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| # DO NOT EDIT, GENERATED AUTOMATICALLY | ||
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| - id: doi:10.1093/nar/gkad1082 | ||
| title: "The Monarch Initiative in 2024: an analytic platform integrating phenotypes,\ | ||
| \ genes\_and diseases across species" | ||
| authors: | ||
| - Tim E Putman | ||
| - Kevin Schaper | ||
| - Nicolas Matentzoglu | ||
| - "Vincent\_P Rubinetti" | ||
| - "Faisal\_S Alquaddoomi" | ||
| - Corey Cox | ||
| - J Harry Caufield | ||
| - Glass Elsarboukh | ||
| - Sarah Gehrke | ||
| - Harshad Hegde | ||
| - "Justin\_T Reese" | ||
| - Ian Braun | ||
| - "Richard\_M Bruskiewich" | ||
| - Luca Cappelletti | ||
| - Seth Carbon | ||
| - "Anita\_R Caron" | ||
| - "Lauren\_E Chan" | ||
| - "Christopher\_G Chute" | ||
| - "Katherina\_G Cortes" | ||
| - "Vin\xEDcius De\_Souza" | ||
| - Tommaso Fontana | ||
| - "Nomi\_L Harris" | ||
| - "Emily\_L Hartley" | ||
| - Eric Hurwitz | ||
| - "Julius\_O B Jacobsen" | ||
| - Madan Krishnamurthy | ||
| - "Bryan\_J Laraway" | ||
| - "James\_A McLaughlin" | ||
| - "Julie\_A McMurry" | ||
| - "Sierra\_A T Moxon" | ||
| - "Kathleen\_R Mullen" | ||
| - "Shawn\_T O\u2019Neil" | ||
| - "Kent\_A Shefchek" | ||
| - Ray Stefancsik | ||
| - Sabrina Toro | ||
| - "Nicole\_A Vasilevsky" | ||
| - "Ramona\_L Walls" | ||
| - "Patricia\_L Whetzel" | ||
| - David Osumi-Sutherland | ||
| - Damian Smedley | ||
| - "Peter\_N Robinson" | ||
| - "Christopher\_J Mungall" | ||
| - "Melissa\_A Haendel" | ||
| - "Monica\_C Munoz-Torres" | ||
| publisher: Nucleic Acids Research | ||
| date: '2023-11-24' | ||
| link: https://doi.org/gs6kmr | ||
| orcid: 0000-0002-4655-3773 | ||
| plugin: orcid.py | ||
| file: orcid.yaml | ||
| - id: doi:10.1101/2023.10.11.560955 | ||
| title: Integration of 168,000 samples reveals global patterns of the human gut microbiome | ||
| authors: | ||
| - Richard J. Abdill | ||
| - Samantha P. Graham | ||
| - Vincent Rubinetti | ||
| - Frank W. Albert | ||
| - Casey S. Greene | ||
| - Sean Davis | ||
| - Ran Blekhman | ||
| publisher: Cold Spring Harbor Laboratory | ||
| date: '2023-10-11' | ||
| link: https://doi.org/gsvf5z | ||
| orcid: 0000-0002-4655-3773 | ||
| plugin: orcid.py | ||
| file: orcid.yaml | ||
| - id: doi:10.1093/nar/gkad289 | ||
| title: 'MyGeneset.info: an interactive and programmatic platform for community-curated | ||
| and user-created collections of genes' | ||
| - id: doi:10.1145/3629260 | ||
| title: "mCaptcha: Replacing CAPTCHAs with Ratelimiters to Improve Security and Accessibility" | ||
| authors: | ||
| - Ricardo Avila | ||
| - Vincent Rubinetti | ||
| - Xinghua Zhou | ||
| - Dongbo Hu | ||
| - Zhongchao Qian | ||
| - Marco Alvarado Cano | ||
| - Everaldo Rodolpho | ||
| - Ginger Tsueng | ||
| - Casey Greene | ||
| - Chunlei Wu | ||
| publisher: Nucleic Acids Research | ||
| date: '2023-04-18' | ||
| link: https://doi.org/gr5hb5 | ||
| orcid: 0000-0002-4655-3773 | ||
| plugin: orcid.py | ||
| file: orcid.yaml | ||
| - id: doi:10.1101/2023.01.05.522941 | ||
| title: Hetnet connectivity search provides rapid insights into how two biomedical | ||
| entities are related | ||
| - Sibi Chakkaravarthy Sethuraman | ||
| - Aravinth TM | ||
| - Devi Priya VS | ||
| publisher: Communications of the ACM | ||
| date: '2024' | ||
| link: https://doi.org/10.1145/3629260 | ||
| plugin: manual | ||
|
|
||
| - id: doi:10.1016/j.cose.2023.103600 | ||
| title: "A Comprehensive Examination of Email Spoofing: Issues and Prospects for Email Security" | ||
| authors: | ||
| - Daniel S. Himmelstein | ||
| - Michael Zietz | ||
| - Vincent Rubinetti | ||
| - Kyle Kloster | ||
| - Benjamin J. Heil | ||
| - Faisal Alquaddoomi | ||
| - Dongbo Hu | ||
| - David N. Nicholson | ||
| - Yun Hao | ||
| - Blair D. Sullivan | ||
| - Michael W. Nagle | ||
| - Casey S. Greene | ||
| publisher: Cold Spring Harbor Laboratory | ||
| date: '2023-01-07' | ||
| link: https://doi.org/grmcb9 | ||
| orcid: 0000-0002-4655-3773 | ||
| plugin: orcid.py | ||
| file: orcid.yaml | ||
| - id: doi:10.1093/gigascience/giad047 | ||
| title: Hetnet connectivity search provides rapid insights into how biomedical entities | ||
| are related | ||
| - Sibi Chakkaravarthy Sethuraman | ||
| - Devi Priya VS | ||
| - Tarun Reddi | ||
| - Mulka Sai Tharun Reddy | ||
| - Muhammad Khurram Khan | ||
| publisher: Computers & Security, Elsevier | ||
| date: '2023' | ||
| link: https://doi.org/10.1016/j.cose.2023.103600 | ||
| plugin: manual | ||
|
|
||
| - id: doi:10.1016/j.cosrev.2023.100600 | ||
| title: "Flow based containerized honeypot approach for network traffic analysis: An empirical study" | ||
| authors: | ||
| - Daniel S Himmelstein | ||
| - Michael Zietz | ||
| - Vincent Rubinetti | ||
| - Kyle Kloster | ||
| - Benjamin J Heil | ||
| - Faisal Alquaddoomi | ||
| - Dongbo Hu | ||
| - David N Nicholson | ||
| - Yun Hao | ||
| - Blair D Sullivan | ||
| - Michael W Nagle | ||
| - Casey S Greene | ||
| publisher: GigaScience | ||
| date: '2022-12-28' | ||
| link: https://doi.org/gsd85n | ||
| orcid: 0000-0002-4655-3773 | ||
| plugin: orcid.py | ||
| file: orcid.yaml | ||
| - id: doi:10.1101/2022.02.18.461833 | ||
| title: 'MolEvolvR: A web-app for characterizing proteins using molecular evolution | ||
| and phylogeny' | ||
| - Sibi Chakkaravarthy Sethuraman | ||
| - Tharshith Goud Jadapalli | ||
| - Devi Priya | ||
| - Saraju P Mohanty | ||
| publisher: Computer Science Review, Elsevier | ||
| date: '2023' | ||
| link: https://doi.org/10.1016/j.cosrev.2023.100600 | ||
| plugin: manual | ||
|
|
||
| - id: doi:10.1109/ACCESS.2022.3212484 | ||
| title: "Loki: A Physical Security Key Compatible IoT Based Lock for Protecting Physical Assets" | ||
| authors: | ||
| - Jacob D Krol | ||
| - Joseph T Burke | ||
| - Samuel Z Chen | ||
| - Lo M Sosinski | ||
| - Faisal S Alquaddoomi | ||
| - Evan P Brenner | ||
| - Ethan P Wolfe | ||
| - Vincent P Rubinetti | ||
| - Shaddai Amolitos | ||
| - Kellen M Reason | ||
| - John B Johnston | ||
| - Janani Ravi | ||
| publisher: Cold Spring Harbor Laboratory | ||
| date: '2022-02-22' | ||
| link: https://doi.org/gstx7j | ||
| orcid: 0000-0002-4655-3773 | ||
| plugin: orcid.py | ||
| file: orcid.yaml | ||
| - id: doi:10.1186/s13059-020-02021-3 | ||
| title: Compressing gene expression data using multiple latent space dimensionalities | ||
| learns complementary biological representations | ||
| - Sibi Chakkaravarthy Sethuraman | ||
| - Aditya Mitra | ||
| - Kuan-Ching Li | ||
| - Anisha Ghosh | ||
| - M Gopinath | ||
| - Nitin Sukhija | ||
| publisher: IEEE Access | ||
| date: '2022' | ||
| link: https://doi.org/10.1109/ACCESS.2022.3212484 | ||
| plugin: manual | ||
|
|
||
| - id: doi:10.1109/TCE.2021.3086445 | ||
| title: "MyWear: A Novel Smart Garment for Automatic Continuous Vital Monitoring" | ||
| authors: | ||
| - Gregory P. Way | ||
| - Michael Zietz | ||
| - Vincent Rubinetti | ||
| - Daniel S. Himmelstein | ||
| - Casey S. Greene | ||
| publisher: Genome Biology | ||
| date: '2020-05-11' | ||
| link: https://doi.org/gg2mjh | ||
| orcid: 0000-0002-4655-3773 | ||
| plugin: orcid.py | ||
| file: orcid.yaml | ||
| - id: doi:10.1371/journal.pcbi.1007128 | ||
| title: Open collaborative writing with Manubot | ||
| - S. Sibi Chakkaravarthy | ||
| - Pranav Kompally | ||
| - Saraju P Mohanty | ||
| - Uma Chopalli | ||
| publisher: IEEE Transactions on Consumer Electronics | ||
| date: '2021' | ||
| link: https://doi.org/10.1109/TCE.2021.3086445 | ||
| plugin: manual | ||
|
|
||
| - id: doi:10.56042/jsir.v80i07.3744 | ||
| title: "VISU: A 3D Printed Functional Robot for Human Pose Replication" | ||
| authors: | ||
| - Daniel S. Himmelstein | ||
| - Vincent Rubinetti | ||
| - David R. Slochower | ||
| - Dongbo Hu | ||
| - Venkat S. Malladi | ||
| - Casey S. Greene | ||
| - Anthony Gitter | ||
| publisher: PLOS Computational Biology | ||
| date: '2020-12-04' | ||
| link: https://doi.org/c7np | ||
| orcid: 0000-0002-4655-3773 | ||
| plugin: sources.py | ||
| file: sources.yaml | ||
| type: paper | ||
| description: Lorem ipsum _dolor_ **sit amet**, consectetur adipiscing elit, sed | ||
| do eiusmod tempor incididunt ut labore et dolore magna aliqua. | ||
| image: https://journals.plos.org/ploscompbiol/article/figure/image?size=inline&id=info:doi/10.1371/journal.pcbi.1007128.g001&rev=2 | ||
| buttons: | ||
| - type: manubot | ||
| link: https://greenelab.github.io/meta-review/ | ||
| - type: source | ||
| text: Manuscript Source | ||
| link: https://github.com/greenelab/meta-review | ||
| - type: website | ||
| link: http://manubot.org/ | ||
| tags: | ||
| - open science | ||
| - collaboration | ||
| repo: greenelab/meta-review | ||
| - id: doi:10.1101/573782 | ||
| title: Sequential compression of gene expression across dimensionalities and methods | ||
| reveals no single best method or dimensionality | ||
| - Pranav Kompally | ||
| - S. Sibi Chakkaravarthy | ||
| - Srikar Reddy | ||
| - Charan Koduri | ||
| - Yaswanth Naidu | ||
| - M.Raghavaiah | ||
| - Sashidhar Reddy | ||
| - Namburi Nikhil | ||
| publisher: Journal of Scientific and Industrial Research (JSIR) | ||
| date: '2021' | ||
| link: https://doi.org/10.56042/jsir.v80i07.3744 | ||
| plugin: manual | ||
|
|
||
| - id: doi:10.1109/MCE.2020.3033269 | ||
| title: "VISU: A 3D Printed Functional Robot for Crowd Surveillance" | ||
| authors: | ||
| - Gregory P. Way | ||
| - Michael Zietz | ||
| - Vincent Rubinetti | ||
| - Daniel S. Himmelstein | ||
| - Casey S. Greene | ||
| publisher: Cold Spring Harbor Laboratory | ||
| date: '2019-03-11' | ||
| link: https://doi.org/gfxjxf | ||
| orcid: 0000-0002-4655-3773 | ||
| plugin: orcid.py | ||
| file: orcid.yaml | ||
| - id: doi:10.1016/j.csbj.2020.05.017 | ||
| title: Constructing knowledge graphs and their biomedical applications | ||
| - S. Sibi Chakkaravarthy | ||
| - Pranav Kompally | ||
| - Srikar Reddy | ||
| publisher: IEEE Consumer Electronics | ||
| date: '2021' | ||
| link: https://doi.org/10.1109/MCE.2020.3033269 | ||
| plugin: manual | ||
|
|
||
| - id: doi:10.1016/j.compeleceng.2022.107751 | ||
| title: "A Decentralized Open Web Cryptographic Standard" | ||
| authors: | ||
| - David N. Nicholson | ||
| - Casey S. Greene | ||
| publisher: Computational and Structural Biotechnology Journal | ||
| date: '2020-01-01' | ||
| link: https://doi.org/gg7m48 | ||
| image: https://ars.els-cdn.com/content/image/1-s2.0-S2001037020302804-gr1.jpg | ||
| plugin: sources.py | ||
| file: sources.yaml | ||
| - id: doi:10.7554/eLife.32822 | ||
| title: Sci-Hub provides access to nearly all scholarly literature | ||
| - Dedipyaman Das | ||
| - S.Sibi Chakkaravarthy | ||
| - Suresh Chandra Satapathy | ||
| publisher: Computers and Electrical Engineering, Elsevier | ||
| date: '2022' | ||
| link: https://doi.org/10.1016/j.compeleceng.2022.107751 | ||
| plugin: manual | ||
|
|
||
| - id: doi:10.1016/j.cosrev.2021.100433 | ||
| title: "Comprehensive Analysis of Embeddings and Pre-Training in NLP" | ||
| authors: | ||
| - Daniel S Himmelstein | ||
| - Ariel Rodriguez Romero | ||
| - Jacob G Levernier | ||
| - Thomas Anthony Munro | ||
| - Stephen Reid McLaughlin | ||
| - Bastian Greshake Tzovaras | ||
| - Casey S Greene | ||
| publisher: eLife | ||
| date: '2018-03-01' | ||
| link: https://doi.org/ckcj | ||
| image: https://iiif.elifesciences.org/lax:32822%2Felife-32822-fig8-v3.tif/full/863,/0/default.webp | ||
| plugin: sources.py | ||
| file: sources.yaml | ||
| - Jatin Karthik Tripathy | ||
| - S.Sibi Chakkaravarthy | ||
| - Meenalosini Vimal Cruz | ||
| - Anupama Namburu | ||
| - Mangalraj P | ||
| - Nandha Kumar R | ||
| - Sudhakar Ilango | ||
| - Vaidehi Vijayakumar | ||
| publisher: Computer Science Review, Elsevier | ||
| date: '2021' | ||
| link: https://doi.org/10.1016/j.cosrev.2021.100433 | ||
| plugin: manual |