New papers to read

[kdahlquist]

The team should check out this article, especially @NAnguiano and @anuvarsh.

Kumar, S., & Dudley, J. (2007). Bioinformatics software for biologists in the genomics era. Bioinformatics, 23(14), 1713-1717.

[kdahlquist]

Here's another one:

List, M., Ebert, P., & Albrecht, F. (2017). Ten Simple Rules for Developing Usable Software in Computational Biology. PLOS Computational Biology, 13(1), e1005265.

[kdahlquist]

I changed the title of this issue for us to post papers of interest to the group as they come in. I got an article alert for this one:

Schäfer, R. A., & Voß, B. (2016). VisualGraphX: interactive graph visualization within Galaxy. Bioinformatics, 32(22), 3525-3527.

and this one:

Mons, B., Neylon, C., Velterop, J., Dumontier, M., da Silva Santos, L. O. B., & Wilkinson, M. D. Cloudy, increasingly FAIR; revisiting the FAIR Data guiding principles for the European Open Science Cloud. Information Services & Use, (Preprint), 1-8.

[kdahlquist]

A paper that will be good for the BioDB course:

McMurry, J., Juty, N., Blomberg, N., Burdett, A., Conlin, T., Conte, N., ... & Gonzalez-Beltran, A. (2017). Identifiers for the 21st century: How to design, provision, and reuse persistent identifiers to maximize utility and impact of life science data. bioRxiv, 117812.

Also, reposting here an earlier comment from @dondi on another issue to keep items to read in one place: https://www.designernews.co/stories/84443-redditors-design-worst-volume-sliders-possible

[jmcmurry]

Hi there, the full peer reviewed version of our above identifiers paper came out 3 weeks ago in Plos Biology (doi:10.1371/journal.pbio.2001414) and it is a lot better than the biorxiv version. If you serve data, please also have a look into Herbert van de Sompel's signposting suggestions, which we couldn't address in detail in the paper. Let us know if you have any feedback or questions. Best of luck...

[kdahlquist]

Thanks @jmcmurry for the update!

[kdahlquist]

Interesting paper on visualization of protein structures, may be useful in the future.

Heinrich, J., Vuong, J., Hammang, C. J., Wu, A., Rittenbruch, M., Hogan, J., ... & O'Donoghue, S. I. (2016, June). Evaluating viewpoint entropy for ribbon representation of protein structure. In Computer Graphics Forum (Vol. 35, No. 3, pp. 181-190).

[kdahlquist]

Goodstadt, M., & Marti‐Renom, M. A. (2017). Challenges for visualizing three‐dimensional data in genomic browsers. FEBS letters.

• This paper is about genome browsers, but fundamentally is about visualizing 3D data in 2D space, a challenge we face with GRNsight.

[kdahlquist]

New book on Data Visualization: https://serialmentor.com/dataviz/index.html Written in R Markdown with source in GitHub at: https://github.com/clauswilke/dataviz

[kdahlquist]

Aouaa, N., Gherbi, R., Meziane, A., Hadjar, H., & Setitra, I. (2018, October). Visual Data Mining by Virtual Reality for Protein-Protein Interaction Networks. In 2018 IEEE/ACS 15th International Conference on Computer Systems and Applications (AICCSA) (pp. 1-8). IEEE.

[kdahlquist]

Ira Herskowitz is credited with first using the arrow and blunt-end marker to mean activation vs. inhibition/repression. See: Botstein, D. (2004). Ira Herskowitz: 1946-2003. Genetics, 166(2), 653-660.

[kdahlquist]

Qu, Z., Lau, C. W., Nguyen, Q. V., Zhou, Y., & Catchpoole, D. R. (2019). Visual Analytics of Genomic and Cancer Data: A Systematic Review. Cancer informatics, 18, 1176935119835546. DOI: 10.1177/1176935119835546

[kdahlquist]

https://the-turing-way.netlify.com/introduction/introduction

[kdahlquist]

O'Donoghue, S. I., Baldi, B. F., Clark, S. J., Darling, A. E., Hogan, J. M., Kaur, S., ... & Swedlow, J. R. (2018). Visualization of biomedical data. Annual Review of Biomedical Data Science, 1, 275-304.

[kdahlquist]

Cruz, A., Arrais, J. P., & Machado, P. (2018). Interactive and coordinated visualization approaches for biological data analysis. Briefings in bioinformatics. DOI: 10.1093/bib/bby019 https://academic.oup.com/bib/article/20/4/1513/4953976

[kdahlquist]

Cruz, A., Arrais, J. P., & Machado, P. (2018, July). Interactive Network Visualization of Gene Expression Time-Series Data. In 2018 22nd International Conference Information Visualisation (IV) (pp. 574-580). IEEE. DOI: 10.1109/iV.2018.00105 https://ieeexplore.ieee.org/abstract/document/8564223

[kdahlquist]

Cruz, A., Arrais, J. P., & Machado, P. (2018). Interactive and coordinated visualization approaches for biological data analysis. Briefings in bioinformatics. https://academic.oup.com/bib/article/20/4/1513/4953976

[kdahlquist]

SCOPE LAB at UCLA http://projects.dma.ucla.edu/scopelab/

[dondi]

Dependency issue: https://medium.com/@alex.birsan/dependency-confusion-4a5d60fec610

[kdahlquist]

Baltoumas, F. A., Zafeiropoulou, S., Karatzas, E., Koutrouli, M., Thanati, F., Voutsadaki, K., ... & Pavlopoulos, G. A. (2021). Biomolecule and Bioentity Interaction Databases in Systems Biology: A Comprehensive Review. Biomolecules, 11(8), 1245. https://www.mdpi.com/2218-273X/11/8/1245

[kdahlquist]

Agapito, G., & Cannataro, M. (2021). Using BioPAX-Parser (BiP) to enrich lists of genes or proteins with pathway data. BMC bioinformatics, 22(13), 1-35. https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-021-04297-z

[kdahlquist]

Guo, M. G., Sosa, D. N., & Altman, R. B. (2022). Challenges and opportunities in network-based solutions for biological questions. Briefings in Bioinformatics, 23(1), bbab437. https://academic.oup.com/bib/article/23/1/bbab437/6438103?login=true

[kdahlquist]

For future iteration of Biological Databases? https://terra.bio/anvil-in-the-classroom-cloud-scale-educational-resources-for-modern-genomics/

[kdahlquist]

Durant, E., Rouard, M., Ganko, E. W., Muller, C., Cleary, A. M., Farmer, A. D., ... & Sabot, F. (2022). Ten simple rules for developing visualization tools in genomics. PLOS Computational Biology, 18(11), e1010622.

[kdahlquist]

Alzahrani, H., & Fernstad, S. (2023). An investigation into various visualization tools for complex biological networks. Information Visualization, 14738716231181545. https://journals.sagepub.com/doi/full/10.1177/14738716231181545

[kdahlquist]

From @nchun2's Annotated Bibliography for HNRS 2000

Tzu-Hsien Yang, Chung-Ching Wang, Yu-Chao Wang, Wei-Sheng Wu, YTRP: a repository for yeast transcriptional regulatory pathways, Database, Volume 2014, 2014, bau014, https://doi.org/10.1093/database/bau014

John A. Choi, John J. Wyrick, RegulatorDB: a resource for the analysis of yeast transcriptional regulation, Database, Volume 2017, 2017, bax058, https://doi.org/10.1093/database/bax058

García-Ríos, E., Alonso-del-Real, J., Lip, K. Y. F., Pinheiro, T., Teixeira, J., van Gulik, W., ... & Guillamón, J. M. (2022). Genome-wide effect of non-optimal temperatures under anaerobic conditions on gene expression in Saccharomyces cerevisiae. Genomics, 114(4), 110386. https://doi.org/10.1016/j.ygeno.2022.110386

Ghorbani, M., Jonckheere, E. A., & Bogdan, P. (2018). Gene Expression Is Not Random: Scaling, Long-Range Cross-Dependence, and Fractal Characteristics of Gene Regulatory Networks. Frontiers in Physiology, 9. https://www.frontiersin.org/articles/10.3389/fphys.2018.01446

[kdahlquist]

Ehlers, H., Villedieu, A., Raidou, R. G., & Wu, H. Y. (2023). Improving readability of static, straight-line graph drawings: A first look at edge crossing resolution through iterative vertex splitting. Computers & Graphics, 116, 448-463. https://doi.org/10.1016/j.cag.2023.09.010