Announcement

List of Recent Publications

2020

  • Singh KK, Chaubey G, Chen JY, Suravajhala P. Decoding SARS-CoV-2 hijacking of host mitochondria in COVID-19 pathogenesis. Am J Physiol Cell Physiol. 2020;319(2):C258-C267. doi:10.1152/ajpcell.00224.2020
  • Katam R, Shokri S, Murthy N, et al. Proteomics, physiological, and biochemical analysis of cross tolerance mechanisms in response to heat and water stresses in soybean. PLoS One. 2020;15(6):e0233905. Published 2020 Jun 5. doi:10.1371/journal.pone.0233905
  • Shukla N, Siva N, Malik B, Suravajhala P. Current Challenges and Implications of Proteogenomic Approaches in Prostate Cancer [published online ahead of print, 2020 Jul 21]. Curr Top Med Chem. 2020;10.2174/1568026620666200722112450.
  • Suravajhala, R.; Parashar, A.; Malik, B.; Nagaraj, A.V.; Padmanaban, G.; Kavi Kishor, P.; Polavarapu, R.; Suravajhala, P. Comparative Docking Studies on Curcumin with COVID-19 Proteins. Preprints 2020, 2020050439 (doi: 10.20944/preprints202005.0439.v1). Under review
  • Yash Shah, Deepak Sharma, Rakesh Sharma, Sourav Singh, Hrishikesh Thakur, William John, Shamsudheen Marakkar, Prashanth Suravajhala, Vijayaraghava Seshadri Sundararajan, Jayaraman Valadi, Khader Shameer, Ramanathan Sowdhamini. Crowdsourcing Machine Intelligence Solutions to Accelerate Biomedical Science: Lessons learned from a machine intelligence ideation contest to improve the prediction of 3D domain swapping. bioRxiv 2020.07.12.199398; doi: https://doi.org/10.1101/2020.07.12.199398 (Under review).
  • Leire Moya, Samaneh Farashi, Prashanth N Suravajhala, Panchadsaram Janaththani, Jyotsna Batra Genes associated with liver damage signalling pathways may impact the severity of COVID-19 symptoms in Spanish and Italian populations . bioRxiv 2020.07.03.179028; doi: https://doi.org/10.1101/2020.07.03.179028 (Under review).
  • Prashanth Suravajhala. Your Passport to a Career in Bioinformatics (Edition 2). 2020. Book. Springer. (In press).

2019

  • Upadhyayula R.S., Solanki P.S., Suravajhala P., Medicherla K.M. (2019) Bioinformatics Tools for Microbial Diversity Analysis. In: Satyanarayana T., Johri B., Das S. (eds) Microbial Diversity in Ecosystem Sustainability and Biotechnological Applications. Springer Nature, Singapore, Vol-I, 2019, pp 23-47
  • Chaturvedi,P., Raina,V., Solanki,P.S., Saxena,V.L.,(2019) In silico Prediction of Anti-plasmodial Activity of Spices: Targeting Malarial Proteases, 13(8), KC01-KC06.
  • Monisha Singhal, Pragya Chaturvedi ,RK Gothwal, MK Mohan, PS Solanki, Comparative study of synonymous codon usage in bacteria growing at extreme temperatures, Int. J. of Bioinformatics Research and Applications , Communicated & Accepted ( In Press)
  • Bharti Malhotra#, Veenu Gupta, Pratibha Sharma, Ruchi Singh, Himanshu Sharma, Madhavi Vyas, RP Mathur, VK Mathur, Deepa Meena, Hemant Malhotra, Pragya D. Yadav, Gajanan Sapkal, Ullas PT, Gururaj Rao Deshpande, Rashmi Gunjikar, Heena Shaman, Devendra T Mourya, Nivedita Gupta, Sujit Singh, P Ravindran, Jitender Tiwari, Dimpal A. Nyayanit, Neeraj Kumar, Sameer Phalke, Anup Chugani, Sudhir Bhandari, Pooran Singh Solanki , Prashanth Suravajhala, Manila Salaria, “Clinico-epidemiological and genomic profile of first Zika Virus outbreak in India at Jaipur city of Rajasthan state”, Journal of Infection and Public Health (In Press)
  • Saxena A, Tiwari P, Wahi N, Soni A, Bansiwal RC, Kumar A, Sharma B, Punjabi P, Gupta N, Malik B, Medicherla KM, Suravajhala P, Mathur SK. Transcriptome profiling reveals association of peripheral adipose tissue pathology with type-2 diabetes in Asian Indians. Adipocyte. 2019 Mar 20:1-12.
  • Tiwari P, Saxena A, Gupta N, Medicherla KM, Suravajhala P, Mathur SK. Systems Genomics of Thigh Adipose Tissue From Asian Indian Type-2 Diabetics Revealed Distinct Protein Interaction Hubs. Front Genet. 2019 Jan 8; 9:679.
  • Ijaq J, Malik G, Kumar A, Das PS, Meena N, Bethi N, Sundararajan VS,Suravajhala P. A model to predict the function of hypothetical proteins through a nine-point classification scoring schema. BMC Bioinformatics. 2019 Jan 8; 20(1):14.
  • Madduru D, Ijaq J, Dhar S, et al. Systems Challenges of Hepatic Carcinomas: A Review. J Clin Exp Hepatol. 2019;9(2):233-244. doi:10.1016/j.jceh.2018.05.002
  • Gupta S, Tiwari P, Gupta N, et al. Is Pouch Specific to Colon and Not Ileum?. Curr Pediatr Rev. 2019;15(4):259-264. doi:10.2174/1573396315666190829155930
  • Suravajhala P. Systems Genomics in the Age of Next Generation Sequencing (Part II). Curr Genomics. 2019;20(8):536.
  • Suravajhala P. Systems Genomics in the Age of Next Generation Sequencing (Part I). Curr Genomics. 2019;20(7):468. doi:10.2174/138920292007200101105336

2018

  • Mathur P, Medicherla KM, Chaudhary S, Patel M, Bagali S and Suravajhala P. Whole Exome Sequencing reveals rare variants linked to Congenital Pouch Colon. Nature Scientific Reports. 2018: 8:6646.
  • Mathur SK, Tiwari P, Gupta S, Gupta N, Nimesh S, Medicherla KM, Suravajhala P. Genetics of Lipodystrophy: Can It Help in Understanding the Pathophysiology of Metabolic Syndrome? Biomolecules. 2018 Jul 6;8(3).
  • Gupta S, Gupta N, Tiwari P, Menon S, Mathur P, Kothari SL, Nallapeta S, Medicherla KM, Suravajhala P. Lnc-EPB41-Protein Interactions Associated with Congenital Pouch Colon. Biomolecules. 2018 Sep 17;8(3).
  • Sundararajan VS, Malik G, Ijaq J, Kumar A, Das PS, Shidhi PR, Nair AS, Suravajhala P, Dhar PK. HYPO: A database of hypothetical human proteins. Protein Pept Lett. 2018 Aug 27.
  • Meena N, Vasundhara M, Reddy MS, Suravajhala P, Raghavender US, Medicherla KM. Draft Genome Sequence of a Fungus (Fusarium tricinctum) Cultured from a Monoisolate Native to the Himalayas. Genome Announc. 2018 May 17;6(20).
  • Kumar A, Pandeya A, Malik G, Sharma M, P HK, S AK, Gahlaut V, Gajula MNVP, Singh KP, Suravajhala P, Balyan HS, Gupta PK. A web resource for nutrient use efficiency-related genes, quantitative trait loci and microRNAs in important cereals and model plants. F1000Res. 2018 May 29;7. pii: ISCB Comm J-673.
  • Mathur P, Nunia V, Sharma R, Simlot A, Medicherla KM. Congenital Pouch Colon: Role of Genetics or Environmental Influence? Pathobiology. 2018 Sep 17:1-10.
  • Singh H, Tiwari P, Bhavi V, Chaudhary PS, Suravajhala P, Mohan MK, Mathur SK. Application of Chromosomal Microarray for Evaluation of Idiopathic Short Stature in Asian Indian Children: A Pilot Study. Indian J Endocrinol Metab. 2018 Jan-Feb;22(1):100-106.
  • Dashtban M, Balafar M, Suravajhala P. Gene selection for tumor classification using a novel bio-inspired multi-objective approach. Genomics. 2018 ;110(1):10-17.
  • Suravajhala P and Fang L. Long Non-coding RNAs in Animal Genomes: Challenges and Promises. In Press. Int. J. Bioinfo. Res. App. 2018.
  • Vijay U, Gupta S, Mathur P, Suravajhala P and Bhatnagar P. Microbial Mutageneicty Assay Test. Bioprotocol: 8(6): e2763 (2018).
  • Tiwari P, Gupta S, Kumar A, Sharma M, Sundararajan VS, Kothari SL, Medicherla KM, Mathur S, Malik B and Suravajhala P. Elsevier. Enclopaedia in Bioinformatics. 2018 (In press).
  • Meena, N., Mathur, P., Medicherla, K. M. and Suravajhala, P. A Bioinformatics Pipeline for Whole Exome Sequencing: Overview of the Processing and Steps from Raw Data to Downstream Analysis. Bio-protocol, 2018; Bio101: e2805.

2017

  • Prakash R, Hossain AM, Pal UN, Kumar N, Khairnar K, Mohan MK. Dielectric Barrier Discharge based Mercury-free plasma UV-lamp for efficient water disinfection. Sci Rep. 2017 Dec 12;7(1):17426 (2017).
  • Suravajhala P, Benso A. Prioritizing single-nucleotide polymorphisms and variants associated with clinical mastitis. Adv Appl Bioinform Chem. 2017;12;10:57-64.
  • Kumari PH, Kumar SA, Sivan P, Katam R, Suravajhala P, Rao KS, Varshney RK, Kishor PB. Overexpression of a Plasma Membrane Bound Na+/H+ Antiporter-Like Protein (SbNHXLP) Confers Salt Tolerance and Improves Fruit Yield in Tomato by Maintaining Ion Homeostasis. Front Plant Sci. 2017 Jan 6;7:2027
  • Raghavender US. Analysis of residue conformations in peptides in Cambridge structural database and protein-peptide structural complexes. Chem Biol Drug Des. (2017 Mar);89(3):428-442. doi: 10.1111/cbdd.12862. pub 2016 Sep 26. PubMed PMID: 27589215.

2016

  • Chandra, S., Saxena, T., Nehra, S. and Krishna Mohan, M. (2016). Quality assessment of supplied drinking water in Jaipur city, India, using PCR–based approach. Envion. Earth Sci., 75:153.
  • Iddamalgoda L, Das PS, Aponso A, Sundararajan VS, Suravajhala P, Valadi JK. Data Mining and Pattern Recognition Models for Identifying Inherited Diseases: Challenges and Implications. Front Genet. 2016 Aug 10;7:136 (2016).
  • Katam R, Sakata K, Suravajhala P, Pechan T, Kambiranda DM, Naik KS, Guo B, Basha SM. Comparative leaf proteomics of drought-tolerant and -susceptible peanut in response to water stress. J Proteomics. 2016 Jun 30;143:209-26.
  • Pappu P, Madduru D, Chandrasekharan M, Modhukur V, Nallapeta S, Suravajhala P. Next generation sequencing analysis of lung cancer datasets: A functional genomics perspective. Indian J Cancer. 2016 Jan-Mar;53(1):1-7.
  • Suravajhala P, Kogelman LJ, Kadarmideen HN. Multi-omic data integration and analysis using systems genomics approaches: methods and applications in animal production, health and welfare. Genet Sel Evol. 2016 Apr 29;48(1):38.
  • Sade H, Meriga B, Surapu V, Gadi J, Sunita MS, Suravajhala P, Kavi Kishor PB. Toxicity and tolerance of aluminum in plants: tailoring plants to suit to acid soils. Biometals. 2016 Apr;29(2):187-210.

2015

  • Meena S., Gothwal R. K., Saxena J., Nehra S., Mohan M. K. and Ghosh P. (2015). Effect of metal ions and chemical compounds on chitinase produced by a newly isolated thermotolerant Paenibacillus sp. BISR-047 and its shelf-life. Int. J. Curr. Microbiol. Appl. Sci., 4(5): 882-891.
  • Upadhyay AK, Chacko AR, Gandhimathi A, Ghosh P, Harini K, Joseph AP, Joshi AG, Karpe SD, Kaushik S, Kuravadi N, Lingu CS, Mahita J, Malarini R, Malhotra S, Malini M, Mathew OK, Mutt E, Naika M, Nitish S, Pasha SN, Raghavender US, Rajamani A, Shilpa S, Shingate PN, Singh HR, Sukhwal A, Sunitha MS, Sumathi M, Ramaswamy S, Gowda M, Sowdhamini R. Genome sequencing of herb Tulsi (Ocimum tenuiflorum) unravels key genes behind its strong medicinal properties. BMC Plant Biol. 2015 Aug 28; 15:212. doi: 10.1186/s12870-015-0562-x. PubMed PMID: 26315624; PubMed Central PMCID: PMC4552454.
  • Metri R, Hariharaputran S, Ramakrishnan G, Anand P, Raghavender US, Ochoa-Montaño B, Higueruelo AP, Sowdhamini R, Chandra NR, Blundell TL, Srinivasan N. SInCRe-structural interactome computational resource for Mycobacterium tuberculosis. Database (Oxford). 2015 Jun 30;2015:bav060. doi: 10.1093/database/bav060. Print 2015.
  • Raghavender US, Sowdhamini R. Mechanistic Basis of Peptide-Protein Interaction in AtPep1-PEPR1 Complex in Arabidopsis thaliana. Protein Pept Lett. 2015;22(7):618-27 (2015). PubMed PMID: 25961822.
  • Saxena T., Kaushik P. and Mohan M. K. (2015). Prevalence of E. coli O157:H7 in water sources: an overview on associated diseases, outbreaks and detection methods. Diagnostic Microbiol. Infect. Dis., 82: 249–264.
  • Yadav H., Gothwal R. K., Mathur S. and Ghosh P. (2015). Bioactivation of Jhamarkotra rock phosphate by a thermotolerant phosphate solubilizing bacterium Bacillus sp. BISR-HY63 isolated from phosphate mines. Archives of Agronomy and Soil Sci., 61 (8): 1125-1135.

2014

  • Ramakrishnan G, Ochoa-Montaño B, Raghavender US, Mudgal R, Joshi AG, Chandra NR, Sowdhamini R, Blundell TL, Srinivasan N. Enriching the annotation of Mycobacterium tuberculosis H37Rv proteome using remote homology detection approaches: insights into structure and function. Tuberculosis (Edinb). 2015 Jan;95(1):14-25. doi: 10.1016/j.tube.2014.10.009. Epub 2014 Nov 6. Review. PubMed PMID: 25467293.
  • Yadav H., Gothwal R. K., Solanki P. S., Nehra S, Sinha-Roy S. and Ghosh P. (2014). Isolation and characterization of thermo-tolerant phosphate-solubilizing bacteria from a phosphate mine and their rock phosphate solubilizing abilities. Geomicrobiology Journal, 32 (6): 475-481.
  • Meena S., Gothwal R. K., Mohan M. K. and Ghosh P. (2014). Production and purification of a hyperthermostable chitinase from Brevibacillus formosus BISR-1 isolated from the Great Indian Desert soils. Extremophiles, 18 (2): 451-462.
  • Meena S., Gothwal R. K., Saxena J., Mohan M. K. and Ghosh P. (2014). Chitinase production by a newly isolated thermotolerant Paenibacillus sp. BISR-047. Annals of Microbiology, 64 (2): 787-797.
  • Varshney A. K., Mohan M. K., Vidyarthi A. S., Nigam V. K. and Ghosh P. (2014). Effect of nitrogen sources and C:N ratio on production of manganese peroxidase using Phanerochaete chrysosporium NCIM 1197. J. Pure Appl. Microbiol., 8: 481-487.
  • Nehra S., Gothwal R. K. and Ghosh P. (2014). Biodiversity conservation: An Indian agenda for the millennium. In: Biodiversity in India: Assessment, Scope and Conservation, Lambert Academic Publishing (LAP), Germany, pp. 323-340.
  • Nehra S., Gothwal R. K., Chandra S., Meena P., Mohan M. K. and Ghosh P. (2014). Role of microbes in bioremediation. In: Applied Microbiology (Ed. Nehra S.), Pointer Publication, Jaipur, pp. 232-248.
  • Nehra S., Gothwal R. K., Chandra S. Meena P., Mohan M. K. and Ghosh, P. (2014). Rhizobium : Nitrogen fixation and agriculture, In: Biofertilizers for sustainable agriculture (Ed. Nehra S.), Pointer Publication, Jaipur, pp. 209-221.
  • Karkho R., Gothwal R. K. and Nehra S. (2014). The treatment of leprosy using various drugs and antileprotic plants: A Review. In: Plant Disease Management and Microbes (Ed. Nehra S.), Aavishkar Publication, Jaipur, pp. 250-258.
  • Saxena T., Varshney A. K., Gothwal R. K., Kaushik P., Mohan M. K. and Nehra S. (2014). Immunological Techniques. In: Plant Disease Management and Microbes (Ed. Nehra S.), Aavishkar Publication, Jaipur, pp. 259-268.
  • Nehra, S. (2014). Plant derived drugs and herbal medicines in healthcare. In: Herbal folk medicine (Ed. Nehra S.), Pointer publication, Jaipur, pp 119-149.
  • Saxena T. and Nehra S. (2014). Biodiversity in aquatic environments. In: Biodiversity in India: Assessment, Scope and Conservation, Lambert Academic Publishing (LAP), Germany.
  • Joshi AG, Raghavender US, Sowdhamini R. Improved performance of sequence search approaches in remote homology detection. Version 2. F1000Res. 2013 Mar 22 [2014 Jan ];2:93. PubMed PMID: 25469226; PubMed Central PMCID: PMC4240247 (2014).

2013

  • Alok K. Varshney, M. K. Mohan, A. S. Vidyarthi, V. K. Nigam and P. Ghosh. (2013). Statistical optimization of medium components to increase the manganese peroxidase productivity by Phanerochaete chrysosporium NCIM 1197. Biotechnol. Bioprocess Eng., 18: 1176-1184.
  • Nehra S., Gothwal R. K., Chandra S. Meena P., Mohan M. K. and Ghosh P. (2013). Mycorrhizae and its application in plant disease management. In: Arbuscular Mycorrhizae in Crop Production (Ed. Nehra S.), Pointer Publication, Jaipur, pp. 20-61.
  • Nehra S., Gothwal R. K., Chandra S. Meena P., Mohan M. K. and Ghosh P. (2013). Biotechnology for medicinal plants: Micropropagation and Improvement, In: Medicinal Plants: Chemistry and Properties, (Ed. Nehra S.), Aavishkar Publication, Jaipur, pp. 146-162.
  • Yadav H., Gothwal R. K., Nigam V. K., Sinha-Roy S. and Ghosh P. (2013). Optimization of culture conditions for phosphate solubilization by a thermo-tolerant phosphate-solubilizing bacterium Brevibacillus sp. BISR-HY65 isolated from phosphate mines. Biocatalysis Agricultural Biotechnol., 2 (3): 217-225.
  • Lalwani S., Mohan M., Solanki P., Singhal S., Mathur S. and Spedicato E. (2013). An application of the ABS algorithm for modeling multiple regression on massive data, predicting the most influencing factors. Appl. Mathematics, 4 (6): 907-913.

 

List of Books Published (Last 5 years): 2013 -18

  • U. S. Raghavender, Methods in Computational Biology, Delve Publishing, (2018) ISBN:9781773612416
  • U. S. Raghavender, Computational Molecular Bioscience: Concepts, Delve Publishing, (2018), ISBN: 9781773612423
  • Biodiversity in India: Assessment, Scope and Conservation, Lambert Academic Publishing (LAP), Germany, 2014 (Eds. Nehra S. Gothwal R. K. and Ghosh P).
  • Plant Disease Management and Microbes. Aavishkar Publishers Distriburors Jaipur, India, 2014 (Ed.Nehra S.)
  • Medicinal Plants: Chemistry and Properties. Aavishkar Publisher & Distributor, Jaipur, India, 2013 (Ed. Nehra S.).
  • Biofertilizers for Sustainable Agriculture. Pointer Publisher & Distributor, Jaipur, India, 2013 (Ed. Nehra S.).