Journal Publications

2021

Bedre, R, Avila, C, Mandadi, KK. HTSQualC: A Flexible and One-Step Quality Control Software for High-throughput Sequence Data Analysis. Accepted in Scientific Reports. 2021 September 3.



Pant S, Irigoyen S, Liu J, Bedre R, Christensen S, Schmelz E, Sedbrook J, Scholthof KB, Mandadi KK. Brachypodium PHENYLALANINE AMMONIA LYASE (PAL) promotes antiviral defenses against Panicum mosaic virus and its satellites. mBio. 2021, 1, e03518-20.

2020

Irigoyen S, Ramasamy M, Pant S, Niraula P, Bedre R, Gurung M, Rossi D, Laughlin C, Gorman Z, Achor D, Levy A, Kolomiets MV, Setamou M, Badillo-Vargas IE, Avila CA, Irey M, Mandadi KK. Plant hairy roots enable high throughput identification of new antimicrobials against Candidatus Liberibacter spp. Nature Communications. 2020, 11, 5802.


Awika H, Cochran K, Joshi V, Bedre R, Mandadi, KK, Avila CA. Single-marker and haplotype-based association analysis of anthracnose (Colletotrichum dematium) resistance in Spinach (Spinacia oleracea). Plant Breeding. 2020 Apr;139(2):402-18

2019

Bedre R, Mandadi, KK. GenFam: A web application and database for gene family-based classification and functional enrichment analysis. Plant Direct. 2019 Dec 1;3(12).


Awika H, Marconi T, Bedre R, Mandadi, KK, Avila CA. Minor Alleles are Associated with White Rust (Albugo occidentalis) Susceptibility in Spinach (Spinacia oleracea). Horticulture Research. 6, 129 (2019) doi:10.1038/s41438-019-0214-7.


Kandel DR, Bedre R, Mandadi, KK, Crosby K, Avila CA. Genetic Diversity and Population Structure of Texas A&M Tomato (Solanum lycopersicum) Breeding Germplasm. American Journal of Plant Sciences. 2019 Jul 11;10(7):1154-80


Bedre, R, Irigoyen, S, Schaker, PDC, Monteiro-Vitorello, CB, Da Silva, JA, Mandadi, KK. Genome-wide alternative splicing landscapes modulated by biotrophic sugarcane smut pathogen.. Scientific Reports. 2019 June 9:8876



Bedre R, Irigoyen S, Petrillo E, Mandadi K. New Era in Plant Alternative Splicing Analysis Enabled by Advances in High-Throughput Sequencing (HTS) Technologies. Frontiers in Plant Science. 2019 June;10:740


Awika H, Bedre R, Yeom J, Marconi T Enciso J, Mandadi K, Jung J, Avila C. Developing Growth-Associated Molecular Markers Via High-Throughput Phenotyping in Spinach. The Plant Genome. 2019 Aug 1

2018

Sengupta S, Mangu V, Sanchez L, Bedre R Joshi R, Rajasekaran K, Baisakh N. An Actin Depolymerizing Factor from the Halophyte Smooth Cordgrass, Spartina alterniflora (SaADF2) is Superior to its Rice homolog (OsADF2) in Conferring Drought and Salt Tolerance when Constitutively Overexpressed in Rice. Plant biotechnology journal. 2019 Jan;17(1):188-205


Mehanathan M, Bedre R, Mangu V, Rajasekaran K, Bhatnagar D, Baisakh N. Identification of candidate resistance genes of cotton against Aspergillus flavus infection using a comparative transcriptomics approach. Physiology and Molecular Biology of Plants. 2018 Mar 22:1-7.


Irigoyen S, Bedre RH, Scholthof KB, Mandadi KK. Genomic Approaches to Analyze Alternative Splicing, A Key Regulator of Transcriptome and Proteome Diversity in Brachypodium distachyon. InBrachypodium Genomics 2018 (pp. 73-85). Humana Press, New York, NY.

2017

Solis J, Gutierrez A, Mangu V, Sanchez E, Bedre R, Linscombe S, Baisakh N. Genetic Mapping of Quantitative Trait Loci for Grain Yield under Drought in Rice under Controlled Greenhouse Conditions. Frontiers in chemistry. 2018 Jan 8;5:129.


Gupta A, Bedre R, Thapa SS, Sabrin A, Wang G, Dassanayake M, Grove A. Global awakening of cryptic biosynthetic gene clusters in Burkholderia thailandensis. ACS chemical biology. 2017 Nov 8;12(12):3012-21.

2016

Bedre R, Ramanarao MV, Sanchez LE, Srivastav S, Baisakh N. Transcriptome Analysis of Smooth Cordgrass (Spartina alterniflora Loisel), A Monocot Halophyte, Reveals Candidate Genes Involved in its Adaptation to Salinity. BMC genomics. 2016 Aug 19;17(1):657.


Bedre RH, Raj U, Misra SP, Varadwaj PK. Antiviral therapy with nucleotide/nucleoside analogues in chronic hepatitis B: A meta-analysis of prospective randomized trials. Indian Journal of Gastroenterology. 2016 Mar:1-8.

2015

Bedre R, Rajasekaran K, Mangu VR, Timm LE, Bhatnagar D, Baisakh N. Genome-wide transcriptome analysis of cotton (Gossypium hirsutum L.) identifies candidate gene signatures in response to aflatoxin producing fungus Aspergillus flavus. PloS one. 2015 Sep 14;10(9):e0138025.


Zandkarimi H, Bedre R, Solis J, Mangu V, Baisakh N. Sequencing and expression analysis of salt-responsive miRNAs and target genes in the halophyte smooth cordgrass (Spartina alterniflora Loisel). Molecular biology reports. 2015 Aug 1;42(8):1341-50.


Joshi R, Mangu VR, Bedre R, Sanchez L, Pilcher W, Zandkarimi H, Baisakh N. Salt adaptation mechanisms of halophytes: improvement of salt tolerance in crop plants. InElucidation of Abiotic Stress Signaling in Plants 2015 (pp. 243-279). Springer New York.

2013

Khan NA*, Bedre R*, Parco A, Bernaola L, Hale A, Kimbeng C, Pontif M, Baisakh N. Identification of cold-responsive genes in energycane for their use in genetic diversity analysis and future functional marker development.. Plant science. 2013 Oct 31;211:122-31. * equal contribution

2012

Lee S, Rajasekaran K, Ramanarao MV, Bedre R, Bhatnagar D, Baisakh N. Identifying cotton (Gossypium hirsutum L.) genes induced in response to Aspergillus flavus infection. Physiological and Molecular Plant Pathology, 80, 35-40.

Workshops

Advanced Bioinformatics Workshop, Nov 20 to Nov 23, 2017 at Guayaquil, Ecuador

Software

• GenFam: Gene Family based classification and enrichment analysis Visit GenFam
• HTSeqQC: automated sequence filtering analysis tool for high-throughput RNA-seq data Visit HTSeqQC
• bioinfokit: Bioinformatics data analysis and visualization toolkit Visit bioinfokit

Presentations, Oral and Conferences

• Kandel, D.R., Awika, H.O., Bedre, R., Mandadi, K.K, Crosby, K., Avila, C.A. 2020. Identification of Fruit Quality Associated Loci in Tomato (Solanum lycopersicum) Using Genome-Wide Association Mapping American Society of Horticultural Sciences (ASHS), Virtual Meeting. August 10-13 .
• Ramasamy, M., Irigoyen, S., Pant, S., Bedre, R., Niraula , P., Avila, C.A., Mandadi, K.K. 2020. Modulation of Salicylic Acid Receptor Activity Confers Resistance to Potato Zebra Chip Disease. American Society of Plant Biology (ASPB), Virtual Meeting. July 27-31 (Oral talk by Ramasamy, M.).
• Bedre, R., Irigoyen, S., Schaker, P.D.C., Monteiro-Vitorello, C.B., Da Silva, J.A., Mandadi, K.K. 2020. Genome-Wide Alternative Splicing Landscapes Modulated by Biotrophic Sugarcane Smut Pathogen. Plant and Animal Genome XXVIII Conference, San Diego, CA. Jan 11- 15 (Oral talk).
• Awika, H.O., Cochran, K., Bedre, R., Mandadi, K.K., Avila, C.A. 2019. Single SNP- and Haplotype-Based Association Analysis of Anthracnose Disease Caused By Colletotrichum Dematium in Spinach (Spinacia oleracea). American Society of Horticultural Sciences, Las Vegas, CA. 21-25 July (Oral talk).
• Awika, H.O., Marconi, T.G., Bedre, R., Mandadi, K.K., Avila, C.A. 2019. Assessing Minor Alleles as Risk Factors in Spinach White Rust Disease Severity. American Society of Horticultural Sciences, Las Vegas, CA. 21-25 July.
• Kandel, D.R., Bedre, R.H., Mandadi, K.K., Crosby, K., Avila, C.A. 2019. Genetic Diversity and Population Structure of Texas A&M Tomato (Solanum lycopersicum) Breeding Germplasm . American Society of Horticultural Sciences, Las Vegas, CA. 21-25 July.
• Devisetty, U., Castillo-Siri, A., Palos, K.R., Bedre, R., Mandadi, K.K., Lyons, E., Beilstein, M.A., Nelson, A. 2019. Comparative Genomic and Transcriptomic Analyses of Functionally Characterized Arabidopsis lncRNAs Reveals Conservation in Unexpected Places. Plant and Animal Genome XXVII Conference, San Diego, CA. 11- 16 January.
• Bedre, R., Irigoyen, S., Schaker, P.D.C., Monteiro-Vitorello, C.B., Da Silva, J.A., Mandadi, K.K. 2019. Characterization of Alternative Splicing Patterns Modulated by Biotrophic Smut Pathogen in Sugarcane. Plant and Animal Genome XXVII Conference, San Diego, CA. 11- 16 January.
• Bernaola, L.,Bedre, R., Stout, M. 2018. Mycorrhizal colonization affects rice gene expression of resistance traits in response to herbivore feeding. International Rice Research Conference (IRRC), Singapore. Oct 15- 17.
• Awika, H.,Bedre, R., Marconi, T., Badillo, I., Mandadi, K.K., Avila, C.A. 2018. Differential gene expression profile between resistant and susceptible tomato genotypes in response to tomato-potato psyllid (Bactericera cockerelli) infestation. American Society of Horticultural Sciences (ASHS), Washington, DC. July 30- August 3.
• Awika, H.,Bedre, R., Marconi, T., Enciso, J., Jung, J., Mandadi, K.K., Avila, C.A. 2018. Development of molecular markers associated to spinach growth parameters. American Society of Horticultural Sciences (ASHS), Washington, DC. July 30- August 3. (Oral)
• Awika, H.,Bedre, R., Marconi, T., Badillo, I., Mandadi, K.K., Avila, C.A. 2018. Resistance to the tomato-potato Psyllid (Bactericera cockerelli) in Solanum habrochaites. American Society of Plant Biology (ASPB), Montréal, Quebec. July 14-18.
• Bedre, R., Scholthof, K.-B.G., Figueroa, M., Djamei, A., Zuccaro, A., Kazan, K., Powell, J., Vogel, J.P., and Mandadi, K.K. 2018. A gene atlas of diverse grass-microbe interactions in Brachypodium and Setaria. The 13th DOE Joint Genome Institute Annual Genomics of Energy & Environment User Meeting Annual Meeting, San Francisco, CA. 13-16 March.
• Bedre, R., Irigoyen, S., Ramasamy, M., and Mandadi, K.K. Integration of Bioinformatics and Omics Technologies in Crop Improvement. The 76th Annual Meeting of the Subtropical Agriculture and Environments Society, February 9, 2018, Monte Alto, TX.
• Badillo-Vargas, I.E., Bedre, R., Esparza-Díaz, G., Avila, C., and Mandadi, K.K. Tissue-specific transcriptional responses of the potato psyllid related to the horizontal and vertical transmission of the bacterial pathogen causing zebra chip disease of potato. The 76th Annual Meeting of the Subtropical Agriculture and Environments Society, February 9, 2018, Monte Alto, TX.
• Bedre R, Irigoyen S, Schaker P, Monteiro-Vitorello C, Mandadi KK. Genome-wide characterization of alternative splicing patterns in sugarcane modulated during infection with smut pathogen, Sporisorium scitamineum. The Annual Meeting of the American Phytopathological Society, August 5-9, 2017, San Antonio, TX.
• Badillo-Vargas, I.E., Bedre, R., Esparza-Díaz, G., Avila, C., and Mandadi, K.K. Tissue-specific transcriptional responses related to the horizontal and vertical transmission of a bacterial pathogen by its insect vector. The Annual Meeting of the American Phytopathological Society, August 5-9, 2017, San Antonio, TX.
• Venkata M, Bedre R, Zandkarimi H, Baisakh N. Looking at the bright side of an invasive species: Spartina alterniflora from an abiotic stress tolerance perspective. Plant and Animal Genome XXIII Conference. In Plant and Animal Genome XXIII Conference, January 10-14, 2015, San Diego, CA.
• Zandkarimi H, Venkata M, Bedre R, Baisakh, N. Expression profiling of miRNAs and their target genes under salt stress in the halophyte smooth cordgrass (Spartina alterniflora Loisel). In Plant and Animal Genome XXIII Conference, January 10-14, 2015, San Diego, CA.
• Venkata M, Timm LS, Joshi R, Bedre R, Baisakh N. Translation of halophyte transcriptome resources to improve salt and drought stress tolerance in rice. 2014 International meeting, At Long Beach, CA, USA.
• Bedre R, Venkata M, Srivastav S, Sanchez E, Solis J, Pereira A & Baisakh N. Genome-wide transcriptome analysis of the halophyte grass Spartina alterniflora reveals molecular basis of its salt adaptation responses. In Plant and Animal Genome XXII Conference, January 11-15, 2014, San Diego, CA.
• Bernaola L, Parco A, Hale A, Bedre R, Kimbeng C, Gravois K, Baisakh N. Mining genes for cold tolerance in sugarcane toward development of functional markers. In Plant and Animal Genome XX Conference, January 14-18, San Diego, CA.