Rajeev K. Azad

Previous Scheduled Teaching

Published Intellectual Contributions

Book Chapter

• McGarry, R.C., Ayre, B.G., Azad, R.K. (2024). Cotton meristem transcriptomes: constructing an RNA-Seq pipeline to explore crop architecture regulation. Methods in molecular biology (Clifton, N.J.). Transcriptome Data Analysis. 215-233. New York, Springer Nature.
• Burks, D.J., Azad, R.K. (2020). Identifying auxin response factor genes and their co-expression networks in Medicago truncatula. The Model Legume Medicago truncatula. 802-808. Wiley/Blackwell.
• Burks, D., Azad, R.K., Wen, J., Dickstein, R. (2018). The M. truncatula genome: genomic data availability. Medicago truncatula: Methods and Protocols. Springer.
• Azad, R.K.. (2008). Genes in prokaryotic genomes and their computational prediction. Computational Methods for Understanding Bacterial and Archaeal Genomes. Xu, Y. and Gogarten, J.P. (eds.) Series on Advances in Bioinformatics and Computational Biology, Vol. 7. Imperial College Press, London. ISBN-13: 978-1-86094-982-1, ISBN-10: 1-86094-982-7..
• Azad, R.K., Lawrence, J.G., Thakur, V. and Ramaswamy, R.. (2007). Segmentation of genomic DNA sequences. Advanced Computational Methods for Biocomputing and Bioimaging, Eds. Pham, T.D., Yan, H. and Crane, D.I., Nova Science Publishers, New York. ISBN: 1600212786..
• Borodovsky, M. and Azad, R.K. (2004). Prokaryotic gene identification in silico. Encyclopedia of Genetics, Genomics, Proteomics and Bioinformatics, Part 4. Bioinformatics, Sec 4.2. Gene Finding and Gene Structure, Eds. Dunn, M.J., Jorde, L.B., Little, P.F.R. and Subramaniam, S. John Wiley & Sons, Ltd., New York. ISBN: 0470849746.

Conference Proceeding

• Ramaswamy, R. and Azad, R.K.. (2003). Analysis of DNA sequences through segmentation: Exploring the mosaic via statistical measures. Physica Scripta T106: 21-25. Physica Scripta T106: 21-25..

Journal Article

• Dixson, J.D., Vumma, L., Azad, R.K. (2024). An Analysis of Combined Molecular Weight and Hydrophobicity Similarity between the Amino Acid Sequences of Spike Protein Receptor Binding Domains of Betacoronaviruses and Functionally Similar Sequences from Other Virus Families.. Other. 12 (10)
• Dixson, J.D., Azad, R.K. (2024). Physicochemical Evaluation of Remote Homology in the Twilight Zone.. Other. 1-13.
• De , R., Jani, M., Azad, R.K. (2024). DICEP: An integrative approach to augmenting genomic island detection.. Other. 388 49-58.
• Pusadkar, V., Mazumder, A., Azad, A., Patil, D., Azad, R.K. (2024). Deciphering Microbial Shifts in the Gut and Lung Microbiomes of COVID-19 Patients.. Other. 12 (6)
• Gore, S., Meche, B., Shao, D., Ginnett, B., Zhou, K., Azad, R.K. (2024). DiseaseNet: a transfer learning approach to noncommunicable disease classification.. BMC Bioinformatics. 25 (1) 107.
• Coxe, T., Burks, D.J., Singh, U., Mittler, R., Azad, R.K. (2024). Benchmarking RNA-Seq Aligners at Base-Level and Junction Base-Level Resolution Using the Arabidopsis thaliana Genome.. Other. 13 (5)
• Sengupta, S., Azad, R.K. (2024). An RNA-Seq Data Analysis Pipeline.. Methods in molecular biology (Clifton, N.J.). 2812 1-9.
• Robledo, J., Nahar, S.R., Ruiz, M.A., Hendricks, R.J., Burks, D.J., Ladage, M.L., Kwon, T., Azad, R.K., Padilla, P.A. (2024). RNA Sequencing Experimental Analysis Workflow Using Caenorhabditis elegans.. Methods in molecular biology (Clifton, N.J.). 2812 115-141.
• Kumar, A., Dixson, J., Azad, R.K. (2024). RNA-Seq Analysis of Mammalian Prion Disease.. Methods in molecular biology (Clifton, N.J.). 2812 367-377.
• Ji, L., Zhang, Z., Liu, S., Zhao, L., Li , Q., Xiao, B., Suzuki, N., Burks, D.J., Azad, R.K., Xie, G. (2024). The OsTIL1 lipocalin protects cell membranes from reactive oxygen species damage and maintains the 18:3-containing glycerolipid biosynthesis under cold stress in rice.. The Plant journal : for cell and molecular biology. 117 (1) 72-91.
• De , R., Whiteley, M., Azad, R.K. (2023). A gene network-driven approach to infer novel pathogenicity-associated genes: application to Pseudomonas aeruginosa PAO1.. mSystems. 8 (6) e0047323.
• Almalki, F., Sunuwar, J., Azad, R.K. (2023). Using Machine Learning to Predict Genes Underlying Differentiation of Multipartite and Unipartite Traits in Bacteria.. Other. 11 (11)
• Coxe, T., Azad, R.K. (2023). Silicon versus Superbug: Assessing Machine Learning's Role in the Fight against Antimicrobial Resistance.. Other. 12 (11)
• Pusadkar, V., Azad, R.K. (2023). Benchmarking Metagenomic Classifiers on Simulated Ancient and Modern Metagenomic Data.. Other. 11 (10)
• Burks, D.J., Pusadkar, V., Azad, R.K. (2023). POSMM: an efficient alignment-free metagenomic profiler that complements alignment-based profiling.. Environmental Microbiome. 18 (1) 16.
• Fichman, Y., Xiong, H., Sengupta, S., Morrow, J., Loog, H., Azad, R.K., Hibberd, J.M., Liscum, E., Mittler, R. (2023). Phytochrome B regulates reactive oxygen signaling during abiotic and biotic stress in plants.. The New Phytologist. 237 (5) 1711-1727.
• Almalki, F., Choudhary, M., Azad, R.K. (2023). Analysis of multipartite bacterial genomes using alignment free and alignment-based pipelines.. Archives of Microbiology. 205 (1) 25.
• Sengupta, S., Azad, R.K. (2023). Leveraging comparative genomics to uncover alien genes in bacterial genomes.. Microbial Genomics. 9 (1)
• De , R., Azad, R.K. (2022). Molecular signatures in the progression of COVID-19 severity.. Scientific Reports. 12 (1) 22058.
• Sengupta, S., Azad, R.K. (2022). Reconstructing horizontal gene flow network to understand prokaryotic evolution.. Other. 12 (11) 220169.
• Sunuwar, J., Azad, R.K. (2022). Identification of Novel Antimicrobial Resistance Genes Using Machine Learning, Homology Modeling, and Molecular Docking.. Other. 10 (11)
• Burks, D.J., Azad, R.K. (2022). Mapping Strengths and Weaknesses of Different Clustering Approaches to Deciphering Bacterial Chimerism.. Other. 26 (8) 422-439.
• Gore, S., Azad, R.K. (2022). CancerNet: a unified deep learning network for pan-cancer diagnostics.. BMC Bioinformatics. 23 (1) 229.
• Pandey, R.S., Azad, R.K. (2022). Factors That Influence the Choice of Markov Model Order in Discriminating DNA Sequences from Different Sources.. Other. 26 (6) 348-355.
• Burks, D.J., Sengupta, S., De , R., Mittler, R., Azad, R.K. (2022). The Arabidopsis gene co-expression network.. Other. 6 (4) e396. https://onlinelibrary.wiley.com/doi/10.1002/pld3.396
• Fallatah, W., De , R., Burks, D., Azad, R.K., Jagadeeswaran, P. (2022). Analysis of transcribed sequences from young and mature zebrafish thrombocytes.. PLOS One. 17 (3) e0264776.
• Phillippi, D., Daniel, S., Pusadkar, V., Youngblood, V., Nguyen, K., Azad, R.K., McFarlin, B.K., Lund, A.K. (2022). Inhaled diesel exhaust particles result in microbiome-related systemic inflammation and altered cardiovascular disease biomarkers in C57Bl/6 male mice.. Particle and Fibre Toxicology.
• Pandey, R.S., Azad, R.K. (2022). A Protocol for Horizontally Acquired Metabolic Gene Detection in Algae.. Methods in molecular biology (Clifton, N.J.). 2396 61-69.
• Sengupta, S., Azad, R.K. (2022). A Protocol for Phylogenetic Reconstruction.. Methods in molecular biology (Clifton, N.J.). 2396 35-46.
• Dixson, J.D., Azad, R.K. (2022). A Protocol for Prion Discovery in Plants.. Methods in molecular biology (Clifton, N.J.). 2396 215-226.
• Burks, D.J., Azad, R.K. (2022). RNA-Seq Data Analysis Pipeline for Plants: Transcriptome Assembly, Alignment, and Differential Expression Analysis.. Methods in molecular biology (Clifton, N.J.). 2396 47-60.
• Alharbi, A., Iyer, N., Al Qaryoute, A., Raman, R., Burks, D.J., Azad, R.K., Jagadeeswaran, P. (2021). Role of ribosomal RNA released from red cells in blood coagulation in zebrafish and humans.. Blood Advances. 5 (22) 4634-4647.
• Sunuwar, J., Azad, R.K. (2021). A machine learning framework to predict antibiotic resistance traits and yet unknown genes underlying resistance to specific antibiotics in bacterial strains.. Briefings in Bioinformatics. 22 (6)
• Ibtehaz, N., Ahmed, I., Ahmed, M.S., Rahman, M.S., Azad, R.K., Bayzid, M.S. (2021). SSG-LUGIA: Single Sequence based Genome Level Unsupervised Genomic Island Prediction Algorithm.. Briefings in Bioinformatics. 22 (6)
• Dixson, J.D., Azad, R.K. (2021). A novel predictor of ACE2-binding ability among betacoronaviruses.. Other. 9 (1) 360-373.
• Jani, M., Azad, R.K. (2021). Discovery of mosaic genomic islands in Pseudomonas spp.. Archives of Microbiology. 203 (5) 2735-2742.
• Zandalinas, S.I., Sengupta, S., Fritschi, F.B., Azad, R.K., Nechushtai, R., Mittler, R. (2021). The impact of multifactorial stress combination on plant growth and survival.. The New Phytologist. 230 (3) 1034-1048.
• Cohen, I., Zandalinas, S.I., Fritschi, F.B., Sengupta, S., Fichman, Y., Azad, R.K., Mittler, R. (2021). The impact of water deficit and heat stress combination on the molecular response, physiology, and seed production of soybean.. Physiologia Plantarum. 172 (1) 41-52.
• Daniel, S., Pusadkar, V., McDonald, J.D., Mirpuri, J., Azad, R.K., Goven, A.J., Lund, A. (2021). Traffic generated emissions alter the lung microbiota by promoting the expansion of Proteobacteria in C57Bl/6 mice placed on a high-fat diet.. Ecotoxicology and Environmental Safety.
• Fichman, Y., Zandalinas, S.I., Sengupta, S., Burks, D., Myers, Jr, R.J., Azad, R.K., Mittler, R. (2020). MYB30 Orchestrates Systemic Reactive Oxygen Signaling and Plant Acclimation.. Plant Physiology. 184 (2) 666-675.
• Upadhyay, R.K., Chatterjee, S., Saha, S., Azad, R.K. (2020). Age-group-targeted testing for COVID-19 as a new prevention strategy.. Other. 1-12, DOI: 10.1007/s11071-020-05879-x.
• Yan, C., Cannon, A.E., Watkins, J., Keereetaweep, J., Khan, B.R., Jones, A.M., Blancaflor, E.B., Azad, R.K., Chapman, K.D. (2020). Seedling Chloroplast Responses Induced by N-Linolenoylethanolamine Require Intact G-Protein Complexes.. Plant Physiology. 184 (1) 459-477.
• Burks, D.J., Azad, R.K. (2020). Higher-order Markov models for metagenomic sequence classification.. Other. 36 (14) 4130-4136.
• Cannon, A.E., Yan, C., Burks, D.J., Rao, X., Azad, R.K., Chapman, K.D. (2020). Lipophilic signals lead to organ-specific gene expression changes in Arabidopsis seedlings.. Other. 4 (7) e00242.
• Dixson, J.D., Azad, R.K. (2020). Prions: Roles in Development and Adaptive Evolution.. Other. 88 (5) 427-434.
• Zandalinas, S.I., Fichman, Y., Devireddy, A.R., Sengupta, S., Azad, R.K., Mittler, R. (2020). Systemic signaling during abiotic stress combination in plants.. Proceedings of the National Academy of Sciences of the United States of America. 117 (24) 13810-13820.
• Sturtevant, D., Lu, S., Zhou, Z.W., Shen, Y., Wang, S., Song, J., Zhong, J., Burks, D.J., Yang, Z.Q., Yang, Q., Cannon, A.E., Herrfurth, C., Feussner, I., Borisjuk, L., Munz, E., Verbeck, G.F., Wang, X., Azad, R.K., Singleton, B., Dyer, J.M., Chen, L.L., Chapman, K.D., Guo, L. (2020). The genome of jojoba (Simmondsia chinensis): A taxonomically isolated species that directs wax ester accumulation in its seeds.. Science Advances. 6 (11) eaay3240.
• Zandalinas, S.I., Song, L., Sengupta, S., McInturf, S.A., Grant, D.G., Marjault, H.B., Castro-Guerrero, N.A., Burks, D., Azad, R.K., Mendoza-Cozatl, D.G., Nechushtai, R., Mittler, R. (2020). Expression of a dominant-negative AtNEET-H89C protein disrupts iron-sulfur metabolism and iron homeostasis in Arabidopsis.. The Plant journal : for cell and molecular biology. 101 (5) 1152-1169.
• Balfagón, D., Sengupta, S., Gómez-Cadenas, A., Fritschi, F.B., Azad, R.K., Mittler, R., Zandalinas, S.I. (2019). Jasmonic Acid Is Required for Plant Acclimation to a Combination of High Light and Heat Stress.. Plant Physiology. 181 (4) 1668-1682.
• Azad, R.K., Shulaev, V. (2019). Metabolomics technology and bioinformatics for precision medicine.. Briefings in Bioinformatics. 20 (6) 1957-1971.
• Jani, M., Azad, R.K. (2019). IslandCafe: Compositional Anomaly and Feature Enrichment Assessment for Delineation of Genomic Islands.. Other. 9 (10) 3273-3285.
• Zhuo, C., Rao, X., Azad, R.K., Pandey, R., Xiao, X., Harkelroad, A., Wang, X., Chen, F., Dixon, R. (2019). Enzymatic basis for C-lignin monomer biosynthesis in the seed coat of Cleome hassleriana.. The Plant journal : for cell and molecular biology. 99 506-520.
• Zandalinas, S.I., Sengupta, S., Burks, D., Azad, R.K., Mittler, R. (2019). Identification and characterization of a core set of ROS wave-associated transcripts involved in the systemic acquired acclimation response of Arabidopsis to excess light.. The Plant journal : for cell and molecular biology. 98 (1) 126-141.
• Sturtevant, D., Romsdahl, T.B., Yu, X., Burks, D.J., Azad, R.K., Shanklin, J., Chapman, K. (2019). Tissue-specific differences in metabolites and transcripts contribute to the heterogeneity of ricinoleic acid accumulation in Ricinus communis L. (castor) seeds. Metabolomics. 15 (1) https://api.elsevier.com/content/abstract/scopus_id/85059652912
• Sengupta, S., Nechushtai, R., Jennings, P.A., Onuchic, J.N., Padilla, P.A., Azad, R., Mittler, R. (2018). Phylogenetic analysis of the CDGSH iron-sulfur binding domain reveals its ancient origin. Scientific Reports. 8
• Choudhury, F.K., Devireddy, A.R., Azad, R.K., Shulaev, V., Mittler, R. (2018). Local and Systemic Metabolic Responses during Light-Induced Rapid Systemic Signaling.. Plant Physiology. 178 (4) 1461-1472.
• Choudhury, F.K., Devireddy, A.R., Azad, R.K., Shulaev, V., Mittler, R. (2018). Rapid accumulation of glutathione during light stress in Arabidopsis.. Other. 59 (9) 1817–1826.
• Azad, R.K., Shulaev, V. (2018). Metabolomics technology and bioinformatics for precision medicine.. Other. 20 (6) 1957–1971.
• Jani, M., Sengupta, S., Hu, K., Azad, R.K. (2017). Deciphering pathogenicity and antibiotic resistance islands in methicillin-resistant Staphylococcus aureus genomes.. Other. 7 (12) pii: 170094.
• Burks, D.J., Norris, S., Kauffman, K.M., Joy, A., Arevalo, P., Azad, R.K., Wildschutte, H. (2017). Environmental vibrios represent a source of antagonistic compounds that inhibit pathogenic Vibrio cholerae and Vibrio parahaemolyticus strains.. Other. 6 (5) e504.
• Karmi, O., Holt, S.H., Song, L., Tamir, S., Luo, Y., Bai, F., Adenwalla, A., Darash-Yahana, M., Sohn, Y.S., Jennings, P.A., Azad, R.K., Onuchic, J.N., Morcos, F., Nechushtai, R., Mittler, R. (2017). Interactions between mitoNEET and NAF-1 in cells.. PLOS One. 12 (4) e0175796.
• Inupakutika, M.A., Sengupta, S., Nechushtai, R., Jennings, P.A., Onuchic, J.N., Azad, R.K., Padilla, P.A., Mittler, R. (2017). Phylogenetic analysis of eukaryotic NEET proteins uncovers a link between a key gene duplication event and the evolution of vertebrates.. Scientific Reports. 7 42571.
• Pandey, R.S., Saxena, G., Bhattacharya, D., Qiu, H., Azad, R.K. (2017). Using complementary approaches to identify trans-domain nuclear gene transfers in the extremophile Galdieria sulphuraria (Rhodophyta).. Other. 53 (1) 7-11.
• Burks, D.J., Azad, R.K. (2016). Identification and Network-Enabled Characterization of Auxin Response Factor Genes in Medicago truncatula.. Frontiers in Plant Science. 7 1857.
• Inupakutika, M.A., Sengupta, S., Devireddy, A.R., Azad, R.K., Mittler, R. (2016). The evolution of reactive oxygen species metabolism.. Journal of Experimental Botany. 67 (21) 5933-5943.
• Ladage, M.L., King, S.D., Burks, D.J., Quan, D.L., Garcia, A.M., Azad, R.K., Padilla, P.A. (2016). Glucose or Altered Ceramide Biosynthesis Mediate Oxygen Deprivation Sensitivity Through Novel Pathways Revealed by Transcriptome Analysis in Caenorhabditis elegans.. G3: Genes, Genomes, Genetics. 6 (10) 3149-3160.
• Jani, M., Mathee, K., Azad, R.K. (2016). Identification of Novel Genomic Islands in Liverpool Epidemic Strain of Pseudomonas aeruginosa Using Segmentation and Clustering.. Frontiers in Microbiology. 7 1210.
• Pandey, R.S., Azad, R.K. (2016). Deciphering evolutionary strata on plant sex chromosomes and fungal mating-type chromosomes through compositional segmentation.. Plant Molecular Biology. 90 (4-5) 359-73.
• Veerappan, V., Jani, M., Kadel, K., Troiani, T., Gale, R., Mayes, T., Shulaev, E., Wen, J., Mysore, K.S., Azad, R.K., Dickstein, R. (2016). Rapid identification of causative insertions underlying Medicago truncatula Tnt1 mutants defective in symbiotic nitrogen fixation from a forward genetic screen by whole genome sequencing.. BMC Genomics. 17 141.
• Suzuki, N., Bassil, E., Hamilton, J.S., Inupakutika, M.A., Zandalinas, S.I., Tripathy, D., Luo, Y., Dion, E., Fukui, G., Kumazaki, A., Nakano, R., Rivero, R.M., Verbeck, G.F., Azad, R.K., Blumwald, E., Mittler, R. (2016). ABA Is Required for Plant Acclimation to a Combination of Salt and Heat Stress.. PLOS One. 11 (1) e0147625.
• Holt, S.H., Darash-Yahana, M., Sohn, Y.S., Song, L., Karmi, O., Tamir, S., Michaeli, D., Luo, Y., Paddock, M.L., Jennings, P.A., Onuchic, J.N., Azad, R.K., Pikarsky, E., Cabantchik, I.Z., Nechushtai, R., Mittler, R. (2016). Activation of apoptosis in NAF-1-deficient human epithelial breast cancer cells.. Journal of Cell Science. 129 (1) 155-65.
• Suzuki, N., Devireddy, A.R., Inupakutika, M.A., Baxter, A., Miller, G., Song, L., Shulaev, E., Azad, R.K., Shulaev, V., Mittler, R. (2015). Ultra-fast alterations in mRNA levels uncover multiple players in light stress acclimation in plants.. The Plant journal : for cell and molecular biology. 84 (4) 760-72.
• Mittal, R., Lisi, C.V., Gerring, R., Mittal, J., Mathee, K., Narasimhan, G., Azad, R.K., Yao, Q., Grati, M., Yan, D., Eshraghi, A.A., Angeli, S.I., Telischi, F.F., Liu, X.Z. (2015). Current concepts in the pathogenesis and treatment of chronic suppurative otitis media.. Journal of Medical Microbiology. 64 (10) 1103-16.
• Garcia, A.M., Ladage, M.L., Dumesnil, D.R., Zaman, K., Shulaev, V., Azad, R.K., Padilla, P.A. (2015). Glucose induces sensitivity to oxygen deprivation and modulates insulin/IGF-1 signaling and lipid biosynthesis in Caenorhabditis elegans.. Genetics. 200 (1) 167-84.
• Ré, M.A., Azad, R.K. (2014). Generalization of entropy based divergence measures for symbolic sequence analysis.. PLOS One. 9 (4) e93532.
• Azad, R.K., Li , J. (2013). Interpreting genomic data via entropic dissection.. Other. 41 (1) e23.
• Pandey, R.S., Wilson Sayres, M.A., Azad, R.K. (2013). Detecting evolutionary strata on the human x chromosome in the absence of gametologous y-linked sequences.. Other. 5 (10) 1863-71.
• Azad RK, Li J.. (2012). Interpreting genomic data via entropic dissection. Nucleic Acids Research 2012; Advance Access published October 3, 2012; doi:10.1093/nar/gks917. Related Links: http://nar.oxfordjournals.org/content/41/1/e23.long.
• Azad, R.K., Lawrence, J.G. (2012). Detecting laterally transferred genes.. Methods in molecular biology (Clifton, N.J.). 855 281-308.
• Azad, R.K., Lawrence, J.G. (2012). Detecting laterally transferred genes.. Methods in molecular biology (Clifton, N.J.). 855 281-308.
• Azad, R.K. (2011). Towards more robust methods of alien gene detection. Azad RK, Lawrence JG. Nucleic Acids Res . 2011 May;39(9):e56. Epub 2011 Feb 4. Related Links: http://www.ncbi.nlm.nih.gov/pubmed/21297116.
• Azad, R.K., Lawrence, J.G. (2011). Towards more robust methods of alien gene detection.. Other. 39 (9) e56.
• Azad, R.K. (2009). Detection of genomic islands via segmental genome heterogeneity. Arvey AJ, Azad RK, Raval A, Lawrence JG. Nucleic Acids Res . 2009 Sep;37(16):5255-66. Epub 2009 Jul 9. Related Links: http://www.ncbi.nlm.nih.gov/pubmed/19589805.
• Arvey, A.J., Azad, R.K., Raval, A., Lawrence, J.G. (2009). Detection of genomic islands via segmental genome heterogeneity.. Other. 37 (16) 5255-66.
• Azad, R.K. (2007). Detecting laterally transferred genes: use of entropic clustering methods and genome position. Azad RK, Lawrence JG. Nucleic Acids Res . 2007;35(14):4629-39. Epub 2007 Jun 25. Related Links: http://www.ncbi.nlm.nih.gov/pubmed/17591616.
• Azad, R.K. (2007). Markov models of genome segmentation. Thakur V, Azad RK, Ramaswamy R. Phys Rev E Stat Nonlin Soft Matter Phys . 2007 Jan;75(1 Pt 1):011915. Epub 2007 Jan 17. Related Links: http://www.ncbi.nlm.nih.gov/pubmed/17358192.
• Azad, R.K., Lawrence, J.G. (2007). Detecting laterally transferred genes: use of entropic clustering methods and genome position.. Other. 35 (14) 4629-39.
• Thakur, V., Azad, R.K., Ramaswamy, R. (2007). Markov models of genome segmentation.. Other. 75 (1 Pt 1) 011915.
• Azad, R.K. (2006). The evolutionary origin of Xanthomonadales genomes and the nature of the horizontal gene transfer process. Comas I, Moya A, Azad RK, Lawrence JG, Gonzalez-Candelas F. Mol Biol Evol . 2006 Nov;23(11):2049-57. Epub 2006 Aug 1. Related Links: http://www.ncbi.nlm.nih.gov/pubmed/16882701.
• Comas, I., Moya, A., Azad, R.K., Lawrence, J.G., Gonzalez-Candelas, F. (2006). The evolutionary origin of Xanthomonadales genomes and the nature of the horizontal gene transfer process.. Other. 23 (11) 2049-57.
• Azad, R.K. (2005). Use of artificial genomes in assessing methods for atypical gene detection. Azad RK, Lawrence JG. PLoS Comput Biol . 2005 Nov;1(6):e56. Epub 2005 Nov 11. Related Links: http://www.ncbi.nlm.nih.gov/pubmed/16292353.
• Azad, R.K., Lawrence, J.G. (2005). Use of artificial genomes in assessing methods for atypical gene detection.. PLOS Computational Biology. 1 (6) e56.
• .. (2004). Effects of choice of DNA sequence model structure on gene identification accuracy. Azad RK, Borodovsky M. Bioinformatics . 2004 May 1;20(7):993-1005. Epub 2004 Jan 29. Related Links: http://www.ncbi.nlm.nih.gov/pubmed/14751980.
• Azad, R.K. (2004). Probabilistic methods of identifying genes in prokaryotic genomes: connections to the HMM theory. Azad RK, Borodovsky M. Brief Bioinform . 2004 Jun;5(2):118-30. Related Links: http://www.ncbi.nlm.nih.gov/pubmed/15260893.
• Azad, R.K., Rao, J.S and Ramaswamy, R.. (2004). Symbol sequence analysis of climatic time signals. Nonlinear Analysis: Real World Applications 5: 487-500. Nonlinear Analysis: Real World Applications 5: 487-500..
• Azad, R.K., Borodovsky, M. (2004). Probabilistic methods of identifying genes in prokaryotic genomes: connections to the HMM theory.. Other. 5 (2) 118-30.
• Azad, R.K., Borodovsky, M. (2004). Effects of choice of DNA sequence model structure on gene identification accuracy.. Other. 20 (7) 993-1005.
• Azad, R.K., Rao, J.S and Ramaswamy, R.. (2002). Information-entropic analysis of chaotic time series: Determination of time-delays and dynamical coupling. Chaos, Solitons & Fractals 14: 633-641. Chaos, Solitons & Fractals 14: 633-641..
• Azad, R.K. (2002). Segmentation of genomic DNA through entropic divergence: power laws and scaling. Azad RK, Bernaola-Galván P, Ramaswamy R, Rao JS. Phys Rev E Stat Nonlin Soft Matter Phys . 2002 May;65(5 Pt 1):051909. Epub 2002 May 8. Related Links: http://www.ncbi.nlm.nih.gov/pubmed/12059595.
• Azad, R.K. (2002). Simplifying the mosaic description of DNA sequences. Azad RK, Rao JS, Li W, Ramaswamy R. Phys Rev E Stat Nonlin Soft Matter Phys . 2002 Sep;66(3 Pt 1):031913. Epub 2002 Sep 25. Related Links: http://www.ncbi.nlm.nih.gov/pubmed/12366158.
• Azad, R.K., Rao, J.S., Li , W., Ramaswamy, R. (2002). Simplifying the mosaic description of DNA sequences.. Other. 66 (3 Pt 1) 031913.
• Azad, R.K., Bernaola-Galván, P., Ramaswamy, R., Rao, J.S. (2002). Segmentation of genomic DNA through entropic divergence: power laws and scaling.. Other. 65 (5 Pt 1) 051909.

Lab Protocol Series- Methods in Molecular Biology

• Azad, R.K. (2024). Transcriptome Data Analysis. Springer Nature.

Review

• Jani, M., Azad, R.K. (2013). Information entropy based methods for genome comparison. Other. 3 (2) NY, USA, ACM New York.

Contracts, Grants and Sponsored Research

Contract

• Azad, R.K. (Principal), "Analysis of RNA-Seq data from blood samples of COVID-19 patients and individuals vaccinated with mRNA COVID-19 vaccines (Contract start date: Sep 1, 2025)," sponsored by Neo7Bioscience Inc., Other, $210000 Funded. (2024 - 2029).
• Azad, R.K., "MBI Early Career Award: Spring 2016- Dynamics of biologically inspired networks," sponsored by Mathematical Biosciences Institute, The Ohio State University (Through NSF), Federal, $20000 Funded. (2016 - 2016).

Fellowship

• Azad, R.K., "Deciphering evolutionary strata and inactivation domains on sex chromosomes," sponsored by University of North Texas (Junior Faculty Summer Research Fellowship), University of North Texas, $2500 Funded. (2013 - 2013).

Grant - Research

• Azad, R.K., Padilla, P. (Principal), Burggren, W. (Co-Principal), "G-RISE at the University of North Texas," sponsored by National Institutes of Health, Federal, $2187228 Funded. (2021 - 2026).
• Lund, A.K. (Principal), Azad, R.K. (Co-Principal), "The Renin-Angiotensin System in Air Pollution-Mediated Exacerbation of Obesity," sponsored by National Institute of Health (NIH) / National Institute of Environmental Health and Safety (NIEHS), Federal, $437496 Funded. (2023 - 2026).
• Xiao, T. (Principal), Ding, J. (Co-Principal), Albert, M.V. (Supporting), Alam, Z.S. (Supporting), Hartmann, F. (Supporting), Wang, Y. (Supporting), Liang, L. (Supporting), Chen, H. (Supporting), Du, J. (Supporting), Azad, R.K. (Supporting), "NSF REU site: Beyond Language: Training to Create and Share Vector Embeddings across Application," sponsored by NSF, Federal, $403547 Funded. (2023 - 2025).
• Azad, R.K. (Co-Principal), Mittler, R. (Principal), "Leaf-to-leaf communication during acclimation to multiple stresses," sponsored by National Science Foundation, Federal, $1080011 Funded. (2019 - 2024).
• Jagadeeswaran, P. (Principal), Azad, R.K. (Co-Principal), "Regulators of von Willebrand Factor Levels," sponsored by NIH, Federal, $891000 Funded. (2021 - 2024).
• Henard, C.A. (Principal), Azad, R.K. (Co-Principal), "Characterization of the carbon dioxide starvation response in a promising greenhouse gas mitigation biocatalyst.," sponsored by BioDiscovery Institute, University of North Texas, $30000 Funded. (2023 - 2024).
• Azad, R.K. (Other), Zhao, H. (Principal), Albert, M. (Co-Principal), "REU Site: Interdisciplinary Research Experience on Accelerated Deep Learning through A Hardware-Software Collaborative Approach," sponsored by National Science Foundation, Federal, $389725 Funded. (2021 - 2024).
• Jagadeeswaran, P. (Principal), Azad, R.K. (Co-Principal), "Zebrafish Thrombopoiesis," sponsored by NIH, Federal, $418980 Funded. (2018 - 2021).
• Azad, R.K. (Principal), Padilla, P.A. (Principal), "Molecular consequences of glucose diet and altered ceramide species impacting oxygen deprivation responses," sponsored by National Institutes of Health, Federal, $445343 Funded. (2016 - 2020).
• Azad, R.K. (Co-Principal), Mittler, R. (Principal), "NSF/MCB-BSF: Integrating ROS, redox and cell metabolism across plant and animal cells," sponsored by National Science Foundation, Federal, $854627 Funded. (2016 - 2020).
• Dixon, R. (Principal), Azad, R.K., Chen, F., Boyd, R.R., D'Souza, N.A., "Biosynthesis, regulation and engineering of C-lignin," sponsored by National Science Foundation, Federal, $833722 Funded. (2015 - 2019).
• Azad, R.K. (Co-Principal), Mittler, R. (Principal), Shulaev, V. (Co-Principal), "Ultrafast omics reveals key players in the response of plants to abiotic stress," sponsored by National Science Foundation, Federal, $720000 Funded. (2014 - 2019).
• Jagadeeswaran, P. (Principal), Azad, R.K. (Principal), "Regulators of von Willebrand Factor Levels," sponsored by National Institutes of Health, FED, Funded. (2021 - 2024).
• Azad, R.K. (Principal), "Leaf-to-leaf communication during acclimation to multiple stresses," sponsored by University of Missouri-Columbia, NFP, Funded. (2019 - 2023).
• Jagadeeswaran, P. (Principal), Azad, R.K. (Co-Principal), "Zebrafish Thrombopoiesis," sponsored by National Institutes of Health, FED, Funded. (2018 - 2022).
• Padilla, P.A. (Principal), Azad, R.K. (Co-Principal), "Molecular Consequences of Glucose Diet and Altered Ceramide Species Impacting Oxygen Deprivation Responses," sponsored by National Institutes of Health, FED, Funded. (2016 - 2020).
• Azad, R.K. (Principal), "MCB-BSF: Integrating ROS, redox and cell metabolism across plant and animal cells," sponsored by University of Missouri-Columbia, NFP, Funded. (2018 - 2020).
• Chen, F. (Co-Principal), D'Souza, N.A. (Principal), Azad, R.K. (Principal), Dixon, R.A. (Principal), Boyd, R.R. (Co-Principal), "Biosynthesis, Regulation and Engineering of C-Lignin," sponsored by National Science Foundation, FED, Funded. (2015 - 2019).
• Azad, R.K. (Principal), Mittler, R. (Principal), "NSF/MCB-BSF: Integrating ROS, redox and cell metabolism across plant and animal cells," sponsored by National Science Foundation, FED, Funded. (2016 - 2018).
• Azad, R.K. (Principal), Mittler, R. (Principal), Shulaev, V. (Co-Principal), "Ultrafast Omics Reveals Key Players in the Response of Plants to Abiotic Stress," sponsored by National Science Foundation, FED, Funded. (2014 - 2018).
• Azad, R.K. (Principal), "MBI Early Career Award: Spring 2016- Dynamics of Biologically Inspired Networks," sponsored by The Ohio State University, NFP, Funded. (2016 - 2016).