{"id":24652623,"url":"https://github.com/jananiravi/papers","last_synced_at":"2026-01-04T15:06:09.525Z","repository":{"id":52673717,"uuid":"190951808","full_name":"jananiravi/papers","owner":"jananiravi","description":null,"archived":false,"fork":false,"pushed_at":"2024-01-04T21:06:47.000Z","size":44385,"stargazers_count":0,"open_issues_count":0,"forks_count":1,"subscribers_count":1,"default_branch":"main","last_synced_at":"2025-01-25T19:44:50.480Z","etag":null,"topics":["comparative-genomics","computational-biology","host-pathogen","molecular-evolution","mycobacterium-tuberculosis","phylogeny","stress-response"],"latest_commit_sha":null,"homepage":"https://jravilab.github.io/publication","language":null,"has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"mit","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/jananiravi.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":null,"funding":null,"license":"LICENSE","code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null,"governance":null,"roadmap":null,"authors":null}},"created_at":"2019-06-09T01:32:30.000Z","updated_at":"2024-02-06T15:29:41.000Z","dependencies_parsed_at":"2024-01-14T22:13:19.521Z","dependency_job_id":null,"html_url":"https://github.com/jananiravi/papers","commit_stats":{"total_commits":12,"total_committers":1,"mean_commits":12.0,"dds":0.0,"last_synced_commit":"9ee9a1b0554c894824eb16509c8da57eb0d3a478"},"previous_names":[],"tags_count":0,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/jananiravi%2Fpapers","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/jananiravi%2Fpapers/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/jananiravi%2Fpapers/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/jananiravi%2Fpapers/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/jananiravi","download_url":"https://codeload.github.com/jananiravi/papers/tar.gz/refs/heads/main","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":244706545,"owners_count":20496571,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2022-07-04T15:15:14.044Z","host_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub","repositories_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories","repository_names_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repository_names","owners_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners"}},"keywords":["comparative-genomics","computational-biology","host-pathogen","molecular-evolution","mycobacterium-tuberculosis","phylogeny","stress-response"],"created_at":"2025-01-25T19:44:55.888Z","updated_at":"2026-01-04T15:06:09.454Z","avatar_url":"https://github.com/jananiravi.png","language":null,"funding_links":[],"categories":[],"sub_categories":[],"readme":"# Papers \u0026 such!\n_**Coming soon!**_ \u003cbr\u003e\n- Lipid metabolism in Mycobacterium tuberculosis-infected macrophages\n- Modeling the START transition in the budding yeast cell cycle\n\n***\n\u003csup\u003e#\u003c/sup\u003eCo-primary authors.\n\u003csup\u003e*\u003c/sup\u003eCo-corresponding authors.\n**In bold:** Members of JRaviLab.\n\n## 2021 Reconciling Multiple Connectivity Scores for Drug Repurposing\n_**Kewalin Samart**\u003csup\u003e#\u003c/sup\u003e, **Phoebe Tuyishime**\u003csup\u003e#\u003c/sup\u003e, Arjun Krishnan\u003csup\u003e*\u003c/sup\u003e, **Janani Ravi\u003csup\u003e*\u003c/sup\u003e**._ **Reconciling Multiple Connectivity Scores for Drug Repurposing.** Briefings in Bioinformatics. 2021\n- [Preprint](https://arxiv.org/abs/2009.09317) | [PDF](https://arxiv.org/pdf/2009.09317)\n- [Live doc](https://jravilab.github.io/connectivity_scores)\n- [Repo](https://github.com/jravilab/connectivity_scores)\n- [Webpage](https://jravilab.github.io/publication/connectivity_scores/)\n\n## 2021 A Broadly Conserved Deoxycytidine Deaminase Protects Bacteria from Phage Infection\n_Geoffrey B Severin\u003csup\u003e#\u003c/sup\u003e, Brian Y Hsueh\u003csup\u003e#\u003c/sup\u003e, 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.\n- [Preprint](https://doi.org/10.1101/2021.03.31.437871) | [PDF](https://www.biorxiv.org/content/10.1101/2021.03.31.437871v1.full.pdf)\n- [Data website](https://jravilab.github.io/phage_defense_dcdv)\n- [Webpage](https://jravilab.github.io/publication/dcdv_vcholerae/)\n\n## 2021 S-layers in Gram-Positive Pathogens\n_**Janani Ravi**\u003csup\u003e#*\u003c/sup\u003e, Fioravanti A\u003csup\u003e#*\u003c/sup\u003e._ **S-layers: the proteinaceous multifunctional armours of Gram-positive pathogens.** Frontiers in Microbiology. 2021\n- [DOI](https://doi.org/10.3389/fmicb.2021.663468) | [PDF](https://www.frontiersin.org/articles/10.3389/fmicb.2021.663468/pdf)\n- [Webpage](https://jravilab.github.io/publication/slps_grampos/)\n\n## 2021 New Brazilian _M. tuberculosis_ lineage\n_Syeda Anum Hadi\u003csup\u003e#\u003c/sup\u003e, Ida V Kolte\u003csup\u003e#\u003c/sup\u003e, Evan P Brenner\u003csup\u003e#\u003c/sup\u003e, Jennifer Gardy, EAT Cunha, L Ferrazoli, DA Villela, RS Santos, **Janani Ravi**, Srinand Sreevatsan\u003csup\u003e*\u003c/sup\u003e, Paulo C Basta\u003csup\u003e*\u003c/sup\u003e._ **Identification of a predominant genotype of Mycobacterium tuberculosis in Brazilian indigenous population.** Scientific Reports. 2021 Jan 13;11(1):1224. PMID: 33441660\n- [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)\n- [Webpage]((//jravilab.github.io/publication/2019/iai))\n\n## 2020 Psp evolution across the tree of life\n_**Janani Ravi\u003csup\u003e*\u003c/sup\u003e**, Vivek Anantharaman, **Samuel Chen**, Pratik Datta, L Aravind\u003csup\u003e*\u003c/sup\u003e, Maria L Gennaro\u003csup\u003e*\u003c/sup\u003e._ **Phage-shock-protein (Psp) Envelope Stress Response: Evolutionary History \u0026 Discovery of Novel Players.** bioRxiv. 2020\n- [Preprint](https://doi.org/10.1101/2020.09.24.301986) | [PDF](https://www.biorxiv.org/content/10.1101/2020.09.24.301986v2.full.pdf)\n- [Webapp](https://jravilab.shinyapps.io/psp-evolution)\n- [Webpage](https://jravilab.github.io/publication/psp_evolution/)\n\n## 2019 Tcy Cystine transporters in _Staphylococcus aureus_\n_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.\n- [PubMed](https://www.ncbi.nlm.nih.gov/pubmed/31843961/) | [PDF](https://jravilab.github.io/files/saureus_tcy.pdf)\n- [Webpage](https://jravilab.github.io/publication/tcy_saureus/)\n\n## 2018 Psp systems in Actinobacteria\n_**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. \n- [PubMed](https://www.ncbi.nlm.nih.gov/pubmed/29488183/) | [PDF](https://github.com/jananiravi/papers/blob/master/2018-Ravi_Psp_actinobacteria_Anto.pdf)\n- [Repo](//github.com/jananiravi/psp-actinobacteria)\n- [Webpage](https://jravilab.github.io/publication/psp_actino/)\n\n## 2017 Psp systems in Gram-positive bacteria\n_contributed to all the figures and computational analyses in this review._ \u003cbr\u003e\n_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.\n- [PubMed](https://www.ncbi.nlm.nih.gov/pubmed/27865622/) | [PDF](https://github.com/jananiravi/papers/blob/master/2016-Psp-TiM-Review.pdf)\n- [Repo](//github.com/jananiravi/psp-variants-review)\n- [Webpage](//jravilab.github.io/publication/2017/tim)\n\n## 2016 Sigma-factor network in Mtb\n_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.\n- [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)\n- [Repo](//github.com/jananiravi/sigmafactor-network-mtb)\n- [Webpage](https://jravilab.github.io/publication/sigfac_mtb/)\n\n## 2015 Psp in Mtb\n_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.\n- [PubMed](https://www.ncbi.nlm.nih.gov/pubmed/25899163/) | [PDF](https://github.com/jananiravi/papers/blob/master/2015-Datta-Psp_Mtb-MolMicro.pdf)\n- [Repo](https://github.com/jananiravi/psp-mtb)\n- [Webpage](https://jravilab.github.io/publication/psp_mtb/)\n\n## 2014 VitD in Mtb-infected macrophages\n_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.\n- [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)\n- [Repo](//github.com/jananiravi/vitamind-lipidmetabolism-mtb-infection)\n- [Webpage](//jravilab.github.io/publication/2014/jimm)\n\n\n_Questions/comments? Email [me](mailto:janani@msu.edu)_\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fjananiravi%2Fpapers","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fjananiravi%2Fpapers","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fjananiravi%2Fpapers/lists"}