Ecosyste.ms: Awesome

An open API service indexing awesome lists of open source software.

Awesome Lists | Featured Topics | Projects

https://github.com/jananiravi/papers

comparative-genomics computational-biology host-pathogen molecular-evolution mycobacterium-tuberculosis phylogeny stress-response

Last synced: 1 day ago
JSON representation

Host: GitHub
URL: https://github.com/jananiravi/papers
Owner: jananiravi
License: mit
Created: 2019-06-09T01:32:30.000Z (over 5 years ago)
Default Branch: main
Last Pushed: 2024-01-04T21:06:47.000Z (about 1 year ago)
Last Synced: 2024-03-20T10:20:42.434Z (10 months ago)
Topics: comparative-genomics, computational-biology, host-pathogen, molecular-evolution, mycobacterium-tuberculosis, phylogeny, stress-response
Homepage: https://jravilab.github.io/publication
Size: 42.3 MB
Stars: 0
Watchers: 1
Forks: 1
Open Issues: 0
Metadata Files:
- Readme: README.md
- License: LICENSE

Awesome Lists containing this project

README

        # Papers & such!

_**Coming soon!**_ 


- Lipid metabolism in Mycobacterium tuberculosis-infected macrophages

- Modeling the START transition in the budding yeast cell cycle

***

^#Co-primary authors.

^*Co-corresponding authors.

**In bold:** Members of JRaviLab.

## 2021 Reconciling Multiple Connectivity Scores for Drug Repurposing

_**Kewalin Samart**^#, **Phoebe Tuyishime**^#, Arjun Krishnan^*, **Janani Ravi^***._ **Reconciling Multiple Connectivity Scores for Drug Repurposing.** Briefings in Bioinformatics. 2021

- [Preprint](https://arxiv.org/abs/2009.09317) | [PDF](https://arxiv.org/pdf/2009.09317)

- [Live doc](https://jravilab.github.io/connectivity_scores)

- [Repo](https://github.com/jravilab/connectivity_scores)

- [Webpage](https://jravilab.github.io/publication/connectivity_scores/)

## 2021 A Broadly Conserved Deoxycytidine Deaminase Protects Bacteria from Phage Infection

_Geoffrey B Severin^#, Brian Y Hsueh^#, Clinton A Elg, John A Dover, Christopher R Rhoades, Alex J Wessel, Benjamin J Ridenhour, Eva M Top, **Janani Ravi**, Kristin D Parent, Chris M Waters._ A Broadly Conserved Deoxycytidine Deaminase Protects Bacteria from Phage Infection. bioRxiv. 2021.

- [Preprint](https://doi.org/10.1101/2021.03.31.437871) | [PDF](https://www.biorxiv.org/content/10.1101/2021.03.31.437871v1.full.pdf)

- [Data website](https://jravilab.github.io/phage_defense_dcdv)

- [Webpage](https://jravilab.github.io/publication/dcdv_vcholerae/)

## 2021 S-layers in Gram-Positive Pathogens

_**Janani Ravi**^#*, Fioravanti A^#*._ **S-layers: the proteinaceous multifunctional armours of Gram-positive pathogens.** Frontiers in Microbiology. 2021

- [DOI](https://doi.org/10.3389/fmicb.2021.663468) | [PDF](https://www.frontiersin.org/articles/10.3389/fmicb.2021.663468/pdf)

- [Webpage](https://jravilab.github.io/publication/slps_grampos/)

## 2021 New Brazilian _M. tuberculosis_ lineage

_Syeda Anum Hadi^#, Ida V Kolte^#, Evan P Brenner^#, Jennifer Gardy, EAT Cunha, L Ferrazoli, DA Villela, RS Santos, **Janani Ravi**, Srinand Sreevatsan^*, Paulo C Basta^*._ **Identification of a predominant genotype of Mycobacterium tuberculosis in Brazilian indigenous population.** Scientific Reports. 2021 Jan 13;11(1):1224. PMID: 33441660

- [PubMed](https://pubmed.ncbi.nlm.nih.gov/33441660/) | [DOI](https://doi.org/10.1038/s41598-020-79621-3) | [PDF](https://www.nature.com/articles/s41598-020-79621-3.pdf)

- [Webpage]((//jravilab.github.io/publication/2019/iai))

## 2020 Psp evolution across the tree of life

_**Janani Ravi^***, Vivek Anantharaman, **Samuel Chen**, Pratik Datta, L Aravind^*, Maria L Gennaro^*._ **Phage-shock-protein (Psp) Envelope Stress Response: Evolutionary History & Discovery of Novel Players.** bioRxiv. 2020

- [Preprint](https://doi.org/10.1101/2020.09.24.301986) | [PDF](https://www.biorxiv.org/content/10.1101/2020.09.24.301986v2.full.pdf)

- [Webapp](https://jravilab.shinyapps.io/psp-evolution)

- [Webpage](https://jravilab.github.io/publication/psp_evolution/)

## 2019 Tcy Cystine transporters in _Staphylococcus aureus_

_Joshua M Lensmire, Jack P Dodson, Brian Y Hsueh, Michael R Wischer, Phillip C Delekta, John C Shook, Elizabeth N Ottosen, Paige J Kies, **Janani Ravi**, Neal D Hammer._ **The Staphylococcus aureus Cystine Transporters TcyABC and TcyP Facilitate Nutrient Sulfur Acquisition during Infection.** Infect Immun. 2020 Feb 20;88(3). doi: 10.1128/IAI.00690-19. Print 2020 Feb 20. PMID: 31843961.

- [PubMed](https://www.ncbi.nlm.nih.gov/pubmed/31843961/) | [PDF](https://jravilab.github.io/files/saureus_tcy.pdf)

- [Webpage](https://jravilab.github.io/publication/tcy_saureus/)

## 2018 Psp systems in Actinobacteria

_**Janani Ravi**, Vivek Anantharaman, L Aravind, Maria L Gennaro._ **Variations on a theme: evolution of the phage-shock-protein system in Actinobacteria.** Antonie Van Leeuwenhoek. 2018 May;111(5):753-760. doi: 10.1007/s10482-018-1053-5. Epub 2018 Feb 27. PubMed PMID: 29488183. 

- [PubMed](https://www.ncbi.nlm.nih.gov/pubmed/29488183/) | [PDF](https://github.com/jananiravi/papers/blob/master/2018-Ravi_Psp_actinobacteria_Anto.pdf)

- [Repo](//github.com/jananiravi/psp-actinobacteria)

- [Webpage](https://jravilab.github.io/publication/psp_actino/)

## 2017 Psp systems in Gram-positive bacteria

_contributed to all the figures and computational analyses in this review._ 


_Manganelli R, Gennaro ML._ **Protecting from Envelope Stress: Variations on the Phage-Shock-Protein Theme.** Trends Microbiol. 2017 Mar;25(3):205-216. doi: 10.1016/j.tim.2016.10.001. Epub 2016 Nov 16. PMID: 27865622.

- [PubMed](https://www.ncbi.nlm.nih.gov/pubmed/27865622/) | [PDF](https://github.com/jananiravi/papers/blob/master/2016-Psp-TiM-Review.pdf)

- [Repo](//github.com/jananiravi/psp-variants-review)

- [Webpage](//jravilab.github.io/publication/2017/tim)

## 2016 Sigma-factor network in Mtb

_Rinki Chauhan, **Janani Ravi**, Pratik Datta, Tian Chen, Dirk Schnappinger, Kevin E Bassler, Gabor Balázsi, Maria L Gennaro._ **Reconstruction and topological characterization of the sigma factor regulatory network of _Mycobacterium tuberculosis_.** Nat Commun. 2016 Mar 31;7:11062. doi: 10.1038/ncomms11062. PMID: 27029515.

- [PubMed](https://www.ncbi.nlm.nih.gov/pubmed/27029515/) | [PDF](https://github.com/jananiravi/papers/blob/master/2016-Chauhan-Sigfac_Mtb-NatComm.pdf) | [Supp Mat](https://github.com/jananiravi/papers/blob/master/2016-Chauhan-Sigfac_Mtb-NatComm_Supp.pdf)

- [Repo](//github.com/jananiravi/sigmafactor-network-mtb)

- [Webpage](https://jravilab.github.io/publication/sigfac_mtb/)

## 2015 Psp in Mtb

_Pratik Datta, **Janani Ravi**, Valentina Guerrini, Rinki Chauhan, Matt B Neiditch, Scarlet S Shell, Sarah M Fortune, Baris Hancioglu, Oleg A Igoshin, Maria L Gennaro._ **The Psp system of _Mycobacterium tuberculosis_ integrates envelope stress-sensing and envelope-preserving functions.** Mol Microbiol. 2015 Aug;97(3):408-22. doi: 10.1111/mmi.13037. Epub 2015 May 26. PMID: 25899163.

- [PubMed](https://www.ncbi.nlm.nih.gov/pubmed/25899163/) | [PDF](https://github.com/jananiravi/papers/blob/master/2015-Datta-Psp_Mtb-MolMicro.pdf)

- [Repo](https://github.com/jananiravi/psp-mtb)

- [Webpage](https://jravilab.github.io/publication/psp_mtb/)

## 2014 VitD in Mtb-infected macrophages

_Hugh Salamon, Natalie Bruiners, Karim Lakehal, Lanbo Shi, **Janani Ravi**, Ken D Yamaguchi, Richard Pine, Maria L Gennaro._ **Cutting edge: Vitamin D regulates lipid metabolism in _Mycobacterium tuberculosis_ infection.** J Immunol. 2014 Jul 1;193(1):30-34. doi: 10.4049/jimmunol.1400736. Epub 2014 Jun 4. PMID: 24899504.

- [PubMed](https://www.ncbi.nlm.nih.gov/pubmed/24899504/) | [PDF w/ Supp Mat](https://github.com/jananiravi/papers/blob/master/2014-VitD_Mtb-JImm_wSupp.pdf)

- [Repo](//github.com/jananiravi/vitamind-lipidmetabolism-mtb-infection)

- [Webpage](//jravilab.github.io/publication/2014/jimm)

_Questions/comments? Email [me](mailto:[email protected])_