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Lessons on gene regulation learnt from the Drosophila melanogaster bithorax complex.
Arumugam Srinivasan and Rakesh K Mishra.
Int J Dev Biol. 2020;64(1-2-3):151-158. doi: 10.1387/ijdb.190167rm [PubMed]

Long-Read Genome Sequencing and Assembly of Leptopilina boulardi: A Specialist Drosophila Parasitoid
Shagufta Khan, Divya Tej Sowpati, Arumugam Srinivasan, Mamilla Soujanya Rakesh K. Mishra
G3 (Bethesda). 2020 May 4;10(5):1485-1494. doi: 10.1534/g3.120.401151. [PubMed]

Sperm methylome alterations following yoga-based lifestyle intervention in patients of primary male infertility: A pilot study
Shilpa Bisht, Sofia Banu, Surabhi Srivastava, Rashmi U. Pathak, Rajeev Kumar, Rima Dada, Rakesh K. Mishra
Andrologia. 2020 May;52(4):e13551. doi: 10.1111/and.13551. [PubMed]

Interactome of vertebrate GAF/ThPOK reveals its diverse functions in gene regulation and DNA repair.
Avinash Srivastava, Rakesh K Mishra
J Biosci (2020) 45:38 doi: 10.1007/s12038-020-0014-0 [PubMed]

Genomic organization of Polycomb Response Elements and its functional implication in Drosophila and other insects.
Arumugam Srinivasan, Rakesh K Mishra
J Biosci (2020) 45:12 DOI: 10.1007/s12038-019-9975-2 [PubMed]

MSDB: a comprehensive, annotated database of microsatellites.
Akshay Kumar Avvaru, Deepak Sharma, Archana Verma, Rakesh K Mishra, Divya Tej Sowpati
Nucleic Acids Res. 2020 Jan 8; 48(D1):D155-D159. doi: 10.1093/nar/gkz886. [PubMed]

SETDB1 modulates the differentiation of both the crystal cells and the lamellocytes in Drosophila
Indira Paddibhatla, Dushyant K Gautam, Rakesh K Mishra
Dev Biol. 2019 Dec 1; 456(1):74-85. doi: 10.1016/j.ydbio.2019.08.008. [PubMed]

Heterochromatic hues of transcription-the diverse roles of noncoding transcripts from constitutive heterochromatin.
Parna Saha, Rakesh K Mishra
FEBS J. 2019 Dec; 286(23):4626-4641. doi: 10.1111/febs.15104. [PubMed]

Activation of Su(Hw)-Controlled Genes Is Associated with Increase in GAF Binding.
P V Elizar'ev, D A Chetverina, L S Melnikova, A Srivastava, Rakesh K Mishra, A K Golovnin, P G Georgiev, M M Erokhin
Dokl Biochem Biophys. 2019 Sep; 488(1):293-295. doi: 10.1134/S1607672919050016. [PubMed]

Patterns of microsatellite distribution across eukaryotic genomes.
Srivastava S, Avvaru AK, Sowpati DT, Mishra RK.
BMC Genomics. 2019 Feb 22;20(1):153. doi: 10.1186/s12864-019-5516-5. [PubMed]

Drosophila Choline transporter non-canonically regulates pupal eclosion and NMJ integrity through a neuronal subset of mushroom body
Runa Hamid, Nikhil Hajirnis, Shikha Kushwaha, Sadaf Saleem, Vimlesh Kumar, Rakesh K. Mishra.
Dev Biol . 2018 Dec 7. doi: 10.1016/j.ydbio.2018.12.006. [PubMed]

Damage-responsive elements in Drosophila regeneration.
Vizcaya-Molina E, Klein CC, Serras F, Mishra RK, Guigó R, Corominas M.
Genome Res. 2018 Dec;28(12):1852-1866. doi: 10.1101/gr.233098.117. [PubMed]

Little imaginal discs, a Trithorax group member, is a constituent of nuclear matrix of Drosophila melanogaster embryos.
Varma P, Mishra RK.
J Biosci. 2018 Sep;43(4):621-633. [PubMed]

Comparison of Nuclear Matrix and Mitotic Chromosome Scaffold proteins in Drosophila S2 cells-Transmission of hallmarks of nuclear organization through mitosis.
Rahul Sureka, Rashi Wadhwa, Suman S Thakur, Rashmi U Pathak* and Rakesh K. Mishra.
Mol Cell Proteomics. 2018 Oct;17(10):1965-1978. doi: 10.1074/mcp.RA118.000591. [PubMed]

Epigenomic and genomic landscape of Drosophila melanogaster heterochromatic genes.
Saha P, Sowpati DT, Mishra RK.
Genomics. 2018 Feb 10. pii: S0888-7543(17)30184-2. doi: 10.1016/j.ygeno.2018.02.001. [Epub ahead of print] [PubMed]

Epigenetic factors Polycomb (Pc) and Suppressor of zeste (Su(z)2) negatively regulate longevity in Drosophila melanogaster.
Dasari V, Srivastava S, Khan S, Mishra RK.
Biogerontology. 2018 Feb;19(1):33-45. doi: 10.1007/s10522-017-9737-1. Epub 2017 Nov 27. [PubMed]

PERF: An Exhaustive Algorithm for Ultra-Fast and Efficient Identification of Microsatellites from Large DNA Sequences.
Avvaru AK, Sowpati DT, Mishra RK.
Bioinformatics. 2017 Nov 7. doi: 10.1093/bioinformatics/btx721. [Epub ahead of print] [PubMed]

Distinguishing States of Arrest: Genome-Wide Descriptions of Cellular Quiescence Using ChIP-Seq and RNA-Seq Analysis.
Srivastava S, Gala HP, Mishra RK, Dhawan J.
Methods Mol Biol. 2018;1686:215-239. doi: 10.1007/978-1-4939-7371-2_16. [PubMed]

C-State: an interactive web app for simultaneous multi-gene visualization and comparative epigenetic pattern search.
Sowpati DT, Srivastava S, Dhawan J, Mishra RK.
BMC Bioinformatics. 2017 Sep 13;18(Suppl 10):392. doi: 10.1186/s12859-017-1786-6. [PubMed]

Ultraconserved Sequences Associated with HoxD Cluster Have Strong Repression Activity.
Kushawah G, Mishra RK.
Genome Biol Evol. 2017 Aug 1;9(8):2049-2054. doi: 10.1093/gbe/evx148. [PubMed]

Vertebrate GAF/ThPOK: emerging functions in chromatin architecture and transcriptional regulation.
Srivastava A, Kumar AS, Mishra RK.
Cell Mol Life Sci. 2017 Aug 30. doi: 10.1007/s00018-017-2633-7. [Epub ahead of print] Review. [PubMed]

MSDB: A Comprehensive Database of Simple Sequence Repeats.
Avvaru AK, Saxena S, Sowpati DT, Mishra RK.
Genome Biol Evol. 2017 Jun 1;9(6):1797-1802. doi: 10.1093/gbe/evx132. [PubMed]

Long Noncoding RNAs in Mammalian Development and Diseases.
Saha P, Verma S, Pathak RU, Mishra RK.
Adv Exp Med Biol. 2017;1008:155-198. doi: 10.1007/978-981-10-5203-3_6. [PubMed] [View]

Simple sequence repeats showing 'length preference' have regulatory functions in humans.
Krishnan J, Athar F, Rani TS, Mishra RK.
Gene. 2017 Jul 13. pii: S0378-1119(17)30533-4. doi: 10.1016/j.gene.2017.07.022. [Epub ahead of print] [PubMed]

The placental gateway of maternal transgenerational epigenetic inheritance.
Sailasree SP, Srivastava S, Mishra RK.
J Genet. 2017 Jul;96(3):465-482. [PubMed]

Single Amino Acid Repeats in the Proteome World: Structural, Functional, and Evolutionary Insights.
Kumar AS, Sowpati DT, Mishra RK
PLOS ONE 11(11): e0166854. 2016 Nov 28. doi: 10.1371/journal.pone.0166854 [View]

Finding clues to the riddle of sex determination in zebrafish.
Nagabhushana A, Mishra RK
J Biosci. 2016 Mar;41(1):145-55 [PubMed]

Reversible loss of reproductive fitness in zebrafish on chronic alcohol exposure
Pooran Singh Dewari, Funmilola Ajani, Gopal Kushawah, Damera Santhosh Kumar, Rakesh K. Mishra
Alcohol Journal. 2015 Dec 18. doi:10.1016/j.alcohol.2015.11.006 [View]

Expansion of the polycomb system and evolution of complexity.
Sowpati DT, Senthilkumar R, Mishra RK.
Mech Dev. 2015 Aug 7. pii: S0925-4773(15)30014-9. doi: 10.1016/j.mod.2015.07.013. [PubMed]

Specific combinations of boundary element and Polycomb response element are required for the regulation of the Hox genes in Drosophila melanogaster.
Singh NP, Mishra RK.
Mech Dev. 2015 Aug 5. pii: S0925-4773(15)30017-4. doi: 10.1016/j.mod.2015.07.016. [PubMed]

Epigenetic mechanisms and boundaries in the regulation of mammalian Hox clusters.
Srivastava S, Dhawan J, Mishra RK.
Mech Dev. 2015 Aug 6. pii: S0925-4773(15)30016-2. doi: 10.1016/j.mod.2015.07.015. [PubMed]

The functional diversity of Drosophila Ino80 in development.
Ghasemi M, Pawar H, Mishra RK, Brahmachari V.
Mech Dev. 2015 Aug 4. pii: S0925-4773(15)30015-0. doi: 10.1016/j.mod.2015.07.014 [PubMed]

A fine balance: epigenetic control of cellular quiescence by the tumor suppressor PRDM2/RIZ at a bivalent domain in the cyclin a gene.
Cheedipudi S, Puri D, Saleh A, Gala HP, Rumman M, Pillai MS, Sreenivas P, Arora R, Sellathurai J, Schroder HD, Mishra RK, Dhawan J.
Nucleic Acids Res. 2015 Jul 27;43(13):6236-56. doi: 10.1093/nar/gkv567. Epub 2015 Jun 3. [PubMed]

Code in the Non-Coding.
Jaya Krishnan, Rakesh K Mishra.
Proceedings of Indian National Science Academy. 2015 Jun.

A fine balance: epigenetic control of cellular quiescence by the tumor suppressor PRDM2/RIZ at a bivalent domain in the cyclin a gene.
Cheedipudi S, Puri D, Saleh A, Gala HP, Rumman M, Pillai MS, Sreenivas P, Arora R, Sellathurai J, Schroeder HD, Mishra RK, Dhawan J.
Nucleic Acids Res. 2015 Jun 3. pii: gkv567. [PubMed]

Drosophila Rif1 is an essential gene and controls late developmental events by direct interaction with PP1-87B.
Sreesankar E, Bharathi V, Mishra RK, Mishra K.
Sci Rep. 2015 May 29;5:10679. doi: 10.1038/srep10679. [PubMed]

CARM1 regulates astroglial lineage through transcriptional regulation of Nanog and posttranscriptional regulation by miR92a.
Selvi BR, Swaminathan A, Maheshwari U, Nagabhushana A, Mishra R K, Kundu TK.
Mol Biol Cell. 2015 Jan 15;26(2):316-26. doi: 10.1091/mbc.E14-01-0019. Epub 2014 Nov 12. [PubMed]

Restraining the enhancers from straying.
Mishra R K.
J Biosci. 2014 Dec;39(5):739-40. [PubMed]

High-wire act: the poised genome and cellular memory.
Puri D, Gala H, Mishra R, Dhawan J.
FEBS J. 2014 Dec 1. doi: 10.1111/febs.13165. [PubMed]

Genome-wide mapping of matrix attachment regions in Drosophila melanogaster.
Pathak RU, Srinivasan A, Mishra R K.
BMC Genomics. 2014 Nov 25;15:1022. doi: 10.1186/1471-2164-15-1022. [PubMed]

Length and sequence dependent accumulation of simple sequence repeats in vertebrates: Potential role in genome organization and regulation.
Ramamoorthy S, Garapati HS, Rakesh K Mishra.
Gene. 2014 Nov 10;551(2):167-75. doi: 10.1016/j.gene.2014.08.052. Epub 2014 Aug 27. [PubMed ]

Role of abd-A and Abd-B in Development of Abdominal Epithelia Breaks Posterior Prevalence Rule.
Singh NP, Rakesh K Mishra.
PLoS Genet. 2014 Oct 23;10(10):e1004717. doi: 10.1371/journal.pgen.1004717. eCollection 2014 Oct. [PubMed ]

Mining the cis-regulatory elements of Hox clusters.
Matharu NK, Rakesh K Mishra.
Methods Mol Biol. 2014;1196:121-31. doi: 10.1007/978-1-4939-1242-1_8. [PubMed ]

Emerging trends of long non-coding RNAs in gene activation.
Krishnan J, Rakesh K Mishra.
FEBS J. 2014 Jan;281(1):34-45. doi: 10.1111/febs.12578. Epub 2013 Nov 13. Review. [PubMed ]

Transposable element 'roo' attaches to nuclear matrix of the Drosophila melanogaster.
Mamillapalli A, Pathak RU, Garapati HS, Rakesh K Mishra.
J Insect Sci. 2013;13:111. doi: 10.1673/031.013.11101. [PubMed ]

A functionally conserved Polycomb response element from mouse HoxD complex responds to heterochromatin factors.
Vasanthi D, Nagabhushan A, Matharu NK, Rakesh K Mishra.
Sci Rep. 2013 Oct 22;3:3011. doi: 10.1038/srep03011. [PubMed ]

GATA simple sequence repeats function as enhancer blocker boundaries.
Ram P. Kumar, Jaya Krishnan, Narendra Pratap Singh, Lalji Singh and Rakesh K Mishra.
Nat Commun. 4:1844, 2013 [PubMed ] [Full Text]

Vertebrate GAGA factor associated insulator elements demarcate homeotic genes in the HOX clusters.
Surabhi Srivastava, Deepika Puri, Hita S Garapati, Jyotsna Dhawan and Rakesh K Mishra.
Epigenetics & Chromatin, 6:8, 2013 [PubMed ] [FREE Full Text]

AAGAG repeat RNA is an essential component of nuclear matrix in Drosophila.
Rashmi U. Pathak, Anitha Mamillapalli, Nandini Rangaraj, Ram P. Kumar, Dasari Vasanthi, Krishnaveni Mishra and Rakesh K Mishra.
RNA Biol. 10 (4), 536-543,2013 [PubMed ] [Full Text]

Functional sub-division of the Drosophila genome via chromatin looping: the emerging importance of CP190.
Sajad H. Ahanger, Yogesh S. Shouche and Rakesh K Mishra.
Nucleus, 4 (2), 115-122, 2013 [PubMed ] [Full Text]

Conserved boundary elements from the Hox complex of mosquito, Anopheles gambiae.
Sajad H. Ahanger, Arumugam Srinivasan, Dasari Vasanthi, Yogesh S. Shouche and Rakesh K Mishra.
Nucleic Acids Res. 41 (2), 804-816, 2013 [PubMed ] [FREE Full Text]

Homeotic gene regulation: a paradigm for epigenetic mechanisms underlying organismal development.
Navneet K. Matharu, Vasanthi Dasari and Rakesh K Mishra.
Subcellular Biochemistry, Volume 61, 177-207, 2013 [PubMed] [FREE Full Text]

Functional diversification of yeast telomere associated protein, Rif1, in higher eukaryotes.
Easwaran Sreesankar, Ramamoorthy Senthilkumar, Vellaichamy Bharathi, Rakesh K Mishra and Krishnaveni Mishra.
BMC Genomics. 13(1):255, 2012 [PubMed ] [FREE Full Text]

Chromatin domain boundary element search tool for Drosophila.
Arumugam Srinivasan and Rakesh K Mishra.
Nucleic Acids Res. 40 (10), 4385-4395, 2012 [PubMed ] [FREE Full Text]

Dynamics of Nuclear Matrix Proteome during Embryonic Development in Drosophila melanogaster.
Parul Varma and Rakesh K Mishra.
J. Biosci. 36 (3), 439-459, 2011. [PubMed ] [FREE Full Text]

A BEAF dependent chromatin domain boundary separates myoglianin and eyeless genes of Drosophila melanogaster.
Hina Sultana, Shreekant Verma and Rakesh K Mishra.
Nucleic Acids Res. 39, 3543-57, 2011 [PubMed ] [FREE Full Text]

Epigenetic profile of the euchromatic region of human Y chromosome.
Narendra Pratap Singh, Sri Ranganayaki Madabhushi, Surabhi Srivastava, R. Senthilkumar, C. Neeraja, Sanjeev Khosla and Rakesh K Mishra.
Nucleic Acids Res. 39, 3594-606, 2011. [PubMed ] [FREE Full Text]

Tone up your chromatin and stay young.
Navneet K Matharu and Rakesh K Mishra.
J. Biosci. 36(1), 5-11, 2011. [PubMed ] [FREE Full Text]

A functionally conserved boundary element from the mouse HoxD locus requires GAGA factor in Drosophila.
Dasari Vasanthi, Mamidi Anant, Surabhi Srivastava and Rakesh K Mishra.
Development 137 (24), 4239-4247, 2010 [PubMed ] [Full Text]

Nuclear matrix proteome analysis of Drosophila melanogaster.
Satish Kallappagoudar, Parul Varma, Rashmi U Pathak, R Senthilkumar and Rakesh K Mishra.
Mol Cell Proteomics 9(9):2005-18, 2010 [PubMed ] [Full Text]

Vertebrate homologue of Drosophila GAGA factor.
Navneet Kaur Matharu, Tanweer Hussain, Rajan Sankaranarayanan and Rakesh K Mishra.
J. Mol. Biol. 400, 437-447, 2010. [PubMed ] [Full Text]

The paternal hidden agenda: Epigenetic inheritance through sperm chromatin.
Deepika Puri, Jyotsna Dhawan and Rakesh K Mishra.
Epigenetics 5, 1-6, 2010. [PubMed ] [Full Text]

Chromatin remodeling protein INO80 influences expression of homeotic genes in Drosophila.
Shipra Bhatia, Hema Pawar, Vasanthi Dasari, Rakesh K Mishra, Shanti Chandrashekaran and Vani Brahmachari.
Genes Cells 15, 725-735, 2010. [PubMed ] [Full Text]

Regulation of cellular chromatin state: insight from quiescence and differentiation.
Surabhi Srivastava, Rakesh K Mishra and Jyotsna Dhawan.
Organogenesis 6, 37-47, 2010. [PubMed ] [FREE Full Text]

Repeat performance: how do genome packaging and regulation depend on simple sequence repeats?
Ram Parikshan Kumar, Ramamoorthy Senthilkumar, Vipin Singh and Rakesh K Mishra.
BioEssays 32, 165-174, 2010. [PubMed ] [Full Text]

Novel motifs distinguish multiple homologues of Polycomb in vertebrates: expansion and diversification of the epigenetic toolkit.
Ramamoorthy Senthilkumar and Rakesh K Mishra.
BMC Genomics 10, 549, 2009. [PubMed ] [FREE Full Text]

Cytogenetic characterization and fluorescence in situ hybridization of (GATA)10 repeats on established primary cell cultures from Indian water snake (Natrix piscator) and Indian mugger (Crocodylus palustris) embryos.
L Rao, R Turlapati, M Patel, B Panda, D Tosh, S Mangalipalli, A Tiwari,VP Orunganti, D Rose, A Anand, MK Kulashekaran, SR Priya, Rakesh K Mishra, K Majumdar, RK Aggarwal, L Singh.
Cytogenet Genome Res. 127, 287-96, 2009. [PubMed ] [Full Text]

SnS-Align: A graphic tool for alignment of distantly related proteins.
Ganiraju Manyam, Ancha Baranova, Mikhail Skoblov and Rakesh K Mishra.
International Journal of Bioinformatics Research & Applications (IJBRA) 5, 663-673, 2009. [PubMed ] [Full Text]

Chromatin and Disease: Now blame it on Epigenetics.
Rakesh K Mishra and Siddhartha Roy.
Current Science (perspective), Current Science 97, 261-262, 2009.

Divide and (epigenetic) rule: Chromatin Domains as Functional and Structural Units of Genomes (book chapter).
Rakesh K Mishra and Sanjeev Galande.
Published by Indian National Academy of Sciences, New Delhi (INSA) platinum jubilee publication, 2009

Differentiation to Dedifferentiation: Induced pluripotent stem cells (book chapter).
Narendra Pratap Singh and Rakesh K Mishra.
Recent Trends in Biotechnology, M P Singh (ed.), Nova Science Publishers, New York, 2009

Polycomb Group of Genes and the Epigenetics of Aging (book chapter).
Krishnaveni Mishra and Rakesh K Mishra.
Epigenetics of Aging, Tollefsbol, Trygve O. (Ed.) Springer (ISBN:978-1-4419-0638-0), 2009, 350 pages. [Link to Table of contents]

Genome to Epigenome (book chapter).
Rakesh K Mishra.
I.K. International Publishing House (ISBN:978-93-80026-21-3), 2009, 222 pages.

Chromosomes to Genome (book).
Rakesh K Mishra (Editor).
I.K. International Publishing House (ISBN:978-93-80026-21-3), 2009, 222 pages.

A double-edged sword to force posterior dominance of Hox genes.
Narendra Pratap Singh and Rakesh K Mishra.
BioEssays 30, 1058-1061, 2008. [PubMed ] [Full Text]

An intronic DNA sequence within the mouse Neuronatin gene exhibits biochemical characteristics of an ICR and acts as a transcriptional activator in Drosophila.
Divya Tej Sowpatia, Devi Thiagarajana, Sudhish Sharmaa, Hina Sultanab, Rosalind Johnc, Azim Surani, Rakesh K Mishra and Sanjeev Khosla.
Mech. Dev. 125, 963-973, 2008. [PubMed ] [Full Text]

Epigenetic regulation of genes during development: A conserved theme from flies to mammals.
Dasari Vasanthi and Rakesh K Mishra.
J. Genet. Genomics 35, 413-429, 2008. [PubMed ] [Full Text]

Transcriptional activation by GAGA factor is through its direct interaction with dmTAF3.
Vivek S Chopra, Arumugam Srinivasan, Ram P Kumar, Krishnaveni Mishra, Denis Basquin, Mylène Docquier, Carole Seum, Daniel Pauli, Rakesh K Mishra.
Dev. Biol. 317, 660-670, 2008. [PubMed ] [Full Text]

Reptin and Pontin antagonistically function with PcG and TrxG complexes to mediate Hox gene control.
Soda Diop, Karine Bertaux, Dasari Vasanthi, Ali Sarkeshik, Benjamin Goirand, Denise Aragnol, Nicholas S. Tolwinski, Michael D. Cole, Jacques Pradel, John R. Yates III, Rakesh K Mishra, Yacine Graba and Andrew J. Saurin.
EMBO Reports 9, 260-266, 2008. [PubMed ] [FREE Full Text]

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