stage of the Proteomic Discovery Process", Neelam N. Deshpande and John A. Springer
  4. "A System for Acquiring and Management of ECG Signals by Using Mobile Devices: a Support for First Intervention in Heart Attacks", Pietro Cinaglia, Giuseppe Tradigo, Pierangelo Veltri

1st International Workshop on Robustness and Stability of Biological Systems and Computational Solutions

Location: San Juan 3

1:00pm – 3:00pm 


Invited Talk

"Robustness of problem-solving procedures in computational biology: A case study with the phylogenetic bootstrap", Bernard Moret

Session I (Regular Talks)

  1. "Feature Extraction in Protein Sequences Classification: a New Stability Measure", Rabie Saidi, Sabeur Aridhi, Mondher Maddouri and Engelbert Mephu Nguifo
  2. "Robustness Measure for an Adeno-Associated Viral Shell Self-Assembly Is Accurately Predicted by Configuration Space Atlasing Using EASAL", Ruijin Wu, Aysegul Ozkan, Antonette Bennett, Mavis Agbandje-Mckenna and Meera Sitharam
  3. "A Monte Carlo Approach to Measure the Robustness of Boolean Networks", Vitor H. P. Louzada, Fabricio M. Lopes, Ronaldo F. Hashimoto


3:15pm-6:00pm         Tutorials

Location: San Juan 2 and San Juan 3

  1. “An Introduction to Evolutionary Computation for Bioinformatics”, Clare Bates Congdon
  2. “A Survey of Computational Approaches to Reconstruct, Partition, and Query Biological Networks”, Thair Judeh and Dongxiao Zhu

Monday, October 8, 2012

8:45am-9:00am          Opening Remarks
Location: San Juan Ballroom


9:00am-10:00am        Keynote Talk
Ying Xu from the University of Georgia, Athens will give a keynote on “Genomic Location is Information: Towards Understanding the Organizational Principles of Bacterial Genomes”.
Location: San Juan Ballroom


10:00am-10:30am      Morning Break


10:30am-Noon           PAPER SESSIONS

PAPER SESSION 1 Systems Biology (San Juan 1)
Session chair: Mehmet Koyuturk

  1. “STEROID: In Silico Heuristic Target Combination Identification for Disease-Related Signaling Networks”, Huey Eng Chua, Sourav S Bhowmick, Lisa Tucker-Kellogg and C Forbes Dewey Jr
  2. “Functional Module Identification by Block Modeling using Simulated Annealing with Path Relinking”, Yijie Wang and Xiaoning Qian
  3. “Complexity reduction of Stochastic Master Equation Simulation based on Kronecker Product Analysis”, Mehmet Umut Caglar and Ranadip Pal

PAPER SESSION 2 Protein and RNA Structure (Short Presentations; San Juan 2)
Session chair: Chris Bystroff

  1. “Memory-Based Local Search for Simplified Protein Structure Prediction”, Swakkhar Shatabda, M.A.Hakim Newton, Duc Nghia Pham and Abdul Sattar
  2. “Towards Biophysical Validation of Constraint Modeling for Rigidity Analysis of Proteins”, Filip Jagodzinski and Ileana Streinu
  3. “Predicting Protective Bacterial Antigens Using Random Forest Classifiers”, Yasser El-Manzalawy, Drena Dobbs and Vasant Honavar
  4. “Simulation and Analysis of Antibody Aggregation on Cell Surfaces Using Motion”, Kasra Manavi, Bridget Wilson and Lydia Tapia
  5. “Protein Structure Prediction from Cryo-Electron Microscopy Volume Data at the Medium Resolution”, Kamal Al Nasr, Lin Chen, Dong Si, Desh Ranjan, Muhammad Zubair and Jing He

PAPER SESSION 3 Invited Talks (San Juan 3)
Session chair: Chris Bailey-Kellogg

  1. “Probabilistic Search Frameworks for Modeling Structures and Motions of Protein Systems”, Amarda Shehu
  2. “ProteinHistorian: Tools for the Comparative Analysis of Eukaryote Protein Origin”, John Capra
  3.  “SMURFLite: combining simplified Markov random fields with simulated evolution improves remote homology detection for beta-structural proteins into the twilight zone”, Lenore Cowen

Noon-1:30pm             Lunch

1:30pm-3:00pm         PAPER SESSIONS

PAPER SESSION 4 Comparative Genomics, Population & Cancer Genomics (San Juan 1)
Session chair: Oliver Eulenstein

  1. “Coalescent-based Method for Learning Parameters of Admixture Events from Large-Scale Genetic Variation Data”, Ming-Chi Tsai, Guy Blelloch, R Ravi and Russell Schwartz
  2. “Ancestry Inference of Admixed Populations with Microarray Probe Intensities”, Chen-Ping Fu, Catherine E. Welsh, Fernando Pardo-Manuel de Villena and Leonard McMillan
  3. “Algorithms for Detecting Complementary SNPs within a Region of Interest That Are Associated with Diseases”, Sinan Erten, Marzieh Ayati, Yu Liu, Mark R. Chance and Mehmet Koyuturk  

PAPER SESSION 5 Algorithms for Sequence Analysis (Short Presentations; San Juan 2)
Session chair: Ferhat Ay

  1. “Parallel Syntenic Alignment on GPUs”, Junjie Li, Sanjay Ranka and Sartaj Sahni
  2. “An Integer Programming Approach to Novel Transcript Reconstruction from Paired-End RNA-Seq Reads”, Serghei Mangul, Adrian Caciula, Sahar Al Seesi, Dumitru Brinza, Abdul Rouf Banday, Rahul N. Kanadia, Ion Mandoiu and Alex Zelikovsky
  3. “A fast computation of pairwise sequence alignment scores between a protein and a set of variants of another protein”, Yongwook Choi
  4. “Scalable Genome Scaffolding using Integer Linear Programming”, James Lindsay, Hamed Salooti, Alex Zelikovsky and Ion Mandoiu
  5. “Alignment seeding strategies using contiguous pyrimidine purine matches”, Minmei Hou, Louxin Zhang and Robert Harris  

PAPER SESSION 6 Invited Talks and Bioimaging (San Juan 3)
Session chair: Wei Wang

  1. “Optimization algorithms for the design of immunotolerant biotherapies”, Chris Bailey-Kellogg
  2. “Deriving protein statistical potential using the Boltzmann law and machine learning”, Jinbo Xu
  3. “Biological Interpretation of Morphological Patterns in Histopathological Whole-Slide Images”, Sonal Kothari, John H. Phan, Adeboye O. Osunkoya and May D. Wang

3:00pm-3:30pm         Afternoon Break

3:30pm -5:00pm        PAPER SESSIONS

PAPER SESSION 7 Protein and RNA Structure (San Juan 1)
Session chair:  Lenore Cowen

  1. “Multi-Directional Rapidly Exploring Random Graphs for Modeling Protein Folding”, Shuvra Nath, Shawna Thomas, Chinwe Ekenna and Nancy Amato
  2. “Biased Decoy Sampling to Aid the Selection of Near-native Protein Conformations”, Kevin Molloy and Amarda Shehu
  3. “Exploring objective functions and cross-terms in the optimization of an energy function for protein design”, Yao-Ming Huang and Chris Bystroff

PAPER SESSION 8 Systems Biology (Short Presentations; San Juan 2)
Session chair: Xiaoning Qian

  1. “Efficient Implementation of the Hybrid Method for Stochastic Simulation of Biochemical Systems”, Shuo Wang and Yang Cao
  2. “Network-based classification of recurrent endometrial cancers using high-throughput DNA methylation data”, Jianhua Ruan, Md. Jamiul Jahid, Fei Gu, Chengwei Lei, Yi-Wen Huang, Ya-Ting Hsu, David G. Mutch, Chun-Liang Chen, Nameer B. Kirma and Tim H. Huang
  3. “ADANET: Inferring Gene Regulatory Networks using Ensemble Classifiers”, Janusz Slawek and Tomasz Arodz
  4. “Microarray vs. RNA-Seq: A comparison for active subnetwork discovery”, Ayat Hatem, Kamer Kaya and Umit Catalyurek
  5. “QSEA for fuzzy subgraph querying of KEGG pathways”, Thair Judeh, Tin Chi Nguyen and Dongxiao Zhu

PAPER SESSION 9 Algorithms for Sequence Analysis (San Juan 3)
Session chair: Wei Wang

  1. “Non-overlapping clone pooling for high-throughput sequencing”, Reginaldo Kuroshu
  2. “Discovering Geometric Patterns in Genomic Data”, Wenxuan Gao, Robert Grossman, Philip Yu, Christopher Brown, Matthew Slattery, Lijia Ma and Kevin White
  3. “PseudoDomain: identification of processed pseudogenes based on protein domain classification”, Yuan Zhang and Yanni Sun

5:00pm-5:40pm         ACM SIG FORUM

Location: San Juan 3


5:40pm-7:00pm         ACM SIG Organization Forum

Location: TBA

6:30pm-8:30pm         POSTER SESSION/RECEPTION

Location: San Juan Ballroom

Tuesday, October 9, 2012

9:00am-10:00am        Keynote Talk
Martha L. Bulyk from Brigham & Women’s Hospital and Harvard Medical School will give a keynote on “Transcription Factors and DNA Regulatory Elements”.
Location: San Juan Ballroom

10:00am-10:30am      Morning Break

10:30am-Noon           PAPER SESSIONS

PAPER SESSION 10 Systems Biology (San Juan 1)
Session chair: Jinbo Xu

  1. “NetPipe: A Network-based Pipeline for Discovery of Genes and Protein Complexes Regulating Meiotic Recombination Hotspots”, Min Wu, Chee Keong Kwoh, Xiaoli Li and Jie Zheng
  2. “Reverse Engineering Molecular Hypergraphs”, Ahsanur Rahman, Christopher L. Poirel, David J. Badger and T. M. Murali
  3. “Supervised Logistic Principal Component Analysis for Pathway Based Genome-Wide Association Studies”, Meng Lu, Jianhua Huang and Xiaoning Qian

PAPER SESSION 11 Comparative Genomics, Population & Cancer Genomics (Short Presentations; San Juan 2)
Session chair: Rui Kuang

  1. “Finding Informative Genes for Prostate Cancer: A General Framework of Integrating Heterogeneous Sources”, Liang Ge, Jing Gao, Nan Du and Aidong Zhang
  2. “Integration of Genomic and Epigenomic Features to Predict Meiotic Recombination Hotspots in Human and Mouse”, Min Wu, Chee Keong Kwoh, Teresa M. Przytycka, Jing Li and Jie Zheng
  3. “Inferring novel associations between SNP sets and gene sets in eQTL study using sparse graphical model”, Wei Cheng, Xiang Zhang, Yubao Wu, Xiaolin Yin, Jing Li, David Heckerman and Wei Wang
  4. “A pattern mining based integrative framework for biomarker discovery”, Sanjoy Dey, Gowtham Atluri, Michael Steinbach, Kelvin Lim, Angus MacDonald and Vipin Kumar
  5. “SNPRank: An Efficient Ranking Method for Genome-wide Association Studies”, Jie Liu, Humberto Vidaillet, Elizabeth Burnside and David Page

PAPER SESSION 12 Protein and RNA Structure and Invited Talk (San Juan 3)
Session chair: Ileana Streinu

  1. “Protein Structure and Sequence Mining for Improving Computational Design of Stable Proteins”, Jianwen Fang
  2. “Protein Blocks Versus Hydrogen Bonds Based Alphabets For Protein Structure Classification”, Dino Franklin
  3. “ArtSurf: A Method for Deformable Partial Matching of Protein Small-Molecule Binding Sites”, Jeffrey Van Voorst, Yiying Tong and Leslie Kuhn

Noon-1:30pm             Lunch & Forum: Women in Bioinformatics

Co-chairs: Wei Wang, UCLA  and May Wang, Georgia Tech

Location: Presidential Suite


1:30pm-3:15pm         PAPER SESSIONS

PAPER SESSION 13 Protein and RNA (San Juan 1)
Session chair: Brian Chen

  1. “Multi-target protein-chemical interaction prediction using task-regularized and boosted multi-task learning”, Jintao Zhang, Gerald Lushington and Jun Huan
  2. “Functional Site Prediction by Exploiting Correlations between Labels of Interacting Residues”,  Saradindu Kar, Deepak Vijayakeerthi, Balaraman Ravindran and Ashish V. Tendulkar
  3. “A Volumetric Method for Representing and Comparing Regions of Electrostatic Focusing in Molecular Structure”, Brian Chen and Debdas Paul

PAPER SESSION 14 Systems Biology and Contributed Presentation (San Juan 2)
Session chair: Amarda Shehu

  1. “Three differentiation states risk-stratify bladder cancer into distinct subtypes”, Jens-Peter Volkmer, Debashis Sahoo, Robert Chin, Philip Ho, Chad Tang, Antonina Kurtova, Stephen Willingham, Senthil Pazhanisamy, Humberto Contreras-Trujillo, Theresa Storm, Yair Lotan, Andrew Beck, Benjamin Chung, Ash Alizadeh, Guilherme Godoy, Seth Lerner, Matt van de Rijn, Linda Shortliffe, Irving Weissman and Keith Chan
  2. “Evolutionary Analysis of Functional Modules in Dynamic PPI Networks”, Nan Du, Yuan Zhang, Kang Li, Jing Gao and Aidong Zhang
  3. “Predicting expression-related features of chromosomal domain organization with network-structured analysis of gene expression and chromosomal location”, Vinodh Rajapakse, Wojciech Czaja, William Reinhold, Yves Pommier and Sudhir Varma
  4. “Remote Homology Detection on Alpha-Structural Proteins Using Simulated Evolution”, Mengfei Cao and Lenore Cowen

PAPER SESSION 15 Text Mining and Contributed Presentations (San Juan 3)
Session chair: Tamer Kahveci

  1. “Protein Function Prediction using Text-based Features extracted from Biomedical Literature: The CAFA Challenge”, Andrew Wong and Hagit Shatkay
  2. “Anaphora Resolution in Biomedical Literature: A Hybrid Approach”, Jennifer D'Souza and Vincent Ng
  3. “OCR-based Image Features for Biomedical Image and Article Classification: Identifying Documents relevant to Cis-Regulatory Elements”, Hagit Shatkay, Ramya Narayanaswamy, Santosh Nagaral, Na Harrington, Rohith Mv, Gowri Somanath, Ryan Tarpine, Kyle Schutter, Tim Johnstone, Dorothea Blostein, Sorin Istrail and Chandra Kambahmettu
  4. “Hybrid pattern matching for complex ontology term recognition”, Jung-Jae Kim and Luu Anh Tuan

3:15pm-3:45pm         Afternoon Break

3:45pm -5:15pm        PAPER SESSIONS

PAPER SESSION 16 Algorithms for Sequence Analysis (San Juan 1)
Session chair: Tony Capra

  1. “Efficient SNP-sensitive alignment and database-assisted SNP calling for low coverage samples”, Ruibang Luo, Chi Man Liu, Thomas Wong, Chang Yu, Tak-Wah Lam, Siu Ming Yiu, Ruiqiang Li and Hingfung Ting
  2. “ERNE-BS5: aligning BS-treated sequences by multiple hits on a 5-letters alphabet”, Nicola Prezza, Cristian Del Fabbro, Francesco Vezzi, Emanuele De Paoli and Alberto Policriti
  3. “Improved Multiple Sequence Alignments using Coupled Pattern Mining”, K. S. M. Tozammel Hossain, Debprakash Patnaik, Srivatsan Laxman, Prateek Jain, Chris Bailey-Kellogg and Naren Ramakrishnan

PAPER SESSION 17 Modeling, Querying and Systems Biology (San Juan 2)
Session chair: Hagit Shatkay

  1. “3D Bone Microarchitecture Modeling and Fracture Risk Prediction”, Hui Li, Xiaoyi Li, Lawrence Bone, Cathy Buyea, Murali Ramanathan and Aidong Zhang
  2. “Semantic Querying over Knowledge in Biomedical Text Corpora Annotated with Multiple Ontologies”, Watson Wei Khong Chua and Jung-Jae Kim
  3. “Parallel Verlet Neighbor List Algorithm for GPU-Optimized MD Simulations”, Tyson Lipscomb, Anqi Zou and Samuel Cho
  4. “Signed Network Propagation for Detecting Differential Gene Expressions and DNA Copy Number Variations”, Wei Zhang, Nicholas Johnson, Baolin Wu and Rui Kuang

PAPER SESSION 18 Invited Talks (San Juan 3)
Session chair: Umit V. Catalyurek

  1. "Assessing and Improving the Reliability of Short Read Alignments for Next Generation Sequencing", Mehmet Koyuturk
  2. “Mining Genetic Interactions in Genome-Wide Association Study”, Wei Wang
  3. “Supertrees and Supertree Problems”, Oliver Eulenstein

6:30pm-8:30pm         BANQUET

Wednesday, October 10, 2012

9:00am-10:00am        Keynote Talk
Pierre Baldi from the University of California, Irvine (UCI) will give a keynote on “Machine Learning Approaches in Proteomics”.
Location: San Juan Ballroom

10:00am-10:30am      Morning Break

10:30am-Noon           PAPER SESSIONS

PAPER SESSION 19 Databases, Knowledgebases & Ontologies (San Juan 1)
Session chair: Jing Gao

  1. "What We Found on Our Way to Building a Classifier: A Critical Analysis of the Screening Questionnaire for Young Athletes", Hagit Shatkay
  2. “Protein Function Prediction using Weak-label Learning”, Guoxian Yu, Guoji Zhang, Huzefa Rangwala, Carlotta Domeniconi and Zhiwen Yu
  3. “Detecting ECG Abnormalities via Transductive Transfer Learning”, Kang Li, Nan Du and Aidong Zhang

PAPER SESSION 20 Algorithms for Sequence Analysis (Short Presentations; San Juan 2)
Session chair: Ion Mandoiu

  1. “A New Algorithm for Finding Enriched Regions in ChIP-Seq Data”, Iman Rezaeian and Luis Rueda
  2. “DACIDR: Deterministic Annealed Clustering with Interpolative Dimension Reduction using Large Collection of 16S rRNA Sequences”, Yang Ruan, Saliya Ekanayake, Mina Rho, Haixu Tang, Seung-Hee Bae, Judy Qiu and Geoffrey C. Fox
  3. “An integrated optimization framework for inferring two-generation kinships and parental genotypes from microsatellite samples”, Daehan Won, Chun-An Chou, W. Art Chaovalitwongse, Tanya Y. Berger-Wolf, Bhaskar Dasgupta, Ashfaq A. Khokhar, Mary V. Ashley, Jason Palagi and Marco Maggioni
  4. “On enumerating the DNA sequences”, M. Oguzhan Kulekci
  5. “Rational design of Orthogonal Libraries of Protein Coding Genes”, Daniel Ryan and Dimitris Papamichail

PAPER SESSION 21 Bioimage Analysis (San Juan 3)
Session chair: May D. Wang

  1. “Automatic Segmentation and Quantification of Filamentous Structures in Electron Tomography”, Leandro Loss, Hang Chang, Purbasha Sarkar, Manfred Auer and Bahram Parvin
  2. “Multivariate Hypergeometric Similarity Measure”, Chanchala Kaddi, R. Mitchell Parry and May D. Wang
  3. “Alignment of Real-Time Live-Cell Growth Data for Quantitative Analysis of Growth at the Shoot Apex of Arabidopsis thaliana”, Oben M Tataw, A. K. Row-Chowdhurry and G.V. Reddy

Noon-1:30pm             Lunch

1:30pm-3:00pm         Panel
Panel topic: Bigdata in Biosciences: Challenges and Opportunities
Panel chair: Srinivas Aluru, Iowa State University
Location: San Juan Ballroom


3:00pm-4:00pm         PHD Forum

Location: San Juan Ballroom