SAMSI-SAVI Workshop on Statistical Methods for Bioinformatics: December 12-14, 2013

This workshop, held in Bangalore, India, consisted of a series of one-hour lectures spanning a broad range of topics of current interest in statistical modeling, data analysis and inference in Bioinformatics. A wide range of topics of current use and interest in bioinformatics and more generally for biological data were presented. These included methods for analysis of micro array data, modeling for dynamics of mixtures, methods for differential methylation using next generation sequencing data, methods for analysis of gene networks and modeling and inference for circadian and directional data. The workshop also touched on themes to be further developed during the SAMSI 2014-15 “Beyond Bioinformatics” research program.

Invited Speakers from the USA

Naomi Altman, Pennsylvania State University
Data Obesity: Inflated Estimation and Irreproducible Results with High Throughput Data

Varghese George, Georgia Regents University
Methods for Differential Methylation with Next Generation Sequencing

Susan Holmes, Stanford University
The Many Sides of the Human Microbiome: Combining Heterogeneous Data in Meaningful Ways

Paul Joyce, University of Idaho
The Role of Statistics in the Theory of Adaptive Evolution Informed by Experimental Data

Olga Vitek, Purdue University
Statistical methods for quantitative mass spectrometry-based proteomics

Contributed Papers

Malay Bhattacharyya, University of Kalyani
MicroRNA Signatures Distinguish Breast Cancer Subtypes?

Posters

See the workshop web site for more details.


Schedule and Supporting Media

Thursday, December 12, 2013
Venue: Lecture Hall – I, Department of Mathematics, IISc, Bangalore

Time Description Speaker Slides Videos
9:00am – 9:30am Registration
9:30am – 10:45am Methods for Differential Methylation with Next Generation Sequencing Varghese George, Georgia Regents University
10:45pm – 12:00pm Multilocus association test in genetic association study using similarity between individuals Indranil Mukhopadhyay, ISI
12:00pm – 1:00pm Lunch
1:00pm – 2:15pm Statistical Techniques for Normalization of Microarray Data S.R. Deshmukh, University of Pune
2:15pm – 3:30pm Data Obesity: Inflated Estimation and Irreproducible Results with High Throughput Data Naomi Altman, Penn State University
3:30pm – 3:45pm Tea
3:45pm – 4:30pm Statistical analysis of gene duplication data Snehalata Huzurbazar, SAMSI
4:30pm – 5:45pm Circular Statistical Inference for Circadian Rhythms in Genomic Data Ashis Sen Gupta, ISI
5:45pm – 6:00pm Discussions

Friday, December 13, 2013
Venue: Lecture Hall – I, Department of Mathematics, IISc, Bangalore

Time Description Speaker Slides Videos
9:00am – 10:15am Towards disease prediction modeling – Analysis of host pathogen interactions through integrated genome-scale networks and Boolean dynamics Nagasuma R. Chandra, IISc
10:15am – 10:30am Tea
10:30am – 11:45am Statistical methods for quantitative mass spectrometry-based proteomics Olga Vitek, Purdue University
11:45am – 12:45pm Likelihood and Bayesian Estimates of Reproduction Numbers through Stochastic Modelling for the Pandemic Influenza A/H1N1 2009 in IndiaComprehensive statistical and functional annotation analysis of data from Affymetrix Human Genome U133 Plus 2.0 array

Study on different gene selection methods: support vector machine classification approach

Contributed Papers (3 speakers):

Sheikh Taslim Ali, Karnatak University

Trinadh Kumar Potina, Tata Consultancy Services

Sandip Shil, Gauhati University

12:45pm – 1:45pm Lunch
1:45pm – 3:00pm Filling-in void and sparse regions in protein sequence space by protein- like artificial sequences enables remarkable enhance mentin remote homology detection capability N. Srinivasan, IISc
3:00pm – 4:15pm Statistical methods for Phylogenetic analysis T. S. Vasulu, ISI
4:15pm – 4:30pm Tea
4:30pm-5:45pm The role of statistics in the theory of adaptive evolution informed by experimental data Paul Joyce, University of Idaho
5:45pm-6:00pm Discussions

Saturday, December 14, 2013
Venue: Lecture Hall – I, Department of Mathematics, IISc, Bangalore

Time Description Speaker Slides Videos
9:00am – 10:15am The many sides of the Human Microbiome:combining heterogeneous data in meaningful ways Susan Holmes, Stanford University
10:15am-10:30am Tea
10:30am-11:45am MicroRNA Signatures Distinguish Breast Cancer Subtypes?A New Distribution on the Torus with Applications to Paired Circular Genome Data

Network Analysis wrt PCOS

Analysis of Boolean Functions based on Interaction Graphs and their influence in System Biology

Contributed Papers (3 speakers):

Malay Bhattacharya, University of Kalyani

H.V. Kulkarni, Shivaji University

Anwesha Pan, ISI

Ranjeet Rout, ISI

11:45am – 12:45pm Lunch
12:45pm – 02:00pm Multi objective Clustering with SVM Based Ensembling for Analysis of Gene Expression Data Sanghamitra Bandopadhyay, ISI