Publications

Papers Conferences Editorials
Papers
Conferences
Editorials

2022

Kataria, R. and Kaundal, R*

TRustDB: A comprehensive bioinformatics resource for understanding the complete Wheat - Stem Rust host-pathogen interactome. Database (in press).

http://bioinfo.usu.edu/trustdb/

Duhan, N.$, Kataria, R.$ and Kaundal, R*

TritiKBdb: A functional annotation resource for deciphering the complete interaction networks in Wheat - Karnal Bunt pathosystem. International Journal of Molecular Sciences 23(13): 7455. PMID: 9267065

https://doi.org/10.3390/ijms23137455

Kataria, R. and Kaundal, R*.

WeCoNET: A Host-Pathogen Interactome Database for Deciphering Crucial Molecular Networks of Wheat-Common bunt Cross-talk Mechanisms. BMC Plant Methods 18, Article number: 73 (2022). PMCID: 9164323

https://doi.org/10.1186/s13007-022-00897-9

Kaundal, R.$*, Loaiza, C.D.$, Duhan, N. and Flann, N.

deepHPI: a comprehensive Deep Learning platform for accurate prediction and visualization of host-pathogen protein-protein interactions. Briefings in Bioinformatics bbac125: 1-11. PMID: 35511057

https://doi.org/10.1093/bib/bbac125

Kataria, R. and Kaundal, R*.

Deciphering the Host-Pathogen Interactome of Wheat-Common bunt system: A Step towards Enhanced Resilience in Next Generation Wheat. International Journal of Molecular Sciences 23(5): 2589. PMCID: 8910311.

https://doi.org/10.3390/ijms23052589

Duhan, N., Norton, J.M. and Kaundal, R*.

deepNEC: a novel alignment-free tool for the identification and classification of nitrogen biochemical network-related enzymes using deep learning. Briefings in Bioinformatics bbac071: 1-16. PMID: 35325031 .

https://doi.org/10.1093/bib/bbac071

Kataria, R., Duhan, N. and Kaundal, R*.

Computational Systems Biology of Alfalfa-Bacterial Blight Host-Pathogen Interactions: Uncovering the Complex Molecular Networks for Developing Durable Disease Resistant Crop. Frontiers in Plant Science 12: 807354. PMCID: 8891223.

https://doi.org/10.3389/fpls.2021.807354

Yang, X., Hu, Xiao-Li., Zhang, J., Kaundal, R., Kataria, R., Jessy L.L., Mitchell, J., Tschaplinski, T., Tuskan, G.A. and Cheng, Zong-Ming (Max).

Diversity and conservation of plant small secreted proteins associated with arbuscular mycorrhizal symbiosis. Horticulture Research uhac043: 1-22. PMCID: 8985099.

https://doi.org/10.1093/hr/uhac043

Rutigliano, H.M., Thomas, A.J., Umbaugh, J.J., Wilhelm, A., Sessions, B.R., Kaundal, R., Duhan, N., Hicks, B.A., Schlafer, D.H., White, K.L. and Davies, C.J.

Increased Expression of Pro-Inflammatory Cytokines at the Fetal-Maternal Interface in Bovine Pregnancies Produced by Cloning. American Journal of Reproductive Immunology, e13520. PMID: 34974639.

https://doi.org/10.1111/aji.13520

2021

Kaundal, R.*, Duhan, N., Acharya, B., Pudussery, M., Ferreira, J., Suarez, D., and Sandhu, D*.

Transcriptional profiling of two contrasting genotypes uncovers molecular mechanisms underlying salt tolerance in alfalfa. Scientific Reports - Nature 11(1): 5210. PMCID: 7933430.

10.1038/s41598-021-84461-w

Loaiza, C.D. and Kaundal, R*.

PredHPI: an integrated web server platform for the detection and visualization of host-pathogen interactions using sequence-based methods. Bioinformatics 37(5): 622-624. PMID: 33027504.

10.1093/bioinformatics/btaa862

Duhan, N. and Kaundal, R*.

LegumeSSRdb: a Comprehensive Microsatellite Marker Database of Legumes for Germplasm Characterization and Crop Improvement. International Journal of Molecular Sciences 22(21): 11350. PMCID: 8583334.

https://doi.org/10.3390/ijms222111350

Loaiza, C.D., Duhan, N. and Kaundal, R*.

GreeningDB: a database of host-pathogen protein-protein interactions and annotation features of the bacteria causing huanglongbing HLB disease. International Journal of Molecular Sciences 22(19): 10897. PMCID: 8509195.

https://doi.org/10.3390/ijms221910897

Loaiza, C.D., Duhan, N., Lister, M., and Kaundal, R*.

In silico prediction of host-pathogen protein interactions in melioidosis pathogen Burkholderia pseudomallei and human reveals novel virulence factors and their targets. Briefings in Bioinformatics 22(3): 1-18. PMID: 32444871.

10.1093/bib/bbz162

Mohammadi, M$., Smith, E.A$^., Stanghellini, M.E., and Kaundal, R.

Insights into the host specificity of a new oomycete root pathogen, Pythium brassicum P1: whole genome sequencing and comparative analysis reveals contracted regulation of metabolism, protein families, and distinct pathogenicity repertoire. International Journal of Molecular Sciences 22(16): 9002. PMCID: 8396444 .

10.3390/ijms22169002

Kataria, R. and Kaundal, R*.

alfaNET: A Database of Alfalfa-Bacterial Stem Blight Protein–Protein Interactions Revealing the Molecular Features of the Disease-causing Bacteria. International Journal of Molecular Sciences 22(15): 8342. PMCID: 8348475.

10.3390/ijms22158342

2020

Duhan, N., Meshram, M., Loaiza, C.D., and Kaundal, R*.

citSATdb: genome wide Simple Sequence Repeats (SSR) marker database of citrus species for germplasm characterization and improvement. Genes 11(12): 1486. PMCID: 7764524.

10.3390/genes11121486

Sahu, S.S., Loaiza, C.D., and Kaundal, R.

Plant-mSubP: a computational framework for the prediction of single- and multi-target protein subcellular localization using integrated machine learning approaches. AoB Plants 12(3): plz068. PMCID: 7274489.

10.1093/aobpla/plz068

2019

Sharma B., Batz T.A., Kaundal R*., Kramer E.M., Sanders U.R.^, Mellano V.J., Duhan N., and Larson R.B.

Developmental and Molecular Changes Underlying the Vernalization-Induced Transition to Flowering in Aquilegia coerulea (James). Genes, 10(10): 734. PMCID: 31546687.

10.3390/genes10100734

Phatak, S.^, Thomas, A., Kaundal, R*., Jones, R., Hintze, K., and Benninghoff, A.

Impact of the Total Western Diet for Rodents on Colon Mucosal Gene Expression in a Multigenerational Murine Model of Colitis-associated Colorectal Cancer. Current Developments in Nutrition, 3(S1): nzz030.OR04-03-19.

10.1093/cdn/nzz030.OR04-03-19

Tello, D., Gil, J., Loaiza, C.D., Riascos, J.J., Cardozo, N., and Duitama, J.

NGSEP3: accurate variant calling across species and sequencing protocols. Bioinformatics, 35(22): 4716-4723. PMCID: PMC6853766.

10.1093/bioinformatics/btz275

2018

Sandhu, D., Pudussery, M.V., Kaundal, R., Suarez, D.L., Kaundal, A., Sekhon, R.S.

Molecular characterization and expression analysis of the Na+/H+ exchanger gene family in Medicago truncatula. Functional & Integrative Genomics, 18(2): 141-153. PMID: 29280022.

10.1007/s10142-017-0581-9

Moley, L.^, Jones, R., Kaundal, R., Thomas, A., Benninghoff, A., and Isom, S.C.

Gene expression analysis and DNA methylation patterns of porcine somatic cell nuclear transfer blastocysts with high and low incidence of apoptosis. Reproduction, Fertility and Development, 31(1): 128-128.

10.1071/RDv31n1Ab5

2016

Volz, D.C., Leet, J.K., Chen, A., Stapleton, H.M., Katiyar, N., Kaundal, R., Yu, Y., Wang, Y.

Tris(1,3-dichloro-2-propyl)phosphate Induces Genome-Wide Hypomethylation within Early Zebrafish Embryos. PMCID: PMC5080636.

10.1021/acs.est.6b03656

2014

Sahu, S.S., Weirick, T., Kaundal, R*.

Predicting genome-scale Arabidopsis-Pseudomonas syringae interactome using domain and interolog-based approaches.PMCID: PMC4251041.

10.1186/1471-2105-15-S11-S13

Weirick, T., Sahu, S.S., Mahalingam, R., Kaundal, R*.

LacSubPred: predicting subtypes of Laccases, an important lignin metabolism-related enzyme class, using in silico approaches.PMCID: PMC4251044.

10.1186/1471-2105-15-S11-S15

2013

Kaundal, R., Sahu, S.S., Verma, R^., Weirick, T.

Identification and characterization of plastid-type proteins from sequence-attributed features using machine learning. PMCID: PMC3851450.

10.1186/1471-2105-14-S14-S7

Ahmed, F., Kaundal, R., Raghava, G.P.

PHDcleav: a SVM based method for predicting human Dicer cleavage sites using sequence and secondary structure of miRNA precursors. PMCID: PMC3851333.

10.1186/1471-2105-14-S14-S9

2010

Kaundal, R., Saini, R. and Zhao, P.X.

Combining machine learning and homology-based approaches to accurately predict subcellular localization in Arabidopsis. Plant Physiology 154(1): 36-54. PMCID: PMC2832251.

10.1104/pp.110.156851

Benedito, V.A., Li, H., Dai, X., Wandrey, M., He, J., Kaundal, R., Torres-Jerez, I., Gomez, S.K., Harrison, M.J., Tang, Y., Zhao, P.X. and Udvardi, M.K.

Genomic inventory and transcriptional analysis of Medicago truncatula transporters. Plant Physiology152(3): 1716-1730. PMCID:PMC2832251.

10.1104/pp.109.148684

2009

Kaundal, R. and Raghava, G.P.S.

RSLpred: predicting subcellular localization of rice proteins combining compositional and evolutionary information. Proteomics 9(9): 2324-2342. PMCID:200700597.

10.1002/pmic.200700597

2007

Kapoor, A.S. and Kaundal, R.

Development of weather based forewarning systems for rice blast. Himachal Journal of Agricultural Research 33(2): 211-217.

2006

Kaundal, R., Kapoor, A.S. and Raghava, G.P.S.

Machine learning techniques in disease forecasting: a case study on rice blast prediction. BMC Bioinformatics 7(1): 485. PMCID: PMC1647291.

10.1186/1471-2105-7-485

Kaundal, R*. and Sharma, B.K.

Genotype x environment interaction and stability analysis for yield and other quantitative traits in maize (Zea mays L.) under rainfed and high rainfall valley areas of the sub-montane. Research on Crops 7(1): 171-180.

2005

Kaundal, R*. and Sharma, B.K.

Genetic variability and association studies for different yield components over the environments in elite cultivars of Zea mays L. Himachal Journal of Agricultural Research 31(1): 31-38.

Kaundal, R. and Kapoor, A.S.

Virulence pattern of Pyricularia grisea in district Kangra of Himachal Pradesh. Himachal Journal of Agricultural Research 31(2): 170-172.

2022

July 10-14
Virtual Presentation
Guevara, D. and Kaundal, R*.
Location: The 30th Annual International Conference on Intelligent Systems for Molecular Biology (ISMB); Monona Terrace Convention Center, Madison (WI), USA;
ProFeatX: a parallelized protein feature extraction suite for machine learning.
July 10-14
Virtual Presentation
Duhan, N. and Kaundal, R*
Location: The 30th Annual International Conference on Intelligent Systems for Molecular Biology (ISMB); Monona Terrace Convention Center, Madison (WI), USA;
An automated Python package for Next-Generation Sequencing data analysis and report generation.
July 10-14
Virtual Presentation
Kataria, R. and Kaundal, R*
Location: The 30th Annual International Conference on Intelligent Systems for Molecular Biology (ISMB); Monona Terrace Convention Center, Madison (WI), USA;
Genome-scale Protein Interactome: Unraveling Novel Host Targets in Wheat-Stem Rust Pathosystem.
June 22-24
Oral
Mahalingam, R., Bregitzer, P., Duhan, N. and Kaundal, R.
Location: Plant and Animal Genomes Conference (PAG Asia). Virtual Conference;
Transcriptome analysis of Barley lines with contrasting responses to abiotic stresses.
May 18
Oral
Kaundal, R*., Duhan, N., Acharya, B.R., Pudussery, M.V., Ferreira, J.F.S., Suarez, D.L. and Sandhu, D*.
Location: Conference on Applied Statistics in Agriculture and Natural Resources; Utah State University (USU), Logan (UT), USA
Transcriptional profiling of two contrasting genotypes uncovers molecular mechanisms underlying salt tolerance in Alfalfa.
May 18
Oral
Guevara, D. and Kaundal, R*.
Location: Conference on Applied Statistics in Agriculture and Natural Resources; Utah State University (USU), Logan (UT), USA
Malivhu: a Web Server for Predicting Human-Virus Protein-Protein Interactions Using Machine Learning Algorithms.
May 18
Oral
Duhan, N. and Kaundal, R*.
Location: Conference on Applied Statistics in Agriculture and Natural Resources; Utah State University (USU), Logan (UT), USA
pySeqRNA: An Automated Python Package for RNA Sequencing Data Analysis.
Feb 8
Poster
Hauck, K. and Kaundal, R*.
Location: Research on Capitol Hill (RCH) event, Utah Capitol Building; Salt Lake City (UT), USA
Developing Human-Covid Protein-Protein Interactions Atlas for recently emerged SARS-CoV-2 strains: a step towards pan-viral vaccine development.

2021

Dec 9
Oral
Hauck, K. and Kaundal, R*.
Location: Fall Student Research Symposium (FSRS); Utah State University (USU), Logan (UT)
Developing Human-Covid Protein-Protein Interactions Atlas for SARS-CoV-2 strains: a step towards pan-viral treatment development.
Dec 1-2
Oral
Kataria, R. and Kaundal, R*.
Location: The 2021 International Society for Molecular Plant-Microbe Interactions Congress (IS-MPMI); Virtual Conference
Computational systems biology of Wheat - Common bunt protein-protein interactions: Uncovering the complex molecular networks in an important host-pathogen interaction system.
Nov 7-10
Oral
Kataria, R. and Kaundal, R*.
Location: The 2021 ASA, CSSA, SSSA International Annual Meeting; Salt Lake City (UT), USA
Translating -omics big data: comprehensive understanding of host-pathogen interactions to control common bunt in wheat using computational approaches.
Nov 7-10
Oral
Jouffray, A. and Kaundal, R*.
Location: The 2021 ASA, CSSA, SSSA International Annual Meeting; Salt Lake City (UT), USA
DeepAugment: a Machine Learning Framework for Autonomous Generation and Annotation of Weeds Detection and Classification.
Nov 7-10
Oral
Duhan, N. and Kaundal, R*.
Location: The 2021 ASA, CSSA, SSSA International Annual Meeting; Salt Lake City (UT), USA
pySeqRNA: an Automated Python Package for Next-Generation Sequencing Data Analysis.
Nov 7-10
Oral
Kataria, R., Duhan, N. and Kaundal, R*.
Location: The 2021 ASA, CSSA, SSSA International Annual Meeting; Salt Lake City (UT), USA
Computational Systems Biology of Alfalfa - Pseudomonas syringae Protein-Protein Interactions: Uncovering the Complex Molecular Networks of Host-Pathogen Interactions to Control Bacterial Blight in Alfalfa.
Nov 7-10
Oral
Duhan, N., Norton, J.M. and Kaundal, R*.
Location: The 2021 ASA, CSSA, SSSA International Annual Meeting; Salt Lake City (UT), USA
deepNEC: a Novel Alignment-Free Tool for the Identification and Classification of Nitrogen Metabolism-related Enzymes for Better Annotation of Agricultural Genomes.
Sept 15-16
Oral
Kataria, R. and Kaundal, R*.
Location: The 2021 International Society for Molecular Plant-Microbe Interactions Congress (IS-MPMI); Virtual Conference
alfaNET: a Database of Alfalfa-Bacterial Stem Blight Protein-Protein Interactions Revealing the Molecular Features of the Disease-causing Bacteria.
July 25-30
Oral,Poster
Guevara, D. and Kaundal, R*.
Location: The 29th Annual International Conference on Intelligent Systems for Molecular Biology (ISMB) / The 20th European Conference on Computational Biology (ECCB); Virtual Conference
Prediction and classification of virus families/sub-families, and human-MERS/SARS-CoV/SARS-CoV-2 protein-protein interactions prediction using machine learning.
July 12-13
Oral
Kataria, R., Duhan, N. and Kaundal, R*.
Location: The 2021 International Society for Molecular Plant-Microbe Interactions Congress (IS-MPMI); Virtual Conference
Translating -omics big data: comprehensive understanding of host-pathogen interactions to control bacterial blight in Alfalfa using computational approaches.
April 14-15
Oral
Duhan, N. and Kaundal, R*.
Location: The Annual Student Research Symposium; Utah State University (USU), Logan (UT), USA
pySeqRNA: an automated Python package for RNA sequencing data analysis.
April 14-15
Oral
Larson, R., Duhan, N. and Kaundal, R*.
Location: The Annual Student Research Symposium; Utah State University (USU), Logan (UT), USA; Virtual Symposium
In silico screening of natural compounds as novel drug targets for the treatment of Multiple Myeloma.
April 14-15
Oral
Duhan, N., Norton, J.M. and Kaundal, R*.
Location: The Annual Student Research Symposium; Utah State University (USU), Logan (UT), USA; Virtual Symposium
deepNEC: a novel alignment-free tool for the identification and classification of nitrification-related enzymes using deep learning.
April 14-15
Oral
Kataria, R., Duhan, N. and Kaundal, R*.
Location: The Annual Student Research Symposium; Utah State University (USU), Logan (UT), USA; Virtual Symposium
Translating -omics big data: comprehensive understanding of host-pathogen interactions to control bacterial blight in Alfalfa using computational approaches.
March 6
Oral
Alcaraz, A., Kaundal, R. and Sharma, B*.
Location: The 9th Annual Research, Scholarship & Creative Activities Conference (RSCA); California State Polytechnic University, Pomona (CA)
Understanding developmental and molecular changes that trigger floral organ abscission in Aquilegia coerulea.

2020

Dec 5
Oral
Duhan, N., Norton, J.M. and Kaundal, R*.
Location: Virtual Conference
deepNEC: a novel alignment-free tool for the identification and classification of nitrification-related enzymes using deep learning. The 2020 Annual ASM Intermountain Branch Meeting, American Society of Microbiology
Nov 9-13
Oral
Mahalingam, R., Bregitzer, P., Duhan, N., and Kaundal, R.
Location: Virtual Conference
Transcriptome analysis of barley varieties with contrasting responses to heat, drought and combined heat and drought stress. The 2020 Annual International Agronomy Meeting, ASA-CSSA-SSSA
Jul 13-16
Oral, Poster
Duhan, N. and Kaundal, R*.
Location: Virtual Conference
pySeqRNA: an automated Python package for RNA sequencing data analysis. The 28th Annual International Conference on Intelligent Systems for Molecular Biology (ISMB)
Jul 13-16
Oral, Poster
Duhan, N., Norton, J.M., and Kaundal, R*.
Location: Virtual Conference
NECminer: a novel alignment-free tool for the identification and classification of Nitrification-related enzymes using Deep Learning. The 28th Annual International Conference on Intelligent Systems for Molecular Biology (ISMB)
Jul 13-16
Oral, Poster
Kurivella, N.S., Duhan, N., and Kaundal, R*.
Location: Virtual Conference
legumeSSRdb: a comprehensive database of microsatellite markers in Legume species for germplasm characterization and crop improvement. The 28th Annual International Conference on Intelligent Systems for Molecular Biology (ISMB)
Jul 13-16
Oral, Poster
Larson, R.B., McCowan, S., and Kaundal, R*.
Location: Virtual Conference
BioinfoCore @ USU: High-performance computing for Bioinformatics and the challenges of big -OMICS data. The 28th Annual International Conference on Intelligent Systems for Molecular Biology (ISMB)
Jul 13-16
Oral, Poster
Loaiza, C.D., Flann, N., and Kaundal, R*.
Location: Virtual Conference
deepHPI: a comparative Deep Learning framework for the efficient prediction of host-pathogen protein-protein interactions using sequence-based features. The 28th Annual International Conference on Intelligent Systems for Molecular Biology (ISMB)
Mar 07
Oral
Alcaraz A., Kaundal, R. and Sharma, B
Location: The 8th Annual Research, Scholarship & Creative Activities Conference (RSCA); California State Polytechnic University, Pomona (CA)
Understanding the developmental changes and genetic pathways that trigger floral organ abscission in Aquilegia coerulea.
Feb 07
Oral
Sharma, B., Batz, T.A., Kaundal, R., Kramer, E.M., Sanders, U.T^, Mellano, V.J., Duhan, N. and Larson, R.B.
Location: The 18th Annual Cal Poly Pomona Agricultural Research Institute (ARI) Showcase; California State Polytechnic University, Pomona (CA)
Analysis of developmental and gene expression changes underlying vernalization-induced transition to flowering in Aquilegia coerulea.
Jan 11-15
Oral, Poster
Duhan, N., Meshram, M., Loaiza, C.D., and Kaundal, R*.
Location: San Diego (CA), USA
citSATdb: Genome-Wide Simple Sequence Repeats (SSR) Marker Database of Citrus Species for Germplasm Characterization and Crop Improvement. Plant and Animal Genomes conference XXVIII (PAG international)
Jan 11-15
Poster
Loaiza, C.D., Duhan, N., and Kaundal, R*.
Location: San Diego (CA), USA
GreeningDB: a Database of Protein Features and Protein-Protein Interactions of the Bacteria causing HLB. Plant and Animal Genomes conference XXVIII (PAG international)
Jan 11-15
Poster
Acharya, B.A., Kaundal, R., Duhan, N., Pudussery, M., Ferreira, J.F.S., Suarez, D.L., and Sandhu, D.
Location: San Diego (CA), USA
Dissecting salt tolerance mechanism in alfalfa using RNA-seq analysis of a tolerant and a sensitive genotype. Plant and Animal Genomes conference XXVIII (PAG international)

2019

Aug 07
Oral
Phatak S.^, Thomas A., Kaundal R., Jones R., Hintze K., and Benninghoff A.
Location: The Animal, Dairy and Veterinary Sciences Summer Student Research Symposium; Utah State University (USU), Logan (UT)
Impact of the Total Western Diet for Rodents on Colon Mucosal Gene Expression in a Multigenerational Murine Model of Colitis-associated Colorectal Cancer. 1st place in flash talk presentation
Jun 8-11
Oral
Phatak S.^, Thomas A., Kaundal R., Jones R., Hintze K., and Benninghoff A.
Location: The Animal, Dairy and Veterinary Sciences Summer Student Research Symposium; Utah State University (USU), Logan (UT)
Impact of the Total Western Diet for Rodents on Colon Mucosal Gene Expression in a Multigenerational Murine Model of Colitis-associated Colorectal Cancer. 1st place in flash talk presentation
Apr 26
Sharma, B., Batz, T., Kaundal, R., Mellano, V and Sanders, U^
Location: 14th Annual Science Research Symposium; California State Polytechnic University, Pomona (CA)
Developmental, and Genetic Changes in Shoot Apical Meristem During Transition to Flowering in Aquilegia coerulea.
Apr 10-11
Oral
Loaiza C.D. and Kaundal R*.
Location: The Annual Student Research Symposium; Utah State University (USU), Logan (UT), USA
Prediction of Host-Pathogen protein-protein interactions using machine learning.
Apr 10-11
Lister M., Larson R.B. and Kaundal R*.
Location: The Annual Student Research Symposium; Utah State University (USU), Logan (UT), USA
Centralizing Bioinformatics via High-Performance Computing: Applications, Opportunities, and Challenges in the Era of Large-scale -Omics Data.
Apr 10-11
Oral
Ediriweera U. and Kaundal R*
Location: The Annual Student Research Symposium; Utah State University (USU), Logan (UT), USA
Computational Prediction of Host-Pathogen Protein Interactions in Melioidosis pathogen Burkholderia pseudomallei and Human reveals novel Virulence Factors and Infectivity Mechanisms
Apr 02
Oral
Lister M., Larson R.B. and Kaundal R*.
Location: The Annual Plants, Soils, and Climate Showcase, College of Agriculture and Applied Sciences; Utah State University (USU), Logan (UT), USA
High-Performance Computing for Bioinformatics and the Challenges of Big -OMICS Data.
Apr 02
Oral
Kaundal R*., Duhan N., Acharya B., Pudussery M.V., Ferreira J.F.S., Suarez D.L. and Sandhu D*.
Location: The Annual Plants, Soils, and Climate Showcase, College of Agriculture and Applied Sciences; Utah State University (USU), Logan (UT), USA
Comparative transcriptomics study of alfalfa (Medicago sativa L.) reveals novel genotype-specific salt tolerance mechanisms.
Apr 02
Oral
Loaiza C.D. and Kaundal R*.
Location: The Annual Plants, Soils, and Climate Showcase, College of Agriculture and Applied Sciences; Utah State University (USU), Logan (UT), USA
Deciphering plant-pathogen interactomes: a study on citrus greening disease.
Mar 28-30
Oral
Ediriweera U. and Kaundal R*
Location: The 16th MidSouth Computational Biology & Bioinformatics Society (MCBIOS) annual conference; University of Alabama, Birmingham (AL), USA
Computational Prediction of Host-Pathogen Protein Interactions in Melioidosis pathogen Burkholderia pseudomallei and Human reveals novel Virulence Factors and Infectivity Mechanisms.
Jan 12-16
Loaiza C.D. and Kaundal R*.
Location: The Plant and Animal Genome XXVII International Conference (PAG); Town and Country Hotel, San Diego (California), USA
An integrated in silico approach to explore Citrus and HLB host- pathogen interactions.
Jan 20-23
Oral, Poster
Moley L.A.^ , Jones R., Kaundal R.*, Thomas, A.J., Benninghoff, A.D. and Isom, C.
Location: The 45 th Annual International Embryo Transfer Society Conference; Sheraton Hotel, New Orleans (LA), USA
Gene expression analysis and DNA methylation patterns of porcine SCNT blastocysts with high and low incidence of apoptosis.

2018

Dec 6-8
Oral, Poster
Loaiza C.D. and Kaundal R*.
Location: The 16th Annual Rocky Mountain Bioinformatics Conference; Viceroy Hotel, Aspen/Snowmass (CO), USA
PredHPI: an integrated web-server platform for the prediction and visualization of host-pathogen interactions.
March 29-31
Invited
Mohammadi M$., Smith E$^., Stanghellini M. and Kaundal R*.
Location: The XVth MidSouth Computational Biology & Bioinformatics Society (MCBIOS) Annual Conference; Mississippi State University, Starkville (MS), USA
Complete genome sequence of Pythium brassicum P1, an oomycete root pathogen: insights into its host specificity to Brassicaceae.
March 29-31
Sahu S.S, Loaiza C.D. and Kaundal R*.
Location: The XVth MidSouth Computational Biology & Bioinformatics Society (MCBIOS) annual conference; Mississippi State University, Starkville (MS), USA
Plant-mSubP: a computational framework for the prediction of single and multi-location protein subcellular localization using integrated machine learning approaches
March 19
Sahu S.S, Loaiza C.D. and Kaundal R*.
Location: Plants, Soils, and Climate Student Showcase; College of Agriculture and Applied Sciences (CAAS); Utah State University, Logan (UT), USA
Plant-mSubP: a computational framework for the prediction of single and multi-location protein subcellular localization using integrated machine learning approaches
Jun 12-15
Batz T., Kaundal R., Mellano V. and Sharma,
Location: The 99th Annual Pacific Division meeting of AAAS (American Association for the Advancement of Science); California State Polytechnic University, Pomona (CA), USA
Molecular and Morphological Analysis of the Floral Transition in Aquilegia coerulea.
Jan 10-13
Moley L.A.^ , Jones R., Kaundal R., Thomas, A.J., Benninghoff, A.D. and Isom, C.
Location: The 51 st Annual Meeting of the Society for the Study of Reproduction (SSR); Hilton New Orleans Riverside, New Orleans (LA), USA
RNA-Seq analysis of porcine SCNT blastocysts with high and low incidence of apoptosis.
Aug 8
Oral
Moley L.A.^ , Jones R., Kaundal R., Thomas, A.J., Benninghoff, A.D. and Isom, C.
Location: The 7th Annual ADVS Student Research Symposium; Utah State University, Logan (UT), USA
Gene expression analysis and DNA methylation patterns of porcine SCNT blastocysts with high and low incidence of apoptosis.
Jan 15
Invited
Sandhu D., Cornacchione M.V., Pudussery M., Kaundal A., Kaundal R., Ferreira J.F.S. and Suarez D.L.
Location: Punjab Agricultural University (PAU), Ludhiana (Punjab), India.
Genetic analysis of salinity responses in Medicago genotypes.

2017

Oct 22-25
Sandhu D., Pudussery M., Kaundal R. and Suarez D.L.
Location: The ASA, CSSA & SSSA International Annual Meetings; Tampa (Florida), USA
Molecular analysis of the Na+/H+ exchanger gene family and its role in salt stress in Medicago truncatula.
Mar 12-16
Kupsco A., Leet J.K., Altomare D., Chen A., Stapleton H.M., Katiyar N., Kaundal R., Yu Y., Wang Y. and Volz D.C.
Location: 56th Annual Meeting and ToxExpo, Society of Toxicology; Baltimore (Maryland), USA
Transcriptome and DNA Methylome profiling of early Zebrafish embryos exposed to Tris (1,3-dichloro-2-propyl) phosphate.

2016

Dec 1-2
Kupsco A., Leet J.K., Altomare D., Chen A., Stapleton H.M., Katiyar N., Kaundal R., Yu Y., Wang Y. and Volz D.C.
Location: International Symposium & Workshop: Fish and amphibian embryos as alternative models in toxicology and teratology; Aulnay-sous-Bois/Paris, France
Transcriptome and DNA Methylome profiling of early Zebrafish embryos exposed to Tris (1,3-dichloro-2-propyl) phosphate.
Nov 2-4
Kupsco A., Leet J.K., Altomare D., Chen A., Stapleton H.M., Katiyar N., Kaundal R., Yu Y., Wang Y. and Volz D.C.
Location: Toxicoepigenetics: The interface of Epigenetics and Risk assessment, Society of Toxicology meeting; Tysons (Virginia), USA
Transcriptome and DNA Methylome profiling of early Zebrafish embryos exposed to Tris (1,3-dichloro-2-propyl) phosphate.
Jan 9-13
Kaundal R*., Hayes J., Katiyar N. and Liu T.
Location: Plant and Animal Genomes conference XXIV (PAG international); San Diego (CA), USA
Centralizing bioinformatics via High-Performance Computing: applications, opportunities, and challenges in the era of large-scale -Omics data.

2015

Mar 13-14
Kaundal R*., Hayes J., Katiyar N. and Pham, V.
Location: The XII th MidSouth Computational Biology & Bioinformatics Society (MCBIOS) annual conference; University of Arkansas, UAMS, Little Rock (AR), USA
Centralizing bioinformatics via High-Performance Computing: applications, opportunities, and challenges in the era of large-scale -Omics data.
Mar 13-14
Sahu S.S., Hayes J. and Kaundal R*.
Location: The XII th MidSouth Computational Biology & Bioinformatics Society (MCBIOS) annual conference; University of Arkansas, UAMS, Little Rock (AR), USA
Computational prediction of single and multi-target protein subcellular localization using machine-learning approach.

2014

Jul 12-16
Sahu S.S., Kaundal A., Rojas C.M., Lee S.,Weirick T., Mysore K.S. and Kaundal R*.
Location: American Society of Plant Biologists (ASPB) meeting; Portland, Oregon, USA
Computational prediction and experimental validation of host-pathogen protein-protein interactome: a case study on Arabidopsis thaliana - Pseudomonas syringae model system.
March 6-8
Weirick T., Sahu S.S., Mahalingam R. and Kaundal R*.
Location: The XII th MidSouth Computational Biology & Bioinformatics Society (MCBIOS) annual conference; University of Arkansas, UAMS, Little Rock (AR), USA
Predicting subtypes of laccases, an important lignin metabolism-related enzyme class, with machine learning.
Mar 6-8
Sahu S.S., Weirick T. and Kaundal R*.
Location: The XI th MidSouth Computational Biology & Bioinformatics Society (MCBIOS) annual conference; Oklahoma State University, Stillwater (OK), USA
Prediction of Arabidopsis-Pseudomonas syringae interactome based on domain and interolog based approaches.

2013

Sep 23-24
Moncrief, R.,Weirick T. and Kaundal R*.
Location: International Plant Genomics Congress; St. Louis (MO), USA
Deciphering genome-scale host-pathogen Protein Interaction Networks using Artificial Intelligence and its applicability to select agents.
Sep 19
Sahu S.S.,Weirick T., Moncrief, R. and Kaundal, R*.
Location: BMB Annual Research Symposium; OSU Stillwater (OK), USA
A Bioinformatics Approach to Predict Host- Pathogen Protein-Protein Interactions Network.
Apr 23
Weirick T., Fathepure B.Z., Mahalingam R. and Kaundal R*.
Location: NSF EPSCoR Annual Bioenergy Conference; Oklahoma State University, Stillwater (OK), USA
LigPred: a Comprehensive Prediction System for the Identification and Classification of Enzymes Related to the Synthesis and Degradation of Lignin.
Sep 19
Weirick T., Fathepure B.Z., Mahalingam R. and Kaundal R*.
Location: NSF EPSCoR Annual Bioenergy Conference; Oklahoma State University, Stillwater (OK), USA
LigPred: a Comprehensive Prediction System for the Identification and Classification of Enzymes Related to the Synthesis and Degradation of Lignin.
Apr 5-6
Kaundal R*. and Verma R^.
Location: The X th MidSouth Computational Biology & Bioinformatics Society (MCBIOS) annual conference; University of Missouri, Columbia (MO), USA
PLpred: a bioinformatics system for the identification and classification of plastid type proteins.
Apr 5-6
Moncrief, R. and Kaundal R*.
Location: The X th MidSouth Computational Biology & Bioinformatics Society (MCBIOS) annual conference; University of Missouri, Columbia (MO), USA
Bioinformatics Approaches to Deciphering Host-Pathogen Protein Interaction Networks (PINs).
Apr 5-6
Sahu S.S. and Kaundal R*.
Location: The X th MidSouth Computational Biology & Bioinformatics Society (MCBIOS) annual conference; University of Missouri, Columbia (MO), USA
Predicting Multi-target Protein Subcellular Localization combining homology and Machine Learning Approaches.
Apr 5-6
Ahmed F., Kaundal R. and Raghava G.P.S.
Location: The X th MidSouth Computational Biology & Bioinformatics Society (MCBIOS) annual conference; University of Missouri, Columbia (MO), USA
PHDcleav: a SVM-based method for predicting human Dicer cleavage sites using sequence and secondary structure of miRNA precursors.
Mar 9-10
Invited Talk and Poster
Moncrief, R. and Kaundal R*.
Location: Gordon Research Conferences (Chemical & Biological Terrorism Defense); Ventura Beach Marriott, Ventura (CA), USA
Artificial Intelligence-based prediction of plant host-pathogen protein interaction networks in select agents.
Mar 3-5
Weirick T., Fathepure B.Z., Mahalingam R. and Kaundal R*.
Location: NSF EPSCoR Bioinformatics Workshop; Arkansas State University, Little Rock (AR), USA
LigPred: a Comprehensive Prediction System for the Identification and Classification of Enzymes Related to the Synthesis and Degradation of Lignin.
Feb 20-21
Kelley, R. and Kaundal, R*.
Location: OSU Annual Research Week & Symposium (2013); Oklahoma State University, Stillwater (OK), USA
Bioinformatics Approaches to Deciphering Genome-wide Host-Pathogen Protein Interaction Networks.
Feb 20-21
Weirick T., Fathepure B.Z., Mahalingam R. and Kaundal R*.
Location: OSU Annual Research Week & Symposium (2013); Oklahoma State University, Stillwater (OK), USA
LigPred: a Comprehensive Prediction System for the Identification and Classification of Enzymes Related to the Synthesis and Degradation of Lignin

2012

Sep 20-21
Kelley, R. and Kaundal, R*.
Location: Biochemistry & Molecular Biology Annual Research Symposium (2012); Oklahoma State University, Stillwater (OK), USA
Bioinformatics Approaches to Deciphering Genome-wide Host-Pathogen Protein Interaction Networks.
Feb 17-18
Verma R.^ and Kaundal R*.
Location: The IX th MidSouth Computational Biology & Bioinformatics Society (MCBIOS) annual conference; University of Mississippi, Oxford (MS), USA
A Support Vector Machine-based prediction method to classify the plastid and non-plastid type proteins.

2010

Jul 10-14
Kaundal R. and Zhao P.X.
Location: The 18 th Annual International Conference on Intelligent Systems for Molecular Biology (ISMB); Boston (MA), USA
A systematic approach to predicting organism-specific subcellular localization suggests species-specific sorting patterns.

2009

Jul 18-22
Kaundal R. and Zhao P.X.
Location: American Society of Plant Biologists (ASPB) meeting; Honolulu, Hawaii, USA
ASLpred: Arabidopsis Subcellular Localization predictor.

2008

Jan 12-16
Kaundal R. and Zhao P.X.
Location: Plant and Animal Genomes conference XVI (PAG meeting); San Diego (CA), USA
An integrated prediction system for protein subcellular localization in Arabidopsis.

2004

Feb 19-21
A.S. Kapoor and R. Kaundal
Location: The 56th Annual meeting and National Symposium on Crop Surveillance: Disease Forecasting and Management; Division of Plant Pathology, Indian Agricultural Research Institute (IARI), New Delhi
Development of weather based forewarning models for rice blast in Himachal Pradesh.
Nov 9-10
A.S. Kapoor and R. Kaundal
Location: National Symposium on Emerging Trends in Plant Disease Management; Department of Plant Pathology, CSK Himachal Pradesh Agricultural University, Palampur, India
Development of weather-based forecasting models for rice neck blast in Himachal Pradesh.

2002

Oct 1-4
Kapoor A.S., Kaundal R and Pratap A.
Location: CSK Himachal Pradesh Agricultural University (HPAU), Palampur, India
Weather based forewarning of rice blast in H.P. International Conference on Challenges and Options for Sustainable Development of the Himalayas - Beyond 2002

Editorials

Wren, J.D., Toby, I., Hong, H., Nanduri, B., Kaundal, R. Dozmorov, M.G. and Thakkar, S.

Proceedings of the 2016 MidSouth Computational Biology and Bioinformatics Society (MCBIOS) Conference. BMC Bioinformatics 17(S13): 356.

https://doi.org/10.1186/s12859-016-1213-4

Wren, J.D., Dozmorov, M.G., Burian, D., Perkins, A., Zhang, C., Hoyt, P. and Kaundal, R.

Proceedings of the 2014 MidSouth Computational Biology and Bioinformatics Society (MCBIOS) Conference. BMC Bioinformatics 15(S11): I1.

https://doi.org/10.1186/1471-2105-15-S11-I1

Wren, J.D., Dozmorov, M.G., Burian, D., Kaundal, R., Perkins, A., Perkins, E., Kupfer, D.M. and Springer, G.K.

Proceedings of the 2013 MidSouth Computational Biology and Bioinformatics Society (MCBIOS) Conference. BMC Bioinformatics 14(S14): S1.

https://doi.org/10.1186/1471-2105-14-S14-S1

Wren, J.D., Dozmorov, M.G., Burian, D., Kaundal, R., Bridges, S. and Kupfer, D.M.

Proceedings of the 2012 MidSouth Computational Biology and Bioinformatics Society (MCBIOS) Conference. BMC Bioinformatics 13(S15): S1.

https://doi.org/10.1186/1471-2105-13-S15-S1