Publications

A gene network driven approach to infer novel pathogenicity associated genes: Application to Pseudomonas aeruginosa PAO1.
De R, Whiteley M, Azad RK (2023)

Remote homology: An analysis of functional/structural similarity between betacoronaviruses and other virus families
Dixson JD, Vumma L, Azad RK (2023)

Published

POSMM: an efficient alignment-free metagenomic profiler that complements alignment-based profiling.
Burks DJ, Pusadkar V, Azad RK.
Environ Microbiome. 2023 Mar 8;18(1):16.
DOI: 10.1186/s40793-023-00476-y.

Leveraging comparative genomics to uncover alien genes in bacterial genomes.
Sengupta S, Azad RK.
Microb Genom. 2023 Jan;9(1):mgen000939.
DOI: 10.1099/mgen.0.000939.

Molecular signatures in the progression of COVID-19 severity.
De R, Azad RK.
Sci Rep. 2022 Dec 21;12(1):22058.
DOI: 10.1038/s41598-022-26657-2.

Analysis of multipartite bacterial genomes using alignment free and alignment-based pipelines.
Almalki F, Choudhary M, Azad RK.
Arch Microbiol. 2022 Dec 14;205(1):25.
DOI: 10.1007/s00203-022-03354-2.

Reconstructing horizontal gene flow network to understand prokaryotic evolution.
Sengupta S, Azad RK.
Open Biol. 2022 Nov;12(11):220169.
DOI: 10.1098/rsob.220169

Phytochrome B regulates reactive oxygen signaling during abiotic and biotic stress in plants.
Fichman Y, Xiong H, Sengupta S, Morrow J, Loog H, Azad RK, Hibberd JM, Liscum E, Mittler R.
New Phytol. 2023 Mar;237(5):1711-1727.
DOI: 10.1111/nph.18626.

Identification of Novel Antimicrobial Resistance Genes Using Machine Learning, Homology Modeling, and Molecular Docking.
Sunuwar J, Azad RK.
Microorganisms. 2022 Oct 23;10(11):2102.
DOI: 10.3390/microorganisms10112102.

Mapping Strengths and Weaknesses of Different Clustering Approaches to Deciphering Bacterial Chimerism.
Burks DJ, Azad RK.
OMICS. 2022 Aug;26(8):422-439.
DOI: 10.1089/omi.2022.0062.

CancerNet: a unified deep learning network for pan-cancer diagnostics.
Gore S, Azad RK.
BMC Bioinformatics. 2022 Jun 13;23(1):229.
DOI: 10.1186/s12859-022-04783-y.

Factors That Influence the Choice of Markov Model Order in Discriminating DNA Sequences from Different Sources.
Pandey RS, Azad RK.
OMICS. 2022 Jun;26(6):348-355.
DOI: 10.1089/omi.2022.0043.

The Arabidopsis gene co-expression network.
Burks DJ, Sengupta S, De R, Mittler R, Azad RK.
Plant Direct. 2022 Apr 26;6(4):e396.
doi: 10.1002/pld3.396.

Analysis of transcribed sequences from young and mature zebrafish thrombocytes.
Fallatah W, De R, Burks D, Azad RK, Jagadeeswaran P.
PLoS One. 2022 Mar 23;17(3):e0264776.
DOI: 10.1371/journal.pone.0264776. eCollection 2022.

Inhaled diesel exhaust particles result in microbiome-related systemic inflammation and altered cardiovascular disease biomarkers in C57Bl/6 male mice.
Phillippi DT, Daniel S, Pusadkar V, Youngblood VL, Nguyen KN, Azad RK, McFarlin BK, Lund AK.
Part Fibre Toxicol. 2022 Feb 9;19(1):10.
DOI: 10.1186/s12989-022-00452-3.

A novel predictor of ACE2-binding ability among betacoronaviruses.
Dixson JD, Azad RK.
Evol Med Public Health. 2021 Oct 13;9(1):360-373.
DOI: 10.1093/emph/eoab032. eCollection 2021

A Protocol for Prion Discovery in Plants.
Dixson JD, Azad RK.
Methods Mol Biol. 2022;2396:215-226.
DOI: 10.1007/978-1-0716-1822-6_16.

A Protocol for Horizontally Acquired Metabolic Gene Detection in Algae.
Pandey RS, Azad RK.
Methods Mol Biol. 2022;2396:61-69.
DOI: 10.1007/978-1-0716-1822-6_6.

RNA-Seq Data Analysis Pipeline for Plants: Transcriptome Assembly, Alignment, and Differential Expression Analysis.
Burks DJ, Azad RK.
Methods Mol Biol. 2022;2396:47-60.
DOI: 10.1007/978-1-0716-1822-6_5.

A Protocol for Phylogenetic Reconstruction.
Sengupta S, Azad RK.
Methods Mol Biol. 2022;2396:35-46.
DOI: 10.1007/978-1-0716-1822-6_4.

Role of ribosomal RNA released from red cells in blood coagulation in zebrafish and humans.
Alharbi A, Iyer N, Al Qaryoute A, Raman R, Burks DJ, Azad RK, Jagadeeswaran P.
Blood Adv. 2021 Nov 23;5(22):4634-4647.
DOI: 10.1182/bloodadvances.2020003325.

SSG-LUGIA: Single Sequence based Genome Level Unsupervised Genomic Island Prediction Algorithm.
Ibtehaz N, Ahmed I, Ahmed MS, Rahman MS, Azad RK, Bayzid MS.
Brief Bioinform. 2021 Nov 5;22(6):bbab116.
DOI: 10.1093/bib/bbab116.

A machine learning framework to predict antibiotic resistance traits and yet unknown genes underlying resistance to specific antibiotics in bacterial strains.
Sunuwar J, Azad RK.
Brief Bioinform. 2021 Nov 5;22(6):bbab179.
DOI: 10.1093/bib/bbab179.

Discovery of mosaic genomic islands in Pseudomonas spp.
Jani M, Azad RK.
Arch Microbiol. 2021 Jul;203(5):2735-2742.
DOI: 10.1007/s00203-021-02253-2.

Traffic generated emissions alter the lung microbiota by promoting the expansion of Proteobacteria in C57Bl/6 mice placed on a high-fat diet.
Daniel S, Pusadkar V, McDonald J, Mirpuri J, Azad RK, Goven A, Lund AK.
Ecotoxicol Environ Saf. 2021 Apr 15;213:112035.
DOI: 10.1016/j.ecoenv.2021.112035.

The impact of multifactorial stress combination on plant growth and survival.
Zandalinas SI, Sengupta S, Fritschi FB, Azad RK, Nechushtai R, Mittler R.
New Phytol. 2021 May;230(3):1034-1048.
DOI: 10.1111/nph.17232.

The impact of water deficit and heat stress combination on the molecular response, physiology, and seed production of soybean.
Cohen I, Zandalinas SI, Fritschi FB, Sengupta S, Fichman Y, Azad RK, Mittler R.
Physiol Plant. 2021 May;172(1):41-52.
DOI: 10.1111/ppl.13269.

Age-group-targeted testing for COVID-19 as a new prevention strategy.
Upadhyay RK, Chatterjee S, Saha S, Azad RK.
Nonlinear Dyn. 2020;101(3):1921-1932.
DOI: 10.1007/s11071-020-05879-x. Epub 2020 Sep 1.

Lipophilic signals lead to organ‐specific gene expression changes in Arabidopsis seedlings
Ashley E. Cannon, Chengshi Yan, David J. Burks, Xiaolan Rao, Rajeev K. Azad, Kent D. Chapman
Plant DirectVolume 4, Issue 7. First published: 15 July 2020
https://doi.org/10.1002/pld3.242

MYB30 orchestrates systemic reactive oxygen signaling and plant acclimation.
Fichman Y, Zandalinas SI, Sengupta S, Burks D, Myers RJ, Azad R, Mittler R.
Plant Physiol. 2020 Jul 22:pp.00859.2020.
DOI: 10.1104/pp.20.00859.

Seedling chloroplast responses induced by N-linolenoylethanolamine require intact G-protein complexes.
Yan C, Cannon A, Watkins J, Keereetaweep J, Khan BR, Jones AM, Blancaflor EB, Azad R, Chapman KD.
Plant Physiol. 2020 Jul 14:pp.01552.2019.
DOI: 10.1104/pp.19.01552.

Higher-order Markov models for metagenomic sequence classification.
Burks DJ, Azad RK.
Bioinformatics. 2020 Aug 15;36(14):4130-4136.
DOI: 10.1093/bioinformatics/btaa562.

Systemic signaling during abiotic stress combination in plants.
Zandalinas SI, Fichman Y, Devireddy AR, Sengupta S, Azad RK, Mittler R.
Proc Natl Acad Sci U S A. 2020 Jun 16;117(24):13810-13820.
DOI: 10.1073/pnas.2005077117.

Prions: Roles in Development and Adaptive Evolution.
Dixson JD, Azad RK.
J Mol Evol. 2020 Jul;88(5):427-434.
DOI: 10.1007/s00239-020-09944-2.

The genome of jojoba (Simmondsia chinensis): A taxonomically isolated species that directs wax ester accumulation in its seeds.
Sturtevant D, Lu S, Zhou ZW, Shen Y, Wang S, Song JM, Zhong J, Burks DJ, Yang ZQ, Yang QY, Cannon AE, Herrfurth C, Feussner I, Borisjuk L, Munz E, Verbeck GF, Wang X, Azad RK, Singleton B, Dyer JM, Chen LL, Chapman KD, Guo L.
Sci Adv. 2020 Mar 11;6(11):eaay3240.
DOI: 10.1126/sciadv.aay3240.

Identifying auxin response factor genes and their co-expression networks in Medicago truncatula.
Burks DJ, Azad RK.
In: The Model Legume Medicago truncatula. de Bruijn FJ (Ed.). Wiley/Blackwell. 2020. https://doi.org/10.1002/9781119409144.ch98.

Jasmonic Acid Is Required for Plant Acclimation to a Combination of High Light and Heat Stress.
Balfagón D, Sengupta S, Gómez-Cadenas A, Fritschi FB, Azad RK, Mittler R, Zandalinas SI.
Plant Physiol. 2019 Dec;181(4):1668-1682.
DOI: 10.1104/pp.19.00956

Expression of a dominant-negative AtNEET-H89C protein disrupts iron-sulfur metabolism and iron homeostasis in Arabidopsis.
Zandalinas SI, Song L, Sengupta S, McInturf S, Grant DG, Marjault HB, Castro-Guerrero NA, Burks D, Azad RK, Mendoza Cozatl DG, Nechushtai R, Mittler R.
Plant J. 2020 Mar;101(5):1152-1169. doi: 10.1111/tpj.14581.
DOI: 10.1111/tpj.14581

IslandCafe: Compositional Anomaly and Feature Enrichment Assessment for Delineation of Genomic Islands.
Jani M, Azad RK.
G3 (Bethesda). 2019 Aug 6. pii: g3.400562.2019.
DOI: 10.1534/g3.119.400562

Enzymatic basis for C-lignin monomer biosynthesis in the seed coat of Cleome hassleriana.
Zhuo C, Rao X, Azad R, Pandey R, Xiao X, Harkelroad A, Wang X, Chen F, Dixon RA
Plant J. 2019 Apr 19.
DOI: 10.1111/tpj.14340

Tissue-specific differences in metabolites and transcripts contribute to the heterogeneity of ricinoleic acid accumulation in Ricinus communis L. (castor) seeds.
Sturtevant D, Romsdahl T, Yu X, Burks D, Azad RK, Shanklin J, Chapman K
Metabolomics (2019)
DOI: 10.1007/s11306-018-1464-3

Identification and characterization of a core set of ROS wave-associated transcripts involved in the systemic acquired acclimation response of Arabidopsis to excess light.
Zandalinas SI, Sengupta S, Burks D, Azad RK, Mittler R
The Plant Journal (2018)
DOI: 10.1111/tpj.14205

Local and Systemic Metabolic Responses during Light-Induced Rapid Systemic Signaling.
Choudhury FK, Devireddy AR, Azad RK, Shulaev V, Mittler R
Plant Physiology (2018)
DOI: 10.1104/pp.18.01031

Rapid accumulation of glutathione during light stress in Arabidopsis.
Choudhury FK, Devireddy AR, Azad RK, Shulaev V, Mittler R
Plant & Cell Physiology (2018)
DOI: 10.1093/pcp/pcy101

Phylogenetic analysis of the CDGSH iron-sulfur binding domain reveals its ancient origin.
Sengupta S, Nechushtai R, Jennings PA, Onuchic JN, Padilla PA, Azad RK, Mittler R
Scientific Reports (2018)
DOI: 10.1038/s41598-018-23305-6

The M. truncatula genome: genomic data availability.
Burks DJ, Azad RK, Dickstein R
Methods in Molecular Biology (2018)
DOI: 10.1007/978-1-4939-8633-0_3

Metabolics technology and bioinformatics for precision medicine.
Azad RK, Shulaev V
Briefings in Bioinformatics (2018)
DOI: 10.1093/bib/bbx170

Deciphering pathogenicity and antibiotic resistance islands in methicillin resistant Staphylococcus aureus genomes.
Jani M, Sengupta S, Hu K, Azad RK
Open Biology (2017)
DOI: 10.1098/rsob.170094

Environmental Vibrios antagonize pathogenic Vibrio cholerae and Vibrio parahaemolyticus strains.
Burks DJ, Norris S, Kauffman K, Joy A, Arevalo P, Azad RK, Wildschutte H
Microbiology Open (2017)
DOI: 10.1002/mbo3.504

Interactions between mitoNEET and NAF-1 in cells.
Karmi O, Holt SH, Song L, Tamir S, Luo Y, Bai F, Adenwalla A, Darash-Yahana M, Sohn YS, Jennings PA, Azad RK, Onuchic JN, Morcos F, Nechushtai R, Mittler R
PLOS One (2017)
DOI: 10.1371/journal.pone.0175796

Phylogenetic analysis of eukaryotic NEET proteins uncovers a link between a key gene duplication event and the evolution of vertebrates.
Inupakutika M, Sengupta S, Nechushtai R, Jennings P, Onuchic J, Azad RK, Padilla P, Mittler R
Scientific Reports (2017)
DOI: 10.1038/srep42571

Identifying auxin response factor genes and their co-expression networks in Medicago truncatula.
Burks DJ, Azad RK
Frontiers in Plant Science. (2016)
DOI: 10.3389/fpls.2016.01857

The evolution of reactive oxygen species metabolism.
Inupakutika MA, Sengupta S, Devireddy AR, Azad RK, Mittler R.
Journal of experimental botany. 2016;
DOI: 10.1093/jxb/erw382

Glucose or Altered Ceramide Biosynthesis Mediate Oxygen Deprivation Sensitivity Through Novel Pathways Revealed by Transcriptome Analysis in Caenorhabditis elegans.
Ladage ML, King SD, Burks DJ, Quan DL, Garcia AM, Azad RK, Padilla PA.
G3 (Bethesda, Md.). 2016; 6(10):3149-3160.
DOI: 10.1534/g3.116.031583

Using complementary approaches to identify trans-domain nuclear gene transfers in the extremophile Galdieria sulphuraria (Rhodophyta).
Pandey RS, Saxena G, Bhattacharya D, Qiu H, Azad RK.
Journal of phycology. 2016;
DOI: 10.1111/jpy.12466

Identification of Novel Genomic Islands in Liverpool Epidemic Strain of Pseudomonas aeruginosa Using Segmentation and Clustering.
Jani M, Mathee K, Azad RK.
Frontiers in microbiology. 2016; 7:1210.
DOI: 10.3389/fmicb.2016.01210

Deciphering evolutionary strata on plant sex chromosomes and fungal mating-type chromosomes through compositional segmentation.
Pandey RS, Azad RK.
Plant molecular biology. 2016; 90(4-5):359-73.
DOI: 10.1007/s11103-015-0422-y

Rapid identification of causative insertions underlying Medicago truncatula Tnt1 mutants defective in symbiotic nitrogen fixation from a forward genetic screen by whole genome sequencing.
Veerappan V, Jani M, Kadel K, Troiani T, Gale R, Mayes T, Shulaev E, Wen J, Mysore KS, Azad RK, Dickstein R.
BMC genomics. 2016; 17:141.
DOI: 10.1186/s12864-016-2452-5

ABA Is Required for Plant Acclimation to a Combination of Salt and Heat Stress.
Suzuki N, Bassil E, Hamilton JS, Inupakutika MA, Zandalinas SI, Tripathy D, Luo Y, Dion E, Fukui G, Kumazaki A, Nakano R, Rivero RM, Verbeck GF, Azad RK, Blumwald E, Mittler R.
PloS one. 2016; 11(1):e0147625.
DOI: 10.1371/journal.pone.0147625

Activation of apoptosis in NAF-1-deficient human epithelial breast cancer cells.
Holt SH, Darash-Yahana M, Sohn YS, Song L, Karmi O, Tamir S, Michaeli D, Luo Y, Paddock ML, Jennings PA, Onuchic JN, Azad RK, Pikarsky E, Cabantchik IZ, Nechushtai R, Mittler R.
Journal of cell science. 2016; 129(1):155-65.
DOI: 10.1242/jcs.178293

Ultra-fast alterations in mRNA levels uncover multiple players in light stress acclimation in plants.
Suzuki N, Devireddy AR, Inupakutika MA, Baxter A, Miller G, Song L, Shulaev E, Azad RK, Shulaev V, Mittler R.
The Plant journal : for cell and molecular biology. 2015; 84(4):760-72.
DOI: 10.1111/tpj.13039

Current concepts in the pathogenesis and treatment of chronic suppurative otitis media.
Mittal R, Lisi CV, Gerring R, Mittal J, Mathee K, Narasimhan G, Azad RK, Yao Q, Grati M, Yan D, Eshraghi AA, Angeli SI, Telischi FF, Liu XZ.
Journal of medical microbiology. 2015; 64(10):1103-16.
DOI: 10.1099/jmm.0.000155

Glucose induces sensitivity to oxygen deprivation and modulates insulin/IGF-1 signaling and lipid biosynthesis in Caenorhabditis elegans.
Garcia AM, Ladage ML, Dumesnil DR, Zaman K, Shulaev V, Azad RK, Padilla PA.
Genetics. 2015; 200(1):167-84. DOI: 10.1534/genetics.115.174631
DOI: 10.1534/genetics.115.174631

Generalization of entropy based divergence measures for symbolic sequence analysis.
Ré MA, Azad RK.
PloS one. 2014; 9(4):e93532.
DOI: 10.1371/journal.pone.0093532

Interpreting genomic data via entropic dissection.
Azad RK, Li J.
Nucleic acids research. 2013; 41(1):e23.
DOI: 10.1093/nar/gks917

Information entropy based methods for genome comparison
Jani M, Azad RK.
ACM SIGBioinformatics Record. 2013; 3(2):2.
DOI: 10.1145/2500124.2500126

Alien gene transfer in Crop Plants: Innovations, Methods and Risk Assessment
Azad RK, Mishra NK, Ahmed F, Kaundal R. Pratap A, Kumar J, editors.
New York: Springer Science + Business Media; 2013.
Bioinformatics approaches to deciphering alien gene transfer: a comprehensive analysis
DOI: 10.1007/978-1-4614-8585-8

Detecting evolutionary strata on the human x chromosome in the absence of gametologous y-linked sequences.
Pandey RS, Wilson Sayres MA, Azad RK.
Genome biology and evolution. 2013; 5(10):1863-71.
DOI: 10.1093/gbe/evt139

Detecting laterally transferred genes.
Azad RK, Lawrence JG.
Methods in molecular biology (Clifton, N.J.). 2012; 855:281-308.
DOI: 10.1007/978-1-61779-582-4_10

Towards more robust methods of alien gene detection.
Azad RK, Lawrence JG.
Nucleic acids research. 2011; 39(9):e56.
DOI: 10.1093/nar/gkr059

Detection of genomic islands via segmental genome heterogeneity.
Arvey AJ, Azad RK, Raval A, Lawrence JG.
Nucleic acids research. 2009; 37(16):5255-66.
DOI: 10.1093/nar/gkp576

Computational Methods for Understanding Bacterial and Archaeal Genomes
Azad RK. Xu Y, Gogarten JP, editors.
London: Imperial College Press; 2008. Chapter 2,
Genes in prokaryotic genomes and their computational prediction

Advanced Computational Methods for Biocomputing and Bioimaging
Azad RK, Lawrence JG, Thakur V, Ramaswamy R. Pham TD, Yan H, Crane DI, editors.
New York: Nova Science Publishers; 2007.
Segmentation of genomic DNA sequences

Detecting laterally transferred genes: use of entropic clustering methods and genome position.
Azad RK, Lawrence JG.
Nucleic acids research. 2007; 35(14):4629-39.
DOI: 10.1093/nar/gkm204

Markov models of genome segmentation.
Thakur V, Azad RK, Ramaswamy R.
Physical review. E, Statistical, nonlinear, and soft matter physics. 2007; 75(1 Pt 1):011915.
DOI: 10.1103/PhysRevE.75.011915

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.
Molecular biology and evolution. 2006; 23(11):2049-57.
DOI: 10.1093/molbev/msl075

Use of artificial genomes in assessing methods for atypical gene detection.
Azad RK, Lawrence JG.
PLoS computational biology. 2005; 1(6):e56.
DOI: 10.1371/journal.pcbi.0010056

Probabilistic methods of identifying genes in prokaryotic genomes: connections to the HMM theory.
Azad RK, Borodovsky M.
Briefings in bioinformatics. 2004; 5(2):118-30.
DOI: 10.1093/bib/5.2.118

Effects of choice of DNA sequence model structure on gene identification accuracy.
Azad RK, Borodovsky M.
Bioinformatics (Oxford, England). 2004; 20(7):993-1005.
DOI: 10.1093/bioinformatics/bth028

Symbol Sequence Analysis of Climatic Time Signals
Azad RK, Rao JS, Ramaswamy R.
Nonlinear Analysis: Real World Applications. 2004; 5:487-500.
DOI: 10.1016/j.nonrwa.2003.11.003

Encyclopedia of Genetics, Genomics, Proteomics and Bioinformatics
Borodovsky M, Azad RK.
Dunn MJ, Jorde LB, Little PFR, Subramaniam S, editors. New York: John Wiley & Sons, Ltd.; 2004.
Prokaryotic gene identification in silico
DOI: 10.1002/047001153X

Analysis of DNA sequences through segmentation: Exploring the mosaic via statistical measures
Ramaswamy R, Azad RK.
Physica Scripta . 2003; T106:21-25.
DOI: 10.1238/Physica.Topical.106a00021

Simplifying the mosaic description of DNAsequences. Physical review. E, Statistical, nonlinear, and soft matter physics.
Azad RK, Rao JS, Li W, Ramaswamy R.
2002; 66(3 Pt 1):031913.
DOI: 10.1103/PhysRevE.66.031913

Segmentation of genomic DNA through entropic divergence: power laws and scaling.
Azad RK, Bernaola-Galván P, Ramaswamy R, Rao JS.
Physical review. E, Statistical, nonlinear, and soft matter physics. 2002; 65(5 Pt 1):051909.
DOI: 10.1103/PhysRevE.65.051909

Information--entropic analysis of chaotic time series: Determination of time--delays and dynamical coupling.
Azad RK, Rao JS, Ramaswamy R.
Chaos, Solitons & Fractals. 2002; 14:633-641.
DOI: 10.1016/S0960-0779(02)00003-6

Publications

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Published