Books, Patents, Publications & Thesis
Selected Publications
Patent Granted & Published:
1. Abhishek Narain Singh, Flashlight Superhelical Photobioreactor, for mass cultivation of algae for biodiesel production and for other suitable purposes. Application Nr: 1135/DEL/2006, Patent Number: 252085 [link]
Patents Published:
2. Abhishek Narain Singh, Method to by-pass allosteric domain activity of an enzyme such as to alter the feed-back or feed-forward inhibition or activation: application in vitamin B5 pathway for its overproduction as an example. Patent Application: 1760/DEL/2010 [link]
Patents Provisional:
3. Abhishek Narain Singh, Deepak Singh Rathore, SWAYANTRA: people, process, performance big data analytics machine. Patent Application: 3328/DEL/2014
4.Abhishek Narain Singh, Genome Repeat Region ALU/LINES Sequencing & Functional characterization & drug re-positioning for AMD and eye disorders Application Nr: 201711031540
Journals and Conferences:
1. Abhishek Narain Singh, Para-Seqs: Parallel Next Generation Sequencing Pattern Match Tools, PaperID# BIC6060, The 18th International Conference on Bioinformatics & Computational Biology, BIOCOMP'17, The 2017 World Congress in Computer Science, Computer Engineering, & Applied Computing, July 17-20, 2017, Las Vegas, USA http://csce.ucmss.com/cr/books/2017/LFS/CSREA2017/BIC6060.pdf
2. Singh AN (2015) JenetStud: A short course on bioinformatics software applications on a typical linux based cluster environment. Nucleus Biotechnology, April 2015 http://nucleusopen.org/jenetstud-a-short-course-on-bioinfo…/
3. Abhishek Narain Singh, A105 Family Decoded: Discovery of Genome-Wide Fingerprints for Personalized Genomic Medicine, page 115-126, Proceedings of the International Congress on Personalized Medicine UPCP 2012 (February 2-5, 2012, Florence, Italy), Medimond Publisher, ScienceMED journal vol.3 issue 2, April 2012. http://www.edlearning.it/ScienceMED/v3_2_2012.pdf
4. Abhishek Narain Singh, Comparative Optimal analysis of de novo assembly tools in pursuit of personalized medicine, page 127-137, Proceedings of the International Congress on Personalized Medicine UPCP 2012 (February 2-5, 2012, Florence, Italy), Medimond Publisher, ScienceMED journal vol.3 issue 2, April 2012. http://www.edlearning.it/ScienceMED/v3_2_2012.pdf
5. Abhishek Narain Singh, Dinesh Gupta and Shahid Jameel, Bioinformatics analysis of the SARS virus X1 protein shows it to be a calcium-binding protein, Current Science, Vol.86,NO.6, 25 MARCH 2004, http://tinyurl.com/sars-x1
6. Abhishek Narain Singh, Customized Biomedical Informatics, BIOCOMP'13, The 14th International Conference on Bioinformatics and Computational Biology, July 22-25, 2013, Las Vegas, USA http://tinyurl.com/BIOCOMB13 .
7. Abhishek Narain Singh, Bioinformatics Component in Personalized Medicine, BIOCOMP'13, The 14th International Conference on Bioinformatics and Computational Biology, July 22-25, 2013, Las Vegas, USA http://tinyurl.com/BIOCOMB13 .
8. D.A. Bader, Y. Li, T. Li, V. Sachdeva, ``BioPerf: A Benchmark Suite to Evaluate HighPerformance Computer Architecture on Bioinformatics Applications,'' The IEEE International Symposium on Workload Characterization (IISWC 2005), Austin, TX, October 6-8, 2005. ( Acknowledgement Author A.N. Singh) https://www.cc.gatech.edu/~bader/papers/BioPerf-IIWSC05.pdf Slides at: https://www.slidedoc.us/david-a-bader
9. Bhavnani, S.K., Abbas, M., McMicken, V., Oezguen, N., Tupa, J., iCircos: Visual Analytics for Translational Bioinformatics. Proceedings of ACM International Health Informatics Symposium, IHI'2012 (Acknowledgement Author Abhishek Narain Singh) http://www.skbhavnani.com/DIVA/papers/Bhavnani_et_al-IHI-2012.pdf
10. Abhishek Narain Singh, Drug Repositioning in Pursuit of Personalized Medicine by Means of Big Data Analytics: An AMD Eye Disorder Point of View to Cure Blindness and to Sequence ALU Isoforms, Biocomp 2018, Las Vegas, USA https://csce.ucmss.com/cr/books/2018/LFS/CSREA2018/BIC3484.pdf
Posters and Meeting reports
10. D. A. Bader, V. Sachdeva, V. Agarwal, G. Gupta and A. N. Singh, Life Science Applications, IBM/DARPA High Productivity Computing Systems (HPCS) Project Meeting, Austin, TX, February 8, 2005.
11. D.A. Bader, V. Sachdeva, V. Agarwal, G. Goel, A.N. Singh, BioSPLASH: A sample workload for bioinformatics and computational biology for optimizing next-generation performance computer systems, Technical Report, University of New Mexico, USA, May 2005. http://www.cc.gatech.edu/~bader/papers/BioSplash-050501.pdf
12. Abhishek Narain Singh, Knowledge Mining and Bioinformatics Tools to Advance Personalized Diagnostics and Therapeutics, USISTF organized Workshop, Florence Nov 2012, Italy http://tinyurl.com/biomining http://hit.fiu.edu/W/pre-report.pdf
13. Abhishek Narain Singh, A105 Family Decoded: Discovery of Genome-Wide Fingerprints for Personalized Genomic Medicine, Poster, 2-5 Feb UPCP 2012, Florence, Italy http://f1000.com/posters/browse/summary/1089898
14. Abhishek Narain Singh, A4C Decoded: Comparative Optimal analysis of de novo assembly tools in pursuit of personalized medicine, Poster, 2-5 Feb UPCP 2012, Florence, Italy http://f1000.com/posters/browse/summary/1089897
15. Abhishek Narain Singh, Variations in Genome Architecture, Poster, International Congress on Personalized Medicine, 2-5 Feb UPCP 2012, Florence, Italy http://f1000.com/posters/browse/summary/1089896
16. Abhishek Narain Singh, Cisca Wijmenga, Lude Franke, Morris Swertz, Members of Genomics Coordination Centre, Comparison of Structural Variation between Build 36 Reference Genome and Celera R27 Genome using GenomeBreak, Posters Connecting Biobanks, BBMRI-NL conference, 21 November 2011, Rotterdam Members of BBMRI-NL rainbow projects ‘Genome of -7- the Netherlands’ & ‘dynamic biobank bioinformatics’, Genome of the Netherlands, Posters Connecting Biobanks, BBMRI-NL conference, 21 November 2011, Rotterdam
17. Abhishek Narain Singh, Parallel Gene Hunting Tools, Poster Presentation, The 2nd Symposium on Systems Genetics, 29-30 September 2011, Groningen
18. Abhishek Narain Singh, Comparison of Structural Variation between Build 36 Reference Genome and Celera R27c Genome using GenomeBreak, Poster Presentation, The 2nd Symposium on Systems Genetics, 29-30 September 2011, Groningen
19. Abhishek Singh, GENOMEBREAK: A versatile computational tool for genome-wide rapid investigation, exploring the human genome, a step towards personalized genomic medicine, Poster 70, Human Genome Meeting 2011, Dubai, March 2011
20. Abhishek Narain Singh, AlgaeTech: Alternative Fuel, Poster Presentation, Algal Biomass Organization Summit 2010, Phoenix, Arizona, September 29- October 2 , 2010.
21. D.A. Bader, V. Sachdeva, A. Trehan, V. Agarwal, G. Gupta, and A.N. Singh, BioSPLASH: A sample workload from bioinformatics and computational biology for optimizing next-generation high-performance computer systems (Poster Session), 13th Annual International Conference on Intelligent Systems for Molecular Biology (ISMB 2005), Detroit, MI, June 25-29, 2005.
22. Abhishek Narain Singh, Customized and Personalized Next Generation Genomic, ASHG '13, 63rd Annual Meeting of the American Society of Human Genetics, October 22-26, 2013, Boston, USA (accepted as poster).
M.Tech Thesis Publication, IIT Delhi:
23. Abhishek Narain Singh, Development of Photobioreactor, M.Tech thesis, 2004-06, IIT Delhi [M.Tech Thesis resulting patent]
PhD Study, CDS, Thesis Publication, Cambridge University:
24. Abhishek Narain Singh, Strategies to increase levels of vitamin B5 in plants and algae, PhD Study, CDS, Thesis 2007-09, University of Cambridge PhD Study, CDS, Cambridge University, UK
MBA Thesis Publication, Leipzig Graduate School of Management:
25. Abhishek Narain Singh, Fail-to-Fail - Trinomial ttha affected optional valuation, MBA Thesis, 2017, Leipzig Graduate School of Management, Germany
26. Abhishek Narain Singh, SVs have higher selection pressure to track inheritance by Y-Chromosome and mtDNA and associated paternal and maternal diseases respectively, while SNPs from them would be more
individual specific, Personalized and Precision Medicine International Conference, PEMED, June 2018, Paris, France (accepted as poster)
27. Abhishek Narain Singh, SVs have higher selection pressure to track inheritance by Y-Chromosome and mtDNA, while SNPs from them would be more individual specific with high rate of mutation & associated paternal and maternal diseases respectively - mtDNA can exhibit more complex scenario than heteroplasmy, In Press
28. Abhishek Narain Singh, ‘SasCsvToolkit’ - A versatile parallel `bag-of-tasks` job submission application on heterogeneous and homogeneous platforms for Big Data Analytics such as for Biomedical Informatics, In Press
29. Abhishek Narain Singh, Precision Genomic Diagnostics & Scientific Discoveries, In Press
30. Abhishek Narain Singh, Peptidomics integrated Multi Omics based Precision Diagnosis, In Press
31. Abhishek Narain Singh, Genome Wide Pattern Search, In Press
32. Abhishek Narain Singh, Genome Assembly by de novo method - Comparative Analysis, In Press
33. Abhishek Narain Singh, Drug Repositioning in pursuit of Personalized Medicine by means of Big Data Analytics, In Press
34. Abhishek Narain Singh, Customized Biomedical Informatics, In Press
35. Abhishek Narain Singh, Big Data Analytics to combat SARS virulence Epidemic: Calcium binding property of cytosolic region of 3a protein can be pro-apoptotic, In Press
36. Abhishek Narain Singh, Metabolic Pathway Engineering by deregulating allosteric domain feedback or feedforward activity of an enzyme and other techniques, In Press
37. Abhishek Narain Singh, ‘Trinomial Risk Appetite Re-joining Tree’ Real Options Valuation - Case Studies in the Biotech & Pharmaceutical sector, In Press
BOOKS
38. Abhishek Narain Singh, Genetic Engineering Strategies, Scholar's Press, September 2, 2016, GenEngg URL, , ISBN 978-3-659-83921-4 (Email me at aby.narain@gmail.com if you need a printed copy of the book).
39. Abhishek Narain Singh, Co-Author, Knowledge Mining and Bioinformatics Techniques, 2014, Web Publication http://cake.fiu.edu/HIT-papers/Book_post_NSF_Workshop_Knowledge_Mining_and_Bioinformatics_Techniques_to_Advance_Personalized_Diagnostics_and_Therapeutics.pdf
Publication from PhD Study, CDS, at Cambridge University, UK
1. Chakauya et. al., Towards engineering increased pantothenate (vitamin B5) levels in plants, Plant Mol Biol (2008) 68:493–503 DOI 10.1007/s11103-008-9386-5
PsychDPC Project Publications where I was Marie Curie Experienced Researcher
Protoclin Project Publications where I was a Marie Curie Experienced Researcher
Klein J, Lacroix C, Caubet C, Siwy J, Zürbig P, Dakna M, Muller F, Breuil B, Stalmach A, Mullen W, Mischak H, Bandin F, Monsarrat B, Bascands JL, Decramer S, Schanstra JP.
Fetal Urinary Peptides to Predict Postnatal Outcome of Renal Disease in Fetuses with Posterior Urethral Valves (PUV). Sci Transl Med. 2013 Aug 14;5(198):198ra106. doi: 10.1126/scitranslmed.3005807. PubMed PMID: 23946195
. Albalat A, Stalmach A, Bitsika V, Siwy J, Schanstra JP, Petropoulos AD, Vlahou, A, Jankowski J, Persson F, Rossing P, Jaskolla TW, Mischak H, Husi H. Improving peptide relative quantification in MALDI-TOF MS for biomarker assessment. Proteomics. 2013 Aug 14. doi: 10.1002/pmic.201300100. [Epub ahead of print] PubMed PMID: 23943474.
Moulos P, Klein J, Jupp S, Stevens R, Bascands JL, Schanstra JP. The KUPNetViz: a biological network viewer for multiple -omics datasets in kidney diseases. BMC Bioinformatics. 2013 Jul 24;14:235. doi: 10.1186/1471-2105-14-235. PubMed PMID: 23883183; PubMed Central PMCID: PMC3725151.
Mischak H, Vlahou A, Ioannidis JP. Technical aspects and inter-laboratory variability in native peptide profiling: the CE-MS experience. Clin Biochem. 2013 Apr;46(6):432-43. doi: 10.1016/j.clinbiochem.2012.09.025. Epub 2012 Oct 4. Stalmach A, Albalat A, Mullen W, Mischak H.
Recent advances in capillary electrophoresis coupled to mass spectrometry for clinical proteomic applications. Electrophoresis. 2013 Mar 20. doi: 10.1002/elps.201200708. [Epub ahead of print] Mischak H. How to get proteomics to the clinic? Issues in clinical proteomics, exemplified by CE-MS. Proteomics Clin Appl. 2012 Oct;6(9-10):437-42. doi: 10.1002/prca.201200027. Epub 2012 Sep 24.
Klein J, Eales J, Zürbig P, Vlahou A, Mischak H, Stevens R. Proteasix: A tool for automated and large-scale prediction of proteases involved in naturally occurring peptide generation. Proteomics. 2013 Apr;13(7):1077-82. doi: 10.1002/pmic.201200493. Epub 2013 Feb 26.
Molin L, Seraglia R, Lapolla A, Ragazzi E, Gonzalez J, Vlahou A, Schanstra JP, Albalat A, Dakna M, Siwy J, Jankowski J, Bitsika V, Mischak H, Zürbig P, Traldi P. A comparison between MALDI-MS and CE-MS data for biomarker assessment in chronic kidney diseases. J Proteomics. 2012 Oct 22;75(18):5888-97. doi: 10.1016/j.jprot.2012.07.024. Epub 2012 Jul 26.
Klein, Jupp, Moulos, Fernandez, Buffin-Meyer, Casemayou, Chaaya, Charonis, Bascands, Stevens, and Schanstra. The KUPKB: a novel Web application to access multiomics data on kidney disease. FASEB J. 2012 May;26(5):2145-53. doi: 10.1096/fj.11-194381. Epub 2012 Feb 17.
Mullen., Albalat, Gonzalez, Zerefos, Siwy, Franke, Mischak Performance of different separation methods interfaced in the same MS-reflection TOF: comparison of performance between CE versus HPLC. Electrophoresis. 2012 Feb;33(4):567- 74. doi: 10.1002/elps.201100415.
Ambati Group Publication during my Scientific Engagement
Kerur N, et.al., cGAS drives noncanonical-inflammasome activation in age-related macular degeneration. Nature Medicine. 2017 Nov 27. doi 10.1038/nm.4450.
Scherer Group Publication during my Scientific Engagement
The diploid genome sequence of an individual human. Levy S, Sutton G, Ng PC, Feuk L, Halpern AL, Walenz BP, Axelrod N, Huang J, Kirkness EF, Denisov G, Lin Y, MacDonald JR, Pang AW, Shago M, Stockwell TB, Tsiamouri A, Bafna V, Bansal V, Kravitz SA, Busam DA, Beeson KY, McIntosh TC, Remington KA, Abril JF, Gill J, Borman J, Rogers YH, Frazier ME, Scherer SW, Strausberg RL, Venter JC. PLoS Biol. 2007 Sep 4;5(10):e254. PMID: 17803354
Genome of The Netherlands (GoNL) publications in which I was involved as an ICT professional.
Sohail, M, Vakhrusheva, OA, Sul, JH, Pulit, SL, Francioli, LC, Genome of the Netherlands Consortium, Alzheimer’s Disease Neuroimaging Initiative, van den Berg, LH, Veldink, JH, de Bakker, PIW, Bazykin, GA, Kondrashov, AS, Sunyaev, SR. 2017. Negative selection in humans and fruit flies involves synergistic epistasis. Science 356:539-542.
Francioli, LC, Cretu-Stancu, M, Garimella, KV, Fromer, M, Kloosterman, WP, Genome of the Netherlands consortium, Samocha, KE, Neale, BM, Daly, MJ, Banks, E, DePristo, MA, de Bakker, PI. 2017. A framework for the detection of de novo mutations in family-based sequencing data. Eur. J. Hum. Genet. 25:227-233.
Hehir-Kwa, JY, Marschall, T, Kloosterman, WP, Francioli, LC, Baaijens, JA, Dijkstra, LJ, Abdellaoui, A, Koval, V, Thung, DT, Wardenaar, R, Renkens, I, Coe, BP, Deelen, P, de Ligt, J, Lameijer, EW, van Dijk, F, Hormozdiari, F, Genome of the Netherlands Consortium, Uitterlinden, AG, van Duijn, CM, Eichler, EE, de Bakker, PI, Swertz, MA, Wijmenga, C, van Ommen, GB, Slagboom, PE, Boomsma, DI, Schönhuth, A, Ye, K, Guryev, V. 2016. A high-quality human reference panel reveals the complexity and distribution of genomic structural variants. Nat Commun 7:12989.
van den Akker, EB, Pitts, SJ, Deelen, J, Moed, MH, Potluri, S, van Rooij, J, Suchiman, HE, Lakenberg, N, de Dijcker, WJ, Uitterlinden, AG, Kraaij, R, Hofman, A, de Craen, AJ, Houwing-Duistermaat, JJ, van Ommen, GJ, Genome of The Netherlands Consortium, Cox, DR, van Meurs, JB, Beekman, M, Reinders, MJ, Slagboom, PE. 2016. Uncompromised 10-year survival of oldest old carrying somatic mutations in DNMT3A and TET2. Blood 127:1512-5.
Palamara, PF, Francioli, LC, Wilton, PR, Genovese, G, Gusev, A, Finucane, HK, Sankararaman, S, Genome of the Netherlands Consortium, Sunyaev, SR, de Bakker, PI, Wakeley, J, Pe'er, I, Price, AL. 2015. Leveraging Distant Relatedness to Quantify Human Mutation and Gene-Conversion Rates. Am. J. Hum. Genet. 97:775-89.
van Leeuwen, EM, Kanterakis, A, Deelen, P, Kattenberg, MV, Genome of the Netherlands Consortium, Slagboom, PE, de Bakker, PI, Wijmenga, C, Swertz, MA, Boomsma, DI, van Duijn, CM, Karssen, LC, Hottenga, JJ. 2015. Population-specific genotype imputations using minimac or IMPUTE2. Nat Protoc 10:1285-96.
Minică, CC, Dolan, CV, Hottenga, JJ, Pool, R, Genome of the Netherlands Consortium, Fedko, IO, Mbarek, H, Huppertz, C, Bartels, M, Boomsma, DI, Vink, JM. 2015. Heritability, SNP- and Gene-Based Analyses of Cannabis Use Initiation and Age at Onset. Behav. Genet. 45:503-13.
Francioli, LC, Polak, PP, Koren, A, Menelaou, A, Chun, S, Renkens, I, Genome of the Netherlands Consortium, van Duijn, CM, Swertz, M, Wijmenga, C, van Ommen, G, Slagboom, PE, Boomsma, DI, Ye, K, Guryev, V, Arndt, PF, Kloosterman, WP, de Bakker, PIW, Sunyaev, SR. 2015. Genome-wide patterns and properties of de novo mutations in humans. Nat. Genet. 47:822-826.
van Leeuwen, EM, Karssen, LC, Deelen, J, Isaacs, A, Medina-Gomez, C, Mbarek, H, Kanterakis, A, Trompet, S, Postmus, I, Verweij, N, van Enckevort, DJ, Huffman, JE, White, CC, Feitosa, MF, Bartz, TM, Manichaikul, A, Joshi, PK, Peloso, GM, Deelen, P, van Dijk, F, Willemsen, G, de Geus, EJ, Milaneschi, Y, Penninx, BW, Francioli, LC, Menelaou, A, Pulit, SL, Rivadeneira, F, Hofman, A, Oostra, BA, Franco, OH, Mateo Leach, I, Beekman, M, de Craen, AJ, Uh, HW, Trochet, H, Hocking, LJ, Porteous, DJ, Sattar, N, Packard, CJ, Buckley, BM, Brody, JA, Bis, JC, Rotter, JI, Mychaleckyj, JC, Campbell, H, Duan, Q, Lange, LA, Wilson, JF, Hayward, C, Polasek, O, Vitart, V, Rudan, I, Wright, AF, Rich, SS, Psaty, BM, Borecki, IB, Kearney, PM, Stott, DJ, Adrienne Cupples, L, Genome of The Netherlands Consortium, Jukema, JW, van der Harst, P, Sijbrands, EJ, Hottenga, JJ, Uitterlinden, AG, Swertz, MA, van Ommen, GJ, de Bakker, PI, Eline Slagboom, P, Boomsma, DI, Wijmenga, C, van Duijn, CM. 2015. Genome of The Netherlands population-specific imputations identify an ABCA6 variant associated with cholesterol levels. Nat Commun 6:6065.
Genome of the Netherlands Consortium. 2014. Whole-genome sequence variation, population structure and demographic history of the Dutch population. Nat. Genet. 46:818-25.