Publications

Asterisk (*) indicates corresponding author and hash (#) indicates equal contribution.

1. Jain Y, Chandradoss KR, A V A, Bhattacharya J, Lal M, Bagadia M, Singh H, Sandhu KS*. Convergent evolution of a genomic rearrangement may explain cancer resistance in hystrico- and sciuromorpha rodents. NPJ Aging Mech Dis. 2021 Sep 1;7(1):20. doi: 10.1038/s41514-021-00072-9.

2. Chandradoss KR#, Chawla B#, Dhuppar S, Nayak R, Ramachandran R, Kurukuti S, Mazumder A, Sandhu KS*. CTCF mediated genome architecture regulates the dosage of mitotically stable mono-allelic expression of autosomal genes. Cell Reports 2020. Oct 27: 33(4)  PubMed  Publisher. 

3. Chandradoss KR,  Guthikonda PK, Kethavath S, Dass M, Singh H, Nayak R, Kurukuti S*, Sandhu KS*. Biased visibility in HiC datasets marks dynamically regulated condensed and decondensed chromatin states genome-wide. BMC Genomics 21, 175 (2020). PubMed  Publisher. 

4. Singh A, Choudhuri P, Chandradoss KR, Lal M, Mishra SK, Sandhu KS*. Does genome surveillance explain the global discrepancy between binding and effect of chromatin factors? FEBS Lett. 2020 Jan 12. doi: 10.1002/1873-3468.13729. PubMed  Publisher.

5. Bhalla P, Shukla A, Vernekar DV, Arimbasseri AG, Sandhu KS, Bhargava P. Yeast PAF1 complex counters the pol III accumulation and replication stress on the tRNA genes. Sci Rep. 2019 Sep 9;9(1):12892.  PubMed  Publisher.  

6. Meenakshi Bagadia#, Keerthivasan Raanin Chandradoss#, Yachna Jain, Harpreet Singh, Mohan Lal, Sandhu KS*. Evolutionary loss of genomic proximity to conserved noncoding elements impacted the gene expression dynamics during mammalian brain development. GENETICS 2019 Apr;211(4):1239-1254; PubMed  Publisher.  

7. Bagadia M, Singh A, Sandhu KS*. Three dimensional organization of genome might have guided the dynamics of gene order evolution in eukaryotes. Genome Biol Evo. Mar 08, 2016. doi: 10.1093/gbe/evw050. PubMed  Publisher.

8. Singh A, Bagadia M, Sandhu KS*. Spatially coordinated replication and minimization of expression noise constrain three-dimensional organization of yeast genome. DNA Res. Feb. 29, 2016. doi:10.1093/dnares/dsw005. PubMed  Publisher (selected as Editor's choice )

9. Reeder C, Closser M, Poh HM, Sandhu KS, Wichterle H, Gifford D. High resolution mapping of enhancer-promoter interactions. PLoS One. 2015 May 13;10(5). PubMed  Publisher

10. Tayal N, Choudhary P, Pandit SB, Sandhu KS*. Evolutionarily conserved and conformationally constrained short peptides might serve as DNA recognition elements in intrinsically disordered regions. Molecular Biosystems 2014 Mar 26. DOI: 10.1039/C3MB70539K.  PubMed  Publisher

11. Mercer TR, Edwards SL, Clark MB, Neph SJ, Wang H, Stergachis AB, John S, Sandstrom R, Li G, Sandhu KS, Ruan Y, Nielsen LK, Mattick JS, Stamatoyannopoulos JA. DNase I-hypersensitive exons colocalize with promoters and distal regulatory elements. Nat. Genet. 2013. doi: 10.1038/ng.2677. PubMed  Publisher

12. Sandhu KS*, Guoliang Li, Huay Mei Poh, Yu Ling Kelly Quek, Yee Yen Sia, Su Qin Peh, Fabianus Hendriyan Mulawadi, Mile Sikic, Francesca Menghi, Anbupalam Thalamuthu, Wing Kin Sung, Xiaoan Ruan, Melissa Jane Fullwood, Edison Liu, Peter Csermely, Yijun Ruan* . Large scale functional organization of long-range chromatin interaction networks. Cell Rep. 2012 Nov 29;2(5):1207-19. PubMed  Publisher

13. ENCODE consortium. An Integrated Encyclopedia of DNA Elements in the Human Genome. Nature 2012; 489(7414):57-74. PubMed  Publisher

14.  Sandhu KS*. Did the modulation of expression noise shape the evolution of three dimensional genome organizations? Nucleus 2012; 3:3,1-4.  PubMed  Publisher

15. Li G#, Ruan X#, Auerbach R#, Sandhu KS#, Ping Wang, Yuriy Orlov, Huay Mei Poh, Yufen Goh, Joanne Lim, Sim Hui Shan, Su Qin Peh, Fabianus Hendriyan Mulawadi, Ong Chin Thing, Steve Landt, Debasish Raha, Ghia Euskirchen, Shuzhen Hong, Herve Thoreau, Chia-Lin Wei, Weihong Ge, Yi Sun, Melissa Fullwood, Edison T. Liu, Edwin Cheung, Wing-Kin Sung, Michael Snyder* and Yijun Ruan*. Extensive promoter centered chromatin interactions provide a architectural basis for transcription regulation in eukaryotes. Cell. 2012 Jan 20;148(1-2):84-98 (#co-first author). PubMed  Publisher 

16.  Sandhu KS, Li G, Sung WK and Ruan Y. Chromatin interaction networks and higher order chromatin architectures of eukaryotic genomes. J Cell Biochem. 2011 Apr 25. doi: 10.1002/jcb.23155. PubMed  Publisher

17. Csermely P, Sandhu KS, Hazai E, Hoksza Z, Kiss HJM, Miozzo F, Veres DV, Piazza F and Nussinov R. Disordered proteins and network disorder in network descriptions of protein structure, dynamics and function. Hypotheses and a comprehensive review. Current Protein & Peptide Science 2011; vol.12. PubMed  Publisher

18.  Reinius B, Shi C, Hengshuo L, Sandhu KS, Radomska K, Rosen GD, Lu L, Kullander K, Williams RW and Jazin E. Female-biased expression of long non-coding RNAs in domains that escape X-inactivation in mouse. BMC Genomics. 2010 Nov 3;11(1):614. PubMed  Publisher

19.  Sandhu KS*. Systems properties of proteins encoded by imprintedse genes. Epigenetics 2010 Oct 01,5 (7). PubMed  Publisher

20.  Sandhu KS, Shi C, Sjolinder M, Zhao Z, Gondor A, Liu L, Tiwari VK, Guibert S, Emilsson L, Imreh MP, Ohlsson R*. Nonallelic transvection of multiple imprinted loci is organized by the H19 imprinting control region during germline development. Genes Dev. 2009; Nov 15; 23: 2592-2597. PubMed  Publisher

21.  Sandhu KS*. Intrinsic disorder explains diverse nuclear roles of chromatin remodeling proteins. J Mol Recognit. 2009 Jan-Feb;22(1):1-8. PubMed  Publisher

22.  Sandhu KS*, Pandey S, Maiti S, Pillai B. GASCO: genetic algorithm simulation for codon optimization. In Silico Biol. 2008;8(2):187-92. PubMed  Publisher

23. Ali A, Jha P, Sandhu KS, Raghuram N*. Spirulina nitrate assimilating enzymes (NR, NiR, GS) have higher specific activities and are more stabile than those of rice. Physiol. Mol. Biol. Plants. 2008 July; 14 (3): 179-182.  PubMed Publisher

24. Prakash T, Sandhu KS, Singh NK, Bhasin Y, Ramakrishnan C, Brahmachari SK*. Structural assessment of glycyl mutations in invariantly conserved motifs. Proteins. 2007 Nov 15;69(3):617-32. PubMed  Publisher

25. Ganapathi M, Singh GP, Sandhu KS, Brahmachari SK, Brahmachari V*. A whole genome analysis of 5' regulatory regions of human genes for putative cis-acting modulators of nucleosome positioning. Gene. 2007 Apr 15;391(1-2):242-51. PubMed  Publisher

26. BioSuite: A comprehensive bioinformatics software package (A unique industry–academia collaboration). The NMITLI-BioSuite Team. Current Science. 2007 Jan 10; 92 (1): 29-38.  Publisher

27. Sandhu KS, Dash D*. Dynamic alpha-helices: conformations that do not conform. Proteins. 2007 Jul 1;68(1):109-22. PubMed  Publisher

28. Zhao Z, Tavoosidana G, Sjölinder M, Göndör A, Mariano P, Wang S, Kanduri C, Lezcano M, Sandhu KS, Singh U, Pant V, Tiwari V, Kurukuti S, Ohlsson R*. Circular chromosome conformation capture (4C) uncovers extensive networks of epigenetically regulated intra- and interchromosomal interactions. Nat Genet. 2006 Nov;38(11):1341-7. PubMed  Publisher 

29. Sandhu KS, Dash D*. Conformational flexibility may explain multiple cellular roles of PEST motifs. Proteins. 2006 Jun 1;63(4):727-32. PubMed  Publisher

30.  Singh GP$, Ganapathi M$, Sandhu KS, Dash D*. Intrinsic unstructuredness and abundance of PEST motifs in eukaryotic proteomes. Proteins. 2006 Feb 1;62(2):309-15. PubMed  Publisher

31. Sandhu KS, Acharya KK*. ExPrimer: to design primers from exon--exon junctions. Bioinformatics. 2005 May 1;21(9):2091-2.  PubMed  Publisher