Publications
Published
2024
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. (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
2023
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*. (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
2022
Muley VY*, König R. (2022): Human transcriptional gene regulatory network compiled from 14 data resources, Biochimie, 2022 Feb 1;193:115-125
2021
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
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*, Bojórquez SAF, Kamble KD. (2021): Nervous System of Invertebrates, Encyclopedia of Animal Cognition and Behavior, 2021 Mar 12: Springer, Cham
2020
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
2019
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*, 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
2018
Muley VY*, Pathania A. (2018): Gene Expression, Encyclopedia of Animal Cognition and Behavior, 2018 Oct 20: Springer, Cham
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
2017
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
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
2016
Muley VY*, Hahn A. (2016): Protein-protein functional linkage predictions: bringing regulation to context, Computational Biology & Bioinformatics: Gene Regulation, 2016 May 12, Taylor & Francis
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
2014
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
2013
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
2012
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
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
In process/Preprints
Muley VY*, Singh A, Gruber K, Kamble KD, Varela-Echavarría A. (2023): 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