Biomedical Informatics Graduate Lab

Journal Club

It is an initiative started by the graduate students and the research staffs of BIL under the guidance of Prof. Jagath C. Rajapakse. The aim of this club is to develop critical thinking, improving presentation skills and learning from peers.

Members of the club meet twice a month, on every alternate Thursday. The meeting starts with a presentation made by one of the members which is followed by discussion.

Completed presentations:

Date	Speaker	Paper
23.08.2007	Prof. Jagath Rajapakse	Markov Encoding for Detecting Signals in Genomic Sequences
13.09.2007	Maria Stepanova	Locating mammalian transcription factor binding sites: A survey of computational and experimental techniques
11.10.2007	Merlin Veronika	An Overview of Image Analysis in Multidimensional Biological Microscopy
17.01.2008	Mundra Piyushkumar	Development of Two-Stage SVM-RFE Gene Selection Strategy for Microarray Expression Data Analysis
21.02.2008	Kavuri Swati Sri	ICA with Reference
20.03.2008	Iti Chaturvedi	Using Protein-Protein Interactions for Refining Gene Networks Estimated from Microarray Data by Bayesian Networks
03.04.2008	Zheng Bo	Multiple-Fiber Reconstruction Algorithms for Diffusion MRI
17.07.2008	Liu Song	A graphical model approach to automated classification of protein subcellular location patterns in multi-cell images
15.08.2008	Li Yongjin	Walking the Interactome for Prioritization of Candidate Disease Genes
11.09.2008	Liu Qian	Noxclass: Prediction of Protein-Protein Interaction Types
09.10.2008	Merlin Veronika	High-throughput Screening of Cellular Features Using High-resolution Light-microscopy: Application for Profiling Drug Effects on Cell Adhesion
06.11.2008	Mundra Piyushkumar	MSVM-RFE: Extensions of SVM-RFE for Multiclass Gene Selection on DNA Microarray Data
04.12.2008	Zheng Bo	A Bayesian Approach for Stochastic White Matter Tractography
16.01.2009	Xu Shuoyu	Second Harmonic Imaging and Scoring of Collagen in Fibrotic Tissues
12.02.2009	Zhu Shiwen	Integrating high-content screening and ligand-target prediction to identify mechanism of action
12.03.2009	Kavuri Swati Sri	A fast algorithm for one unit ICA-R
09.04.2009	Iti Chaturvedi	Modeling Multiple Time Units Delayed Gene Regulatory Network Using Dynamic Bayesian Network.
07.05.2009	Alvin Ng	Variable Selection for Model-Based Clustering.
04.06.2009	Yan Feng	The peaking phenomenon in the presence of feature-selection.
02.07. 2009	Li Yongjin	Efficient similarity search and classification via rank aggregation
30.07. 2009	Liu SONG	A comparison of methods for multi-class support vector machines
20.08.2009	Zhao Liang	Machine learning approaches for prediction of linear B-cell epitopes on proteins
17.09.2009	Liu Qian	Identification of hot-spot residues in protein-protein interactions by computational docking.
12.11.2009	Alvin Ng	Synthetic Images of High-Throughput Microscopy for Validation of Image Analysis Methods.
19.11.2009	Cheng Jierong	A biosegmentation benchmark for evaluation of bioimage analysis methods.
03.12.2009	Divya Jain	Assessment of prediction accuracy of protein function from protein–protein interaction data.
07.01.2010	Fransiskus Xaverius Ivan	Identification of differentially expressed subnetworks based on multivariate ANOVA.
21.01.2010	Iti Chaturvedi	Systematic component selection for gene-network refinement.
04.02.2010	Mundra Piyushkumar	Genetic algorithms for simultaneous variable and sample selection in metabonomics.
18.02.2010	Li Yongjin	QNet: a tool for querying protein interaction networks.
04.03.2010	Liu Qian	Human Cancer Protein-Protein Interaction Network: A Structural Perspective.
18.03.2010	Liu Song	A framework for the automated analysis of sub-cellular patterns in human protein atlas images.
08.04.2010	Merlin Veronika	Phenotypic profiling of the human genome by time-lapse microscopy reveals cell division genes.
22.04.2010	Kavuri Swathi Sri	Sensorimotor Rhythm-Based Brain–Computer Interface (BCI): Feature Selection by Regression Improves Performance.
06.05.2010	Xu Shuoyu	Sampling the spatial patterns of cancer: Optimized biopsy procedures for estimating prostate cancer volume and Gleason Score.
20.05.2010	Zhao Liang	Accurate prediction of peptide binding sites on protein surfaces.
03.06.2010	Zhu Shiwen	3D cell nuclei segmentation based on gradient flow tracking.
17.06.2010	Le Zhenhua	PCRPi: Presaging Critical Residues in Protein interfaces, a new computational tool to chart hot spots in protein interfaces.
02.07.2010	Adrianto Wirawan	High Performance Protein Sequence Database Scanning on the Cell Broadband Engine Processor.
15.07.2010	Thidathip Wongsurawat	Genome-wide analyses of recombination prone regions predict role of DNA structural motif in recombination.
29.07.2010	Lei Lin	Building Disease-Specific Drug-Protein Connectivity Maps from Molecular Interaction Networks and PubMed Abstracts.
12.08.2010	Shamima Banu Binte SM Rashid	Prediction of protein–RNA binding sites by a random forest method with combined features.
26.08.2010	Yang Peng	Align human interactome with phenome to identify causative genes and networks underlying disease families.
20.09.2010	Su Tran To Chinh	FRODOCK: a new approach for fast rotational protein–protein docking.
04.10.2010	Jierong Cheng	A computational framework for studying neuron morphology from in vitro high content neuron based screening.
18.10.2010	Stephanus Daniel Handoko	AutoDock Vina: Improving the speed and accuracy of docking with a new scoring function, efficient optimization and multithreading.
02.12.2010	Fransiskus Xaverius Ivan	Novel regulators of stem cell fates identified by a multivariate phenotype screen of small compounds on human embryonic stem cell colonies.
13.01.2011	Divya Jain	Improving disease gene prioritization using the semantic similarity of Gene Ontology terms.
27.01.2011	Liu Qian	Predicting disease-associated substitution of a single amino acid by analyzing residue interactions.
24.02.2011	Li Zhenhua	Geometric Similarities of Protein–Protein Interfaces at Atomic Resolution Are Only Observed within Homologous Families: An Exhaustive Structural Classification Study.
07.03.2011	Ouyang Xuchang	A machine learning approach to predicting protein–ligand binding affinity with applications to molecular docking.
24.03.2011	Xu Shuoyu	Image-based multiscale modeling predicts tissue-level and network-level fiber reorganization in stretched cell-compacted collagen gels.
28.04.2011	Mundra Piyushkumar Arjunlal	Robust biomarker identification for cancer diagnosis with ensemble feature selection methods.
19.05.2011	Iti Charturvedi	Estimation of nonlinear gene regulatory networks via L1 regularized NVAR from time series gene expression data.
02.06.2011	Yang Peng	Associating genes and protein complexes with disease via network propagation.
23.06.2011	Zhu Shiwen	Local cell metrics: a novel method for analysis of cell-cell interactions.
30.06.2011	Kavuri Swathi Sri	On semi-blind source separation using spatial constraints with application in EEG analysis.
14.07.2011	Zhao Liang	Preferential use of protein domain pairs as interaction mediators: order and transitivity.
28.07.2011	Shamima Banu	Structure-based prediction of RNA-binding domains and RNA-binding sites and application to structural genomics targets.

Upcoming presentations:

Time: 4.00 – 5.00pm

Venue: Data Management and Analytics Graduate Lab (DMAL) meeting room, N4-B3c-14

Anyone interested in participating in BIL Journal Club should write to the Journal Club Coordinator, Merlin Veronika.