In conjunction with ACM SIGKDD International Conference on Knowledge Discovery and Data Mining (SIGKDD '16)

BIOKDD'16 Workshop

Workshop Home

  Important Dates
  Organizers and Program Committee



Bioinformatics is the science of managing, mining, and interpreting information from biological data. Various genome projects have contributed to an exponential growth in DNA and protein sequence databases. Rapid advances in high-throughput technologies, such as microarrays, mass spectrometry and new/next-generation sequencing, can monitor quantitatively the presence or activity of thousands of genes, RNAs, proteins, metabolites, and compounds in a given biological state. The ongoing influx of these data, the pressing need to address complex biomedical challenges, and the gap between the two have collectively created exciting opportunities for data mining researchers.

While tremendous progress has been made over the years, many of the fundamental problems in bioinformatics, such as protein structure prediction, gene-environment interaction, and regulatory network mapping, have not been convincingly addressed. Besides these, new technologies such as next-generation sequencing are now producing massive amounts of sequence data; managing, mining and compressing these data raise challenging issues. Finally, there is a pressing need to use these data coupled with efficient and effective computational techniques to build models of complex biological processes and disease phenotypes. Data mining will play an essential role in addressing these fundamental problems and in the development of novel therapeutic/diagnostic/prognostic solutions in the post-genomics era of medicine.

The goal of the 16th International Workshop on Data Mining in Bioinformatics (BIOKDD'16) is to encourage KDD researchers to tackle the numerous challenges of mining and learning in Bioinformatics, Biomedical and Health Informatics. Thus this year, the workshop will feature the theme of “Latest Advances of Mining and Learning in Bioinformatics, Biomedical and Health Informatics”. This field focuses on the use of data mining and machine learning approaches for the analysis of the large amount of heterogeneous complex biological and medical data being generated together with innovative applications in biomedical and health informatics. The key goal is thus to build accurate predictive or descriptive models from data enabling either novel discoveries in basic biology and medicine or an effective use of the latest advances of data mining in healthcare.

We encourage papers that propose novel data mining techniques for areas including but not limited to

  • Predictive modeling for complex phenotypes from large-scale biological data
  • Discovery of biological networks and pathways underlying biological processes and diseases
  • Processing of new/next-generation sequencing (NGS) data
  • Discovery of genotype-phenotype associations
  • Biomarker discovery in clinical and genomic data
  • Data analytics for clinical informatics
  • Data integration for biomedical applications
  • Comparative genomics
  • Metagenome analysis using sequencing data
  • RNA-seq and microarray-based gene expression analysis
  • Genome-wide analysis of non-coding RNAs
  • Genome-wide regulatory motif discovery
  • Structural bioinformatics
  • Correlating NGS with proteomics data analysis
  • Functional annotation of genes and proteins
  • Cheminformatics
  • Special biological data management techniques
  • Information visualization and Visual analytics for biomedical data
  • Predictive modeling for personalized treatment
  • Semantic web and ontology in Biomedicine
  • Privacy and security issues in genomics and healthcare
  • Text mining for biomedical literature and clinical notes
  • Information retrieval for healthcare and Biomedical applications
  • Biomedical signal analysis and processing
  • Intelligent medical data management
  • Collaboration technologies for biomedicine
  • Social networks for biomedicine

Program Overview

13:00-13:10   Welcome Remarks

13:10-14:00   Invited Talk: Prof. Jun Huan, Professor, Dept. of EECS, University of Kansas, Lawrence, KS.

14:00-14:30   Vipin Vijayan and Tijana Milenkovic.

                     Multiple network alignment via multiMAGNA++

14:30-15:00   Marco Frasca and Nicolo Cesa-Bianchi.

                     Multi-Task Label Propagation with Dissimilarity Measures

15:00-15:30   Tanay Kumar Saha, Ataur Katebi and Mohammad Al Hasan.

Discovery of Functional Motifs from the Interface Region of    Oligomeric Proteins using Frequent Subgraph Mining Method

15:30-16:00   Coffee Break

16:00-16:50   Invited Talk: Prof. Shuiwang Ji, Associate Professor, School of  EECS, Washington State University, Pullman, WA.

16:50-17:00   Closing Remarks


Important Dates

June 10th, 2016 (Extended) Deadline for Submission of Papers
June 15th, 2016 Notification of Acceptance; Workshop Registration Open
June 30th, 2016 Submission of Camera-ready Papers
August 14th, 2016 Workshop Presentation

All deadlines are at 11:59 PM Pacific Standard Time.


Papers should be at most 10 pages long, single-spaced, in font size 10 or larger with one-inch margins on all sides. Using the ACM Proceedings Format is highly recommended. Paper should be submitted in PDF format through EasyChair at the following link:

Papers will be published in the webpage. A selection of accepted papers will also be invited to be submitted to a special section of the reputed IEEE Transactions on Computational Biology and Bioinformatics.


To be available.

Workshop Organizers

Program Chairs

Sara C. Madeira
Department of Computer Science and Engineering
Instituto Superior Técnico, Universidade de Lisboa
Av. Rovisco Pais, 1
1049-001 Lisbon, Portugal

Web site:

Chandan K. Reddy
Department of Computer Science
Virginia Tech
900 North Glebe Rd., Office 5-178
Arlington, VA 22203

Web site:

General Chairs

Mohammed J. Zaki, Ph.D.
Department of Computer Science
Rensselaer Polytechnic Institute
Troy, NY 12180-3590

Web site:


Jake Y. Chen, Ph.D.
University of Alabama at Birmingham
1900 University Blvd, THT 1st Floor
Birmingham, AL 35233

Web site:

Program Committee

Alexandra M. Carvalho IST, University of Lisbon, Portugal
Alexandre P. Francisco IST, University of Lisbon, Portugal
Asa Ben-Hur Colorato State University, USA
Florentino Fdez-Riverola University of Vigo, Spain
Jie Zheng Nanyang Technical University, Singapore
Joana P. Goncalves Delft University of Technology, The Netherlands
Joao Carrico Instituto de Medicina Molecular, Portugal
Joaquin Dopazo Principe Felipe Research Center, Spain
Jose Luis Oliveira Universidade de Aveiro, Portugal
Kris Lauken University of Antwerpen, Belgium
Luis Pedro Coelho EMBL, Germany
Mehmet Koyuturk Case Western Reserve University, USA
Manuele Bicego University of Padova, Italy
Miguel Rocha Universidade do Minho, Portugal
Naren Ramakrishnan Virginia Tech, USA
Olivier Gevaert Stanford University, USA
Pedro T Monteiro INESC-ID, Portugal
Pier Luigi Martelli University of Bologna, Italy
Piero Fariselli University of Padova, Italy
Raf Van de Plas Delft University of Technology, The Netherlands
Rita Casadio University of Bologna, Italy
Rui Chang Icahn School of Medicine at Mount Sinai, USA
Saeed Salem North Dakota State University, USA
Stefan Kramer Johannes Guternberg University Mainze, Germany
Susana Vinga IDMEC, Portugal
T. M. Murali Virginia Tech University, USA
Tae Hyun Hwang University of Texas Southwest Medical Center, USA
Tamer Kahveci University of Florida, USA
Tijl De Bie University of Bristol, United Kingdom
Vladimir Pavlovic Rutgers University, USA
Xia Ning Indiana University Purdue University Indianapolis, USA
Yves Moreau KULeuven, Belgium

Workshop History

Information on past workshops is available at:

Data Mining

For more information on data mining see SIGKDD and kdnuggets