Publications: Tiratha Raj Singh

[Refereed Journals] [Refereed Proceedings] [Book Chapters] [Abstracts and Posters]

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Refereed Journals:

[46] Ashwani Kumar and Tiratha Raj Singh (2017) Analysis for biological network properties of Alzheimer’s disease associated gene set by enrichment and topological examinations, IJBRA. , Accepted [PubMed].

[45] Vineet Mehta, Arun Parashar, Arun Sharma, Tiratha Raj Singh, Udayabanu Malairaman (2017) Quercetin ameliorates chronic unpredicted stress mediated memory dysfunction in male Swiss albino mice by attenuating insulin resistance and elevating hippocampal GLUT4 levels independent of insulin receptor expression. Hormones and Behavior , [PubMed].

[44] Ashwani Kumar and Tiratha Raj Singh (2017) A New Decision Tree to Solve the Puzzle of Alzheimer's Disease Pathogenesis Through Standard Diagnosis Scoring System, Interdiscip Sci.: CLS , 9(1),107-115 [PubMed].

[43] Ahmed Moussa, Brigitte Vannier, Raghu M. Yennamalli, and Tiratha Raj Singh (2016) Recent Trends and Developments in Bioinformatics: Challenges and Opportunities. CSI Communications , 40 (7), 28-31 [PubMed].

[42] Ankita Shukla, Ahmed Moussa, and Tiratha Raj Singh (2016) DREMECELS: A Curated Database for Base Excision and Mismatch Repair Mechanisms Associated Human Malignancies. PlosOne , 11(6):e0157031 [PubMed].

[41] Manika Sehgal, Rajinder Gupta, Ahmed Moussa, and Tiratha Raj Singh (2015) An Integrative Approach for Mapping Differentially Expressed Genes and Network Components Using Novel Parameters to Elucidate Key Regulatory Genes in Colorectal Cancer, PlosOne , 10(7):e0133901 [PubMed].

[40] Varun Kumar, Neha Sharma, Kirti Shitiz, Tiratha Raj Singh, Chanderdeep Tandon, Hemant Sood, and Rajinder Singh Chauhan (2015) An insight into conflux of metabolic traffic leading to picroside-I biosynthesis by tracking molecular time course changes in a medicinal herb, Picrorhiza kurroa. , Plant Cell, Tissue and Organ Culture: Journal of Plant Biotechnology , : [PubMed].

[39] Varun Kumar, Tiratha Raj Singh, Alkesh Hada, Monica Jolly, Andy Ganapathi, Archana Sachdev (2015) Probing Phosphorus Efficient Low Phytic Acid Content Soybean Genotypes with Phosphorus Starvation in Hydroponics Growth System., Applied Biochemistry and Biotechnology , : [PubMed].

[38] Prashanth Survajhala and Tiratha Raj Singh, (2015) Is HNF4A a candidate to study zinc finger protein slug?, IJBRA , 11(4):366-373 [PubMed].

[37] Jibesh Padhan, Varun Kumar, Hemant Sood, Tiratha Raj Singh, and Rajinder Singh Chauhan (2015) Contents of Therapeutic Metabolites in Swertia chirayita Correlate with the Expression Profiles of Multiple Genes in Corresponding Biosynthesis Pathways, Phytochemistry , : [PubMed].

[36] Ankita Shukla, Manika Sehgal, and Tiratha Raj Singh, (2015) Hydroxymethylation and its potential implication in DNA repair system: A review and future perspectives, Gene , 564:109-118 [PubMed].

[35] Ira Vashisht, Prashant Mishra, Tarun Pal, Sreekrishna Chanumolu, Tiratha Raj Singh, Rajinder Singh Chauhan (2015) 2. Mining NGS transcriptomes for miRNAs and dissecting their role in regulating growth, development, and secondary metabolites production in different organs of a medicinal herb, Picrorhiza kurroa, Planta , (DOI 10.1007/s00425-015-2255-y): [PubMed].

[34] Rohit Randhawa, Manika Sehgal, Tiratha Raj Singh, Ajay Duseja, Harish Changotra (2015) Unc-51 like kinase 1 (ULK1) in silico analysis for biomarkers identification: A vital component of autophagy, Gene , 562:40-49 [PubMed].

[33] Sarra HAMZAOUI, Smail BOUZERGANE, Tiratha Raj Singh, Hassan BADIR, and Ahmed MOUSSA(2015) Analysis of Mass Spectrometry data: Significance Analysis of Microarrays for SELDI-MS Data in Proteomics, IJCB , 4(1):05-12 [PubMed].

[32] Manika Sehgal, and Tiratha Raj Singh (2014) Systems biology approach for mutational and site-specific structural investigation of DNA repair genes for xeroderma pigmentosum, Gene , 543 (1):108-117 [PubMed].

[31] Nikhil Malhotra, Varun Kumar, Hemant Sood, Tiratha Raj Singh, and Rajinder Singh Chauhan (2014) Multiple genes of mevalonate and non-mevalonate pathways contribute to high aconites content in an endangered medicinal herb, Aconitum heterophyllum, Phytochemistry , DOI: 10.1016/j.phytochem.2014.08.025: [PubMed].

[30] Manika Sehgal, and Tiratha Raj Singh (2014) DR-GAS: A database of functional genetic variants and their phosphorylation states in human DNA repair systems, DNA Repair , 16: 97-103 [PubMed].

[29] Abhay Pratap, Setu Taliyan, and Tiratha Raj Singh (2014) NMDB: Network Motif Database Envisaged and Explicated from Human Disease Specific Pathways, Journal of Biological Systems , 22(1): 89-100 [PubMed].

[28] Arun Gupta, Sharat Chandra, and Tiratha Raj Singh (2014) HLAB27Pred: SVM Based Precise Method for Predicting HLA-B*2705 Binding Peptides in Antigenic Sequences, Netw Model Anal Health Inform Bioinforma : [PubMed].

[27] Abhik Seal, Arun Gupta, M. Mahalaxmi, Riju A. Tiratha Raj Singh, and V. Arunachalam (2014) Tools, resources and databases for SNPs and indels in sequences: A review., IJBRA 10(3): 264-96 [PubMed].

[26] Meethanshu Mittal, Rahul Singh, and Tiratha Raj Singh (2014) Prediction of ligand binding sites in RNA binding protein pockets using Support Vector Machines, Journal of Biomedical Sciences , : [PubMed].

[25] Praharshit Sharma, Bhupendra Kumar Pathak, and Tiratha Raj Singh (2014) A mathematical model of central dogma of molecular biology employing a novel irrational- integral-imaginary (i3) encoding and numerical approximation based on cellular automaton, International Journal for Computational Biology , 3(1):40-43.

[24] O. Kaissi, E.Nimpaye, Tiratha Raj Singh, B.Vannier, A.Ibrahimi, A.Ghacham, A.Moussa (2013) Gene Selection Comparative Study in Microarray Data Analysis, Bioinformation , 9(20):1019-22 [PubMed].

[23] Tiratha Raj Singh (2013) Mitochondrial genomes and frameshift mutations: hidden stop codons, their functional consequences and disease associations, International Journal of Genomic Medicine , 1: 108 [PubMed].

[22] Priya P. Panigrahi and Tiratha Raj Singh (2013) Computational studies on Alzheimer’s disease associated pathways and regulatory patterns using microarray gene expression and network data: revealed association with aging and other diseases, Journal of Theoretical Biology 334:109-121 [PubMed].

[21] Tiratha Raj Singh, Arun Gupta and Prashanth Suravajhala (2013) Challenges in the miRNA research, IJBRA , 9/6: 576-583[pdf] [PubMed]

[20] Ashwani Kumar and Tiratha Raj Singh (2013) Simulation Studies of Gene-Regulatory Pathways in Baccilus subtilis for Virulence and Competence Phenotype by Quorum Sensing, Systems and Synthetic Biology, 7:33-39.

[19] Arun Gupta and Tiratha Raj Singh (2013) SHIFT: Server for Hidden stops In frameshifted Translations, BMC Research Notes , 6:68. [PubMed] .

[18] Pooja Kaushik, C.K. Jain, R. Gabrani, and Tiratha Raj Singh (2013) Study on variability assessment and evolutionary relationships of glutamate racemase in Pseudomonas species, Interdisplinary Sciences: Computational Life Sciences . 5(4):247-57 [PubMed].

[17] Sharat Chandra, and Tiratha Raj Singh (2012) Linear B-cell epitopes prediction for epitope vaccine design against meningococcal disease and their computational validations through physicochemical properties, Netw Model Anal Health Inform Bioinforma 1(4):153-59.

[16] Digvijay Singh Chauhan, Sharat Chandra, Arun Gupta, and Tiratha Raj Singh (2012) Molecular modelling, docking and interaction studies of Human-plasmogen and Salmonella-enolase with enolase inhibitors, Bioinformation, 8/4: 185-87 [PubMed]

[15] Manika Sehgal, and Tiratha Raj Singh (2012) Identification and analysis of biomarkers for repair proteins: a bioinformatic approach, JNSBM, 2/3: 139-46 [PubMed].

[14] Priya P. Panigrahi, and Tiratha Raj Singh (2012) Computational analysis for functional and evolutionary aspects of BACE-1 and associated Alzheimer’s related proteins, IJCIStudies, 1/4: 322-32.

[13] Tiratha Raj Singh (2011) Phylogenetic Networks: Concepts, Algorithms and Applications, Book Review, Current Science 100/10:1570-71 [pdf] [PubMed]

[12] Tiratha Raj Singh, Arun Gupta, Abhik Seal, M. Mahalaxmi, Riju A. and V. Arunachalam (2011) Computational identification and analysis of single-nucleotide polymorphisms and insertions/deletions in expressed sequence tag data of Eucalyptus., Journal of Genetics 90:e34-38[pdf] [PubMed]

[11] Arun Gupta, Dinesh Chaukiker, and Tiratha Raj Singh (2011) Comparative analysis of epitope predictions: Proposed library of putative vaccine candidates for HIV, Bioinformation 5/9:386-389[pdf] [PubMed]

[10] Sharat Chandra, Digvijay Singh Chauhan, and Tiratha Raj Singh (2010) Prediction of T-cell epitopes from outer membrane protein of outer membrane vesicles of Neisseria meningitidis serogroup B, Bioinformation 5/4:155-161 [pdf] [PubMed]

[9] Prashanth Suravajhala, Jeffrey W. Bizzaro, Pritish Varadwaj, Tiratha Raj Singh and Arun Gupta (2010) Influence of virtual conferences on bioinformatics in India and developing nations. Current Science , 98(11). [pdf]

[8] Tiratha Raj Singh (2010) WEBFARM: Web Server for Finite Automated Restriction Mapping, Bioinformation 4/8:341-343 [pdf] [PubMed]

[7] Tiratha Raj Singh, Georgia Tsagkogeorga, Frederic Delsuc, Samuel Blanquart, Noa Shenkar, Yossi Loya, Emmanuel JP Douzery, and Dorothee Huchon (2009) Tunicate mitogenomics and phylogenetics: peculiarities of the Herdmania momus mitochondrial genome and support for the new chordate phylogeny, BMC Genomics 10:534.[pdf] [PubMed]

[6] Tiratha Raj Singh and K.R. Pardasani (2009) Ambush hypothesis revisited: evidences for phylogenetic trends, Computational Biology and Chemistry 33/3:239-244.[pdf] [PubMed]

[5] Tiratha Raj Singh and K.R. Pardasani (2008) In Silico Analysis of Evolutionary Patterns in Restriction Endonucleases, In Silico Biology 9:0005. [Link to the article] [PubMed]

[4] Tiratha Raj Singh (2008) Mitochondrial Gene Rearrangements: New Paradigm in Evolutionary Biology and Systematics, Bioinformation 3/2:95-97. [pdf] [PubMed]

[3] Tiratha Raj Singh, Ophir Shneor, and Dorothee Huchon (2008) Bird Mitochondrial Gene Order: Insight from 3 Warbler Mitochondrial Genomes, Mol.Biol.Evol. 25/3:475-477.[pdf] [PubMed]

[2] Tiratha Raj Singh and K.R. Pardasani (2007) Computational Model for DNA Fragment Extraction, GAMS J of Math. Biosciences 3/1:70-78.

[1] Tiratha Raj Singh and K.R. Pardasani (2007) Computational protocol for the identification and in silico analysis of Protein Tyrosine Phosphatases (PTPs), Bioinformatics Trends, 2/1:9-16. [Abstract]

Refereed Proceedings:

[12] Manika Sehgal, and Tiratha Raj Singh (2014) Bioinformatics applications to resolve the mystery of diseases associated with Human DNA repair system. , Proceedings of the Annual Conference of Indian Association of Biomedical Scientists,HPCSK Univ., Palampur, India : 14-16 July 2014, pp.39-41., [Abstract]

[11] Ankita Shukla, Manika Sehgal, and Tiratha Raj Singh (2014) Hydroxymethylation and its Role in DNA Repair Associated Disease, Proceedings of the International Conference on Life Sciences, Informatics, Food and Environment ,Noida, India : 29-30, August 2014, [Abstract]

[10] Manika Sehgal, Ankita Shukla, and Tiratha Raj Singh (2014) Functional Enrichment of Pathways Implicated in DNA Repair using Top Down Approach, Proceedings of the International Conference on Life Sciences, Informatics, Food and Environment ,Noida, India : 29-30, August 2014, [Abstract]

[9] Manika Sehgal, and Tiratha Raj Singh (2014) Computational Approach for the Identification of Plausible Biomarkers from Composite Networks and Gene Expression data Associated with Colorectal Cancer, Proceedings of the World Congress on Stem Cell Research, Cancer Biology and Applied Biotechnology,New Delhi, India : 3-4, May 2014, [Abstract]

[8] Ashwani kumar, Abhay Pratap, Urvashi, Rajinder S. Chauhan, and Tiratha Raj Singh (2013) SMDB: Soybean Marker Database, Proceedings of the IFIP International Conference of Bioinformatics,Bhopal, India : 23-26 September, 2013,, [Abstract]

[7] Manika Sehgal, and Tiratha Raj Singh (2011) Identification and analysis of biomarkers for repair proteins: a bioinformatic approach, Proceedings of I-ISC International Conference on Bioinformatics,Nov. 15-17, New Delhi, JNSBM (Special Issue: Vol.2, Issue 3), [Abstract]

[6] Mokshada Kaushik, Madhurika Sharma, and Tiratha Raj Singh (2011) WISA : Web server for interactive sequence alignment, JNSBM, (Special Issue: Vol.2, Issue 3), [Abstract] [pdf] [PubMed]

[5] Payal Bhargava, Megha Gupta, Arun Gupta and Tiratha Raj Singh (2011) WebGenPro: a Web Server for Genomic and Proteomic Analysis, IInd IFIP International Conference, Sept., 22-25, Goa, India. [Abstract]

[4] Tanya Singhania, Gurnoor Singh, Arun Gupta and Tiratha Raj Singh (2011) DOMOS: Domain and Motif Server for Functional Information, IInd IFIP International Conference, Sept., 22-25, Goa, India. [Abstract]

[3] Tiratha Raj Singh and K.R. Pardasani (2008) Bioinformatics Studies on Evolutionary Patterns in Restriction Endonucleases, Proceedings of GAMS International Conference, Jan., 10-13, Agra-Jaipur, India. [Abstract]

[2] Niket Bhargava, Amit Sugandhi, Tiratha Raj Singh and Manish Manoria (2004) In silico analysis for the construction of multiple sequence alignment and phylogenetic evaluation for the CEAL1, BRCA3 and BRCA3 related mRNA and proteins, E-Proceedings, National Conference, YCCE, Nagpur, 2004, Electronic Publication. [Abstract]

[1] Amit Sugandhi, Niket Bhargava, Tiratha Raj Singh and Manish Manoria (2004) The Biology Behind: Understanding Protein Engineering, Immunotoxins, and Drug Designing Issues and Their Application for Finding Breast Cancer Antigen Marker , E-Proceedings, National Conference, YCCE, Nagpur, 2004, Electronic Publication. [Abstract]

Book Chapters:

[5] Manika Sehgal, Tiratha Raj Singh, (2017). Principles and Analysis of Biological Networks: Biological Pathways and Network Motifs. In , Library and Information Services for Bioinformatics Education and Research (pp. 112-129). : IGI Global. [ISBN : 9781522518716].

[4] Priya P Panigrahi, Tiratha Raj Singh, (2017). Data Mining, Big Data, Data Analytics: Big Data Analytics in Bioinformatics. In , Library and Information Services for Bioinformatics Education and Research (pp. 112-129). : IGI Global. [ISBN : 9781522518716].

[3] Tiratha Raj Singh, Brigitte Vannier, Ahmed Moussa (2016). Extraction of Differentially Expressed Genes in Microarray Data. In Mourad Elloumi, Costas S. Iliopoulos, Jason T. L. Wang and Albert Y. Zomaya, Pattern Recognitin in Computational Molecular Biology: TECHNIQUES AND APPROACHES (International, pp. 335-345). : Wiley. [ISBN : 978-1-118-89368-5].

[2] Tiratha Raj Singh (2015). Mitogenomics: Mitochondrial Gene Rearrangements, its Implications and Applications. In R. Keshavchandran, S. Raji Radhakrishnan, Agriculture Bioinformatics (pp. 259-69). New Delhi: New India Publishing Agency. [ISBN : 978-93-83305-42-1].

[1] Tiratha Raj Singh (2014). Machine Learning with Special Emphasis on Support Vector Machines (SVMs) in Systems Biology: A Plant Perspective. In Kavi Kishor, Rajib Bandopadhyay, Prashanth Suravajhala, Agricultural Bioinformatics (pp. 273-281). New Delhi: Springer India. [ISBN : 978-81-322-1879-1].

Abstracts & Posters:

[8] Manika Sehgal, and Tiratha Raj Singh (2014) Decoding the intricate biological pathways for biomarkers implicated in Human DNA repair system , SYSCON-2014: Recent Advances in Biological Sciences, Dec., 10, 2014, AIIMS, New Delhi. [Abstract]

[7] Gurnoor Singh, Tanya Singhania, Arun Gupta and Tiratha Raj Singh (2013) SHIFTDB: Database of hidden stop codons in frame-shifted translation in mitochondrial genomic sequences , ISMB-ECCB, July, 21-23, Berlin, Germany. [Abstract]

[6] Ankit Gupta, Gautam Mehta, Priya P. Panigrahi, Ahmed Moussa, and Tiratha Raj Singh (2013) MiND: web repository for Mitochondrial and Neurological associated human Disease , SCB Africa ASCBC Conference, 13-15 March 2013, Morocco. [Abstract]

[5] Digvijay Singh Chauhan Abhishek Das, Priya P. Panigrahi, and Tiratha Raj Singh (2012) Development of early phase diagnostics for Alzheimer’s disease: use of diabetes mellitus as surrogate biomarker, InCoB, 2012, Thailand Bangkok, [Abstract: Poster]

[4] Digvijay Singh Chauhan and Tiratha Raj Singh (2012) Chaos as Positive and Negative adaptation, InCoB, 2012, Thailand Bangkok, [Abstract: Poster]

[3] Priya P. Panigrahi, Ashish Shankar and Tiratha Raj Singh (2010) DBSSR: Database of Simple Sequence Repeats, 98th Indian Science Congress, [Abstract: Poster]

[2] Kavita Yadav, Sachin Pundhir, Tiratha Raj Singh, and Anil Kumar (2009) GGRP: GenBank Genome Record parser, 5th World Congress of Cellular and Molecular Biology , Nov. 2-6, 2009, at DAVV, Indore, India.[Link to the poster]

[1] Tiratha Raj Singh, C.K. Verma, Ganesh N., Namita Srivastava and K.R. Pardasani (2005) In silico analysis of biological sequences by using bioinformatics tools, National Conference on Bioinformatics and Contemporary Drifts in Life Science , Dec. 12th to 15th, 2005 at NITTR , Bhopal, India. [Awarded best in Bioinformatics Section]