Publications
Journal articles
Muley VY*, Delahaye-Duriez Andree* (2025): Transcriptional coordination between intergenic RNA polymerase II-bound regions and nearby genes reveals functional specialization and disease association in peripheral blood, Computational and Structural Biotechnology Journal, 2025 Nov 26:27(1):5523-5536
Jamdhade AR, Jadhav BR, Muley VY, Hivrale VK* (2025): Exploring the Biochemical Profile of Pheretima posthuma Intestinal Proteases: Unlocking Industrial and Biotechnological Opportunities, Industrial Biotechnology, 2025 Apr 7
Singh MS, Pyati A, Rubi RD, Subramanian R, Muley VY, Ahmed A, Yellaboina S*. (2024): Systems-wide view of host-pathogen interactions across COVID-19 severities using integrated omics analysis, iScience, 2024 Mar 15;27(3):109087
Rakshit S, More A, Gaikwad S, Gade A, Seniya C, Muley VY, Mukherjee A*, Kamble K*. (2024): Role of Diosgenin in suppression of HIV-1 replication: An in vitro preclinical study, Heliyon, 2024 Jan 12;10(2):e24350
Muley VY. (2023): Editorial: Gene expression: epigenetic and transcriptional regulation in neurodegenerative diseases and ageing, Front Neurosci. 2023 Dec 12;17:1342890.
Robles-Rodríguez C, Muley VY, González-Dávalos LM, Shimada A, Varela-Echavarría A, Mora O*. (2023): Microbial colonization dynamics of the postnatal digestive tract of Bos indicus calves, Animal Science Journal. 2023 Sept 5;94(1):e13872
Muley VY*, König R. (2022): Human transcriptional gene regulatory network compiled from 14 data resources, Biochimie, 2022 Feb 1;193:115-125
Aviña-Padilla K, Ramírez-Rafael JA, Herrera-Oropeza GE, Muley VY, Valdivia DI, Díaz-Valenzuela E, García-García A, Varela-Echavarría A, Hernández-Rosales M. (2021): Evolutionary Perspective and Expression Analysis of Intronless Genes Highlight the Conservation of Their Regulatory Role, Frontiers in Genetics, 2021 Jul 9;12:654256
Muley VY*, López-Victorio CJ, Ayala-Sumuano JT, González-Gallardo A, González-Santos L, Lozano-Flores C, Wray G, Hernández-Rosales M, Varela-Echavarría A. (2020): Conserved and divergent expression dynamics during early patterning of the telencephalon in mouse and chick embryos, Progress in Neurobiology, 2020 Mar 1;186:101735
Muley VY*, Akhter Y, Galande S. (2019): PDZ Domains Across the Microbial World: Molecular Link to the Proteases, Stress Response, and Protein Synthesis, Genome Biology and Evolution, 2019 Mar 1;11(3):644-659
Jangid RK, Kelkar A, Muley VY, Galande S. (2018): Bidirectional promoters exhibit characteristic chromatin modification signature associated with transcription elongation in both sense and antisense directions, BMC Genomics, 2018 May 2;19(1):313
VenkatRao V, Kumar SK, Sridevi P, Muley VY, Chaitanya RK. (2017): Cloning, characterization and transmission blocking potential of midgut carboxypeptidase A in Anopheles stephensi, Acta Tropica, 2017 Apr;168:21-28
Haldar KK, Muley VY, Datar S, Patra A. (2017): Structural and electronic investigation of metal-semiconductor hybrid tetrapod hetero-structures, Gold Bulletin, 2017 Mar 9;50:105–110
Salah FS, Ebbinghaus M, Muley VY, Zhou Z, Al-Saadi KR, Pacyna-Gengelbach M, O’Sullivan GA, Betz H, König R, Wang ZQ, Bräuer R, Petersen I. (2016): Tumor suppression in mice lacking GABARAP, an Atg8/LC3 family member implicated in autophagy, is associated with alterations in cytokine secretion and cell death, Cell Death & Disease, 2016 Apr 28;7(4):e2205
Karmodiya K, Anamika K, Muley VY, Pradhan SJ, Bhide Y, Galande S. (2014): Camello, a novel family of Histone Acetyltransferases that acetylate histone H4 and is essential for zebrafish development, Scientific Reports, 2014 Aug 15;4:6076
Muley VY, Ranjan A. (2013): Evaluation of physical and functional protein-protein interaction prediction methods for detecting biological pathways, PLOS One, 2013 Jan 17;8(1):e54325
Muley VY, Ranjan A. (2012): Effect of reference genome selection on the performance of computational methods for genome-wide protein-protein interaction prediction, PLOS One, 2012 Jul 26;7(7):e42057
Kamble KD, Bidwe PR, Muley VY, Kamble LH, Bhadange DG, Musaddiq M. (2012): Characterization of L-asparaginase producing bacteria from water, farm and saline soil, Bioscience discovery, 2012 Jan 1;3 (1), 116-119
Kamble KD, More A, Muley VY. (2012): Effect of incubation on DNase production by a moderate thermophilic bacterium screened from arid land, Journal of Pure and Applied Microbiology, 2012 Mar 31;6(1):265-269
Books
Muley, VY (Ed.). (2025): Computational virology, Methods in Molecular Biology, 2025 May, Humana press, Springer Nature, New York, NY (ISBN 978-1-0716-4545-1)
Muley VY, Acharya V. (2012): Genome-wide prediction and analysis of protein-protein functional linkages in bacteria, SpringerBriefs in Systems Biology, 2012 Jul 28:Volume 2, Springer Nature (ISBN 978-1-4614-4705-4)
Book chapters
PubMed indexed protocols
Muley VY*. (2025): Host Transcriptional Responses to Viral Infections: RNA-Seq Analysis with Rsubread, HISAT2, and STAR with Public RNA-Seq Data, In: Muley, V.Y. (eds) Computational Virology. Methods in Molecular Biology, 2025;2927:23-50
Le HTT, Ahamad I, Muley VY*. (2025): Deciphering Host Differential Gene Expression in Viral Infections Through Public RNA-Seq Data from NCBI GEO, In: Muley, V.Y. (eds) Computational Virology. Methods in Molecular Biology, 2025;2927:51-74
Muley VY*. (2025): Exploring Virus Protein Domains: Detection and Evolutionary Insights, In: Muley, V.Y. (eds) Computational Virology. Methods in Molecular Biology, 2025;2927:165-172
Muley VY*. (2025): Functional Insights Through Gene Ontology, Disease Ontology, and KEGG Pathway Enrichment, In: Muley, V.Y. (eds) Computational Virology. Methods in Molecular Biology, 2025;2927:75-98
Muley VY*. (2024): Prediction and Analysis of Transcription Factor Binding Sites: Practical Examples and Case Studies Using R Programming, In: Mandal, S. (eds) Reverse Engineering of Regulatory Networks. Methods in Molecular Biology, 2024;2719:199–225
Muley VY*. (2024): Deep Learning for Predicting Gene Regulatory Networks: A Step-by-Step Protocol in R, In: Mandal, S. (eds) Reverse Engineering of Regulatory Networks. Methods in Molecular Biology, 2024;2719:265–294
Muley VY*. (2023): Centrality Analysis of Protein-Protein Interaction Networks Using R, In: Mukhtar, S. (eds) Protein-Protein Interactions*, In: Mukhtar, S. (eds) Protein-Protein Interactions, Methods in Molecular Biology. 2023 Jul 15;2690:445-456
Muley VY*. (2023): Search, Retrieve, Visualize and Analyze Protein-Protein Interactions From Multiple Databases: A Guide to Experimental Biologists, In: Mukhtar, S. (eds) Protein-Protein Interactions, Methods in Molecular Biology. 2023 Jul 15;2690:429-443
Muley VY*. (2021): Mathematical Linear Programming to Model MicroRNAs-Mediated Gene Regulation Using Gurobi Optimizer, In: MUKHTAR, S. (eds) Modeling Transcriptional Regulation, Methods in Molecular Biology, 2021 Jul 13;2328:287-301
Muley VY*. (2021): Mathematical Programming for Modeling Expression of a Gene Using Gurobi Optimizer to Identify Its Transcriptional Regulators, In: MUKHTAR, S. (eds) Modeling Transcriptional Regulation, Methods in Molecular Biology, 2021 Jul 13;2328:99-113
Reference book chapters
Jamdhade AR, Hivrale VK, Muley VY*. (2024): Darwin, Charles: On Evolutionary Foundation. In: Shackelford, T. (eds) Encyclopedia of Religious Psychology and Behavior, 2024 July 23: Springer, Cham
Muley VY*, Bojórquez SAF, Kamble KD. (2021): Nervous System of Invertebrates, Encyclopedia of Animal Cognition and Behavior, 2021 Mar 12: Springer, Cham
Muley VY*, Larriva-Sánchez F. (2019): Nervous System, The, Encyclopedia of Animal Cognition and Behavior, 2019 Aug 29: Springer, Cham
Muley VY*, Gijón CET, García IM, Cueva LX. (2019): Vertebrate Nervous System, Encyclopedia of Animal Cognition and Behavior, 2019 Jun 26: Springer, Cham
Muley VY*, Pathania A. (2018): Gene Expression, Encyclopedia of Animal Cognition and Behavior, 2018 Oct 20: Springer, Cham
Muley VY*. (2017): Bioinformatics, Encyclopedia of Animal Cognition and Behavior, 2017 Sept 5: Springer, Cham
Pathania A, Muley VY*. (2017): Gene Expression Profiling, Encyclopedia of Animal Cognition and Behavior, 2017 Aug 22: Springer, Cham
Muley VY*, Hahn A. (2016): Protein-protein functional linkage predictions: bringing regulation to context, Computational Biology & Bioinformatics: Gene Regulation, 2016 May 12, Taylor & Francis
In process/Preprints
Joma MR, Bertho G, Muley VY, Caradeuc C, Pansiot J, Tabet L, Saleh R, Biesaga E, Lebourgeois S, Canesi F, Mauvais F, Bouchneb W, Giraud N, Goubard A, Delahaye A, Marshall E, Pellegrin I, Salmon-Ceron D, Chaisemartin LD, Laforge M*: New biomarkers for long COVID diagnosis reveal specific signatures of metabolic and mitochondrial dysregulation, tissue inflammation, and vascular damage linked to pathophysiology, Under Review
Mohammed SA, Saini AK, Aman S, Muley VY, Wairokpam GK, Parray ZA, Sahani A, Pathania A*: Global Proteome Remodelling in Rhodococcus jialingiae RS1 to Decipher its Plant Growth-Promoting and Biofertilizer Properties: Gene Identification for Transgenics, Under Review
Muley VY*.: Origin of Life. In: Shackelford, T. (eds) Encyclopedia of Religious Psychology and Behavior: Springer Nature, Under Review
Muley VY*, Jamdhade AR, Hivrale VK.: Brain Evolution. In: Shackelford, T. (eds) Encyclopedia of Religious Psychology and Behavior: Springer Nature, Under Review
Muley VY*, Singh A, Gruber K, Kamble KD, Varela-Echavarría A.: Potential functions of the amino-terminal cytoplasmic region of SARS-CoV-2 entry protein TMPRSS2 in virion assembly and early secretory pathway, In preparation, A part of this work is available as a preprint at BioRxiv