2014 ACM International Workshop on Big Data in Life Sciences (BigLS'14)

http://www.bigls.org
Saturday, September 20, 2014 (Location: Salon 3) Held in conjunction with the ACM BCB'14 conference, Newport Beach, CA
Organizers:
Jaroslaw Zola, Assistant Professor, Dept. Computer Science and Engineering, SUNY Buffalo
Ananth Kalyanaraman, Associate Professor, School of Elect. Eng. And Computer Science, Washington State University

Technical Program

8:45am - 10:30am SESSION I: INVITED TALKS

8:45am-9am: Opening remarks
Jaroslaw Zola and Ananth Kalyanaraman

9am-9:45am: invited paper
"Feature subset selection for inferring relative importance of taxonomy"
Gregory Ditzler and Gail Rosen

9:45am-10:30am: invited talk
"Promises and challenges in analysis of biological big data"
Jason McDermott, Pacific Northwest National Laboratory

10:30am-11am Coffee break

11am - 12:30pm SESSION II: KEYNOTE ADDDRESS

"Quantifying Your Superorganism Body Using Big Data Supercomputing"
Larry Smarr
Founding Director of Calit2,
Harry E. Gruber Professor in Computer Science and Engineering,
University of California, San Diego, CA

2pm-3:30pm SESSION III: PEER REVIEWED PAPERS

2pm-2:30pm:
"Big Data challenges for estimating genome assembler quality"
Abhishek Biswas, David Gauthier, Desh Ranjan, Mohammad Zubair

2:30pm-3:00pm:
"RNA-Seq gene and transcript expression analysis using the BioExtract Server and iPlant Collaborative"
Etienne Gnimpieba, Chango Abalo, Carol M. Lushbough

3pm-3:30pm:
"AlignMR: Mass spectrometry peak alignment using Hadoop MapReduce"
Urmi Bhayani and John Springer

3:30pm-5pm SESSION IV: STUDENT POSTERS AND STUDENT MENTORING SESSION

3:30pm-4pm Student poster presentations

4pm-5pm: Mentoring interaction with faculty/researchers and students. Coffee/refreshments will be available between 4-4:30pm. List of poster presenters to be announced after student travel scholarships have been awarded. Please look for updates on the BigLS workshop webpage: http://www.bigls.org





3rd International Workshop on
Parallel and Cloud-based Bioinformatics and Biomedicine (ParBio 2014)


Saturday September 20, 2014
2:00pm - 4:00pm

Location: Salon 1&2
Mario Cannataro, University Magna Graecia of Catanzaro, Italy and
John A. Springer, Purdue University, USA

2:00 - 2:10 - Opening Remarks, Mario Cannataro and John A. Springer

2:10 - 2:35 - Automatic Biosystems Comparison Using Semantic and Name Similarity, Mathialakan, Thavappiragasam, Carol M. Lushbough, Etienne Z. Gnimpieba - (Presenter: Mathialakan Thavappiragasam, University of South Dakota, USA)

2:35 - 3:00 - Pheno2GRN: a workflow for phenotype to gene network studies and reverse engineering comparison, Nick Weinandt, Etienne Z. Gnimpieba, Laura Jackson, Carol Lushbough - (Presenter: Laura Jackson, University of South Dakota, USA)

3:00 - 3:25 - A taxonomy for bioinformatics tools: exploiting semantics, parallelism, and services for analyzing omics data, Mario Cannataro, Pietro Hiram Guzzi - (Presenter: Mario Cannataro, University Magna Graecia of Catanzaro, Italy)

3:25 - 3:50 - A system for ubiquitous distributed acquisition of voice alteration samples through a mobile application, Pietro Cinaglia, Manuela Macri, Barbara Calabrese, Patrizia Vizza, Giuseppe Tradigo, Pierangelo Veltri - (Presenter: Pierangelo Veltri, University Magna Graecia of Catanzaro, Italy)


3:50 - 4:00 - Closing Remarks, Mario Cannataro and John A. Springer



Workshop on Computational Network Biology: Modeling, Analysis, and Control (CNB-MAC)

Saturday September 20, 2014
9:20am - 4:40pm
Location: Salon 5

Dr. Byung-Jun Yoon, Department of Electrical and Computer Engineering
Texas A&M University

Dr. Xiaoning Qian, Department of Electrical and Computer Engineering
Texas A&M University


Workshop Program:

09:20-09:30 Opening Remarks

09:30-10:30 Invited Keynote Talk by Dr. Fengzhu Sun

  • Molecular Networks and the Internet: Are They Similar?


    • 10:30-11:30 Highlight Talks
  • Zhandong Liu: Combinatorial Therapy Discovery using Mixed Integer Linear Programming.
  • Ranadip Pal: Mathematical Design and Validation of Synergistic Anti-Cancer Drug Combinations.

    • 11:30-13:00 Lunch Break

    13:00-14:00 Invited Tutorial by Dr. Lori Dalton
  • Optimal Bayes Classification


    • 14:00-14:20 Five-Minute Lightning Talks for Posters
  • Yijie Wang and Xiaoning Qian: Biological network clustering by robust NMF.
  • Hyundoo Jeong and Byung-Jun Yoon: A Novel Context-Sensitive Random Walk Model for Estimating Node Correspondence Between Two Biological Networks.
  • Amin Ahmadi Adl and Xiaoning Qian: Network-regularized Bi-clique Finding For Tumor Stratification.
  • Mansuck Kim, Huan Zhang, Charles Woloshuk, Won-Bo Shim, and Byung-Jun Yoon: Computational Identification of Functional Network Modules that are Associated with the Pathogenicity of Fusarium verticillioides.

    • 14:20-15:30 Poster Presentations & Coffee Break

    15:30-16:30 Paper Presentations
  • Navadon Khunlertgit and Byung-Jun Yoon: Simultaneous Identification of Robust Synergistic Subnetwork Markers for Effective Cancer Prognosis.
  • Mohammadmahdi Rezaei Yousefi and Lori Dalton: Optimal Cancer Prognosis Under Network Uncertainty.

    • 16:30-16:40 Closing Remarks





    ICIW 2014: the Fifth Immunoinformatics and Computational Immunology Workshop

    Saturday September 20, 2014
    9:20am - 4:40pm
    Location: Cardiff

    Vasant Honavar (Penn State University, PA, USA)
    Guanglan Zhang (Boston University, MA, USA) - contact Guanglan for matters related to submissions
    Lou Chitkushev (Boston University, MA, USA)
    Vladimir Brusic (Dana-Farber Cancer Institute, Harvard Medical School, USA)

    8:30-9:30AM Invited keynote talk by Dr. Christian Schoenbach
    Bridging the gaps between prediction of T-cell epitopes and what impacts immunity.

    9:30-10:30AM Session I (Paper Presentations)
  • Salvador Eugenio C. Caoili. An Integrative Framework for Structure-Based Prediction of Biological Effects Mediated by Antipeptide Antibodies.
  • Sinu Paul, John Sidney, Bjoern Peters, Alessandro Sette. Development and validation of a broad scheme for prediction of HLA class II restricted T cell epitopes.
  • Anne Bresciani, Jason Greenbaum, Cecilia S. Lindestam Arlehamn, Alessandro Sette, Morten Nielsen, Bjoern Peters. The interplay of sequence conservation and T cell immune recognition.

    • 10:30-11:00AM Morning break

    11:00AM-12:30PM Session II (Paper & Poster Presentations)
  • Francesco Pappalardo, Marzio Pennisi, Abdul Mateen Rajput, Ferdinando Chiacchio, Santo Motta. Relapsing-Remitting Multiple Scleroris and the role of Vitamin D: an agent based model.
  • Hariharane Ramasamy, Tulasi Ravuri and Sanheev Mishra. Advanced Search Grammar Tool for identification of Functional Noncoding Elements.
  • Chen-Chieh Fan, Chun-Fan Chang, Hsueh-Ting Chu, Thai-Yen Ling and Cheng-Yan Kao. Better docking affinity to HLA B*57:01 pit with putative structures of self-peptides due to hypersensitivity causative drugs of Abacavir and its likely kin Famotidine.

    • 12:30-2:00PM Lunch

    2:00-2:30PM Session III (Poster Presentations)
  • Sandra Andorf, Jennifer B. Bollyky, Patrick Dunn, Jeffrey A. Wiser, Sanchita Bhattacharya and Atul J. Butte. Towards the characterization of normal peripheral immune cells with data from ImmPort.

    • 2:30-4:00PM Session IV (Tutorial: bring your laptop for hands-on exercises!)
  • Ravi Shankar, Sandra Andorf, Sanchita Bhattacharya, Jeffrey Wiser and Atul Butte. RImmPort: enabling ready-for-analysis immunology research data. & Hands-on tutorial on using RImmPort to access publicly-available individuallevel immunology research data


    • CSBW 2014 - The 7th Computational Structural Bioinformatics Workshop

    http://www.cs.odu.edu/~lchen/CSBW.htm
    Saturday, September 20, 2014 (Location: Salon 4)
    8:30am - 12:30pm
    Held in conjunction with the ACM BCB'14 conference, Newport Beach, CA

    Organizers: Jing He, Amarda Shehu, Nurit Haspel, and Brian Chen

    8:30-8:40: Opening remarks (Jing He)
    Session 1 (session chair Nurit Haspel)

    8:40-9:00 Orientations of β-strand Traces and Near Maximum Twist. Dong Si and Jing He.

    9:00-9:20 A Computational Model for Data Acquisition in SAXS. Hui Dong and Gregory Chirikjian

    9:20-9:40 Highlight talk - Nurit Haspel, University of Massachusetts at Boston

    9:40-10:00 An Analysis of Conformational Changes upon RNA-Protein Binding. Kannan Sankar, Rasna R. Walia, Carla M. Mann, Robert L. Jernigan, Vasant G. Honavar, and Drena Dobbs.

    10:00-10:20 Highlight Talk - Jianlin Cheng, University of Missouri

    10:20-11:00: Break + poster session

    Session 2 (session chair: Kamal Al Nasr)

     11:00-11:20 Variational Bayesian Clustering on Protein Cavity Conformations for Detecting Influential Amino Acids. Ziyi Guo, and Brian Chen.

    11:20-11:40 Construction of Protein Backbone Pieces Using Segment based FBCCD and Cryo-EM Skeleton. Kamal Al Nasr and Jing He.

    11:40-12:00 Improving Decoy Databases for Protein Folding Algorithms. Aaron Lindsey, Hsin-Yi Yeh, Chih-Peng Wu, Shawna Thomas, and Nancy Amato

    12:00-12:20 Highlight talk - Amarda Shehu, George Mason University

    12:20 - 12:30 Concluding remarks (Amarda Shehu, Brian Chen)



    8th International Workshop on Biomolecular Network Analysis (IWBNA)

    Saturday September 20, 2014
    4:30pm - 6:00pm
    Location: Salon 1&2

     Organizers: Young-Rae Cho, Pietro H. Guzzi, and Pierangelo Veltri

    4:30 4:45 Incremental Network Querying in Biological Networks. Md Mahmudul Hasan and Tamer Kahveci.

    4:40 5:00 On the Impact of Data Integration and Edge Enrichment in Mining Significant Signals from Biological Networks. Sean West and Hesham Ali.

    5:00 5:15 Evidence of post translational modification bias extracted from the tRNA and corresponding amino acid interplay across a set of diverse organisms. Oliver Bonham-Carter, Ishwor Thapa, and Dhundy Bastola.

    5:15 5:30 Heuristic Parallelizable Algorithm for Similarity Based Biosystems Comparison. Mathialakan Thavappiragasam, Carol Lushbough, and Etienne Gnimpieba.

    5:30 5:45 An R-based tool for miRNA data analysis and correlation with clinical ontologies. Francesca Cristiano and Pierangelo Veltri.

    5:45 6:00 Closing Remark. Pierangelo Veltri


    Deep Learning in Bio- and Health Informatics (DL 2014)

    Saturday, September 20, 2014
    2:00 pm - 4:00 pm
    Location: Salon 4

     Organizer: Pierre Baldi, University of California, Irvine

    2:00pm - 4:00pm

    2:00-2:30 Deep Learning to Predict Chemical Properties and Reactions. Pierre Baldi.

    2:30-3:00 Deep Learning for Protein Structure Prediction. Jianlin Cheng.

    3:00-3:30 Applications of Deep Learning to Large-Scale Genomic Data. Xiaohui Xie.

    3:30-4:00 A Multi-label Deep Belief Network for Predicting Multiple Diseases. Aidong Zhang and Hui Li.