Department of Biological Sciences

Indian Institute of Science Education and Research Mohali
(0172) 229 3152
headbiology@iisermohali.ac.in
Education
  • 2010-2012

    Post-doctoral Research Fellow

    Genome Institute of Singapore

  • 2007-2010

    PhD (Medicine)

    Karolinksa Institute, Stockholm, Sweden

People
Keerthivasan Chandradoss PhD (alumnus)

Ken joined our group in Aug, 2014. He completed his MS integrated degree from Institute of Bioinformatics and Applied Biotechnology (IBAB), Bangalore. He worked upon role of genome architecture in guiding mono-alleleic expression of genes. He is presently working as post- doctoral fellow in University of Pennsylvania.

Yachna Jain PhD (alumnus)

Yachna joined our group in Aug, 2017. Before joiining us, she worked at IIT-K and NABI as a project associate. She studied the role of genome organisation in cancer resistance in certain rodent clades. Yachna is presently working as a data scientist with a corporate.

Meenakshi Bagadia PhD (alumnus)

Meenakshi Joined our group in Aug, 2014. She completed her BS-MS integrated degree from IISER-Mohali. She has been interested in evolution of linear genome order. She is presently working in as data scientist in corporate sector.

Arashdeep Singh PhD (alumnus)

Arash Joined our group in Aug, 2013. He completed his BS-MS integrated degree from IISER-Mohali. He has been interested in evolutionary and functional constraints of eukaryotic genome organization. He is presently working as post-doc at National Cancer Institute (NCI), NIH.

Teaching
BIO411 - Bioinfomatics lab Sequence composition analysis, ab intio gene prediction, Motif finding algorithms, Primer designing algorithm, Codon optimization, Sequence alignment algorithms, Phylogenetic analysis, Protein structure analysis, Molecular modelling and dynamics

IDC407 - Network Science History of network models, Mathematics of networks, Local and global network attributes, Paths, Percolation, Price's model, Network dynamics, Network models of epidemic, Controllability

BIO459 - Epigenetics Trans-generational epigenetic inheritance, Molecular mechanisms and evolution of epigenetic modifications, Linear and 3D genome organization, Epigenetic reprogramming during development and diseases, Genome technologies

IDC306 - Biocomputing Practical computing for biologists using PERL/Python and R

IDC409 - Introduction to Data Science Introduction to big data, data storage, Hadoop, mySQL, HiveQl, missing value imputation, data scaling and normalization, exploratory data analyses, data distributions, correlograms, dimension reduction using PCA, SVD, K-means, SOM and t-SNE, machine leanring using PLA, SVM, DT, XgBoost, Naive Bayes, CNN etc.

BIO606 - Biostatistics Set theory, Probability, Conditional probability and Bayes theorem, Descriptive statistics, Probability distributions (Binomial, Geometric, Normal, Pareto's, Poisson, Exponential, Gamma, Beta, Chi-square, t-distribution), Contgency tables and Chi-square test, Hypothesis testing, type I and II error, P-value, Power, parametric and non-parametric tests of signifcance, Linear regression, Correlation, Partial correlation, PCA, Causal inference

BIO401 - Genome Structure and Function Review of Genome composition, GC and CpG content, Gene attributes, Promoter properties, DNA transposons & retrotransposons, piRNA, miRNAs, Linear organisation of genome, evolution of gene-clusters, Epigenetic modifications and 3D organisation of genome, Epigenetic reprogramming of genome during development and diseases, Genome technologies

BIO512 - Topics in Biology Systems biology section: Introduction to scale-free networks, Gene regulatory networks, Hill's equation, Negative and positive Auto regulatory loops, Feed-forward, feed-back loops, oscillators etc.

IDC101 - Introduction to Computation (tutored) Linux and Python

IDC620 - Computational Biology Data-mining and Machine Learning section

Publication
Preferred left-handed conformations of glycyls with pathogenic variants protect against aggregation 2024, Purva Mishra, Rajesh Potlia, Kuljeet Singh Sandhu. bioRxiv

Loss of conserved noncoding elements likely shaped the evolution of regressed phenotypes in cavefish 2024, Mohan Lal, Jui Bhattacharya, Kuljeet Singh Sandhu. bioRxiv

Convergent evolution of a genomic rearrangement may explain cancer resistance in hystrico- and sciuromorpha rodents. 2022, Jain Y, Chandradoss KR, A V A, Bhattacharya J, Lal M, Bagadia M, Singh H, Sandhu KS*. NPJ Aging Mech Dis., 7 (1), 20

CTCF mediated genome architecture regulates the dosage of mitotically stable mono-allelic expression of autosomal genes. 2020, Chandradoss KR#, Chawla B#, Dhuppar S, Nayak R, Ramachandran R, Kurukuti S, Mazumder A, Sandhu KS*. Cell Reports, 33 (4), 108302

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

Does genome surveillance explain the global discrepancy between binding and effect of chromatin factors? 2020, Singh A, Choudhuri P, Chandradoss KR, Lal M, Mishra SK, Sandhu KS*.. FEBS Lett., 594 (8), 1339-1353

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

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

Three dimensional organization of genome might have guided the dynamics of gene order evolution in eukaryotes. 2016, Bagadia M, Singh A, Sandhu KS*. Genome Biol Evo., 8 (3), 946–954

Spatially coordinated replication and minimization of expression noise constrain three-dimensional organization of yeast genome. 2016, Singh A, Bagadia M, Sandhu KS*. DNA Res., 23 (2), 155–169

High resolution mapping of enhancer-promoter interactions. 2015, Reeder C, Closser M, Poh HM, Sandhu KS, Wichterle H, Gifford D.. PLoS One., 10 (5),  e0122420

Evolutionarily conserved and conformationally constrained short peptides might serve as DNA recognition elements in intrinsically disordered regions. Molecular Biosystems 2014, Tayal N, Choudhary P, Pandit SB, Sandhu KS*.. Molecular BioSystems, 10 (), 469-1480

DNase I-hypersensitive exons colocalize with promoters and distal regulatory elements. 2013, 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.. Nat. Genet., 45 (), 852–859

ENCODE consortium. 2012, An Integrated Encyclopedia of DNA Elements in the Human Genome.. Nature, 489 (7414), 57-74

Large scale functional organization of long-range chromatin interaction networks. 2012, 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* .. Cell Reports, 2 (5), 1207-19

An Integrated Encyclopedia of DNA Elements in the Human Genome. 2012, ENCODE consortium.. Nature, 489 (7414), 57-74

Did the modulation of expression noise shape the evolution of three dimensional genome organizations? 2012, Sandhu KS*.. Nucleus, 3 (3), (1-4)

Extensive promoter centered chromatin interactions provide a architectural basis for transcription regulation in eukaryotes. 2012, 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*.. Cell, 148 (1-2), 84-98

Chromatin interaction networks and higher order chromatin architectures of eukaryotic genomes. 2011, Sandhu KS, Li G, Sung WK and Ruan Y.. J Cell Biochem., 112 (9), 2218-2221

Disordered proteins and network disorder in network descriptions of protein structure, dynamics and function. Hypotheses and a comprehensive review. 2011, Csermely P, Sandhu KS, Hazai E, Hoksza Z, Kiss HJM, Miozzo F, Veres DV, Piazza F and Nussinov R.. Current Protein & Peptide Science, 13 (1),  19 - 33

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

Systems properties of proteins encoded by imprintedse genes. 2010, Sandhu KS*.. Epigenetics, 5 (7, 627-636

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

Intrinsic disorder explains diverse nuclear roles of chromatin remodeling proteins. 2009, Sandhu KS*. J Mol Recognit. 22(1):1-8.

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

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

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

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

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

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

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

Circular chromosome conformation capture (4C) uncovers extensive networks of epigenetically regulated intra- and interchromosomal interactions. 2006, 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*.. Nat Genet. 38(11):1341-7.

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

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

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

Contact
Work Email: sandhuks[at]iisermohali[dot]ac[dot]in Address: 4F9, Academic Block II, IISER-Mohali, Sector 81, SAS Nagar 140306

Indian Institute of Science Education and Research (IISER)- Mohali
Knowledge City, Sector 81, SAS nagar 140306, INDIA
headbiology@iisermohali.ac.in| +91 172 2240266

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