Personal

• Name: Kuljeet Sandhu
• Date of birth: Oct 1, 1982
• Sex: Male
• Nationality: Indian
• Marital status: Single
• Email:
  

Education:

• Doctorate of Philosophy, 2007-2010
  Dept. of Microbiology, Tumour and Cell Biology (MTC)
  Karolinska Institute, Stockholm, Sweden
• Thesis: "Networks in Epigenetics"
  We decipher and annotate novel networks in context of epigenetics. In particular, we identify a chromatin interaction network (CIN) centered on one of the Achilles' heels in mammalian development, namely H19-imprinting control region or H19-ICR. We attempt to characterize functional and mechanical insights of these interactions. We further extend to protein interaction networks (PINs) and identified a development and metabolism related, highly central network-module that compromises with robustness of whole human PIN when malfunction. In yet another study we uncovered a common structural feature supposedly responsible for high degree and diversity of protein interactions, again in context of epigenetics. A summary of the thesis is included in the attached appendix.
  Supervisor: Prof. Rolf Ohlsson
• Masters of Science in Bioinformatics, 2006
  79% aggregate, Sikkim Manipal Univsersity, Sikkim, India.
• Post Graduate Diploma in Bioinformatics, 2004
  74% aggregate, Institute of Bioinformatics and Applied Biotechnology (IBAB), Bangalore,India.
• Bachelor of Science in Zoology, Botany and Chemistry, 2001
  71% aggregate, Lucknow Christian Post Graduate College, Lucknow, India.
  

Employment

• 2010- postdoctoral fellow of the Genome Institute of Singapore
  Laboratory of Yijun Ruan elucidating the structure and dynamics of functional DNA elements in complex genomes through transcriptome characterization.
• 2007-10, Uppsala university, Uppsala and Karolinska Institute, Stockholm, Sweden.
  I worked under the able supervision of Prof. Rolf Ohlsson. The work primarily includes computational analysis of large scale chromatin interaction data resulted from an in-house developed technique named Circular Chromosome Conformation Capture (4C) combined with tiling array. As per requirement in the lab, I spent quite a good amount of time in wet lab performing bulk of in-situ experiments.  The PhD program also includes regular course work, journal clubs, work seminars and post-graduate teaching.
• 2004-06, Institute of Genomics and Integrative Biology (IGIB), Delhi, India.
  I worked at GN Ramachandran Center of Genome Informatics with Prof. Samir Brahmchari and Dr. Debasis Dash. The work includes large scale analysis of protein structures, algorithm/ database development and microarray analysis.
• Apr-Sep 04, Institute of Bioinformatics and Applied Bioinformatics, Bangalore, India.
  I work with Dr. Kshitish Acharya to develop algorithms for primer designing and text mining.
• Oct, 03-March, 04, IBM Software Labs, Bangalore, India
  I worked in Technology Incubation Center (TIC) with their bioinformatics team. We proposed a novel regulon based method to characterize large scale cancer gene expression data.

Skills

• Computational skills
  • Operating systems: Linux, Unix, Wiindows
  • Programming: Proficient in PERL and R, working knowledge of C and JAVA.
  • Web: HTML, XML, CGI, Apache server configuration
  • GUI: TCL, PERL-Tk, VB
  • Database: mySQL, DBI
  • Others: Most bioinformatics s/w utilities available online.
• Experimental skills
  • Cell culture: MEFs, ES cells, cancer cell lines and siRNA tranfection
  • Microbiology: Bacterial cell culture, BAC/plasmid isolation.
  • Mol. Biology: Chromatin/DNA/RNA preparation, ChIP, Q-PCR.
  • In-situ: Multicolor DNA FISH and IF
  • Microscopy: Carl Zeiss Meta LSM, Grid confocal (OptiGrid) and others

References

• Prof. Rolf Ohlsson
  Strategic Professor in Genome Integrity
  Dept. of Microbiology, Tumor and Cell biology
  Karolinska Institute, Nobel vag 16, Solna
  Stockholm, Sweden 171 77
  E-mail: Rolf.ohlsson [at] ki.se
  Phone: 00 46 8 52486203
• Dr. Debasis Dash
  Faculty Scientist
  GN Ramachandran Knowledge Center
  for Genome Informatics, Institute of
  Genomics and Integrative Biology (IGIB),
  CSIR, Mall Road, Delhi-110 007, India.
  E-mail: ddash [at] igib.res.in
  Phone: 91 11 41708323 extn 121
• Dr. Chandrasekhar Kanduri
  Associate Professor
  Dept. of Genetics & Pathology
  Rudbeck Laboratory, Uppsala University
  Uppsala Sweden 751 85
  E-mail: kanduri.chandrasekhar [at] genpat.uu.se
  Phone: 00 46 18 4714821
• Dr. N. Raghuram
  Associate Professor
  University School of Biotechnology, GGS IP University, Kashmere Gate, Delhi-
  110403, INdia
  E-mail: raghuram98 [at] hotmail.com
  Phone: 91 11 23900222, 23900223

Conference presentations

1. Networks in Epigenetics. Genome Institute of Singapore (GIS), Singapore. Aug 17, 2010 (Invited talk)
2. Network Paradigm in Epigenetics. Frederich Meischer Institute (FMI), Basel, Switzerland Feb, 2010 (Invited talk)
3. Chromsomal Networks: A higher order structure-function paradigm. A Swedish Network in Epigenetics, 2nd Annual Meeting Stockholm, Sweden, 2008 October 23-24 (talk)
4. Chromosomal Networks and Epigenetic Reprogramming. 2nd Epigenome Mapping Workshop of the NOE “The Epigenome”. Max-Planck Tagungsstätte, Berlin, Germany. 2007 Sept 9 (talk)
5. Role of CTCF in genome-wide chromosomal interactions. 4th International Conference on “CTCF and BORIS in Development, Epigenetics and Disease” . Santander, Spain, 2007 Sept 19-22 (talk)
6. Chromosomal interactions: dating in the nucleus. EBC Symposium. Evolutionary Biology Center, Uppsala University, Sweden. 2007  Nov 22 (talk)
7. Mining the genome-wide screens of chromosomal networks. Stockholm-Uppsala Chromatin Meeting, Stockholm, Sweden, 2007 May 29 (talk)  
8. Epigenetically controlled chromosomal networks. A Swedish Network in Epigenetics, 1st Annual Meeting, Johannesberges Castle Stockholm, Sweden, 2007 Sept 27-28 (poster)
9. Developmentally regulated chromosomal networks. EBC Symposium. Evolutionary Biology Center, Uppsala University, Uppsala 75236, Sweden. 2007 Nov 22 (Poster)
10. Exprimer: A novel tool to design primers from exon-junctions. Symposium on Bioinformatics for Genome Analysis. Bose Institute, Kolkata, India. 2004 January 29-30 (Poster)
11. High on metabolism, high on protein: A comparison of N metabolising enzymes in rice and Spirulina. Society of Biological Chemists, annual conference, PAU, Ludhiyana, India. 2002 Nov 14-16 (Poster) 

Teaching experience

I delivered a lecture series on “Introduction to modern epigenetics” to post-graduate students at Uppsala University in year 2008. (Course coordinator: Dr. Elena Jazin, Dept. of Animal Developmen and Genetics, Evolutionary Biology Center, Uppsala University). The program includes interactive lectures, designing assignments and round-table discussions.

Awards and Scholarships

1. Foundation of Zoological Research, Uppsala University (2007-09)
2. Sartorius scholarship for the best life science student at IBAB (2003-04).
3. IBM scholarship for interns (2003-04).
4. Bronze medal for scoring 3rd rank in B.Sc. in the college (2001).
5. 2nd rank in  10+2 standard.
6. Award for scoring highest marks in Biology and Social Science in high school (1996).
7. 1st rank in high school (1996).

Publications

• Total research articles: 15
• 1st author articles: 8
• Corresponding author: 3

1. Sandhu KS, Zhao Z, Shi C, Ohlsson R*. Genome-wide chromatin interactions of mouse H19 imprinting control locus negate a general link to CTCF. Manuscript, 2010
2. Reinius B, Shi C, Hengshuo L, Sandhu KS, Radomska K, Rosen GD, Lu L, Kullander K, Williams RW and Jazin E. Female-biased non-coding RNAs are co-localized with protein-coding X-inactivation escapee genes on mouse X-chromosome. BMC Genomics, 2010 (under review)
3. Sandhu KS*. Systems properties of proteins encoded by imprinted genes. Epigenetics, 2010; 5 (7) (early online).
4. 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.
5. Sandhu KS*. Intrinsic disorder explains diverse nuclear roles of chromatin remodeling proteins. J Mol Recognit. 2009 Jan-Feb;22(1):1-8.
6. Sandhu KS*, Pandey S, Maiti S, Pillai B. GASCO: genetic algorithm simulation for codon optimization. In Silico Biol. 2008;8(2):187-92.
7. 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.
8. 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.
9. Sandhu KS, Dash D*. Dynamic alpha-helices: conformations that do not conform. Proteins. 2007 Jul 1;68(1):109-22.
10. 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.
11. BioSuite: A comprehensive bioinformatics software package (A unique industry–academia pcollaboration). The NMITLI-BioSuite Team. Current Science. 2007 Jan 10; 92 (1): 29-38.
12. 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.
13. Sandhu KS, Dash D*. Conformational flexibility may explain multiple cellular roles of PEST motifs. Proteins. 2006 Jun 1;63(4):727-32.
14. 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.
15. Sandhu KS, Acharya KK*. ExPrimer: to design primers from exon--exon junctions. Bioinformatics. 2005 May 1;21(9):2091-2.