Date: Thursday, Jun 23, 2016
Presenter:
 Deepak Tanwar. Research Scholar, Department of Pathology, Informatics Division.
Seminar:
PLINK: a toolset for whole genome association analysis (Part I)
Reference Material: http://pngu.mgh.harvard.edu/~purcell/plink/tutorial.shtml

Date:
 
Thursday, June 16, 2016
Presenter: 
Emanuel Diego dos Santos Penha, Research Assistant, Department of Pathology.
Seminar: 
Rare and Low Frequency Variant Stratification in the UK Population: Description and Impact on Association Tests.
Paper:
 Babron, M.-C., Tayrac, M. de, Rutledge, D. N., Zeggini, E. & Génin, E. Rare and Low Frequency Variant Stratification in the UK Population: Description and Impact on Association Tests. PLOS ONE 7, e46519 (2012). 
PMID:23071581

Date:
 Thursday, June 9, 2016
Presenter:
 Malay K Basu, Assistant Professor, Department of Pathology.
Seminar:
 Comparison of co-expression measures: mutual information, correlation, and model based indices
Paper:
 Song, L., Langfelder, P. & Horvath, S. Comparison of co-expression measures: mutual information, correlation, and model based indices. BMC Bioinformatics 13, 328 (2012).
PMID:23217028

Date:
 Thursday, May 26, 2016
Presenter:
 Deepak Tanwar. Research Scholar, Department of Pathology, Informatics Division.
Seminar: 
A short introduction to Machine Learning with R using Caret package
Reference Material: http://appliedpredictivemodeling.com/

Date:
 Thursday, May 19, 2016
Presenter:
 Alexander Stepanov, Ph.D. Research Associate, Pharmacology/Toxicology Department
Seminar:
How to get the most out of your high-throughput screen data

Date:
 Thursday, May 12, 2016
Presenter:
 Emanuel Diego dos Santos Penha, Research Assistant, Department of Pathology.
Seminar:
 Utilizing the Jaccard index to reveal population stratification in sequencing data: a simulation study and an application to the 1000 Genomes Project
Paper:
Prokopenko, D. et al. Utilizing the Jaccard index to reveal population stratification in sequencing data: a simulation study and an application to the 1000 Genomes Project. Bioinformatics 32, 1366–1372 (2016).
PMID:26722118

Date:
 Thursday, May 5, 2015
Presenter:
 Malay K Basu, Assistant Professor, Department of Pathology.
Seminar:
Complex archaea that bridge the gap between prokaryotes and eukaryotes
Paper: 
Spang, A. et al. Complex archaea that bridge the gap between prokaryotes and eukaryotes. Nature 521, 173–179 (2015).
PMID:25945739

Date:
 Thursday, April 21, 2016
Presenter:
 Emanuel Diego dos Santos Penha, Research Assistant, Department of Pathology.
Seminar:
Visualization of genomic data with the Hilbert curve
Paper:
Anders, S. Visualization of genomic data with the Hilbert curve. Bioinformatics 25, 1231–1235 (2009).
PMID:19297348

Date:
 Thursday, April 14, 2016
Presenter:
 Deepak Tanwar. Research Scholar, Department of Pathology, Informatics Division.
Seminar:
 Flux Balance Analysis
Paper:
 Orth, J. D., Thiele, I. & Palsson, B. Ø. What is flux balance analysis? Nat Biotechnol 28, 245–248 (2010).
PMCID:3108565

Date:
 Thursday, April 7, 2015
Presenter:
 Malay K Basu, Assistant Professor, Department of Pathology.
Seminar:
Agile Project management for research labs: SCRUM and SCORE 101
Resources: http://www.scrumguides.org/ and http://www.cs.umd.edu/projects/PL/score/

Date:
 Thursday, Mar 24, 2016
Presenter:
 Deepak Tanwar. Research Scholar, Department of Pathology, Informatics Division.
Seminar:
 Evolution of Genome complexity

Date:
 Thursday, March 17, 2016
Presenter:
Tatjana Coric, PhD. Assistant Professor, Department of Pharmacology and Toxicology, UAB
Seminar:
Novel class of rexinoids for breast cancer chemoprevention

Date:
 Thursday, March 10, 2016
Presenter:
 Christos Vaklavas, MD. Assistant Professor Division of Hematology & Oncology
Seminar:
 Upstream ORFs are prevalent translational repressors in vertebrates
Paper:
 Johnstone, T. G., Bazzini, A. A. & Giraldez, A. J. Upstream ORFs are prevalent translational repressors in vertebrates. The EMBO Journal (2016). doi:10.15252/embj.201592759
PMID:26896445

Date:
 Thursday, March 03, 2016
Presenter:
 Emanuel Diego dos Santos Penha, Research Assistant, Department of Pathology.
Seminar:
 Quantifying Position-Dependent Codon Usage Bias
Paper:
 Hockenberry, A. J., Sirer, M. I., Amaral, L. A. N. & Jewett, M. C. Quantifying Position-Dependent Codon Usage Bias. Mol Biol Evol 31, 1880–1893 (2014).
PMCID:4069614

Date:
 Thursday, February 11, 2016
Presenter:
 Tim Kennell Jr., MD-PhD Student, NIH Medical Scientist Training Program
Seminar:
 Functional evaluation of out-of-the-box text-mining tools for data-mining tasks
Paper:
 Jung, K. et al. Functional evaluation of out-of-the-box text-mining tools for data-mining tasks. J Am Med Inform Assoc 22, 121–131 (2015).
PMID: 25863278

Date:
 Thursday, February 4, 2016
Presenter:
 Hyunmin Koo, Ms, PhD candidate, Biology Department
Seminar:
Highly divergent ancient gene families in metagenomic samples are compatible with additional divisions of life
Paper:
Lopez, P., Halary, S. & Bapteste, E. Highly divergent ancient gene families in metagenomic samples are compatible with additional divisions of life. Biol. Direct 10, 64 (2015).
PMID: 26502935

Date: Thursday, January 21, 2016
Presenter:
 Emanuel Diego dos Santos Penha, Research Assistant, Department of Pathology.
Seminar:
 Adjusting for background mutation frequency biases improves the identification of cancer driver genes.
Paper:
 Evans, P., Avey, S., Kong, Y. & Krauthammer, M. Adjusting for Background Mutation Frequency Biases Improves the Identification of Cancer Driver Genes. IEEE Transactions on NanoBioscience 12, 150–157 (2013).
PMID: 23694700

Date:
 Thursday, January 14, 2015
Presenter:
 Deepak Tanwar, Research Scholar, Department of Pathology.
Seminar:
 ssGSEA: A method for Gene Set Enrichment Analysis
https://www.broadinstitute.org/cancer/software/genepattern/modules/docs/ssGSEAProjection/4

Date: Thursday, January 7, 2015
Presenter: Malay K Basu, Assistant Professor, Department of Pathology.
Seminar: Synonymous mutations frequently act as driver mutations in human cancers 
Paper: Supek, F., Miñana, B., Valcárcel, J., Gabaldón, T. & Lehner, B. Synonymous mutations frequently act as driver mutations in human cancers. Cell 156, 1324–1335 (2014).
PMID:25336595