Simardeep Kaur, Karishma Seem, Naveen Duhan, Suresh Kumar, Rakesh Kaundal, Trilochan Mohapatra

Comparative miRNome and transcriptome analyses reveal the expression of novel miRNAs in the panicle of rice implicated in sustained agronomic performance under terminal drought stress

Jack H Nunberg, Jonna B Westover, Joanne York, Kie Hoon Jung, Kevin W Bailey, Kirsten M Boardman, Minghao Li, Rachel S Furnell, Samantha R Wasson, Justin S Murray, Rakesh Kaundal, Aaron J Thomas, Brian B Gowen

Restoration of virulence in the attenuated Candid#1 vaccine virus requires reversion at both positions 168 and 427 in the envelope glycoprotein GPC

Simardeep Kaur, Karishma Seem, Deepesh Kumar, Suresh Kumar, Rakesh Kaundal, Trilochan Mohapatra

Biogenesis to functional significance of microRNAs under drought stress in rice: Recent advances and future perspectives

Duhan, N,Kaur, S^{^} and Kaundal, R^*

ranchSATdb: a Genome-wide Simple Sequence Repeat (SSR) Markers Database of Livestock Species for Mutant Germplasm Characterization and Improving Farm Animal Health. Genes 14(7): 1481

Kaur, S^{^}, Seem K, Kumar, S^*, Kaundal, R^*, and Mohapatra, T

Comparative Genome-wide Analysis of MicroRNAs and Their Target Genes in Roots of Contrasting Indica Rice Cultivars under Reproductive-Stage Drought. Genes 14(7): 1390

Kataria, R, Kaur, S^{^} and Kaundal, R^*

Deciphering the Complete Human-Monkeypox Virus Interactome: Identifying Immune Responses and Potential Drug Targets. Frontiers in Immunology 14: 1116988.

Duhan, N and Kaundal, R^*

HuCoPIA: An atlas of Human vs SARS-CoV-2 interactome and the comparative analysis with other Coronaviridae family viruses. Viruses 15(2): 492.

Kaur, S^{^}, Seem K, Duhan, N, Kumar, S^*, Kaundal, R^*, and Mohapatra, T

Transcriptome and Physio-Biochemical Profiling Reveals Differential Responses of Rice Cultivars at Reproductive-stage Drought Stress. International Journal of Molecular Sciences 24(2): 1002.

Guevara, D and R^*

ProFeatX: a parallelized protein feature extraction suite for machine learning. Computational and Structural Biotechnology Journal 21: 796-801.

Mahalingam, R^*,Duhan, N, Kaundal, R, Smertenko, A, Nazarov, T and Bregitzer, P

Heat and drought induced transcriptomic changes in barley varieties with contrasting stress response phenotypes. Frontiers in Plant Science 13: 1066421

Kataria, R. and Kaundal, R^*

TRustDB: A comprehensive bioinformatics resource for understanding the complete Wheat - Stem Rust host-pathogen interactome. Database Volume 2022, baac068

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

Kataria, R. and Kaundal, R^*.

Deciphering the Crosstalk Mechanisms of Wheat-Stem Rust pathosystem: Genome-scale prediction Unravels Novel Host Targets. Frontiers in Plant Science. PMID: 35800602

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

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

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.

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 .

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.

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.

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.

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.

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.

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.

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.

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.

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 .

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.

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.

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.

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.

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.

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.

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.

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.

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.

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

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

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.

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.

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.

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.

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.

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.

Kapoor, A.S. and Kaundal, R.

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

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.

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.

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.