Personal information

Verified email domains

Plant genomics, Gramene database, cell-signaling, orgnellar biogenesis, transcriptome analysis, plan
United States

Biography

Dr. Sushma Naithani has an M.S. in Biotechnology and a Ph.D. in Botany. In 1998, she emigrated from India to the USA and worked as a Postdoc at Iowa State University and later at Cornell University. At present, Naithani is an Associate Professor Senior Research in the Department of Botany and Plant Pathology at Oregon State University, USA. Her research focuses on understanding information flow in living systems and how evolution shapes this flow. Naithani employs cutting-edge systems-level pathway modeling approach, supported by meticulous biocuration, gene-orthology-based predictions, and thorough analysis of omics data. She serves as the lead biocurator for the Plant Reactome knowledgebase (https://plantreactome.gramene.org). She also developed species-specific metabolic networks for grapevine (VitisCyc) and strawberry (FragariaCyc), available free-of-cost to support the plant research community (accessible at http://pathways.cgrb.oregonstate.edu/metabolic.html).

Naithani collaborates with various scientists on a range of plant genomics and transcriptomics research projects (for selected publications see https://pubmed.ncbi.nlm.nih.gov/?term=sushma+naithani and for a full list, see https://orcid.org/0000-0001-7819-4552). In addition to her research contributions, Dr. Naithani plays a pivotal role in standardizing genomic data curation and annotation. She is committed to making data FAIR (Findable, Accessible, Reusable, and Interoperable) and is a Steering Committee member for the AgBioData consortium (since 2022) and a NASA Space Biology working group member (also since 2022). Her past contributions include committee roles with the International Society for Biocuration (from 2021 to 2023) and the Grape Information System (from 2015 to 2020).

Naithani serves as an Editor and peer-reviewer for scientific journals. Notably, she held the position of the Editor-in-chief of the Current Plant Biology journal from 2017-2023. Currently, she is an Associate Editor of Frontiers in Plant Science, Editor of PeerJ Life and Environment, Editorial Board member of the Current Plant Biology, and Editorial Board member of Plants (Basel) for Plant Genetics, Genomics and Biotechnology section.

Beyond her academic pursuits, Dr. Naithani is deeply passionate about science communication and enhancing public scientific literacy. She authored an Open Textbook titled "History and Science of Cultivated Plants" (published by Oregon State University Open Educational Resources in 2021), which is accessible at https://open.oregonstate.education/cultivatedplants. Additionally, she authored a popular science book on the history of Agriculture in the Hindi language, published by the National Book Trust of India in 2020 (ISBN: 978-81-237-9265-1).

Activities

Employment (6)

Oregon State University: Corvallis, OR, US

2020-07-01 to present | Associate Professor Senior research (Botany and Plant Pathology)
Employment
Source: Self-asserted source
Sushma Naithani

Oregon State University: Corvallis, OR, US

2012 to 2020-06-30 | Assistant Professor Research (Botany and Plant Pathology)
Employment
Source: Self-asserted source
Sushma Naithani

Oregon State University: Corvallis, OR, US

2008 to 2012 | Assistant Professor Reserach (Horticulture)
Employment
Source: Self-asserted source
Sushma Naithani

Cornell University: Ithaca, NY, US

2006 to 2007 | Lecturer (Plant Breeding and Genetics)
Employment
Source: Self-asserted source
Sushma Naithani

Cornell University: Ithaca, NY, US

2002 to 2006 | Research Associate (Plant Biology)
Employment
Source: Self-asserted source
Sushma Naithani

Cornell University: Ithaca, NY, US

1999 to 2002 | Postdoc Associate (Molecular Biology and Genetics)
Employment
Source: Self-asserted source
Sushma Naithani

Education and qualifications (2)

University of Lucknow Faculty of Science: Lucknow, Uttar Pradesh, IN

Ph.D. (Botany)
Education
Source: Self-asserted source
Sushma Naithani

Maharaja Sayajirao University of Baroda: Vadodara, Gujarat, IN

M. Sc. (Biotechnology)
Education
Source: Self-asserted source
Sushma Naithani

Professional activities (3)

American Society of Plant Biologists: Rockville, MD, US

2023-07-07 to present | Silver (Primary SectionAgriculture, Food, and Renewable Resources (Section O) Secondary SectionHistory and Philosophy of Science (Section L) Tertiary SectionInformation, Computing, and Communication (Section T))
Membership
Source: Self-asserted source
Sushma Naithani

American Association For The Advancement of Science: Washington D.C., District of Columbia, US

2023 to present | Silver (Primary Section: Agriculture, Food, and Renewable Resources (Section O); Secondary Section: History and Philosophy of Science (Section L); Tertiary Section: Information, Computing, and Communication (Section T))
Membership
Source: Self-asserted source
Sushma Naithani

International Society for Biocuration : Lausanne, CH

2021-10 to present | Elected member of the Executive Council
Membership
Source: Self-asserted source
Sushma Naithani

Works (50 of 62)

Items per page:
Page 1 of 2

Detecting novel plant pathogen threats to food system security by integrating the Plant Reactome and remote sensing

Current Opinion in Plant Biology
2025-02 | Journal article
Contributors: Seth C. Murray; Aart Verhoef; Alper Adak; Dipankar Sen; Riva Salzman; Pankaj Jaiswal; Sushma Naithani
Source: check_circle
Crossref

Reference genome of the nutrition-rich orphan crop chia (Salvia hispanica) and its implications for future breeding

Frontiers in Plant Science
2023-12-14 | Journal article
Part of ISSN: 1664-462X
Contributors: Parul Gupta; Matthew Geniza; Justin Elser; Noor Al-Bader; Rachel Baschieri; Jeremy Levi Phillips; Ebaad Haq; Justin Preece; Sushma Naithani; Pankaj Jaiswal
Source: Self-asserted source
Sushma Naithani

Genotype and phenotype data standardization, utilization and integration in the big data era for agricultural sciences

Database
2023-12-11 | Journal article
Contributors: Cecilia H Deng; Sushma Naithani; Sunita Kumari; Irene Cobo-Simón; Elsa H Quezada-Rodríguez; Maria Skrabisova; Nick Gladman; Melanie J Correll; Akeem Babatunde Sikiru; Olusola O Afuwape et al.
Source: check_circle
Crossref

Exploring Pan-Genomes: An Overview of Resources and Tools for Unraveling Structure, Function, and Evolution of Crop Genes and Genomes

Biomolecules
2023-09-17 | Journal article
Contributors: Sushma Naithani; Cecilia H. Deng; Sunil Kumar Sahu; Pankaj Jaiswal
Source: check_circle
Crossref
grade
Preferred source (of 2)‎

Exploring Pan-Genomes of Crops: Genomic Resources and Tools for Unraveling Gene Evolution, Function, and Adaptation

2023-08-23 | Preprint
Contributors: Sushma Naithani; Cecilia H. Deng; Sunil Kumar Sahu; Pankaj Jaiswal
Source: check_circle
Crossref
grade
Preferred source (of 2)‎

Biocuration of a Transcription Factors Network Involved in Submergence Tolerance during Seed Germination and Coleoptile Elongation in Rice (Oryza sativa)

Plants
2023-05-29 | Journal article
Contributors: Sushma Naithani; Bijayalaxmi Mohanty; Justin Elser; Peter D’Eustachio; Pankaj Jaiswal
Source: check_circle
Crossref
grade
Preferred source (of 2)‎

Plant Reactome and PubChem: The Plant Pathway and (Bio)Chemical Entity Knowledgebases

2022 | Book chapter
Contributors: Parul Gupta; Sushma Naithani; Justin Preece; Sunghwan Kim; Tiejun Cheng; Peter D’Eustachio; Justin Elser; Evan E. Bolton; Pankaj Jaiswal
Source: check_circle
Crossref

Correction to: Govindjee’s 90th birthday: a life dedicated to photosynthesis

Plant Physiology Reports
2022-12 | Journal article
Contributors: Alexandrina Stirbet; Dmitry Shevela; Ashwani Pareek; Sushma Naithani; Lars Olof Björn; Julian J. Eaton-Rye; Arthur Nonomura
Source: check_circle
Crossref

Govindjee’s 90th birthday – Congratulations from friends and colleagues

Current Plant Biology
2022-12 | Journal article
Contributors: Sushma Naithani; Alexandrina Stirbet; Dmitry Shevela; Ashwani Pareek; Lars Olof Björn; Julian J. Eaton-Rye; Arthur Nonomura
Source: check_circle
Crossref

Govindjee’s 90th birthday: a life dedicated to photosynthesis

Plant Physiology Reports
2022-12 | Journal article
Contributors: Alexandrina Stirbet; Dmitry Shevela; Ashwani Pareek; Sushma Naithani; Lars Olof Björn; Julian J. Eaton-Rye; Arthur Nonomura
Source: check_circle
Crossref

Plant lectins and their many roles: Carbohydrate-binding and beyond

Journal of Plant Physiology
2021-11 | Journal article
Contributors: Sushma Naithani; Sneha Sudha Komath; Arthur Nonomura; Govindjee Govindjee
Source: check_circle
Crossref

Ensembl Genomes 2022: an expanding genome resource for non-vertebrates.

Nucleic acids research
2021-11-13 | Journal article
Source: Self-asserted source
Sushma Naithani

Chia (Salvia hispanica) Gene Expression Atlas Elucidates Dynamic Spatio-Temporal Changes Associated With Plant Growth and Development

Frontiers in Plant Science
2021-07-20 | Journal article
Part of ISSN: 1664-462X
Source: Self-asserted source
Sushma Naithani

Plant genetics and genomics for building a sustainable agriculture system

Current Plant Biology
2021-06 | Journal article
Part of ISSN: 2214-6628
Source: Self-asserted source
Sushma Naithani

Remembering Johannes Manjrekar (5 June 1957–09 February 2020)

Current Plant Biology
2021-06 | Journal article
Part of ISSN: 2214-6628
Source: Self-asserted source
Sushma Naithani

Beyond gene ontology (GO): using biocuration approach to improve the gene nomenclature and functional annotation of rice S-domain kinase subfamily

PeerJ
2021-03-15 | Journal article
Contributors: Sushma Naithani; Daemon Dikeman; Priyanka Garg; Noor Al-Bader; Pankaj Jaiswal
Source: check_circle
Crossref

Lalit Mohan Srivastava (1931–2012): a highly-respected authority on plant growth, hormones, and environment

Current Plant Biology
2021-01 | Journal article
Part of ISSN: 2214-6628
Source: Self-asserted source
Sushma Naithani

Gramene 2021: harnessing the power of comparative genomics and pathways for plant research

Nucleic Acids Research
2021-01-08 | Journal article
Contributors: Marcela K Tello-Ruiz; Sushma Naithani; Parul Gupta; Andrew Olson; Sharon Wei; Justin Preece; Yinping Jiao; Bo Wang; Kapeel Chougule; Priyanka Garg et al.
Source: check_circle
Crossref

Editorial Special Issue: Plant interactions with microbes and environment

Current Plant Biology
2020-09 | Journal article
Part of ISSN: 2214-6628
Source: Self-asserted source
Sushma Naithani

Current biology special issue: AGRI2019

Current Plant Biology
2020-06 | Journal article
Part of ISSN: 2214-6628
Source: Self-asserted source
Sushma Naithani

Editorial for Special Issue: Plant Genomics and Bioinformatics 2020

Current Plant Biology
2020-01 | Journal article
Part of ISSN: 2214-6628
Source: Self-asserted source
Sushma Naithani

Ensembl Genomes 2020—enabling non-vertebrate genomic research

Nucleic Acids Research
2020-01-08 | Journal article
Part of ISSN: 0305-1048
Part of ISSN: 1362-4962
Source: Self-asserted source
Sushma Naithani
grade
Preferred source (of 2)‎

Remembering Donald J. Armstrong (1937–2019)

Current Plant Biology
2019-12 | Journal article
Part of ISSN: 2214-6628
Source: Self-asserted source
Sushma Naithani

Plant Reactome: a knowledgebase and resource for comparative pathway analysis

Nucleic Acids Research
2019-11-04 | Journal article
Contributors: Sushma Naithani; Parul Gupta; Justin Preece; Peter D’Eustachio; Justin L Elser; Priyanka Garg; Daemon A Dikeman; Jason Kiff; Justin Cook; Andrew Olson et al.
Source: check_circle
Crossref

A role of high-throughput data and predictive modeling in crop management

Current Plant Biology
2019-09 | Journal article
Part of ISSN: 2214-6628
Source: Self-asserted source
Sushma Naithani

Special issue: Plant genomics and bioinformatics

Current Plant Biology
2019-05 | Journal article
Part of ISSN: 2214-6628
Source: Self-asserted source
Sushma Naithani

Gramene 2018: Unifying comparative genomics and pathway resources for plant research

Nucleic Acids Research
2018 | Journal article
EID:

2-s2.0-85040926094

Contributors: Tello-Ruiz, M.K.; Naithani, S.; Stein, J.C.; Gupta, P.; Campbell, M.; Olson, A.; Wei, S.; Preece, J.; Geniza, M.J.; Jiao, Y. et al.
Source: Self-asserted source
Sushma Naithani via Scopus - Elsevier

Editorial Regular issue (Volume 16, Dec 2018)

Current Plant Biology
2018-12 | Journal article
Part of ISSN: 2214-6628
Source: Self-asserted source
Sushma Naithani

Exploring genomics and transcriptomics: the way forward in improving crops and other economically important plant species

Current Plant Biology
2018-09 | Journal article
Part of ISSN: 2214-6628
Source: Self-asserted source
Sushma Naithani

Editorial Regular issue

Current Plant Biology
2018-04 | Journal article
Part of ISSN: 2214-6628
Source: Self-asserted source
Sushma Naithani

Remembering Professor Prasanna K. Mohanty (April 1, 1934 – March 9, 2013)

Current Plant Biology
2018-04 | Journal article
Part of ISSN: 2214-6628
Source: Self-asserted source
Sushma Naithani

AgBioData consortium recommendations for sustainable genomics and genetics databases for agriculture

Database
2018-01-01 | Journal article
Part of ISSN: 1758-0463
Source: Self-asserted source
Sushma Naithani

Pathway analysis and omics data visualization using pathway genome databases: Fragariacyc, a case study

Methods in Molecular Biology
2017 | Book
EID:

2-s2.0-85007170327

Contributors: Naithani, S.; Jaiswal, P.
Source: Self-asserted source
Sushma Naithani via Scopus - Elsevier

Plant Reactome: A resource for plant pathways and comparative analysis

Nucleic Acids Research
2017 | Journal article
EID:

2-s2.0-85015991202

Contributors: Naithani, S.; Preece, J.; D'Eustachio, P.; Gupta, P.; Amarasinghe, V.; Dharmawardhana, P.D.; Wu, G.; Fabregat, A.; Elser, J.L.; Weiser, J. et al.
Source: Self-asserted source
Sushma Naithani via Scopus - Elsevier

Variant effect prediction analysis using resources available at gramene database

Methods in Molecular Biology
2017 | Book
EID:

2-s2.0-85007206663

Contributors: Naithani, S.; Geniza, M.; Jaiswal, P.
Source: Self-asserted source
Sushma Naithani via Scopus - Elsevier

Resources and Tools for Generating and Mining Big Data

Current Plant Biology
2017-09 | Journal article
Part of ISSN: 2214-6628
Source: Self-asserted source
Sushma Naithani
grade
Preferred source (of 2)‎

Editorial Plant Development Volume -9 (June 2017)

Current Plant Biology
2017-06 | Journal article
Part of ISSN: 2214-6628
Source: Self-asserted source
Sushma Naithani
grade
Preferred source (of 2)‎

Exploring Crossroads Between Seed Development and Stress Response

Mechanism of Plant Hormone Signaling under Stress
2017-03-24 | Book chapter
Part of ISBN: 9781118889022
Part of ISBN: 9781118888926
Source: Self-asserted source
Sushma Naithani

FragariaCyc: A metabolic pathway database for woodland strawberry fragaria vesca

Frontiers in Plant Science
2016 | Journal article
EID:

2-s2.0-84960124182

Contributors: Naithani, S.; Partipilo, C.M.; Raja, R.; Elser, J.L.; Jaiswal, P.
Source: Self-asserted source
Sushma Naithani via Scopus - Elsevier

Genomic resources and databases for plant research community

Current Plant Biology
2016 | Journal article
EID:

2-s2.0-85007298528

Contributors: Naithani, S.; Van de Peer, Y.
Source: Self-asserted source
Sushma Naithani via Scopus - Elsevier

Gramene 2016: Comparative plant genomics and pathway resources

Nucleic Acids Research
2016 | Journal article
EID:

2-s2.0-84979255809

Contributors: Tello-Ruiz, M.K.; Stein, J.; Wei, S.; Preece, J.; Olson, A.; Naithani, S.; Amarasinghe, V.; Dharmawardhana, P.; Jiao, Y.; Mulvaney, J. et al.
Source: Self-asserted source
Sushma Naithani via Scopus - Elsevier

Gramene database: Navigating plant comparative genomics resources

Current Plant Biology
2016 | Journal article
EID:

2-s2.0-85007289026

Contributors: Gupta, P.; Naithani, S.; Tello-Ruiz, M.K.; Chougule, K.; D'Eustachio, P.; Fabregat, A.; Jiao, Y.; Keays, M.; Lee, Y.K.; Kumari, S. et al.
Source: Self-asserted source
Sushma Naithani via Scopus - Elsevier

Plants and global climate change: A need for sustainable agriculture: Volume – 2 (July–October 2016)

Current Plant Biology
2016 | Journal article
EID:

2-s2.0-84996590279

Contributors: Naithani, S.
Source: Self-asserted source
Sushma Naithani via Scopus - Elsevier

Towards an open grapevine information system

Horticulture Research
2016 | Journal article
EID:

2-s2.0-84997281846

Contributors: Adam-Blondon, A.-F.; Alaux, M.; Pommier, C.; Cantu, D.; Cheng, Z.-M.; Cramer, G.; Davies, C.; Delrot, S.; Deluc, L.; Di Gaspero, G. et al.
Source: Self-asserted source
Sushma Naithani via Scopus - Elsevier

The floral transcriptome of Eucalyptus grandis

New Phytologist
2015 | Journal article
EID:

2-s2.0-84928923070

Contributors: Vining, K.J.; Romanel, E.; Jones, R.C.; Klocko, A.; Alves-Ferreira, M.; Hefer, C.A.; Amarasinghe, V.; Dharmawardhana, P.; Naithani, S.; Ranik, M. et al.
Source: Self-asserted source
Sushma Naithani via Scopus - Elsevier

De novo transcriptome assembly and analyses of gene expression during photomorphogenesis in diploid wheat Triticum monococcum

PLoS ONE
2014 | Journal article
EID:

2-s2.0-84901250709

Contributors: Fox, S.E.; Geniza, M.; Hanumappa, M.; Naithani, S.; Sullivan, C.; Preece, J.; Tiwari, V.K.; Elser, J.; Leonard, J.M.; Sage, A. et al.
Source: Self-asserted source
Sushma Naithani via Scopus - Elsevier

Gramene 2013: Comparative plant genomics resources

Nucleic Acids Research
2014 | Journal article
EID:

2-s2.0-84891793130

Contributors: Monaco, M.K.; Stein, J.; Naithani, S.; Wei, S.; Dharmawardhana, P.; Kumari, S.; Amarasinghe, V.; Youens-Clark, K.; Thomason, J.; Preece, J. et al.
Source: Self-asserted source
Sushma Naithani via Scopus - Elsevier

The genome of Eucalyptus grandis

Nature
2014 | Journal article
EID:

2-s2.0-84903203459

Contributors: Myburg, A.A.; Grattapaglia, D.; Tuskan, G.A.; Hellsten, U.; Hayes, R.D.; Grimwood, J.; Jenkins, J.; Lindquist, E.; Tice, H.; Bauer, D. et al.
Source: Self-asserted source
Sushma Naithani via Scopus - Elsevier

VitisCyc: A metabolic pathway knowledgebase for grapevine (Vitis vinifera)

Frontiers in Plant Science
2014 | Journal article
EID:

2-s2.0-84917692206

Contributors: Naithani, S.; Raja, R.; Waddell, E.N.; Elser, J.; Gouthu, S.; Deluc, L.G.; Jaiswal, P.
Source: Self-asserted source
Sushma Naithani via Scopus - Elsevier

Maize metabolic network construction and transcriptome analysis

Plant Genome
2013 | Journal article
EID:

2-s2.0-84881220997

Contributors: Monaco, M.K.; Sen, T.Z.; Dharmawardhana, P.D.; Ren, L.; Schaeffer, M.; Naithani, S.; Amarasinghe, V.; Thomason, J.; Harper, L.; Gardiner, J. et al.
Source: Self-asserted source
Sushma Naithani via Scopus - Elsevier
Items per page:
Page 1 of 2