Sushma Naithani

Associate Professor (Sr Res)

she/her

sushma.naithani [at] oregonstate.edu

Office: 541-737-8022

Area of Expertise: Systems biology, Genomics, Cell-cell signaling, Self-incompatibility, Mitochondria biogenesis, Photosynthesis, and Chloroplast biology, Plant pathway biocuration, and gene-gene network modeling

The current research focus of Naithani lab is on the development of the system-level models of crops and model plants of evolutionary importance by utilizing publicly available genomic data to understand how genetic diversity and a plant's immediate environment relate to yield, stress tolerance, and quality traits. We implement a variety of approaches rooted in biochemistry, genetics, genomics, and bioinformatics to dissect complex interactions between a plant’s genetic, metabolic, and signaling networks. The long-term goal is to develop models in a probabilistic framework that can assess the impacts of abiotic stresses on the yield and quality traits of crop plants.

Species-specific Plant Metabolic Pathway databases
Plant Reactome Knowledgebase
Gramene

Lab website

http://naithanilab.cgrb.oregonstate.edu/

Lab Members

Research Associate, Software Developer

2023-present Dr. Justin Elser

Undergraduate Honors Thesis students:

2021-2022 Sarah El-Husseini#, Biohealth Major

2019-2020 Daemon Dikeman*#, Biology Major

STEM Leaders Undergraduate Research Program Fellows (winter and spring term)

2023 Joie Beasley-Bennett#, Botany Major

Undergraduate Research, Scholarship, & the Arts (URSA) fellows (winter and spring terms)

2024 Carolyn Crofford#, Bioresource and sustainability major
2024 Isabella Ramirez#, Microbiology major
2024 Siena Buchanan#, Biology major
2023 Riley Callahan#, Biochemistry & Molecular Biology major
2023 Jenna Rosenau#, Biochemistry and Biophysics
2023 Annette Tongsak#, Computer Science major
2022 Elizabeth Hooks*#, Botany Major (e-campus)
2022 Kennedy A. Sparks#, Bioengineering major
2021 Quentin Beers#, Biochemistry and Molecular Biology major
2021 Gwendolyn Michna#, Biochemistry and Molecular Biology major
2021 Olivia Worley#, Biochemistry and Molecular Biology major
2021 Madeline Goebel#, Biochemistry major
2021 Sarah El-Husseini#, Biohealth Science major
2021 Amitavo Ganguli#, Geography and Geospatial Science major
2020 Callan Stowell#, Biology major

Experiential Learning Activity (one term)

2023 Madeleine Zeller#, Botany Major (e-campus)
2020 Shayla Rao#, Computer Science major
2014. Kelsey M. Nadeau, Biology major
2013. Kate Threlfall, Biology major
2011 Ali Alnakhli, Pharmacy major
2009 Jimmy Hoang (work-study), Biology major
2009 Tracy Nguyen, (work-study), Biology major

Grant-funded Undergraduate Biocurators

2022-2023 Elizabeth Hooks*#, Botany Major (e-campus), Plant Reactome database

2018-19 Priya Garg*#, Plant Reactome database

2014-16: Christina M*#. Partipilo, FragariaCyc database

2013-14 Eli N. Waddell#*, VitisCyc database

Note: *co-authors of one or more published papers. #co-authors of the conference presentations/abstracts.

At OSU

Affiliated with:

Ag Botany / Plant Path

Career Links:

Department of Botany and Plant Pathology

Naithani Lab

Center for Genome Research and Biocomputing

Gramene

Plant Reactome

Courses Taught:

Research Mentoring and Experiential Learning Activities (ELA) related courses:

2021 -present BOT 003 (non-credit grading mode, transcript-visible research experience)
2019-present BOT 401 (undergraduate research with earned credits),
2019-present BOT 403 (undergraduate honors thesis)
2021-2024 BOT 004 (non-credit grading mode, transcript-visible research internship),
2021-2024 BOT 410 (undergraduate research internship with earned credits).

Credit Courses and Guest Lectures:

2020-present - BOT 332 (Laboratory Techniques in Plant Biology; an e-campus course), 1 guest lecture entitled ‘Functional Genomics in Plants’, spring term.
2012-2021 - CSS330 (World Food Crops), Guest Instructor
2019 - MCB599 (Biological Data Science Capstone Course), supervised 3 graduate students on a research project, spring term.
2009-2020 - BOTANY 101 (Botany: A Human Concern)
2009-2010 - BIOLOGY 314 (Cell and Molecular Biology)

Outreach for K-12 Educators and Students:

2013-2017 - OSU STEM ACADEMY: DNA Biology and Bioinformatics Summer Camp for 8th-10th Grade students. This was a two weeks/year. I contributed to the planning and coordinating the whole event and conducted a one-day workshop.
2010 - Organized and conducted three hours workshop entitled ‘Markers, Molecules, and Morphology’ using Oregon Wolfe Barleys’ for High School teachers with Kari van Zee, for STEPS (Scientists and Teachers in Education Partnerships) program funded by USDA

Professional Accomplishments

Professional Affiliations:

2012-present Lead Biocuration Scientist, Plant Reactome Knowledgebase

2012-present Affiliate Faculty, Center for Quantitative Life Sciences, OSU

2017-2023 Editor-in-chief, Current Plant Biology

2022-present Associate Editor, Frontiers in Plant Science-Plant Biotechnology

2022-present Editorial Board Member, Plants (Basel): Plant Genetics, Genomics and Biotechnology section

2012-2020 Outreach Coordinator for NSF-funded Gramene Database Project

2014-2017 Associate Managing Editor, Current Plant Biology

Employment:

2020-present Associate Professor Senior Research, Department of Botany and Plant Pathology (BPP), Oregon State University (OSU), Corvallis, OR, USA

2021-2024 Lead Undergraduate Advisor Botany (on-campus), OSU, Corvallis, OR, USA

2012-2020 Assistant Professor Senior Research, BPP, OSU, Corvallis, OR, USA

2008-2012 Assistant Professor Senior Research, Dept. of Horticulture, OSU, Corvallis, OR, USA

2006-2007 Lecturer, Department of Plant Breeding and Genetics, Cornell University, Ithaca, NY, USA

2002-2006 Research Associate, Department of Plant Biology, Cornell University, Ithaca, NY, USA

1999-2002 Postdoctoral Associate, Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, USA

1998-1999 Postdoctoral Associate, Department of Biophysics, Biochemistry and Molecular Biology, Iowa State University, Ames, IA, USA

Education:

Ph. D., Botany (Plant Molecular Biology), National Botanical Research Institute Lucknow and University of Lucknow, Lucknow, India.

Service:

i. Department Committees

2021-present Member of Botany Curriculum Committee, OSU

2020-2022 Member of BPP Seminar Committee

2021 Organizer of the Fall 2021 Seminar Series, OSU

2021-2022. Served as a P&T mentor for one faculty BPP, OSU

2019-2020 BPP Computer Committee, OSU

2019-present Graduate Faculty, Botany and Plant Pathology (BPP), OSU

2008-Present Graduate Faculty, Molecular and Cellular Biology Program, OSU

2008-present Graduate Faculty, Department of Horticulture, OSU

ii. College and University Committees

2019-present Member of the President's Commission on the Status of Women (PCOSW)
2018- present Graduate Council Representative (GCR), OSU

iii. Service to the profession

Review and evaluation

2016- Present: served as a reviewer and panel member for the National Science Foundation (NSF), the National Aeronautics and Space Administration (NASA), and the U.S.-Israel Binational Science Foundation (BSF).
2023 Conducted review and evaluation of a database portal of the Swiss Institute of Bioinformatics (SIB), Lausanne - Switzerland knowledge
2018 &2023 Provided peer review for two book proposals to the Elsevier publication.
2000-present provided peer reviews for ~800 manuscripts for ~20 scientific journals.

Offices/roles in professional societies

2022-present Member of the steering committee of the AgBioData, a consortium of agricultural biological databases and associated resources (https://www.agbiodata.org)
2024 -Served as a member of Scientific Committee of the 17th Annual International Biocuration Conference (AIBC) 2024 organized by Indian Biological Data Centre (IBDC), Faridabad, India, and the International Society for Biocuration (ISB)
2024 -Served as Chair for Session VI: Data Curation & Standards (II) of the 17th Annual International Biocuration Conference (AIBC) 2024, organized by the Indian Biological Data Centre (IBDC), Faridabad, India, and ISB.
2024 -Served as a panelist for “Supporting Agricultural Genomics Through Bioinformatics workshop” supported by The Agriculture Genome to Phenome Initiative (AG2PI) project funded by the U.S. Department of Agriculture’s (USDA) National Institute of Food and Agriculture (NIFA).
2022 -Served as Co-chair of the 15th Annual Biocuration Conference held virtually in 2022 due to the ongoing COVID-19 pandemic (https://www.biocuration.org/15th-annual-biocuration-conference-virtual/)
2022 -Served as a mentor for JR Biotek-Plant Cell Atlas (PCA) Africa Ph.D. Scholars Mentoring Program. This program aims to mentor a new cadre of African crop scientists and global research leaders (https://www.jrbiotekfoundation.org/jr-bioscience-mentoring-academy). I mentored Tokunbo Gbadeyan, a Ph.D. student in Plant Science (Pathology), Obafemi Awolowo University, Nigeria.
2021-2022 -Elected member of the Executive Committee of the International Society for Biocuration (ISB)
2021-2022 -Chair of Equity Diversity and Inclusion subcommittee of ISB
2010-present - A Member of the American Society of Plant Biologists (ASPB), Botanical Society of America (BSA), and the International Society for Biocuration (ISB)

iv. Service to the Public: Science Communication

Popular Science Books

A brief history of Agriculture (‘Anna Kahan Se Ata Hai’ in Hindi), published by National Book Trust, India. Delhi, India. 1st edition, ISBN: 978-81-237-9265-1

Open Text Book

Naithani S.1,3 (2021). History and Science of Cultivated Plants published by OSU Open Educational Resources, EBOOK ISBN: 978-1-955101-08-0. https://open.oregonstate.education/cultivatedplants .

Newspapers and magazines

New study eyes nutrition-rich chia seed for potential to improve human health, 13 December 2023. OSU Today NEWS reported by Sean Nealon, https://today.oregonstate.edu/news/new-study-eyes-nutrition-rich-chia-seed-potential-improve-human-health
The Tiny Seed With Mighty Secrets: Scientists Unlock Chia’s Genetic Code. (December 29, 2023), https://scitechdaily.com/the-tiny-seed-with-mighty-secrets-scientists-unlock-chias-genetic-code/?fbclid=IwAR0nwV_l3QT0Oz31YAdOJ8b9KJsf_WGwtfkA23XEIjE0Phs58uSXlcPxtV0
Are chia seeds good for you? - study. (December 14, 2023), https://www.jpost.com/health-and-wellness/article-778110?fbclid=IwAR2PojIDy6QH4TO4WsACMFOvBiTEfuzqgW_IsR6TlpSyzyk30UnhXqr2mbI#google_vignette
Researchers Sequence Chia Genome. (December 14, 2023), https://www.sci.news/genetics/chia-genome-12533.html?fbclid=IwAR3LKFVRZ-AURR-vL99qJ5nWZVTv_lj4xnb6Y9WBITWeHzMcnk7Hs51mJAQ
New study eyes nutrition-rich chia seed for potential to improve human health. (December 13, 2023). https://today.oregonstate.edu/news/new-study-eyes-nutrition-rich-chia-seed-potential-improve-human-health?fbclid=IwAR35-CfmE3eCGwU-zX79oP3mMsJzhQcW83Ydzw7d4qNh4IuP9QIxa3NsSSs
New Study Says Chia Seeds Could Change the Future of Health and Medicine. (December 13, 2023), https://vegnews.com/vegan-news/chia-seeds-study-health-medicine
STEM camp ‘DNA Biology and Bioinformatics-2016’, Gazette Times, July 15th 2016 Edition http://www.gazettetimes.com/news/local/stem-camp/article_feb771e5-916c-5710-9b53-19dabe58825c.html
Plant Metabolic Pathways Now Powered by iPlant Collaborative by Shelley Littin, June 18, 2015, iplantcollaborative news and features at http://thelma.iplantcollaborative.org/blog/news/plant-metabolic-pathways-now-powered-iplant-collaborative#main-content
OSU helps decode strawberry genome in bid to improve fruit. OSU Public release date: 26-Dec-2010. http://www.eurekalert.org/pub_releases/2010-12/osu-ohd122110.php
Strawberry shortcuts: Decode DNA to cut crop chemical use. KVAL News video by Tom Adams. KVAL News http://www.kval.com/news/local/112533799.html
Strawberry fields forever, The Telegraph, India, Monday, December 27, 2010, by TV Jayan http://www.telegraphindia.com/1101227/jsp/knowhow/story_13351625.jsp
Strawberry genome sequencing will lead to genetic improvements, December 27, 2010, by Tiffany Woods. http://westernfarmpress.com/orchard-crops/strawberry-genome-sequencing-will-lead-genetic-improvements

My Awards

Honors and Awards:

2024 The Excellence in Biocuration Advanced Career Award by the International Society for Biocuration (https://www.biocuration.org). The Advanced Career Award annually recognizes one biocurator who has been involved in a biocuration-relevant field for seven years or more and has made sustained contributions to the field.

2024 Sustained Research Parasitism (aka the merozoite) award (https://researchparasite.com/) by Pacific Symposium on Biocomputing, GigaByte, and GigaScience. This award is given annually to one senior researcher for exemplary contributions to the meticulous secondary analysis of publicly available genomic data and the discovery of new knowledge and novel insights.

2023 START Superhero certificate for advising from the Office of OSU Office of Student Orientation in 2023. START advising is one of the very important tasks for advisors and requires knowledge, commitment, and participation in advising first-year students.

2017 Travel Support for Plant Genome Evolution 2017 conference, Elsevier Publishers.

2017 Excellent Scholar Award from the Organizing Committee of the XIX International Botanical Congress, held in Shenzhen, China.

2017 Travel Award, International Society of Biocuration, for attending the annual biocuration conference.

2013 Travel fellowship to attend ‘11th International Rice -Functional Genomics 2013 meeting’, USDA.

2013 Travel fellowship to attend ‘Metabolic Pathway Analysis-2013 meeting’, NSF.

1997 ARS-NET certified for Assistant Professorship in National and State Agriculture Universities in India.

1994-97 Senior Research Fellowship, Council of Scientific and Industrial Research, Govt. of India.

1995 Best Poster Award by the Society for Plant Biochemistry and Biotechnology, India.

1992-94 Junior Research Fellowship, Council of Scientific and Industrial Research, Govt. of India.

1992 General Aptitude Test in Engineering (GATE) fellowship from Indian Institute of Technology Delhi, India.

Ranked in the top 7.5 % nationally (92.8 percentile) (declined).

1990-92 Govt. of India Biotechnology Fellowship for M. Sc. (Based on National level exam).

My Publications

Proceedings and Conference Presentations:

Total 120 conference presentations (details can be provided upon request)

My Media

My News Articles:

Unlocking the genome and secrets of Chia seed: The Nutritional Powerhouse

chia seeds and a graph of it's genome assembly

Chia, a tiny seed from Southern Mexico and Central America, might just be the next big thing in healthy eating!

OSU Press Release

New Paper in Plant Genomics and Bioinformatics

Read full story

Primary tabs

Sushma Naithani

Cordley Hall

2701 SW Campus Way

Naithani Lab

Lab website

Lab Members

Research Associate, Software Developer

Undergraduate Honors Thesis students:

STEM Leaders Undergraduate Research Program Fellows (winter and spring term)

Undergraduate Research, Scholarship, & the Arts (URSA) fellows (winter and spring terms)

Experiential Learning Activity (one term)

Grant-funded Undergraduate Biocurators

i. Department Committees

ii. College and University Committees

iii. Service to the profession

iv. Service to the Public: Science Communication

Unlocking the genome and secrets of Chia seed: The Nutritional Powerhouse

Unlocking the genome and secrets of Chia seed: The Nutritional Powerhouse

New Paper in Plant Genomics and Bioinformatics

New Paper in Plant Genomics and Bioinformatics

Student Resources

Employee Resources

New Employees