| Course Info |
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CSE 590C is a weekly seminar on Readings and Research in Computational Biology, open to all
graduate students in computational, biological, and mathematical sciences.
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| Email |
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| Theme |
This quarter's discussion will focus on an assortment of student-selected topics. |
| Schedule |
| Date |
Presenters/Participants |
Topic |
Details |
 | | 01/07 | ---- Organizational Meeting ---- |
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| 01/14 | Daniel; Wang | Estimating Immune Cell Content From Bulk + sc RNAseq | Details |
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| 01/21 | Holiday |
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| 01/28 | Ian; Noble | Polypharm Side Effects & Graph Convolutional Nets | Details |
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| 02/04 | Gabe; Ruzzo | ***Snow Day*** Dynamic Network Prediction | Details |
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| 02/11 | Shunfu; Kanan | ***Snow Day*** Comparative analysis of single-cell RNA-seq | Details |
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| 02/18 | Holiday |
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| 02/25 | Alex; Ruzzo | A Predictive Model of Transcription | Details |
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| 03/04 | Nao; Ruzzo | DeepVariant (Deep learning for SNP calling) | Details |
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| 03/11 | Johannes; Ruzzo | DeepSEA (Deep learning for chromatin code) | Details |
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| Papers, etc. |
 Note on Electronic Access to Journals
The UW Library is generally a paid subscriber to non-open-access journals we cite. You can freely access these
articles from on-campus computers. For off-campus access, follow the "[offcampus]" links below or look at the
library "proxy server" instructions. You will be
prompted for your UW net ID and password.
01/07: -- ---- Organizational Meeting ----
01/14: Estimating Immune Cell Content From Bulk + sc RNAseq -- Daniel; Wang
- M Schelker, S Feau, J Du, N Ranu, E Klipp, G MacBeath, B Schoeberl, A Raue, "Estimation of immune cell content in tumour tissue using single-cell RNA-seq data." Nat Commun, 8, #1 (2017) 2032.
[offcampus]
01/21: -- Holiday
01/28: Polypharm Side Effects & Graph Convolutional Nets -- Ian; Noble
02/04: ***Snow Day*** Dynamic Network Prediction -- Gabe; Ruzzo
02/11: ***Snow Day*** Comparative analysis of single-cell RNA-seq -- Shunfu; Kanan
02/18: -- Holiday
02/25: A Predictive Model of Transcription -- Alex; Ruzzo
- R Bonneau, MT Facciotti, DJ Reiss, AK Schmid, M Pan, A Kaur, V Thorsson, P Shannon, MH Johnson, JC Bare, W Longabaugh, M Vuthoori, K Whitehead, A Madar, L Suzuki, et 6 al., "A predictive model for transcriptional control of physiology in a free living cell." Cell, 131, #7 (2007) 1354-65.
[offcampus]
03/04: DeepVariant (Deep learning for SNP calling) -- Nao; Ruzzo
- R Poplin, PC Chang, D Alexander, S Schwartz, T Colthurst, A Ku, D Newburger, J Dijamco, N Nguyen, PT Afshar, SS Gross, L Dorfman, CY McLean, MA DePristo, "A universal SNP and small-indel variant caller using deep neural networks." Nat. Biotechnol., 36, #10 (2018) 983-987.
[offcampus]
03/11: DeepSEA (Deep learning for chromatin code) -- Johannes; Ruzzo
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| Other Papers |
Other suggested topics/papers that didn't fit the schedule:
- Alex suggested: gene regulatory network inference and the applications of GRNs in understanding biological
phenomena could be an interesting theme. In addition to two already picked for presentation on
2/4
and
2/25,
other potentially relevant papers include:
- JS Desai, RC Sartor, LM Lawas, SVK Jagadish, CJ Doherty, "Improving Gene Regulatory Network Inference by Incorporating Rates of Transcriptional Changes." Sci Rep, 7, #1 (2017) 17244.
[offcampus]
- Yuliang suggested transcriptomic profiling of the tumor microenvironment, including
our 1/14 paper (a computational benchmarking of several methods aimed at enumerating immune cell infiltration in the tumor
microenvironment)
and
- E Azizi, AJ Carr, G Plitas, AE Cornish, C Konopacki, S Prabhakaran, J Nainys, K Wu, V Kiseliovas, M Setty, K Choi, RM Fromme, P Dao, PT McKenney, RC Wasti, et 4 al., "Single-Cell Map of Diverse Immune Phenotypes in the Breast Tumor Microenvironment." Cell, 174, #5 (2018) 1293-1308.e36.
[offcampus]
(single cell RNA-seq of several breast cancer samples from different subtypes. It's
biologically interesting, and there is also some computational method (clustering, batch effects etc.)
discussed.)
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| Other Seminars |
Past quarters of CSE 590C
COMBI & Genome Sciences Seminars
Biostatistics Seminars
Microbiology Department Seminars
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| Resources |
Molecular Biology for Computer Scientists, a primer by Lawrence Hunter (46 pages)
A comprehensive FAQ at bioinformatics.org, including annotated links to online tutorials and lectures.
CSE 527: Computational Biology
CSEP 527: Computational Biology (Professional Masters Program)
Genome 540/541: Introduction to Computational Molecular Biology: Genome and Protein Sequence Analysis
CSE's Computational Molecular Biology research group
Interdisciplinary Ph.D. program in Computational Molecular Biology
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CSE Home 