Assistant Professor

Dr Sandeep Singh

Department of Biological Sciences

Interests

  1. Development of computational tools
  2. Machine learning based predictive models
  3. Structure prediction of peptides.

Education

2007

Allahabad Agricultural Institute
Deemed University
India
BTech

2009

Indian Institute of Information Technology Allahabad
India
MTech

2017

CSIR-Institute of Microbial Technology Chandigarh
India
PhD

Experience

  • 1 year 9 months – Assistant Professor – Lovely Professional University, Punjab
  • 5 years – Research Associate – University of Virginia, USA

Research

  • Development of computational tools to analyse genomics/transcriptomics data.
    Identification of full length chimeric RNAs from long sequencing reads.
    Development of fast screening method to screen a panel of known chimeric RNAs on a large scale cancer transcriptomic data.
  • Machine learning based predictive models for disease diagnosis and therapeutics.
    Integration of chimeric RNA expression profile and gene expression/other genetic features to improve disease diagnosis.
  • Structural Bioinformatics.
    Development of peptide structure prediction methods.
    Modeling of protein-peptide/peptide ligand interactions.

Awards & Fellowships

  • 2007 – GATE – IIT Kanpur
  • 2010 – CSIR-JRF/NET – Council of Scientific and Industrial Research
  • Dr V C Vora Best PhD Thesis Award (2017) awarded by CSIR-Institute of Microbial Technology Chandigarh

Publications

  • 1. Xie Z, Janczyk P, Shi X, Wang Q, Singh S, Cornelison R, Xu J, Mandell J.W., Barr F.G., Li H*. (2022). Rhabdomyosarcomas are oncogene addicted to the activation of AVIL. Proceedings of the National Academy of Sciences 119(24):1-10. doi: 10.1073/pnas.2118048119
  • 2. Comparative study of bioinformatic tools for the identification of chimeric RNAs from RNA Sequencing - Singh S and Li H* - RNA Biology 2021, 1-13 (2021) doi: 10.1080/15476286.2021.1940047
  • 3. A cytoskeleton regulator AVIL drives tumorigenesis in glioblastoma - Xie Z, Janczyk PL, Zhang Y, Liu A, Shi X, Singh S, Facemire L, Kubow K, Li Z, Jia Y, Schafer D, Mandell JW, Abounader R, Li H* - Nature Communications 11(3457), 1-15 (2020) doi: 10.1038/s41467-020-17279-1
  • 4. Landscape characterization of chimeric RNAs in colorectal cancer - Wu H, Singh S, Xie Z, Li X, Li H* - Cancer Letters 489, 56-65 (2020) doi: 10.1016/j.canlet.2020.05.037
  • 5. Topoisomerase II contributes to DNA secondary structure-mediated double- stranded breaks - Szlachta K#, Manukyan A#, Raimer HM#, Singh S, Salamon A, Guo W, Lobachev KS, Wang YH* - Nucleic Acids Res 48, 6654-6671 (2020) doi: 10.1093/nar/gkaa483
  • 6. Pausing sites of RNA polymerase II on actively transcribed genes are enriched with DNA double-stranded breaks. - Singh S#, Szlachta K#, Manukyan A, Raimer HM, Dinda M, Bekiranov S and Wang YH* - J. Biol. Chem 295, 3990-4000 (2020) doi: 10.1074/jbc.RA119.011665
  • 7. The Landscape of Chimeric RNAs in Non-Diseased Tissues and Cells - Singh S#, Qin F#, Kumar S, Elfman J, Lin E, Pham, LP, Yang A and Li H* - Nucleic Acids Res 48(4), 1764-1778 (2020) doi: 10.1093/nar/gkz1223
  • 8. RUNX3 Levels In Human Hematopoietic Progenitors Are Regulated By Aging And Dictate Erythroid-Myeloid Balance. - Balogh P, Adelman ER, Pluvinage JV, Capaldo BJ, Freeman KC, Singh S, Elagib KE, Nakamura Y, Kurita R, Sashida G, Zunder ER, Li H, Gru AA, Price EA, Schrier SL, Weissman IL, Figueroa ME, Pang WW, Goldfarb AN* - Haematologica 105, 905-913 (2020) doi: 10.3324/haematol.2018.208918
  • 9. Functional heritage: The evolution of chimeric RNA into a gene - Wu H, Singh S, Shi X, Xie Z, Lin E, Li X and Li Hui* - RNA Biology 2019, 1-10 (2019) doi: 10.1080/15476286.2019.1670038
  • 10. The Landscape of Chimeric RNAs in Bladder Urothelial Carcinoma - Zhu D, Singh S, Chen X, Zheng Z, Huang J, Lin T and Li H. - Int. J. Biochem. Cell Biol 110, 50-58 (2019) doi: 10.1016/j.biocel.2019.02.007
  • 11. Benchmarking of different molecular docking methods for protein-peptide docking. - Agrawal P#, Singh H#, Srivastava HK, Singh S, Kishor G and Raghava GPS. - BMC Bioinformatics 19(13), 426 (2019) doi: 10.1186/s12859-018-2449-y
  • 12. A cell-based splicing reporter system to identify regulators of cis-splicing between adjacent genes - Katarzyna Chwalenia#, Fujun Qin#, Sandeep Singh, Hui Li - Nucleic Acids Res 47(4), e24 (2018) doi: 10.1093/nar/gky1288
  • 13. The Landscape and Implications of Chimeric RNAs in Cervical Cancer - Peng Wu, Shuo Yang, Sandeep Singh, Fujun Qin, Shailesh Kumar, Ling Wang, Ding Ma, Hui Li - EBioMedicine 37, 158-167 (2018) doi: 10.1016/j.ebiom.2018.10.059
  • 14. AntiTbPdb: a knowledgebase of anti-tubercular peptides - Salman Sadullah Usmani, Rajesh Kumar, Vinod Kumar, Sandeep Singh, Gajendra PS Raghava - Database 2018, bay025 (2018) doi: 10.1093/database/bay025
  • 15. In silico approaches for predicting the half-life of natural and modified peptides in blood - Deepika Mathur, Sandeep Singh, Mehta A, Piyush Agrawal and GPS Raghava - PloS one 13 (6), e0196829 (2018) doi: 10.1371/journal.pone.0196829
  • 16. Connections between Transcription Downstream of Genes and cis-SAGe Chimeric RNA - Katarzyna Chwalenia, Fujun Qin, Sandeep Singh, Panjapon Tangtrongstittikul, Hui Li - Genes 8 (11), 338 (2017) doi: 10.3390/genes8110338
  • 17. THPdb: Database of FDA-approved peptide and protein therapeutics. - Usmani SS#, Bedi G#, Samuel JS#, Singh S, Kalra S, Kumar P, Ahuja AA, Sharma M, Gautam A*, Raghava GPS*. - PloS one 12(7), e0181748 (2017) doi: 10.1371/journal.pone.0181748
  • 18. Assessing therapeutic potential of molecules: molecular property diagnostic suite for tuberculosis (MPDSTB). - Anamika Singh Gaur, Anshu Bhardwaj, Arun Sharma, Lijo John, M Ram Vivek, Neha Tripathi, Prasad V Bharatam, Rakesh Kumar, Sridhara Janardhan, Abhaysinh Mori, Anirban Banerji, Andrew M Lynn, Anmol J Hemrom, Anurag Passi, Aparna Singh, Asheesh Kumar, Charuvaka Muvva, Chinmai Madhuri, Chinmayee Choudhury, D Arun Kumar, Deepak Pandit, Deepak R. Bharti, Devesh Kumar, ER Azhagiya Singam, Gajendra PS Raghava, Hari Sailaja, Harish Jangra, Kaamini Raithatha, Karunakar Tanneeru, Kumardeep Chaudhary, M Karthikeyan, M Prasanthi, Nandan Kumar, N Yedukondalu, Neeraj K Rajput, P Sri Saranya, Pankaj Narang, Prasun Dutta, R Venkata Krishnan, Reetu Sharma, R Srinithi, Ruchi Mishra, S Hemasri, Sandeep Singh, Subramanian Venkatesan, Suresh Kumar, Uca Jaleel, Vijay Khedkar, Yogesh Joshi, G Narahari Sastry - J. Chem. Sci. 129(5), p515-531 (2017) doi: 10.1007/s12039-017-1268-4
  • 19. Computer-aided designing of immunosuppressive peptides based on IL-10 inducing potential. - Nagpal G#, Usmani SS#, Dhanda SK#, Kaur H, Singh S, Sharma M and Raghava GPS - Sci. Rep. 7, 42851 (2017) doi: 10.1038/srep42851
  • 20. SATPdb: A database of structurally annotated therapeutic peptides. - Singh S, Chaudhary K, Dhanda SK, Bhalla S, Usmani SS, Gautam A, Tuknait A, Agrawal P, Mathur D and Raghava GPS - Nucleic Acids Res 44 (D1), D1119-D1126 (2016) doi: 10.1093/nar/gkv1114
  • 21. PEPlife: A Repository of the Half-life of Peptides. - Mathur D, Prakash S, Anand P, Kaur H, Agrawal P, Mehta A, Kumar R, Singh S and Raghava GPS. - Sci. Rep. 6, 36617 (2016) doi: 10.1038/srep36617
  • 22. ZikaVR: An integrated zika virus resource for genomics, proteomics, phylogenetic and therapeutic analysis. - Gupta AK#, Kaur K#, Rajput A#, Dhanda SK#, Sehgal M#, Khan MS#, Monga I, Dar SA, Singh S, Nagpal G, Usmani SS, Thakur A, Kaur G, Sharma S, Bhardwaj A, Qureshi A, Raghava GPS and Kumar M. - Sci. Rep. 6, 32713 (2016) doi: 10.1038/srep32713
  • 23. Prediction of anticancer molecules using hybrid model developed on molecules screened against NCI-60 cancer cell lines. - Singh H, Kumar R, Singh S, Chaudhary K, Gautam A and Raghava GPS. - BMC Cancer 16, 77 (2016) doi: 10.1186/s12885- 016-2082-y
  • 24. CPPsite 2.0. A repository of experimentally validated cell-penetrating peptides. - Agrawal P#, Bhalla S#, Usmani SS#, Singh S, Chaudhary K, Raghava GPS* and Gautam A*. - Nucleic Acids Res 44 (D1), D1098-D1103 (2016) doi: 10.1093/nar/gkv1266
  • 25. A web server and mobile app for computing hemolytic potency of peptides. - Chaudhary K#, Kumar R#, Singh S#, Tuknait A, Gautam A, Mathur D, Anand P, Varshney GC and Raghava GPS. - Sci. Rep. 6, 22843 (2016) doi: 10.1038/srep22843
  • 26. PEPstrMOD: structure prediction of peptides containing natural, non-natural and modified residues. - Singh S, Singh H, Tuknait T, Chaudhary K, Singh B, Kumaran S and Raghava GP - Biology Direct 10, 73 (2015) doi: 10.1186/s13062-015-0103-4
  • 27. Antiangiopred: A server for prediction of anti-angiogenic peptides. - Ramaprasad ASE, Singh S, Raghava GPS and Venkatesan S. - PloS one 10 (9), e0136990 (2015) doi: 10.1371/journal.pone.0136990
  • 28. In silico platform for predicting and initiating beta-turns in a protein at desired locations. - Singh H#, Singh S# and Raghava GPS. - Prot. Struct. Func. Bio. 83, 910- 921 (2015) doi: 10.1002/prot.24783
  • 29. QSAR based model for discriminating EGFR inhibitors and non-inhibitors using Random Forest. - Singh H, Singh S, Singla D, Agarwal SM and Raghava GPS. - Biology Direct 10, 10 (2015) doi: 10.1186/s13062-015-0046-9
  • 30. AHTPDB: a comprehensive platform for analysis and presentation of antihypertensive peptides. - Kumar R, Chaudhary K, Sharma M, Nagpal G, Chauhan JS, Singh S, Gautam A, Raghava GP - Nucleic Acids Res 43 (D1), D956-962 (2015) doi: 10.1093/nar/gku1141
  • 31. CancerPPD: a database of anticancer peptides and proteins. - Tyagi A, Anand P, Gupta S, Sharma M, Mathur D, Joshi A, Singh S, Gautam A, and Raghava G.P.S. - Nucleic Acids Res 43 (D1), D837-843 (2014) doi: 10.1093/nar/gku892
  • 32. Evaluation of Protein Dihedral Angle Prediction Methods. - Singh H#, Singh S# and Raghava GPS - PloS one 9(8), e105667 (2014) doi: 10.1371/journal.pone.0105667
  • 33. ParaPep: a web resource for experimentally validated antiparasitic peptide sequences and their structures. - Mehta D#, Anand P#, Kumar V#, Joshi A#, Mathur D#, Singh S, Tuknait A, Chaudhary K, Gautam SK, Gautam A, Varshney GC*, Raghava GPS* - Database 2014, bau051 (2014) doi: 10.1093/database/bau051
  • 34. Hemolytik: a database of experimentally determined hemolytic and non-hemolytic peptides. - Gautam A#, Chaudhary K#, Singh S#, Joshi A, Anand P, Tuknait A, Mathur D, Varshney GC, and Raghava GPS* - Nucleic Acids Res 42, D444-449 (2014) doi: 10.1093/nar/gkt1008

Contact Details

  • E-mail id: sandeep.s@srmap.edu.in
TOP