STAT
581
Bioinformatics
Seminar (Spring 2022)
Time: 12:30-1:20pm
Location: zoom
link
Schedule
1.
Tuesday,
January 11, 2022
Min Zhang, Department of Statistics, Purdue
University
·
Course
information: Only registered students should attend.
2.
Tuesday,
January 18, 2022
Yunlong
Liu,
Director of Bioinformatics Core; Director of Center for Medical Genomics;
Professor of Molecular and Medical Genetics; Indiana University School of
Medicine
·
Title: Roles of
Regulatory Variants in Complex Diseases
·
Abstract
·
Associated reading: Allele-specific expression and
high-throughput reporter assay reveal functional genetic variants associated
with alcohol use disorders. Rao X, Thapa KS, Chen AB, Lin H, Gao H, Reiter
JL, Hargreaves KA, Ipe J, Lai D, Xuei X, Wang Y, Gu
H, Kapoor M, Farris SP, Tischfield J, Foroud T, Goate AM, Skaar TC, Mayfield RD, Edenberg
HJ, Liu Y. Mol Psychiatry. 2021 Apr;26(4):1142-1151. doi:
10.1038/s41380-019-0508-z. Epub 2019 Sep 2.
PMID: 31477794
3.
Tuesday,
January 25, 2022
Fei Xue, Department of
Statistics, Purdue University
·
Title: Heterogeneous
Mediation Analysis on Epigenomic PTSD and Traumatic Stress in a Predominantly
African American Cohort
·
Abstract
·
Associated reading: Heterogeneous
Mediation Analysis on Epigenomic PTSD and Traumatic Stress in a Predominantly
African American Cohort
4.
Tuesday,
February 1, 2022
Chongli Yuan, Davidson School of Chemical Engineering,
Purdue University
·
Title: Towards
elucidating the impact of environmental exposure on epigenome and long-term
health risk
·
Abstract
·
Associated
reading: Pre-differentiation
exposure to low-dose of atrazine results in persistent
phenotypic changes in human neuronal cell lines
5.
Tuesday,
February 8, 2022 (cancelled)
6.
Tuesday,
February 15, 2022
Zhabiz Golkar, Voorhees College
·
Title: Engineering
Embryos Using CRISPR-Cas9, Scientific and Ethical Considerations
·
Abstract
·
Associated
reading: https://genetics.thetech.org/ask/ask373
7.
Tuesday,
February 22, 2022
Lucia Petito, Feinberg School
of Medicine, Northwestern University
·
Title: Considerations
when Leveraging Electronic Health Records to Address Comparative Effectiveness
Questions: A “Create Your Own Data” Adventure
·
Abstract
·
Associated
reading:
o
Hernán M.A. & Robins
J.M. (2016). Using big data to emulate a target trial when a randomized trial
is not available. American Journal of Epidemiology, 183(8):758-764.
https://doi.org/10.1093/aje/kwv254
o
Hernán, M. A., Sauer, B.
C., Hernández-Díaz, S., Platt, R., & Shrier, I.
(2016). Specifying a target trial prevents immortal time bias and other self-inflicted
injuries in observational analyses. Journal of clinical epidemiology,
79, 70-75. https://doi.org/10.1016/j.jclinepi.2016.04.014
o
Hernán, M. A. (2018).
How to estimate the effect of treatment duration on survival outcomes using
observational data. Bmj, 360.
https://doi.org/10.1136/bmj.k182
o
Petito, L. C., García-Albéniz, X., Logan, R. W., Howlader,
N., Mariotto, A. B., Dahabreh,
I. J., & Hernán, M. A. (2020). Estimates of
overall survival in patients with cancer receiving different treatment regimens: emulating hypothetical target trials in the
Surveillance, Epidemiology, and End Results (SEER)–Medicare Linked Database.
JAMA network open, 3(3), e200452. https://doi.org/10.1001/jamanetworkopen.2020.0452
8.
Tuesday,
March 1, 2022 (CGC seminar series – Part 1)
Zélia Worman, Program Manager,
Seven Bridges
·
Title: The Cancer
Genomics Cloud: A secure and scalable cloud-based platform to access, share,
and analyze multi-omics datasets
·
Abstract
·
Associated
reading:
o
website:
https://www.cancergenomicscloud.org/
o
Publication:
https://aacrjournals.org/cancerres/article/77/21/e3/662625/The-Cancer-Genomics-Cloud-Collaborative
·
Slides
·
Video
9.
Tuesday,
March 8, 2022 (CGC seminar series – Part 2)
Phil Webster, Genomic
Scientist, Seven Bridges
·
Title: RNA-seq analysis
and differential expression in the cloud
·
Abstract
·
Slides
·
Video
·
Note: If you have issues with the workflow runs, please review the Seminar
Workflow Fix.
10.
Tuesday,
March 15, 2022 (No seminar – Spring break)
11.
Tuesday,
March 22, 2022 (CGC seminar series – Part 3)
Phil Webster, Genomic
Scientist, Seven Bridges
·
Title: Using the power of
cloud computing to scale single-cell analysis with the CGC
·
Abstract
·
Slides
·
Video
12.
Tuesday,
March 29, 2022 (CGC seminar series – Part 4)
Manisha Ray
·
Title: Uploading your own
data on the CGC – the power of big data, at the tip of your hands
·
Abstract
·
Slides
·
Video
13.
Tuesday,
April 5, 2022
Saurabh
Sinha,
Thomas M. Siebel Center for Computer Science, University of Illinois
Urbana-Champaign
·
Title: New challenges
and opportunities presented by advances in transcriptomics
·
Abstract
·
Associated
reading:
[Spatial
single-cell transcriptomics]
Emanuel,
G., & He, J. (2021). MERFISH Enables Mapping of Cellular Diversity with
Spatial Context at Subcellular Resolution. Microscopy Today, 29(4), 30-33.
doi:10.1017/S1551929521000894
[Transcriptomic
profile deconvolution]
Jaakkola MK, Elo LL.
Computational deconvolution to estimate cell type-specific gene expression from
bulk data. NAR Genom Bioinform.
2021 Jan 12;3(1):lqaa110. doi:
10.1093/nargab/lqaa110. PMID: 33575652; PMCID:
PMC7803005.
Hao Y, Yan M,
Heath BR, Lei YL, Xie Y. Fast and robust deconvolution of tumor infiltrating
lymphocyte from expression profiles using least trimmed squares. PLoS Comput Biol. 2019 May 6;15(5):e1006976. doi:
10.1371/journal.pcbi.1006976. PMID: 31059559; PMCID: PMC6522071.
14.
Tuesday,
April 12, 2022 – Cancelled
15.
Tuesday,
April 19, 2022
Jinhui
Wang, Integrative Genomics Core, Beckman Research Institute
of City of Hope
Lu
Yang, Department of Systems Biology,
Beckman Research Institute of City of Hope
·
Title: Introduction of next
generation sequencing application and analysis
·
Abstract
·
Associated
reading:
An overview of Next-Generation Sequencing.
Athina Gkazi. Genomics Rsearch. https://www.technologynetworks.com/genomics/articles/an-overview-of-next-generation-sequencing-346532
Nanopore-based fourth-generation DNA
sequencing technology.Feng
Y, Zhang Y, Ying C, Wang D, Du C. Genomics Proteomics Bioinformatics. 2015
Feb;13(1):4-16. doi: 10.1016/j.gpb.2015.01.009. Epub 2015 Mar 2.
Third-Generation Sequencing: The Spearhead
towards the Radical Transformation of Modern Genomics. Athanasopoulou
K, Boti MA, Adamopoulos PG,
Skourou PC, Scorilas A.Life (Basel). 2021 Dec
26;12(1):30. doi: 10.3390/life12010030.
Shade A, Teal TK (2015) Computing
Workflows for Biologists: A Roadmap. PLoS Biol 13(11):e1002303.
Cock PJ, Fields CJ, Goto
N et al. (2010) The Sanger FASTQ file format for sequences with quality scores,
and the Solexa/Illumina FASTQ variants. Nucleic Acids
Res 38(6):1767-1771.
Ewing B, Green P (1998) Base-calling of
automated sequencer traces using phred. II. Error
probabilities. Genome Res 8(3): 186-194.
Conesa, A., Madrigal, P., Tarazona, S. et al. A survey of best practices for RNA-seq
data analysis. Genome Biol 17, 13 (2016).
Nakato R, Shirahige K. Recent advances in ChIP-seq
analysis: from quality management to whole-genome annotation. Brief Bioinform. 2017;18(2):279-290.
Haque, A., Engel, J., Teichmann,
S.A. et al. A practical guide to single-cell RNA-sequencing for biomedical
research and clinical applications. Genome Med 9, 75 (2017).
Hwang, B., Lee, J.H. & Bang, D.
Single-cell RNA sequencing technologies and bioinformatics pipelines. Exp Mol
Med 50, 1–14 (2018).