Jayaram Kancherla

Publications

A more comprehensive list of publications is available at ORCID and ResearchGate.

PUBLICATIONS

  1. itemsep=0.1ex, leftmargin=0.6cm[equal contribution] Aaron Lun, Kancherla, Jayaram*. Powering single-cell analyses in the browser with WebAssembly. Journal of Open Source Software 8.89 (2023): 5603.

  2. Lun, Aaron TL, and Jayaram Kancherla. gesel: a JavaScript package for client-side gene set enrichment. Journal of Open Source Software 8.90 (2023): 5777.

  3. [Preprint] Mohamed K. Gunady, Jayaram Kancherla, Héctor Corrada Bravo, Soheil Feizi. scGAIN: Single Cell RNA-seq Data Imputation using Generative Adversarial Networks. bioRxiv 837302; doi: [https://doi.org/10.1101/837302||10.1101/837302]

  4. BRAIN Initiative Cell Census Network, et al. A multimodal cell census and atlas of the mammalian primary motor cortex. bioRxiv 2020.10.19.343129; doi: [https://doi.org/10.1101/2020.10.19.343129||10.1101/2020.10.19.343129]

  5. Bakken, Trygve E., et al. Comparative cellular analysis of motor cortex of human, marmoset monkey, and mouse. bioRxiv 2020.03.31.016972; doi: [https://doi.org/10.1101/2020.03.31.016972||10.1101/2020.03.31.016972]

  6. Zizhen Yao., et al. A transcriptomic and epigenomic cell atlas of mouse primary motor cortex. 2020.02.29.970558; doi: [https://doi.org/10.1101/2020.02.29.970558||10.1101/2020.02.29.970558]

  7. Orvis, Joshua, Brian Gottfried, Jayaram Kancherla, Ricky S. Adkins, Yang Song, Amiel A. Dror, Dustin Olley et al. “gEAR: gene Expression Analysis Resource portal for community-driven, multi-omic data exploration.” Nature methods (2021): 1-2.

  8. Jayaram Kancherla, Yifan Yang, Hyeyun Chae, Hector Corrada Bravo, Epiviz File Server: Query, transform and interactively explore data from indexed genomic files, Bioinformatics, Volume 36, Issue 18, 15 September 2020, Pages 4682–4690, doi: [https://doi.org/10.1093/bioinformatics/btaa591||10.1093/bioinformatics/btaa591]

  9. Wagner J, Kancherla J, Braccia D et al. Interactive exploratory data analysis of Integrative Human Microbiome Project data using Metaviz. F1000Research 2020, 9:601. doi: [https://doi.org/10.12688/f1000research.24345.1||10.12688/f1000research.24345.1]

  10. [equal contribution] Jayaram Kancherla, Shruti Rao*, Krithika Bhuvaneshwar, Rebecca B. Riggins, Robert A. Beckman, Subha Madhavan, Héctor Corrada Bravo, Simina M. Boca. An evidence-based network approach to recommending targeted cancer therapies. JCO Clinical Cancer Informatics no. 4 (2020) 71-88; doi: [https://doi.org/10.1200/CCI.19.00097||10.1200/CCI.19.00097]

  11. Z. Cui, J. Kancherla, H. C. Bravo and N. Elmqvist, Sherpa: Leveraging User Attention for Computational Steering in Visual Analytics. 2019 IEEE Visualization in Data Science (VDS), Vancouver, BC, Canada, 2019, pp. 48-57. doi: [https://doi.org/10.1109/VDS48975.2019.8973384||10.1109/VDS48975.2019.8973384]

  12. [equal contribution] Zhe Cui, Jayaram Kancherla*, Kyle W Chang, Niklas Elmqvist, Héctor Corrada Bravo, Proactive visual and statistical analysis of genomic data in Epiviz, Bioinformatics, btz883, doi: [https://doi.org/10.1093/bioinformatics/btz883||10.1093/bioinformatics/btz883]

  13. Nathan D Olson, Nidhi Shah, Jayaram Kancherla, Justin Wagner, Joseph N Paulson, Héctor Corrada Bravo. metagenomeFeatures: an R package for working with 16S rRNA reference databases and marker-gene survey feature data, Bioinformatics, btz136, doi: [https://doi.org/10.1093/bioinformatics/btz136||10.1093/bioinformatics/btz136]

  14. Kancherla J, Zhang A, Gottfried B and Bravo HC. Epiviz Web Components: reusable and extensible component library to visualize functional genomic datasets. F1000Research 2018, 7:1096; doi: [http://doi.org/10.12688/f1000research.15433.1||10.12688/f1000research.15433.1]

  15. [equal contribution] Justin Wagner, Florin Chelaru*, Jayaram Kancherla*, Joseph N Paulson*, Alexander Zhang, Victor Felix, Anup Mahurkar, Niklas Elmqvist, Héctor Corrada Bravo; Metaviz: interactive statistical and visual analysis of metagenomic data, Nucleic Acids Research, Volume 46, Issue 6, 6 April 2018, Pages 2777–2787, doi: [http://doi.org/10.1093/nar/gky136||10.1093/nar/gky136]

  16. Gary Ginsberg, Suryanarayana V Vulimiri, Yu-Sheng Lin, Jayaram Kancherla, Brenda Foos & Babasaheb Sonawane (2017) A framework and case studies for evaluation of enzyme ontogeny in children’s health risk evaluation, Journal of Toxicology and Environmental Health, Part A, 80:10-12, 569-593, doi: [http://doi.org/10.1080/15287394.2017.1369915||10.1080/15287394.2017.1369915]

  17. Mansouri, Kamel et al. Collaborative Estrogen Receptor Prediction Project for EDSP Prioritization. Environmental Health Perspectives (2016); doi: [http://dx.doi.org/10.1289/ehp.1510267||10.1289/ehp.1510267]

  18. Richard M.A. et al. The ToxCast Chemical Landscape: Paving the Road to 21st Century Toxicology. Chemical Research in Toxicology (2016) doi: [http://doi.org/10.1021/acs.chemrestox.6b00135||10.1021/acs.chemrestox.6b00135]

BOOK CHAPTERS

WORKSHOPS

• itemsep=0.1ex, leftmargin=0.6cmBiocPy: Facilitate Bioconductor workflows in Python - Jul 24-26, 2024[https://github.com/BiocPy/BiocWorkshop2024||https://github.com/BiocPy/BiocWorkshop2024]

• BICCN Omics Workshop - Jan 20 & 27, 2021[https://nemoarchive.org/biccn-omics-workshop/]

• Interactive visualization and data analysis with Epiviz web - Jul 27-28, 2017components (Differential Gene Expression analysis using minfi)Jayaram Kancherla, Brian Gottfried, Héctor Corrada Bravo[https://bioconductor.org/help/course-materials/2017/BioC2017/#main-conference||BioC 2017], Dana Farber Cancer Institute, Boston, MA

• Metaviz Interactive Statistical and Visual Analysis using data Jun 2017from Human Microbiome ProjectJustin Wagner, Jayaram Kancherla, Héctor Corrada Bravo[https://www.igs.umaryland.edu/education/wkshp_metagenome.php||University of Maryland Institute of Genomic Science], Baltimore, MD

• Interactive visualization of microbiome data using Metaviz Nov 1-2, 2016Jayaram Kancherla, Héctor Corrada Bravo[http://blog.umd.edu/m3/2016/12/09/m3-kick-off-event-took-place-november-1-2-2016/comment-page-1||Mid Atlantic Microbiome Conference], College Park, MD

• Interactive visualization with epiviz Jun 25-26, 2016Héctor Corrada Bravo, Jayaram Kancherla, Justin Wagner, Deok Park[https://bioconductor.org/help/course-materials/2016/BioC2016/#main-conference||BioC 2016], Stanford University, Stanford, CA

• Interactive Genomic Data Analysis and Visualization using Epiviz Jun 15, 2016Jayaram Kancherla[https://iscb-dc-rsg.github.io/2016-summer-workshop/||International Society for Computational Biology], DC RSG

PRESENTATIONS & ABSTRACTS

  1. itemsep=0.1ex, leftmargin=0.6cmSingle-cell Hub at gRED, IGVF Catalog working group, Jan 2024 (Presentation)

  2. Jayaram Kancherla: Enabling Bioconductor workflows in Python, Bioc2023, Boston (Presentation)

  3. Jayaram Kancherla, Aaron Lun, Hector Corrada Bravo. Kana: Interactive visualization and analysis of single-cell RNA-seq datasets. BioVis, International Society for Molecular Biology (ISMB/ECCB 2022), July 10-14, 2021 (Presentation)

  4. Jayaram Kancherla, Kazi Tasnim Zinat, Hector Corrada Bravo, Stephanie Hicks. Hierarchical interactive exploration and analysis of single cell RNA-seq datasets, BioVis, International Society for Molecular Biology (ISMB/ECCB 2021), July 25-30, 2021 (Presentation & Poster)

  5. B. Fowler, B. Sonawane, A. M. Kadry, and J. Kancherla. Health Risk Assessment Challenges of Handling and Disposal of Electronic Waste (E-waste) Society of Toxicology, March 12-26 2021 (Poster)

  6. Jayaram Kancherla, Kazi Zinat Tasnim, Hector Corrada Bravo, Hierarchical interactive exploration and analysis of single cell RNA-seq datasets, Biological Data Science, November 4-6 2020. [https://meetings.cshl.edu/meetings.aspx?meet=data&year=20||CSHL BDS] (Presentation & Poster)

  7. Jayaram Kancherla, Héctor Corrada Bravo. Quickly compose custom interactive genomic visualization apps in R/Bioc with epiviz components. BioC 2020, July 29 - 31, 2020. (Presentation).

Follow me on ResearchGate

ORCID iD iconorcid.org/0000-0001-5855-5031

Publons - http://publons.com/a/1523821

Scopus - http://www.scopus.com/inward/authorDetails.url?authorID=57190063218&partnerID=MN8TOARS