The faculty of IBAB publish their research and other thought pieces in some of the best journals, nationally and internationally. For an institute with big commitments to teaching it has been a remarkable achievement and this has allowed the institute to gain considerable recognition among its peers
 |  |  |
2024
-
Kalakoti Y, Gawande S and Sundar D
Estimating protein-ligand interactions with geometric deep learning and mixture density models.
Journal of Biosciences, 49: 97 doi: 10.1007/s12038-024-00478-z (2024) -
Kaushal S, Gupta S, Shefrin S, Vora D S, Kaul S C, Sundar D, Wadhwa R and Dhanjal J K
Synthetic and natural inhibitors of mortalin for cancer therapy.
Cancers, 16(20): 3470 doi: 10.3390/cancers16203470 (2024) - Kshitish K A; Sravanthi D; Pawan K
A Review of Protein-Protein Interaction Databases
Reference Module in Life Sciences, doi: 10.1016/B978-0-323-95502-7.00076-2 (2024) - Roy, U., Desai, S. S., Kumari, S., Bushra, T., Choudhary, B., & Raghavan, S. C.
Understanding the Role of miR-29a in the Regulation of RAG1, a Gene Associated with the Development of the Immune System
The Journal of Immunology, doi: 10.4049/jimmunol.2300344 (2024) - Magar, S., Kolte, V., Sharma, G., & Govindarajan, S.
Exploring pangenomic diversity and CRISPR-Cas evasion potential in jumbo phages: a comparative genomics study
Microbiology Spectrum, e04200-23, doi: 10.1128/spectrum.04200-23 (2024) - Nayak, S., Regati, D.R. & Sowdhamini, R.
Computational analysis of human gut microbial prolyl oligopeptidases (POPs) reveal candidate genes as therapeutics for celiac disease
Scientific Reports, 14-1, 19641, doi: 10.1038/s41598-024-70079-1 (2024) - Bulusu, S.N., Bavikatte, A., Shah, S., Murthy, S., Mariaselvam, C.M., Kavadichanda, C., Vembar, S., Thabah, M. and Negi, V.S.,
OA25 Transcriptome analysis of peripheral blood and renal tissue identifies genes that predict treatment response in proliferative lupus nephritis: a prospective observational study
Rheumatology, 63, sup-1, keae163.025, doi: 10.1093/rheumatology/keae163.025 (2024) - Kshitish K A, Sravanthi D, and Pawan K
A Review of Protein-Protein Interaction Databases. In: Reference Module in Life Sciences,
Elsevier, doi:10.1016/B978-0-323-95502-7.00076-2 (2024) - Saberwal, G.
Clinical trial registries: The good, and the not so good
Journal of Biosciences, 49: 90 doi: 10.1007/s12038-024-00477-0 (2024) - Borah R, Dhal, AD, Mendiratta, J, Mishra, M and Saberwal G
Identifying trials run in India that are registered in other clinical trial registries: A cross-sectional study.
BMC Medical Research Methodology, 24:201 doi: 10.1186/s12874-024-02336-w (2024). - Wadhwa, R., Wang, J., Shefrin, S., Zhang, H., Sundar, D. and Kaul, S.C.
Molecular insights into the anticancer activity of Withaferin-A: inhibition of Survivin signaling.
Cancers, 16: 3090 doi: 10.3390/cancers16173090 (2024) - Vishwakarma A, Padmashali N, and Thiyagarajan S
AnnoDUF: A Web-Based Tool for Annotating Functions of Proteins Having Domains of Unknown Function
J. Proteome Res., doi: 10.1021/acs.jproteome.4c00251 (2024) - Kumari S, Ghosh S, Joshi S, Guenther R, Siegmund V, Doerner A
Systematic mutational analysis reveals an essential role of N275 in IgE stability
Biotechnology and Bioengineering, doi: 10.1002/bit.28826 (2024) - Shyam S R, Yali Z, Ashraf Y, Kristiina T
Machine Learning Prediction of Autism Spectrum Disorder From a Minimal Set of Medical and Background Information
JAMA Network Open., 7(8):e2429229. doi: 10.1001/jamanetworkopen.2024.29229 (2024) - Borah R, Samanta AD, Rajueni K, Vaswani V and Saberwal G
In India, most principal investigators have run very few trials over the years.
Front. Med., 11:1424570. doi: 10.3389/fmed.2024.1424570 (2024) - Madhavan A, Paramasivam S, V V Dhanesh, Deepak P R S, Gopinath S, Adwitiya D, Hosamani M, B P Sreenivasa, R P T Selvan, Aniket S, Samta G,S Thiyagarajan, Pallab C
Diagnostic and prophylactic potential of a stabilized foot-and-mouth disease serotype Asia1 virus like particles designed through a structure guided approach
International Journal of Biological Macromolecules, doi: 10.1016/j.ijbiomac.2024.134366 (2024) -
Maity U, Aggarwal R, Balasubramanian R, Venkatraman DL, Hegde SR
Devising Isolation Forest-Based Method to Investigate the sRNAome of Mycobacterium tuberculosis Using sRNA-seq Data.
Bioinformatics and Biology Insights, 18 doi:10.1177/11779322241263674 (2024) - Namita M, Kaushiki K, Moushmi G, Anmol S, Subhashini S
Caught in the act of triplication: TNF superfamily
bioRxiv preprint, doi: doi.org/10.1101/2024.07.27.603686 (2024) - Abhishek S, C R Chandrashekar, Sudhir K and Computational Analysis of the accumulation of mutations in therapeutically important RNA viral proteins during pandemics with special emphasis on SARS-CoV-2
Journal of Molecular Biology, doi: 10.1016/j.jmb.2024.168716 (2024) - Saberwal, G.
Drug Prices (Editorial)
Current Science 127 (2), 131–132 (2024) - Swathik C P, Yogesh K, and D Sundar
Identifying High-Quality Leads among Screened Anticancerous Compounds Using SMILES Representations
ACS Omega, doi:10.1021/acsomega.4c02801 (2024) - Kshitish K A, Davuluri S, Goswami M, Ashikha K, Belakeri B, Sanjana B. M, Bajpai A, Dosemane D
Biomedical Text Mining: Biocuration and Literature Search Engines, In: Reference Module in Life Sciences,
Elsevier, doi:10.1016/B978-0-323-95502-7.00101-9 (2024) - Saberwal, G.
Anti-vaxxers (Editorial)
Current Science, 126 (12), 1411–1412 (2024) - Samanta A D, Borah R and Saberwal G
Three levels of discrepancies in the records of trial sites in India, registered with the European Union Clinical Trials Register
Front. Med. 11:1357930 doi: 10.3389/fmed.2024.1357930 (2024) - Saberwal, G.
Institution building (Editorial)
Current Science, 126 (9), 987–988 (2024) - Sharma S, Rani H, Mahesh Y, Jolly M. K., Dixit J., Mahadevan V.
Loss of p53 epigenetically modulates epithelial to mesenchymal transition in colorectal cancer
Translational Oncology, 43, 101848 doi: 10.1016/j.tranon.2023.101848 (2024) - Gehring A, Huebner K, Rani H, Erlenbach-Wuensch K, Merkel S, Mahadevan V,
Grutzmann R, Hartmann A, Schneider-Stock R.
DNA demethylation and tri-methylation of H3K4 at the TACSTD2 promoter are complementary players for TROP2 regulation in colorectal cancer cells
Scientific Reports, 14-1, 2683 doi: 10.1038/s41598-024-52437-1 (2024) - Maruthesh H.; Katagi M.S.; Samuel J.; Nandeshwarappa B.P.
Design, Synthesis, and Computational Characterization of Interesting Schiff Base Scaffolds as Antibacterial, Antimycobacterial, and Antifungal Agents
Russian Journal of Organic Chemistry, 59-10, 1783-1796 doi: 10.1134/S1070428023100147 (2024) - Saini S.; Rathore A.; Sharma S.; Saini A.
Exploratory data analysis of physicochemical parameters of natural antimicrobial and anticancer peptides: Unraveling the patterns and trends for the rational design of novel peptides
BioImpacts, 14-1, 26438, doi: 10.34172/bi.2023.26438 (2024) - Gopalakrishnan V.; Roy U.; Srivastava S.; Kariya K.M.; Sharma S.; Javedakar S.M.; Choudhary B.; Raghavan S.C.
Delineating the mechanism of fragility at BCL6 breakpoint region associated with translocations in diffuse large B cell lymphoma
Cellular and Molecular Life Sciences, 81-1, 21, doi: 10.1007/s00018-023-05042-w (2024) - Ashraf Yahia, Danyang Li, Sanna Lejerkrans, Shyam Rajagopalan, Nelli Kalnak & Kristiina Tammimies.
Whole exome sequencing and polygenic assessment of a Swedish cohort with severe developmental language disorder.
Hum. Genet. doi: 10.1007/s00439-023-02636-z (2024) - Bhalla I S, Ravindranath A G, Vaswani R , Saberwal G
Data from the Indian drug regulator and from Clinical Trials Registry-India does not always match
Front. Med. 11:1346208. doi: 10.3389/fmed.2024.1346208 (2024) - Samuel, J, Ghosh S and Thiyagarajan S
Identification and characterization of domain-specific inhibitors of DENV NS3 and NS5 proteins by in silico screening methods
J. Biomol. Struct. Dyn. doi: 10.1080/07391102.2024.2313161 (2024) - Prajapati A, Yogisharadhya R, Mohanty NN, Mendem SK, Chanda MM, Siddaramappa S, Shivachandra SB.
Comparative genome analysis of Pasteurella multocida strains of porcine origin.
Genome., Aug 28. doi: 10.1139/gen-2023-00 (2024)
ACS Omega, May 30;9(23):24520-24537. doi: 10.1021/acsomega.4c00523 (2024)
Proteins, May 30. doi: 10.1002/prot.26707 (2024)
Front Microbiol, May 15;15:1335310. doi: 10.3389/fmicb.2024.1335310 (2024)
Int J Mol Sci., Jun 12;25(12):6485. doi: 10.3390/ijms25126485 (2024)- Mendiratta J, Pillamarapu M, Saberwal G.
In Clinical Trials Registry-India, the classification of sponsors needs to be standardised.
Indian J. Med. Ethics, doi: 10.20529/IJME.2023.071 (2024)
- 2023
- Mam B.; Karpe S.D.; Sowdhamini R.
Minus-C subfamily has diverged from Classic odorant-binding proteins in honeybees
Apidologie, 54-2, 19, doi: 10.1007/s13592-022-00988-5n (2023) - Maruthesh H.; Katagi M.S.; Samuel J.; Aladakatti R.H.; Nandeshwarappa B.P.
Synthesis and Characterization of Substituted 5-(2-Chloroquinolin-3-yl)-1,3,4-oxadiazole-2-amines: Computational, In Silico ADME, Molecular Docking, and Biological Activities
Russian Journal of Bioorganic Chemistry, 49-6, 1422-1437, doi: 10.1134/S1068162023060225 (2023) - Praveen Kumar C.H.; Katagi M.S.; Samuel J.; Nandeshwarappa B.P.
Synthesis, Characterization and Structural Studies of Novel Pyrazoline Derivatives as Potential Inhibitors of NAD+ Synthetase in Bacteria and Cytochrome P450 51 in Fungi
ChemistrySelect, 8-12, e202300427 doi: 10.1002/slct.202300427 (2023) - Yadav C K.; Basavaraju M.; Mussuvir Pasha K.M.; Samuel J.; Nandeshwarappa B.P.
Benzothiazole-Hydrazone Chromophores: Synthesis, Solvatochromism, Computational and Antimycobacterial Activity Studies
ChemistrySelect, 8-28, e202301432, doi: 10.1002/slct.202301432 (2023) - Kharbikar L.; Konwarh R.; Chakraborty M.; Nandanwar S.; Marathe A.; Yele Y.; Ghosh P.K.; Sanan-Mishra N.; Singh A.P.
3Bs of CRISPR-Cas mediated genome editing in plants: exploring the basics, bioinformatics and biosafety landscape
Physiology and Molecular Biology of Plants, doi: 10.1007/s12298-023-01397-3 (2023) - Kataria A and Saberwal G.
FAIR principles, Data transparency and Drug approvals. (Editorial)
Current Science, 125 (12), 1287–1288 (2023) - Kumari R, Roy U, Desai S, Mondal A, Nair RR, Nilavar N, Choudhary B, Raghavan SC.
MicroRNA, miR-501 Regulate the V(D)J Recombination in B Cells.
Biochem J., Dec 12:BCJ20230250. doi: 10.1042/BCJ20230250 (2023) -
Sahana NS, Yadava ST, Choudhary B, Ravindran F, Khatoon H, Kulkarni M.Expression of circulating tumour cells in oral squamous cell carcinoma: An ex vivo pilot study.Journal of Oral and Maxillofacial Pathology., 1;27(3):489-93 doi: 10.4103/jomfp.jomfp_131_23 (2023)
- Sidhanta SPD, Sowdhamini R, Srinivasan N.
Comparative analysis of permanent and transient domain-domain interactiDoi: https://doi.org/10.1134/S1068162023060225ons in multi-domain proteins.
Proteins. 2023 Oct 12. doi: 10.1002/prot.26581 (2023) - Prabantu VM, Tandon H, Sandhya S, Sowdhamini R, Srinivasan N.
The alteration of structural network upon transient association between proteins studied using graph theory.
Proteins. 2023 Oct 30. doi: 10.1002/prot.26606 (2023) - Sharma NS, Choudhary B
Good Cop, Bad Cop: Profiling the Immune Landscape in Multiple Myeloma
Biomolecules.,13, 1629 doi: 10.3390/biom13111629 (2023) - Ravindran F., Mhatre A., Koroth J., Narayan S., & Choudhary B.
Curcumin modulates cell type-specific miRNA networks to induce cytotoxicity in ovarian cancer cells.
Life Sciences, Volume 334, doi: 10.1016/j.lfs.2023.122224 (2023) - Kumari N, Das K, Sharma S, Dahal S, Desai SS, Roy U, Sharma A, Manjunath M, Gopalakrishnan V, Retheesh ST, Javadekar SM, Choudhary B, Raghavan SC
Evaluation of Potential Role of R-Loop and G-quadruplex DNA in the Fragility of c-MYC during Chromosomal Translocation Associated with Burkitt’s Lymphoma.
Journal of Biological Chemistry, doi: 10.1016/j.jbc.2023.105431 (2023) - Nirgude S, Shahana M V, Ravindran F, Kumar S, Sharma S, Mahadeva R, Mhatre A, Karki SS, Choudhary B.
A Coumarin-Imidazothiadiazole Derivative, SP11 Abrogates Tumor Growth by Targeting HSP90 and Its Client Proteins.
Molecules., 5;28(13):5226. doi: 10.3390/molecules28135226 (2023) - Nirgude S, Desai S, Khanchandani V, Nagarajan V, Thumsi J, Choudhary B
Integration of exome-seq and mRNA-seq using DawnRank, identified genes involved in innate immunity as drivers of breast cancer in the Indian cohort.
PeerJ, doi: 10.7717/peerj.16033 (2023) - Bhat S, Banerjee A, Alagesan S.
AraC-Based Biosensor for the Detection of Isoprene in E. coli.
ACS Omega, 18;8(30):26806-26815. doi: 10.1021/acsomega.3c01164.2023 (2023) - Anbuhl KL, Cazares O, Hubert KA, Mahapatra R, Morgan JD.
Navigating a research career with a disability.
Development, 15;150(16):dev201906. doi: 10.1242/dev.201906. (2023) - Singhvi N, Talwar C, Mahanta U, Kaur J, Mondal K, Ahmad N, Tyagi I, Sharma G, Gupta V.
Comparative genomics and integrated system biology approach unveiled undirected phylogeny patterns, mutational hotspots, functional patterns, and molecule repurposing for monkeypox virus.
Funct Integr Genomics., 11;23(3):231. doi: 10.1007/s10142-023-01168-z (2023) - Kakkar RA, Haneen MA, Parida chandra A, Sharma G
The Known, Unknown, and the Intriguing about members of a Critically Endangered Traditional Medicinal Plant Genus Aconitum
Front. Plant Sci., Volume 14 https://doi.org/10.3389/fpls.2023.1139215 (2023) - Verma S, Reddy P, Sowdhamini R
Integrated approaches for the recognition of small molecule inhibitors for Toll-like receptor 4.
Computational and Structural Biotechnology Journal, 21, 3680-3689 (2023) - Arole, A.H., Deshmukh, P., Sridhar, A., Mathur, S., Mahalingaswamy, M., Subramanya, H., Dalavaikodihalli Nanjaiah, N. & Padmanabhan, B.
Structural and biochemical insights into purine-based drug molecules in hBRD2 delineate a unique binding mode opening new vistas in the design of inhibitors of the BET family
Acta Cryst., D79, doi:10.1107/S2059798323005211 (2023) - Chauhan PK, Sowdhamini R.
Transcriptome data analysis of primary cardiomyopathies reveals perturbations in arachidonic acid metabolism.
Front Cardiovasc Med., 23;10:1110119 doi: 10.3389/fcvm.2023.1110119 (2023) - Saberwal G and Kaushik K. (Eds)
IRIWI. I Realised I Wasn’t Interested ... Inspirational stories of science career transitions.
IndiaBioScience, https://indiabioscience.org/indiabioreads/iriwi-i- realized-i-wasnt-interested (2023) - Saberwal G.
Clinical trial transparency - Status and Prospects (Editorial)
Current Science, 124 (11) 1239-1240 (2023) - Yang H, Huebner K, Hampel C, Erlenbach-Wuensch K, Selvamani SB, Shukla V, Geppert CI, Hartmann A, Mahadevan V, Schneider-Stock R.
ATF2 loss promotes 5-FU resistance in colon cancer cells via activation of the ATR-Chk1 damage response pathway.
BMC Cancer., 27;23(1):480. doi: 10.1186/s12885-023-10940-0 (2023) - Meenakshi S I, Rao M, Mayor S, Sowdhamini R.
A census of actin-associated proteins in humans.
Front Cell Dev Biol., 28;11:1168050 (2023)
doi: 10.3389/fcell.2023.1168050. PMID: 37187613; PMCID: PMC10175787. - Rajaratnam S, Soman AP, Phalguna KS, Pradhan SS, Manjunath M, Rao RK, Dandamudi RB, Bhagavatham SKS, Pulukool SK, Rathnakumar S, Kocherlakota S, Pargaonkar A, Veeranna RP, Arumugam N, Almansour AI, Choudhary B, Sivaramakrishnan V.
Integrated Omic Analysis Delineates Pathways Modulating Toxic TDP-43 Protein Aggregates in Amyotrophic Lateral Sclerosis.
Cells, 24;12(9):1228. doi: 10.3390/cells12091228. (2023) - Desai SS, Ravindran F, Panchal A, Ojha N, Jadhav S, Choudhary B.
Whole transcriptome sequencing reveals HOXD11-AGAP3, a novel fusion transcript in the Indian acute leukemia cohort.
Front Genet, 11;14:1100587. doi: 10.3389/fgene.2023.1100587. (2023) - Mhatre A, Koroth J, Manjunath M, Kumar S S, Gawari R, Choudhary B.
Multi-omics analysis of the Indian ovarian cancer cohort revealed histotype-specific mutation and gene expression patterns.
Front Genet, 6;14:1102114. doi: 10.3389/fgene.2023.1102114. (2023) - Chauhan PK, Sowdhamini R.
Computational analysis of the flexibility in the disordered linker region connecting LIM domains in cysteine-glycine-rich protein.
Front Genet, 29;14:1134509. doi: 10.3389/fgene.2023.1134509. (2023) - Mendiratta J, Pillamarapu M, Chakraborty I, Vaswani R, Kapoor M, Vadlamani S, Saberwal G.
Ethnic representation in interventional clinical trials run in India
The Lancet Regional Health – Southeast Asia, 15: 100230 (2023) - Jaiswal V, Varghese SA, Ghosh S
Validation of CRISPR activation system in Aedes cells using multicistronic plasmid vectors
Front. Bioeng. Biotechnol., 11, https://doi.org/10.3389/fbioe.2023.1142415 (2023) - Mendiratta J, Vaswani R N, Saberwal G
Representation from India in multinational, interventional, Phase 2 or 3 trials registered in Clinical Trials Registry-India: A cross-sectional study
PLOS ONE, 18(9): e0284434. https://doi.org/10.1371/journal.pone.0284434 (2023) - Balagannavar G, Basavaraju K, Bajpai AK, Davuluri S, Kannan S, S Srini V, S Chandrashekar D, Chitturi N, K Acharya K.
Transcriptomic analysis of the Non-Obstructive Azoospermia (NOA) to address gene expression regulation in human testis.
Syst Biol Reprod Med., 8:1-19. doi: 10.1080/19396368.2023.2176268 (2023) - Ghosh C, Kumar N, Kushwah RBS, M S, Joshi SG, Ramanjini CK, Alalamath T, Srinivasan S, Subramani S, Kumar S, Swain S.
Enrichment of phenotype among biological forms of Anopheles stephensi Liston through establishment of isofemale lines.
Parasit Vectors, 28;16(1):79. doi: 10.1186/s13071-023-05696-2 (2023) - Saberwal, G.
The need for a new keyword – ‘Trial registry-metaresearch’ – to track certain uses of clinical trial registry records.
Trials, 24, 190 doi: 10.1186/s13063-023-07231-1 (2023) - Sharma A, Krishna S, Sowdhamini R.
Bioinformatics analysis of mutations sheds light on the evolution of Dengue NS1 protein with implications in
the identification of potential functional and druggable sites.
Mol Biol Evol., 16:msad033. doi: 10.1093/molbev/msad033. (2023) - Pradhan SS, Rao KR, Manjunath M, Saiswaroop R, Patnana DP, Phalguna KS, Choudhary B, Sivaramakrishnan V.
Vitamin B6, B12 and folate modulate deregulated pathways and protein aggregation in yeast model of Huntington disease.
3 Biotech., 13(3):96. doi: 10.1007/s13205-023-03525-y. (2023) - Islam ST, Jolivet NY, Cuzin C, Belgrave AM, My L, Fleuchot B, Faure LM, Mahanta U, Kezzo AA, Saïdi F, Sharma G, Fiche JB, Bratton BP, Herrou J, Nollmann M, Shaevitz JW, Durand E, Mignot T.
Unmasking of the von Willebrand A-domain surface adhesin CglB at bacterial focal adhesions mediates myxobacterial gliding motility.
Sci Adv., 22;9(8):eabq0619. doi: 10.1126/sciadv.abq0619. (2023) - Ahmad E, Mitra A, Ahmed W, Mahapatra V, Hegde SR, Sala C, Cole ST, Nagaraja V.
Rho-dependent transcription termination is the dominant mechanism in Mycobacterium tuberculosis.
Biochim Biophys Acta Gene Regul Mech., 21:194923. doi: 10.1016/j.bbagrm.2023.194923 (2023) - Saberwal G.
How to make Clinical Trials Registry-India world-class.
Current Science, 124 (7), 785–789 doi: 10.18520/cs/v124/i7/785-789 (2023) - Ray U, Gopinatha VK, Sharma S, Goyary L, Choudhary B, Mantelingu K, Rangappa KS, Raghavan SC.
Identification and characterization of mercaptopyrimidine-based small molecules as inhibitors of nonhomologous DNA end joining.
FEBS J, 290(3):796-820. doi: 10.1111/febs.16615 (2023) - Karmakar K, Kumar S, Roy D, Singh M, Kolte V, Choudhury A, Sharma G.
Comparative genomics reveals the diversity of CRISPR-Cas locus in Azotobacter organisms.
Lett Appl Microbiol., 23;76(1):ovac004. doi: 10.1093/lambio/ovac004 (2023) - Imran M, Sachdeva G, Menon S, Das D, Davuluri S, Acharya K, Chaudhari U.
Therapeutic metformin concentrations positively regulate proliferation in endometrial epithelial cells via mTOR activation and augmented mitochondrial strength.
Can J Physiol Pharmacol., 101(1):52-64. doi: 10.1139/cjpp-2022-0307 (2023) - Sai Swaroop R, Akhil PS, Sai Sanwid P, Bandana P, Raksha RK, Meghana M, Bibha C, Sivaramakrishnan V.
Integrated multi-omic data analysis and validation with yeast model show oxidative phosphorylation modulates protein aggregation in amyotrophic lateral sclerosis
Journal of Biomolecular Structure and Dynamics, 41-12, 5548-5567, doi: 10.1080/07391102.2022.2090441. (2023) - Ravindran F, Jain A, Desai S, Menon N, Srivastava K, Bawa PS, Sateesh K, Srivatsa N, Raghunath SK, Srinivasan S, Choudhary B.
Whole-exome sequencing of Indian prostate cancer reveals a novel therapeutic target: POLQ
Journal of Cancer Research and Clinical Oncology, 149-6, 2451-2462, doi: 10.1007/s00432-022-04111-0 (2023)
- 2022
- Adwait G. Joshi, Praveen P., Uma Ramakrishnan and Ramanathan Sowdhamini
Draft genome sequence of the invasive plant Lantana camara L.
Bioinformation, 18(9): 739-741 doi: 10.6026/97320630018739 (2022) - Bheemireddy S, Sandhya S, Srinivasan N, Sowdhamini R.
Computational tools to study RNA-protein complexes
Front Mol Biosci., 9: 954926. doi: 10.3389/fmolb.2022.954926 (2022) - Saberwal, G., Choudhury MC, and Chakraborty I
Facilitating audits of clinical trial data in documents of the Food and Drug Administration.
The Journal of Scientific Practice and Integrity, doi: 10.35122/001c.57582 (2022) - Mahajan R, Hudson BS, Sharma D, Kolte V, Sharma G, Goel G.
Transcriptome Analysis of Podoscypha petalodes Strain GGF6 Reveals the Diversity of Proteins Involved in Lignocellulose Degradation and Ligninolytic Function
Indian J Microbiol, 2(4):569-582. doi: 10.1007/s12088-022-01037-6 (2022)
- Saïdi F et al.
Evaluation of Azido 3‑Deoxy‑D-manno-oct-2-ulosonic Acid (Kdo) Analogues for Click Chemistry-Mediated Metabolic Labeling of Myxococcus xanthus DZ2 Lipopolysaccharide
ACS Omega, 7:39, doi: 10.1021/acsomega.2c03711 (2022)
- Chauhan P K and Sowdhamini, R
Integrative network analysis interweaves the missing links in cardiomyopathy diseasome
Sci Rep., 12(1):19670. doi: 10.1038/s41598-022-24246-x (2022)
- Shafi KM, Sajeevan RS, Kouser S, Vishnuprasad CN, Sowdhamini R.
Transcriptome profiling of two Moringa species and insights into their antihyperglycemic activity
BMC Plant Biol., 22(1):561. doi: 10.1186/s12870-022-03938-6 (2022)
- Manjunath M, Nirgude S, Mhatre A, Vemuri SG, Nataraj M, Thumsi J, Choudhary B.
Transcriptomic profiling of Indian breast cancer patients revealed subtype-specific mRNA and lncRNA signatures.
Front Genet., 13:932060 doi: 10.3389/fgene.2022.932060 (2022)
- Kalmankar NV, Gehi BR, Sowdhamini R.
Effects of a plant cyclotide on conformational dynamics and destabilization of β-amyloid fibrils through molecular dynamics simulations
Front Mol Biosci., 30;9:986704 doi: 10.3389/fmolb.2022.986704 (2022) - Nirgude S, Desai S, Choudhary B.
Genome-wide differential DNA methylation analysis of MDA-MB-231 breast cancer cells treated with curcumin derivatives, ST08 and ST09.
BMC Genomics, 6;23(1):807 doi : 10.1186/s12864-022-09041-2 (2022)
- Srinivasan S et al.
Identification of a TNF-TNFR-like system in malaria vectors (Anopheles stephensi) likely to influence Plasmodium resistance.
Sci Rep., 9;12(1):19079. doi: 10.1038/s41598-022-23780-y (2022) - Kapoor M, Ravi S and Saberwal G
Conducting clinical trials only in India’s large cities is unlikely to sample the country’s ethnicity well enough.
Current Science, 123 (12), 1514-1517 doi: 10.18520/cs/v123/i12/1514-1517 (2022) - Esvaran et al.
Cloning, Expression and Characterization of Spore Wall proProtein (SWP5) of Indian isoIsolate K-1 S of Nosema bombycis
The Protein Journal, 41, 596–612 doi: 10.1007/s10930-022-10078 (2022) - ParanjapeI AM, Desai S, Nishana M, Roy U, Nilavar NM, Mondal A, Kumari R, Radha G, Katapadi V, Choudhary B, Raghavan SC
Nonamer dependent RAG cleavage at CpGs can explain mechanism of chromosomal translocations associated to lymphoid cancers
PLOS Genetics, doi: doi.org/10.1371/journal.pgen.1010421 (2022) - Chakraborty M , Ramaiah A, Adolfi A, Halas P, Kaduskar B, Ngo L T, Jayaprasad S , Paul K, Whadgar S, Srinivasan S, Subramani S, Bier E, James A A, Emerson J J
Author Correction: Hidden genomic features of an invasive malaria vector, Anopheles stephensi, revealed by a chromosome-level genome assembly
BMC Biology, 20:96 doi: 10.1186/s12915-022-01314-2 (2022) - Ray U, Gopinatha VK, Sharma S, Goyary L, Choudhary B, Mantelingu K, Rangappa KS, Raghavan SC.
Identification and characterization of mercaptopyrimidine-based small molecules as inhibitors of nonhomologous DNA end joining
FEBS J., doi: 10.1111/febs.16615. Epub ahead of print. (2022)
- Thomas E, Gopalakrishnan V, Somasagara RR, Choudhary B, Raghavan SC.
Extract of Vernonia condensata, Inhibits Tumor Progression and Improves Survival of Tumor-allograft Bearing Mouse
Sci Rep., 24;6:23255. doi: 10.1038/srep23255. (2022) - Manjunath M, Swaroop S, Pradhan SS, Rao K R, Mahadeva R, Sivaramakrishnan V, Choudhary B.
Integrated Transcriptome and Metabolomic Analysis Reveal Anti-Angiogenic Properties of Disarib, a Novel Bcl2-Specific Inhibitor
Genes (Basel)., 13(7):1208. doi: 10.3390/genes13071208. (2022) - Gromiha MM, Orengo C, Sowdhamini R, Thornton J.
Srinivasan (1962-2021) in Bioinformatics and beyond.
Bioinformatics, 38(8):2377–9. doi: 10.1093/bioinformatics/btac054. Epub ahead of print. (2022) - Rebehmed J, de Brevern AG, Sowdhamini R, Joseph AP.
Advances in Molecular Docking and Structure-Based Modelling.
Front Mol Biosci., 9:839826. doi: 10.3389/fmolb.2022.839826 (2022) - Kalmankar NV, Pavalam M, Indrakumar S, Srinivasan N, Sowdhamini R.
DSDBASE 2.0: updated version of DiSulphide dataBASE, a database on disulphide bonds in proteins.
Database (Oxford), baac005. doi: 10.1093/database/baac005 (2022) - Verma S, Sowdhamini R.
A genome-wide search of Toll/Interleukin-1 receptor (TIR) domain-containing adapter molecule (TICAM) and their evolutionary divergence from other TIR domain containing proteins.
Biol Direct, 17(1):24. doi: 10.1186/s13062-022-00335-9 (2022) - Ambardar S, Vakhlu J, Sowdhamini R.
Insights from the analysis of draft genome sequence of Crocus sativus L.
Bioinformation, 18(1):1-13. doi: 10.6026/97320630018001 (2022) - Chakraborty, I, Shreya, A, Mendiratta, J, Bhan, A. and Saberwal, G.
An analysis of deficiencies in the Ethics Committee data of interventional trials registered with the Clinical Trials Registry – India.
PLOS Global Public Health, 2(10): e0000617 doi:10.1371/journal.pgph.0000617 (2022) - Huebner, K., Erlenbach-Wuensch, K., Prochazka, J. et al.
ATF2 loss promotes tumor invasion in colorectal cancer cells via upregulation of cancer driver TROP2.
Cell. Mol. Life Sci. 79, 423 doi: doi.org/10.1007/s00018-022-04445-5 (2022) - Nirati, Y., Purushotham, N. ; Alagesan, S.
Quantitative insight into the metabolism of isoprene-producingSynechocystis sp. PCC 6803 using steady state 13 C-MFA.
Photosynth Res, doi: 10.1007/s11120-022-00957-0 (2022) - Chakraborty M, Choudhury MC, Chakraborty I and Saberwal, G.
Rare disease patients in India are rarely involved in international orphan drug trials.
PLOS Global Public Health, 2(8): e0000890 doi:10.1371/journal.pgph.0000890 (2022) - Vaigundan D, Yuvaraj I, Sunita P, Sekar K, Murthy, M R N, Krishnaswamy, P R.
Structural characterization of a putative recombinant L-amino acid oxidase from Leptospira interrogans.
Current Science, 895–906, doi: 10.18520/cs/v123/i7/895-906. (2022) - Desai SS, Whadgar S, Raghavan SC and Choudhary B
MiRAGDB: A knowledgebase of RAG regulators
Frontiers in Immunology, 13: 863110 doi: 10.3389/fimmu.2022.863110 (2022) - Panda A, Islam S T, and Sharma G
Harmonizing Prokaryotic Nomenclature: Fixing the Fuss over Phylum Name Flipping.
mBio, 13(3): e00970-22 doi: 10.1128/mbio.00970-22 (2022) - Karmakar K, Bhattacharya R, Sharma A, Parmar A, Nath U, Nataraj K N, Earanna N, Sharma G, Chakravortty D
Lysinibacillus macroides mediated control of cellulose producing morphotype of Salmonella.
Journal of the Science of Food and Agriculture, doi: 10.1002/jsfa.12016 (2022) - Saïdi F, Mahanta U, Panda A, Jolivet N Y, Bitazar R, John G, Martinez M, Mellouk A, Calmettes C, Chang Y-W, Sharma G, Islam S T
Bacterial outer-membrane polysaccharide export (OPX) proteins occupy three structural classes with selective β-barrel porin requirements for polymer secretion.
bioRxiv, doi: 10.1101/2022.02.11.480155v1 (2022) - Moisander PH, Daley MC, Shoemaker KM, Kolte V, Sharma G, Garlick K.
Nitrogen fixation influenced by phosphorus and nitrogen availability in the benthic bloom-forming cyanobacterium Hydrocoleum sp. identified in a temperate marine lagoon.
Journal of Phycology, 58(3): 377-391 doi: 10.1111/jpy.13244 (2022) - Choudhury M. C., Chakraborty I and Saberwal, G.
Discrepancies between FDA documents and ClinicalTrials.gov for Orphan Drug-related clinical trial data.
PLOS Global Public Health, 2(4): e0000261 doi: 10.1371/journal.pgph.0000261 (2022) - Mahanta U, Saberwal G and Sharma G
Are countries becoming better at SARS-CoV-2 genomic surveillance?
Frontiers in Public Health, 10:887955 doi: 10.3389/fpubh.2022.887955 (2022)
- Gadkar S, Thakur M, Desouza J, Bhowmick S, Patel V, Chaudhari U, Acharya K K, Sachdeva G
Estrogen Receptor Expression is Modulated in Human and Mouse Prostate Epithelial Cells during Cancer Progression
Steroids, 184:109036 doi: 10.1016/j.steroids.2022.109036 (2022) - Ambaru B , Gangadharan G M, Subramanya H S, Gupta CM
Profilin is involved in G1 to S phase progression and mitotic spindle orientation during Leishmania donovani cell division cycle
PLOS ONE, 17(3): e0265692 doi: 10.1371/journal.pone.0265692 (2022) - Thakare, A., Ghosh, C., Alalamath, T. et al.
The genome trilogy of Anopheles stephensi, an urban malaria vector, reveals structure of a locus associated with adaptation to environmental heterogeneity.
Sci Rep, 12, 3610 doi: 10.1038/s41598-022-07462-3 (2022) - Acharya, K K
Precision molecular imaging can perhaps be enhanced for lung cancer management via integrated analysis of general parameters such as age, gender, genetics, and lifestyle.
Detection Systems in Lung Cancer and Imaging. Editors El-Baz A and Suri J S, Volume 1 Ch7 doi: 10.1088/978-0-7503-3355-9ch7 (2022) - Acharya, K.
Building bio-technical capacity among future researchers and industrial work-force in developing countries.
Academia Letters, 4672 doi: 10.20935/AL4672 (2022) -
Nirgude S, Desai S, Choudhary B
Curcumin alters distinct molecular pathways in breast cancer subtypes revealed by integrated miRNA/mRNA expression analysisCancer Reports, e1596. doi: 10.1002/cnr2.1596 (2022) - Ravi, S. et al.
Development of an SNP Assay for Marker-Assisted Selection of Soil-Borne Rhizoctonia solani AG-2-2-IIIB Resistance in Sugar Beet
Biology (Basil), 11(1), 49 doi: 10.3390/biology11010049 (2022) - Chakraborty, I and Saberwal, G.
CTRI requirement of prospective trial registration: Not always consistent.
Indian J Med Ethics, 7(4) NS: 312-314 doi: 10.20529/IJME.2022.033 (2022) - Mondal P, Natesha J, Abdul Salam A A, Thiyagarajan S and Meeran S M
Traditional Medicinal Plants against Replication, Maturation and Transmission Targets of SARS-CoV-2: Computational Investigation
J. Biomol. Struct. Dyn., 40(6): 2715-2732 doi: 10.1080/07391102.2020.1842246 (2022) - Awasthi A, Sharma G, Agrawal P
Chapter 20: Computational approaches for vaccine designing.
Book "Bioinformatics: Methods and Applications" by Elsevier Publications, 317–335 doi: 10.1016/B978-0-323-89775-4.00011-0 (2022) - Govindkumar B, Kavyashree B, Patel K, Sasidharan K, Arumugam T S, Thomas L , Praveena BKG, Raksha HN, Menon R, and Acharya KK
Ex-Ex Primer: An experimentally validated tool for designing oligonucleotides spanning spliced nucleic acid regions from multiple species
Journal of Biotechnology, 343; 1- 6 doi: 10.1016/j.jbiotec.2021.10.009 (2022) - Das A, Greco G, Kumar S, Catanzaro E, Morigi R, Locatelli A, Schols D, Alici H, Tahtaci H, Ravindran F, Fimognari C, Karki SS.
Synthesis, in vitro cytotoxicity, molecular docking and ADME study of some indolin-2-one linked 1,2,3-triazole derivatives
Comput Biol Chem., 97:107641. doi: 10.1016/j.compbiolchem.2022.107641. (2022) - Koroth J, Mahadeva R, Ravindran F, Parashar TR, Teja V, Karki SS, Choudhary B.
Curcumin derivative 1, 2-bis [(3E, 5E)-3, 5-bis [(2-chlorophenyl) methylene]-4-oxo-1-piperidyl] ethane-1, 2-dione (ST03) induces mitochondria mediated apoptosis in ovarian cancer cells and inhibits tumor progression in EAC mouse model
Transl Oncol., 5(1):101280. doi: 10.1016/j.tranon.2021.101280. (2022) - Harshan S, Dey P and Raghunathan S
Altered Transcriptional Regulation of Glycolysis in Circulating CD8+ T Cells of Rheumatoid Arthritis Patients
Genes, 13(7), 1216 doi: 10.3390/genes13071216 (2022) - Jose S, Gupta M, Sharma U, Quintero-Saumeth J, Dwivedi M.
Potential of phytocompounds from Brassica oleracea targeting S2-domain of SARS-CoV-2 spike glycoproteins: Structural and molecular insights
J Mol Struct., 1254:132369. doi: 10.1016/j.molstruc.2022.132369. (2022) - Nirgude S, Desai S, Mahadeva R, Ravindran F, Choudhary B.
ST08 Altered NF-κB Pathway in Breast Cancer Cells In Vitro as Revealed by miRNA-mRNA Analysis and Enhanced the Effect of Cisplatin on Tumour Reduction in EAC Mouse Model
Front Oncol., 12:835027. doi: 10.3389/fonc.2022.835027. (2022) - Srividya K, Mir S S, Thiyagarajan S , Nazir A
Dietary factors and SARS-CoV-2 contagion: in silico studies on modulation of viral and host proteins by spice actives
J. Biomol. Struct. Dyn, doi: 10.1080/07391102.2021.1948448 (2022)
- 2021
- Verma K.; Dixit S.; Alam A.
Cross talk between heme Oxygenase 1 and lateral root development for salt tolerance
Harsh Environment and Plant Resilience: Molecular and Functional Aspects, 355-365, doi: 10.1007/978-3-030-65912-7_14 (2021) - Baveja P.; Garg K.M.; Chattopadhyay B.; Sadanandan K.R.; Prawiradilaga D.M.; Yuda P.; Lee J.G.H.; Rheindt F.E.
Using historical genome-wide DNA to unravel the confused taxonomy in a songbird lineage that is extinct in the wild
Evolutionary Applications, 14-3, 698-709, doi: 10.1111/eva.13149 (2021) - Gopalakrishnan V, Sharma S, Ray U, Manjunath M, Lakshmanan D, Vartak SV, Gopinatha VK, Srivastava M, Kempegowda M, Choudhary B, Raghavan SC.
SCR7, an inhibitor of NHEJ can sensitize tumor cells to ionization radiation
Mol Carcinog., 60(9):627-643. doi: 10.1002/mc.23329. Epub 2021 Jun 30. PMID: 34192388 (2021)
- Desai SS, K RR, Jain A, Bawa PS, Dutta P, Atre G, Subhash A, Rao VUS, J S, Srinivasan S, Choudhary B.
Multidimensional Mutational Profiling of the Indian HNSCC Sub-Population Provides IRAK1, a Novel Driver Gene and Potential Druggable Target.
Front Oncol., 2;11:723162. PMID: 34796107; PMCID: PMC8593415 doi: 10.3389/fonc.2021.723162 (2021) - Madhavan A, Dhanesh VV, Selvaraj DPR, Gopinath S, Sreenivasa BP, Tamil Selvan RP, Sanyal A, Thiyagarajan S and Saravanan P
An optimized protocol for purification of virus-like particles of foot-and-mouth disease virus produced in the baculovirus expression system
The Pharma Innovation Journal. 10(10S): 33-37 (2021) - Murthy, M R N
Protein hydration
Current Science, 120 (1), 186 – 192 doi: 10.18520/cs/v120/i1/186-192 (2021) - Saberwal G
The many uses of data in public clinical trial registries
Curr. Sci., 120 (11): 1686 – 1691 doi: 10.18520/cs/v120/i11/1686-1691 (2021)
- Chakraborty, M., Ramaiah, A., Adolfi, A. et al.
Hidden genomic features of an invasive malaria vector, Anopheles stephensi, revealed by a chromosome-level genome assembly.
BMC Biology, 19: 28 doi: 10.1186/s12915-021-00963-z (2021) - Ravindran F, Koroth J, Manjunath M, Narayan S, Choudhary B
Curcumin derivative ST09 modulates the miR‑199a‑5p/DDR1 axis and regulates proliferation and migration in ovarian cancer cells
Scientific Reports, 11:23025 doi: 10.1038/s41598-021-02454-1 (2021) - Pal S, Sharma G, and Subramanian S
Complete genome sequence and identification of polyunsaturated fatty acid biosynthesis genes of the myxobacterium Minicystis rosea DSM 24000T
BMC Genomics, 22, 655 doi: 10.1186/s12864-021-07955-x (2021) - Singh RP, Saini N, Sharma G, Rahisuddin R, Patel M, Kaushik A, and Kumaran S.
Moonlighting Biochemistry of Cysteine Synthase: A Species-specific Global Regulator
Journal of Molecular Biology, 433 (22) 167255 doi: 10.1016/j.jmb.2021.167255 (2021) - Gupta S, Kulshreshtha P, Sharma D, Aggarwal D, Jiwani G, and Sharma G.
Microstructure observations of Lemna aequinoctialis ecotype.
Journal of Scientific Research, 65 (5); 164-171 doi: 10.37398/JSR.2021.650518 (2021) - Satheesh, K S K, Rani, H, Jolly, M K and Mahadevan, V.
Epigenetics of epithelial to mesenchymal transition (EMT) in cancer
Translational Epigenetics : Epigenetics and Metabolomics, Volume 28, Chapter 9, pages 237 - 264 doi: 10.1016/B978-0-323-85652-2.00001-4 (2021) - Rawat M, Kanyal A, Sahasrabudhe A, Vembar SS, Lopez-Rubio J-J, Karmodiya K.
Histone acetyltransferase PfGCN5 regulates stress responsive and artemisinin resistance related genes in Plasmodium falciparum.
Sci Rep. 11(1):852 doi: 10.1038/s41598-020-79539-w (2021)
- Venkatraman DL, Pulimamidi D, Shukla HG and Hegde SR
Tumor relevant protein functional interactions identified using bipartite graph analyses
Scientific Reports, 11, 21530 doi: 10.1038/s41598-021-00879-2 (2021) - Ravi S, Campagna G, Lucia M C D, Broccanello C, Bertoldo G, Chiodi C, Maretto L, Moro M, Eslami A S, Srinivasan S, Squartini A, Concheri G, Stevanato P
SNP Alleles Associated With Low Bolting Tendency in Sugar Beet
Front. Plant Sci., 12: 693285 doi: 10.3389/fpls.2021.693285 (2021) - Kumari R, Roy U, Desai S, Nilavar NM, Nieuwenhuijze AV, Paranjape A, Radha G, Bawa P, Srivastava M, Nambiar M, Balaji KN, Liston A, Choudhary B, Raghavan SC
MicroRNA miR-29c regulates RAG1 expression and modulates V(D)J recombination during B cell development
Cell Reports, 36(2), 109390 doi: 10.1016/j.celrep.2021.109390 (2021) - Kalia, K, Saberwal, G. and Sharma, G.
The lag in SARS-CoV-2 genome submissions to GISAID
Nature Biotechnology, 39: 1058–1060 doi: 10.1038/s41587-021-01040-0 (2021) - Garg, KM and Chattopadhyay, B
Gene Flow in Volant Vertebrates: Species Biology, Ecology and Climate Change
J. Indian Inst. Sci., 101(2):165-176 doi: 10.1007/s41745-021-00239-z (2021) - Sharma S, Varsha K K, Ray U, Siddiqua H, Jose AE Muninarasimaiah S, Raghavan SC, Choudhary B
Acute toxicity analysis of an inhibitor of BCL2, Disarib, in rats
Scientific Reports, 11:9982 doi: 10.1038/s41598-021-89387-x (2021) - Manjunath M and Choudhary B
Triple‑negative breast cancer: A run‑through of features, classification and current therapies (Review)
Oncology Letters, 22(1): 512 doi: 10.3892/ol.2021.12773 (2021) - Venugopal, N and Saberwal, G
A comparative analysis of important public trial registries, and a proposal for an interim ideal one.
PLoS ONE, 16(5): e0251191. doi: 10.1371/journal.pone.0251191 (2021) - Pan Y, Siddaramappa S, Sandal I, Dickerman A, Bandara AB, Inzana TJ.
The role of luxS in Histophilus somni virulence and biofilm formation.
Infection and Immunity, 89(2): e00567-20 doi: 10.1128/IAI.00567-20 (2021) - Siddaramappa S.
Comparative genomics of the Pasteurella multocida toxin.
Genome, 64(7): 679-692 doi: 10.1139/gen-2020-0176 (2021) - Nadig S, Murthy S, Vandanashree M, Subramanya HS, Gopal B, Vembar S.
Draft Genome Sequence of the Community-Associated Staphylococcus aureus Sequence Type 88 Strain LVP-7, Isolated from an Ocular Infection
Microbiology Resource Announcements, 10(7) e00077-21 doi: 10.1128/MRA.00077-21 (2021) - Manjunath M, Choudhary B, Raghavan S C
SCR7, a potent cancer therapeutic agent and a biochemical inhibitor of nonhomologous DNA end-joining
Cancer Reports, 4(3): e1341 doi: 10.1002/cnr2.1341 (2021). - Sharma G, Yao A. I., Smaldone G. T., Liang J., Long M., Facciotti M. T., Singer M.
Global gene expression analysis of the Myxococcus xanthus developmental time course.
Genomics, 113 (1): 120-134 doi: 10.1016/j.ygeno.2020.11.030 (2021) - Nirgude S, Choudhary B
Insights into the role of GPX3, a highly efficient plasma antioxidant, in cancer
Biochem Pharmacol, 184:114365 doi: 10.1016/j.bcp.2020.114365 (2021) - Davuluri S, Bajpai AK, Thirumurugan K, Acharya KK
The molecular basis of gender disparities in smoking lung cancer patients
Life Sci, 267; 118927 doi: 10.1016/j.lfs.2020.118927 (2021) - Kumar V, Sekar M, Sarkar P, Acharya KK, Thirumurugan K
Dynamics of HOX gene expression and regulation in adipocyte development
Gene, 768, 145308 doi: 10.1016/j.gene.2020.145308 (2021) - Hudson BS, Kolte V, Khan A and Sharma G.
Dynamic tracking of variant frequencies depicts the evolution of mutation sites amongst SARS-CoV-2 genomes from India.
Journal of Medical Virology, doi: 93(4) 2534-2537 doi: 10.1002/jmv.26756 (2021)
- 2020
-
Gwee C.Y.; Garg K.M.; Chattopadhyay B.; Sadanandan K.R.; Prawiradilaga D.M.; Irestedt M.; Lei F.; Bloch L.M.; Lee J.G.H.; Irham M.; Haryoko T.; Soh M.C.K.; Peh K.S.-H.; Rowe K.M.C.; Ferasyi T.R.; Wu S.; Wogan G.O.U.; Bowie R.C.K.; Rheindt F.E.
Phylogenomics of white-eyes, a ‘great speciator’, reveals indonesian archipelago as the center of lineage diversity
eLife, 9, e62765, doi: 10.7554/eLife.62765 (2020) -
Yasir M.; Qureshi A.K.; Srinivasan S.; Ullah R.; Bibi F.; Rehan M.; Khan S.B.; Azhar E.I.
Domination of Filamentous Anoxygenic Phototrophic Bacteria and Prediction of Metabolic Pathways in Microbial Mats from the Hot Springs of Al Aridhah
Folia Biologica (Czech Republic), 66-1, 24-35, https://fb.cuni.cz/volume-66-2020-no-1 (2020) -
Chellappan S.; Mathivanan S.; Thippeswamy R.; Nagesh M.; Savithri H.S.; Murthy M.R.N.
Crystal structure of oxalate decarboxylase from Photorhabdus luminescens, a symbiotic bacterium associated with entomopathogenic nematodes
Current Science, 119-8, https://www.currentscience.ac.in/show.issue.php?volume=119&issue=8 (2020) -
Behera N.
Analysis of microarray gene expression data using information theory and stochastic algorithm
Handbook of Statistics, 43, 349-378, doi: 10.1016/bs.host.2020.02.002 (2020) -
Whitfield D L, Sharma G, Smaldone G T and Singer M.
CglB adhesins secreted at bacterial focal adhesions mediate gliding motility
Genomics, 112-2, 1588-1597, doi: 10.1016/j.ygeno.2019.09.008 (2020) - Sharma S, Varsha KK, Kumari S, Gopalakrishnan V, Jose AE, Choudhary B, Mantelingu K, Raghavan SC.
Acute toxicity analysis of Disarib, an inhibitor of BCL2
Scientific Reports, 10:15188 doi: 10.1038/s41598-020-72058-8 (2020) - Nilavar NM, Nishana M, Paranjape AM, Mahadeva R, Kumari R, Choudhary B, Raghavan SC.
Znc2 module of RAG1 contributes towards structure-specific nuclease activity of RAGs
Biochem J, Volume 477 Issue 18 doi: 10.1042/BCJ20200361 (2020) - Chandrashekar DS, Chakravarthi BVSK, Robinson AD, Anderson JC, Agarwal S, Balasubramanya SAH, Eich ML, Bajpai AK, Davuluri S, Guru MS, Guru AS, Naik G, Della Manna DL, Acharya KK, Carskadon S, Manne U, Crossman DK, Ferguson JE, Grizzle WE, Palanisamy N, Willey CD, Crowley MR, Netto GJ, Yang ES, Varambally S, Sonpavde G.
Therapeutically actionable PAK4 is amplified, overexpressed and involved in bladder
Oncogene, volume 39, pages 4077–4091 doi: 10.1038/s41388-020-1275-7 (2020) - Kaur R, Arora N, Jamakhani MA, Malik S, Kumar P, Anjum F, Tripathi S, Mishra A, Prasad A.
Development of multi-epitope chimeric vaccine against Taenia solium by exploring its proteome: an in silico approach
2020 Informa UK Limited, trading as Taylor & Francis Group, Volume 19, 2020 - Issue 1 Pages 105-114 doi: 10.1080/14760584.2019.1711057 (2020) - Baveja P, Garg KM, Chattopadhyay B, Sadanandan KR, Prawiradilaga DM, Yuda P, Lee JGH, Rheindt FE
Using historical genome-wide DNA to unravel the confused taxonomy in a songbird lineage that is extinct in the wild.
Evol Appl., 7;14(3):698-709. doi: 10.1111/eva.13149 (2020) - Murugesan K, Srinivasan P, Mahadeva R, Gupta CM, Haq W
Tuftsin-Bearing Liposomes Co-Encapsulated with Doxorubicin and Curcumin Efficiently Inhibit EAC Tumor Growth in Mice
International Journal of Nanomedicine , 15, 10547–10559 doi: 10.2147/IJN.S276336 (2020) - Chida AR, Ravi S, Jayaprasad S, Paul K, Saha J, Suresh C, Whadgar S, Kumar N, Rao K R, Ghosh C, Choudhary B, Subramani S, Srinivasan S
A near-chromosome level genome assembly of Anopheles stephensi
Front. Genet., 11:565626 doi: 10.3389/fgene.2020.565626 (2020) - Deb S, Jayaprasad J, Ravi S, Rao K R, Whadgar S, Hariharan N, Dixit S, Sunil M, Choudhary B, Stevanato P, Ramireddy E, Srinivasan S
Classification of Grain Amaranths Using Chromosome-Level Genome Assembly of Ramdana, A. hypochondriacus
Front. Plant Sci. 11: 579529 doi: 10.3389/fpls.2020.579529 (2020) - Unni S, Aouti S, Thiyagarajan S and Padmanabhan B
Identification of a repurposed drug as an inhibitor of Spike protein of human coronavirus SARS-CoV-2 by computational methods
J. BioSci, 45(1):130 doi: 10.1007/s12038-020-00102-w (2020) - Nirgude S, Mahadeva R , Koroth J, Kumar S , Kumar K S S, Gopalakrishnan V, Karki S S, and Choudhary B
ST09, A Novel Curcumin Derivative, Blocks Cell Migration by Inhibiting Matrix Metalloproteases in Breast Cancer Cells and Inhibits Tumor Progression in EAC Mouse Tumor Models
Molecules, 25(19), 4499 doi: 10.3390/molecules25194499 (2020) - Gupta CM, Ambaru B, Bajaj R
Emerging Functions of Actins and Actin Binding Proteins in Trypanosomatids
Frontiers in Cell and Developmental Biology, 8:587685 doi: 10.3389/fcell.2020.587685 (2020) - Kumari S, Subramanya HS
Network pharmacology study of Curcuma longa L.: potential target proteins and their functional enrichment analysis
BMC Res Notes, 13(1):468 doi: 10.21203/rs.3.rs-31985/v3 (2020) - Kumar M, Martin A, Nirgude S, Chaudhary B, Mondal S, Sarkar A
Quinacrine inhibits GSTA1 activity and induces apoptosis through G1/S arrest and generation of ROS in human non-small cell lung cancer cell lines
Oncotarget, 11(18): 1603–1617 doi: 10.18632/oncotarget.27558 (2020) - Parlikar A, Kalia K, Sinha S, Patnaik S, Sharma N, Vemuri SG, Sharma G
Understanding genomic diversity, pan-genome, and evolution of SARS-CoV-2
PeerJ, 8:e9576 doi: 10.7717/peerj.9576 (2020) - Islam ST, My L, Jolivet NY, Belgrave AM, Fleuchot B, Brasseur G, Faure LM, Sharma G, Lemon DJ, Saidi F, Fiche J-B, Bratton BP, Singer M, Garza AG, Nollmann M, Shaevitz JW, Mignot T
CglB adhesins secreted at bacterial focal adhesions mediate gliding motility
bioRxiv, doi: 10.1101/2020.07.22.216333 (2020) - Islam ST, Alvarez I V, Saïdi F, Guiseppi A, Vinogradov E, Sharma G, Espinosa L, Morrone C, Brasseur G, Guillemot J-F, Benarouche A, Bridot J-L, Ravicoularamin G, Cagna A, Gauthier C, Singer M, Fierobe H-P, Mignot T, Mauriello EMF
Modulation of bacterial multicellularity via spatio-specific polysaccharide secretion.
PLoS Biology, 18(6): e3000728 doi: 10.1371/journal.pbio.3000728 (2020) - Balasubramanian R and Hegde SR
Integrating multi-omics data to investigate pseudogene expression in Mycolicibacterium smegmatis
Gene, 755: 144908 doi: 10.1016/j.gene.2020.144908 (2020) - Kumari, S. Mohan, A. and Saberwal, G
Hidden duplicates: 10s or 100s of Indian trials, registered with ClinicalTrials.gov, have not been registered in India, as required by law
PLoS One, 15(6): e0234925 doi: 10.1371/journal.pone.0234925 (2020) - Saberwal, G.
Breaking all the rules, at lightning speed (Editorial)
Current Science, 119(1), 7 – 8 (2020) - Ambaru B, Gopalsamy A, Tammana TVS, Subramanya HS, Gupta CM
Actin sequestering protein, profilin, regulates intracellular vesicle transport in Leishmania
Molecular & Biochemical Parasitology, 238, 111280 doi: 10.1016/j.molbiopara.2020.111280 (2020) - Bajaj R, Ambaru B, Gupta CM
Deciphering the role of UBA-like domains in intraflagellar distribution and functions of myosin XXI in Leishmania.
PLoS One, 15(4): e0232116 doi: 10.1371/journal.pone.0232116 (2020) - Viswanathan V, Thiyagarajan S, Erbe V, Raghunathan S, Rajendran V, Siddaramappa S
Characterization of Heumann’s pigmented and non-pigmented strains of [Pseudomonas] Sphingomonas echinoides
Biologia, 75: 1445-1453 doi: 10.2478/s11756-020-00447-5 (2020) - Ami VKG, Balasubramanian R, Hegde SR
Genome-wide identification of the context-dependent sRNA expression in Mycobacterium tuberculosis
BMC Genomics, 21(1):167 doi: 10.1186/s12864-020-6573-5 (2020) - Alka M, Chatterjee S, Parchure A, Mahantesh S, Davuluri S, Kumar AA, Avinash T, Padma M, Premalata CS, Sinha M, Chugani A, Vishnu Priya R, Acharya KK, Jayshree R.S
Natural Killer Cell transcriptome during primary EBV infection and EBV associated Hodgkin Lymphoma in children – a preliminary observation
Immunobiology, 225(3):151907 doi: 10.1016/j.imbio.2020.151907 (2020) - Bajpai AK, Davuluri S, Tiwary K, Narayanan S, Oguru S, Basavaraju K, Dayalan D, Thirumurugan K, Acharya KK
Systematic comparison of the protein-protein interaction databases from a user’s perspective
J Biomed Inform., 103:103380 doi: 10.1016/j.jbi.2020.103380 (2020) - Hegde SR
Computational Identification of the proteins associated with quorum sensing and biofilm formation in Mycobacterium tuberculosis
Frontiers in Microbiology, 10:3011 doi: 10.3389/fmicb.2019.03011 (2020) - Nuttall RA, Sharma G, Moisander PH.
Draft Genome Sequence of Marinobacter hydrocarbonoclasticus NCT7M, Obtained from the Microbiome of a Marine Copepod
Microbiology Resource Announcements, 9 (11) e01459-19 doi: 10.1128/MRA.01459-19 (2020) - Lindner, P, Paul, S, Eckstein, M, Hampel C, Muenzner JK, Erlenback-Wuensch K, Ahmed H P, Mahadevan V, Brabletz T, Hartmann A, Vero J, Schneider-Stock, R
EMT transcription factor ZEB1 alters the epigenetic landscape of colorectal cancer cells
Cell Death and Disease, 11: 147 doi: 10.1038/s41419-020-2340-4 (2020) - Pillamarapu M, Mohan A and Saberwal G
Response to the Letter on: “An analysis of deficiencies in the data of interventional drug trials registered with Clinical Trials Registry – India”
Trials, 21: 39 doi: 10.1186/s13063-019-4011-2 (2020) - Ahmad E, Hegde SR and Nagaraja V
Revisiting intrinsic transcription termination in mycobacteria: U-tract downstream of secondary structure is dispensable for termination.
Biochem Biophys Res Commun, 522(1):226-232 doi: doi: 10.1016/j.bbrc.2019.11.062 (2020) - Whitfield D L, Sharma G, Smaldone G T and Singer M.
Peripheral rods: a specialized developmental cell type in Myxococcus xanthus.
Genomics, 112 (2), 1588-1597 doi: 10.1016/j.ygeno.2019.09.008 (2020) - Bernard V, Moudgalya S, Reegan D, Sreekanthreddy P, Mohan A, Subramanya HS, Vembar SS, Ghosh S
Whole Genome Sequences of Aedes aegypti (Linn.) Field Isolates from Southern India
bioRxiv, doi: 10.1101/2020.05.08.083949 (2020)
- 2019
- Herrera‐Solorio, A.M.; Vembar, S.S.; MacPherson, C.R.; Lozano‐Amado, D.; Meza, G.R.; Xoconostle‐Cazares, B.; Martins, R.M.; Chen, P.; Vargas, M.; Scherf, A. and Hernández‐Rivas, R.,
Clipped histone H3 is integrated into nucleosomes of DNA replication genes in the human malaria parasite Plasmodium falciparum
EMBO reports, 20-4, e46331, doi: 10.15252/embr.201846331 (2019) - Murugesan, K., Koroth, J., Srinivasan, P.P., Singh, A., Mukundan, S., Karki, S.S., Choudhary, B. and Gupta, C.M.,
Effects of green synthesised silver nanoparticles (ST06-AgNPs) using curcumin derivative (ST06) on human cervical cancer cells (HeLa) in vitro and EAC tumor bearing mice models
International Journal of Nanomedicine, 2019-14, 5257—5270, doi: 10.2147/IJN.S202404 (2019) - Bangera, M., Gowda K, G., Sagurthi, S. R., & Murthy, M. R. N.
Structural and functional insights into phosphomannose isomerase: the role of zinc and catalytic residues
Acta Crystallographica Section D: Structural Biology, 75-5, 475-487, doi:10.1107/S2059798319004169 (2019) - Kumari N, Vartak SV, Dahal S, Kumari S, Desai SS, Gopalakrishnan V, Choudhary B, Raghavan SC.
G-quadruplex Structures Contribute to Differential Radiosensitivity of the Human Genome
I Science, 21, 22 288-307 doi: 10.1016/j.isci.2019.10.033 (2019) - Krishnan NM, Katoh H, Palve V, Pareek M, Sato R, Ishikawa S, Panda B.
Functional genomics screen with pooled shRNA library and gene expression profiling with extracts of Azadirachta indica identify potential pathways for therapeutic targets in head and neck squamous cell carcinoma
PeerJ, 7:e6464 1-20 doi: 10.7717/peerj.6464 (2019) - Khatri I, Sharma G, Subramanian S.
Composite genome sequence of Bacillus clausii, a probiotic commercially available as Enterogermina ®, and insights into its probiotic properties
BMC Microbiology, 19:307 doi: 10.1186/s12866-019-1680-7 (2019)
- Ahmed P H, V V, More RP, Viswanath B, Jain S, Rao MS, Mukherjee O; ADBS Consortium
The Indian Exome Reference Database (Phase I)
Journal of Computational Biology, Vol. 26, No. 3 doi: 10.1089/cmb.2018.0199 (2019) - Mbiribindi B, Mukherjee S, Wellington D, Das J and Khakoo S I
Corrigendum: Spatial Clustering of Receptors and Signaling Molecules Regulates NK Cell Response to Peptide Repertoire Changes
Frontiers in Immunology, 10:2370 doi: 10.3389/fimmu.2019.02370 (2019) - Panga V, Kallor AA, Nair A, Harshan S, Raghunathan S
Mitochondrial dysfunction in rheumatoid arthritis: A comprehensive analysis by integrating gene expression, protein-protein interactions and gene ontology data
PLoS ONE, 14(11): e0224632 doi: 10.1371/journal.pone.0224632 (2019) - Pillamarapu, M., Mohan, A. and Saberwal, G.
An analysis of deficiencies in the data of interventional drug trials registered with Clinical Trials Registry – India.
Trials, 20: 535 doi: 10.1186/S13063-019-3592-0 (2019) - Balagannavar G, Basavaraju K, Bajpai AK, Davuluri S, Kannan S, Vasan SS, Madhusudhan M, Darshan SC, Chitturi N, Balagannavar V,Oguru S, and Acharya K K
Listing candidate diagnostic markers and transcriptomic exploration of the molecular basis of a type of male infertility (Non-Obstructive Azoospermia), via next generation sequencing methods
bioRxiv, doi: 10.1101/778670 (2019) - Vadivel K, Schreuder HA, Liesum A, Schmidt AE, Goldsmith G, Bajaj SP
Sodium-site in serine protease domain of human coagulation factor IXa: evidence from the crystal structure and molecular dynamics simulations study.
J Thromb Haemost, 17 (4):574-584 doi: 10.1111/jth.14401 (2019) - Abbey D, Singh G, Verma I, Derebail S, Kolkundkar U, Chandrashekar DS, Acharya KK, Vemuri MC and Seshagiri PB
Successful derivation of an induced pluripotent stem cell line from a genetically nonpermissive enhanced Green Fluorescent Protein-transgenic FVB/N mouse strain.
Cellular Programming, (5): 270 – 284 doi: 10.1089/cell.2019.0019 (2019) - Sinha, M., Sundar, K., Premalata, C.S. et al.
Pro-oncogenic, intra host viral quasispecies in Diffuse large B cell lymphoma patients with occult Hepatitis B Virus infection.
Scientific Reports, 9: 14516 doi: 10.1038/s41598-019-51157-1 (2019) - Rani H, Mahadevan V
Histone and DNA Methylome in Neurodegenerative, Neuropsychiatric and Neurodevelopmental Disorders
Springer Nature, book: The DNA, RNA, and Histone Methylomes, 63-102 doi: 10.1007/978-3-030-14792-1 (2019) - Siddaramappa S, Narjala A, Viswanathan V, Maliye C, and Lakshminarayanan R.
Phylogenetic insights into the diversity of Chryseobacterium species
Access Microbiology, 2019; 1(3): e000019 doi: 10.1099/acmi.0.000019 (2019) - Nuttall R, Sharma G, Moisander PH.
Draft genome sequence of Vibrio cyclitrophicus NCT10V, cultivated from the microbiome of a marine copepod.
Microbiology Resource Announcements, 8 (44) e01208-19 doi: 10.1128/MRA.01208-19 (2019). - Parales RE, Sharma G, Zhang X, Subuyuj GA, Langner JT, Wright ME, Ditty JL and Dawson SC
Draft Genome Sequence of the Caffeine-Degrading Methylotroph Methylorubrum populi PINKEL
Microbiology Resource Announcements, Nov; 8(47): e01300-19 doi: 10.1128/MRA.01208-19 (2019) - Berglar AV, Vembar SS.
Past, Present and Future of Malaria Prevalence and Eradication in the Light of Climate Change.
Encyclopedia of Environmental Health (Second Edition), Pages 49-67 doi: 10.1016/B978-0-12-409548-9.11416-2 (2019) - Gopalakrishnan V, Dahal S, Radha G, Sharma S, Raghavan SC, Choudhary B.
Characterization of DNA double-strand break repair pathways in diffuse large B cell lymphoma.
Mol Carcinog, 58 (2):219-233 doi: 10.1002/mc.22921 (2019). - Pandey M, Gopalakrishnan V, Swarup H A, Kumar S, Gudapurreddy R, Jose A E, Vartak S V, Sebastian R, Srivastava M, Choudhary B, Mantelingu K, Karki S S, Raghavan S C
Water soluble version of SCR7-pyrazine inhibits DNA repair and abrogates tumour cell proliferation.
J Radiat Cancer Res., 10:27-43 doi: 10.4103/jrcr.jrcr_24_18 (2019) - Koroth J, Nirgude S, Tiwari S, Gopalakrishnan V, Mahadeva R, Kumar S, Karki SS, Choudhary B.
Investigation of anti-cancer and migrastatic properties of novel curcumin derivatives on breast and ovarian cancer cell lines.
BMC Complement. Altern. Med., 19:273 doi: 10.1186/s12906-019-2685-3 (2019) - Mbiribindi B, Mukherjee S, Wellington D, Das J, Khakoo SI.
Spatial Clustering of Receptors and Signaling Molecules Regulates NK Cell Response to Peptide Repertoire Changes.
Frontiers in Immunology, 10: 605 doi: 10.3389/fimmu.2019.00605 (2019) - Huebner K, Prochazka J, Monteiro AC, Mahadevan V, Schneider-Stock R
The Activating Transcription Factor 2: an influencer of cancer progression
Mutagenesis, 34(5-6): 375-389 doi: 10.1093/mutage/gez041 (2019) - Choudhury M. C. and Saberwal, G.
The work, goals, challenges, achievements, and recommendations of orphan medicinal product organizations in India: an interview-based study
Orphanet J Rare Dis., 14, 241 doi: 10.1186/s13023-019-1224-0 (2019) - Unni S, Thiyagarajan S, Bharath MMS, and Padmanabhan B
Tryptophan Oxidation in the UQCRC1 Subunit of Mitochondrial Complex III (Ubiquinol-Cytochrome C Reductase) in a Mouse Model of Myodegeneration Causes Large Structural Changes in the Complex: A Molecular Dynamics Simulation Study.
Sci. Rep., 9:10694 doi: 10.1038/s41598-019-47018-6 (2019) - Trebbi, D., Ravi, S., Broccanello, C., Chiodi, C., Francis, G., Oliver, J., Mulpuri, S., Srinivasan, S., Stevanato, P.
Identification and validation of SNP markers linked to seed toxicity in Jatropha curcas L.
Scientific Reports, 9:10220 doi: 10.1038/s41598-019-46698-4 (2019) - Shukla, H. G., Bawa, P.S. and Srinivasan, S.
hg19KIndel: Ethnicity normalized human reference genome.
BMC Genomics, 20:459 doi: 10.1186/s12864-019-5854-3 (2019) - Prabaharan C, Kandavelu P, Packianathan C, Rosen BP4, and Thiyagarajan S
Structures of two ArsR As(III)-responsive transcriptional repressors: Implications for the mechanism of derepression.
J. Struct. Biol., 207 (2):209-217 doi: 10.1016/j.jsb.2019.05.009 (2019) - Choudhury M. C. and Saberwal, G.
The role of patient organizations in the rare disease ecosystem in India: An interview-based study.
Orphanet J Rare Dis., 14:117 doi: 10.1186/s13023-019-1093-6 (2019) - Chaturvedi, N, Mehrotra, B, Kumari, S, Gupta, S, Subramanya, H S and Saberwal, G.
Some data quality issues at ClinicalTrials.gov.
Trials, 20:378 doi: 10.1186/s13063-019-3408-2 (2019) - Saberwal, G.
India to power the more widespread use of biosimilars? (Guest Editorial)
Curr. Sci., 116 (9), 1451–1453 (2019) - Subramanya, H. S. and Saberwal, G.
India needs more policy research. (Guest Editorial)
Curr. Sci., 116 (8), 1279–1280 (2019) - Vijayakumari D, Sharma A K, Bawa PS, Kumar R, Srinivasan S and Vijayraghavan U.
Early splicing functions of fission yeast Prp16 and its unexpected requirement for gene Silencing is governed by intronic features.
RNA Biology, 16 (6), 754-769 doi: 10.1080/15476286.2019.1585737 (2019) - Choudhury, M. C., and Saberwal, G.
Patient advocacy. (Guest Editorial)
Curr. Sci., 116 (3), 345–346 (2019) - Saberwal G
Will our education system enable India to be a super-power any time soon? (Guest Editorial)
Curr. Sci., 116 (4), 509–510 (2019)
- 2018
- Mehrotra P, Ami VKG, Srinivasan N.
Clustering of multi-domain protein sequences
Proteins: Structure, Function and Bioinformatics, 86, 7: 759-776 doi: 10.1002/prot.25510 (2018)
- Amrutha RN, Shrivastav A, Shravani RS, Buddana SK, Deshpande U, Prakasham RS
Complete Genome Sequence of α-1,3-Glucanase-Producing Strain
ASM Journals, 7:14 doi: 10.1128/MRA.01095-18 (2018)
- Palve V, Pareek M, Krishnan NM, Siddappa G, Suresh A, Kuriakose MA, Panda B.
A minimal set of internal control genes for gene expression studies in head and neck squamous cell carcinoma
PeerJ, 6:e5207 doi: 10.7717/peerj.5207 (2018)
- Palve V, Bagwan J, Krishnan NM, Pareek M, Chandola U, Suresh A, Siddappa G, James BL, Kekatpure V, Kuriakose MA, Panda B.
Detection of High-Risk Human Papillomavirus in Oral Cavity Squamous Cell Carcinoma Using Multiple Analytes and Their Role in Patient Survival
American Society of Clinical Oncology, 4 1-38 doi: 10.1200/JGO.18.00058 (2018)
- Mahalingam N, Manivannan B, Khamari B, Siddaramappa S, Adak S, Bulagonda EP
Detection of Antibiotic Resistance Determinants and Their Transmissibility among Clinically Isolated Carbapenem-Resistant Escherichia coli from South India
Med Princ Pract, 27:428–435, doi: 10.1159/000489885 (2018)
- Manu S, Thiyagarajan S, Acharya KK
Systematic analyses of autosomal recombination rates from the 1000 genomes project uncovers the global recombination landscape in humans.
bioRxiv, https://www.biorxiv.org/content/early/2018/01/12/246702 (2018) - Saberwal G
Regulatory harmonization: a view from India. (Guest Editorial)
Current Science, 114, 423–424 (2018)
- Hariharan N, Ravi S, Pradeep BE, Subramanyam KN, Choudhary B, Srinivasan S, Khanchandani P
A novel loss-of-function mutation in HACE1 is linked to a genetic disorder in a patient from India
Human Genome Variation, 5, 17061; doi: 10.1038/hgv.2017.61 (2018) - Dash, SP and Saberwal, G.
The bio-incubation boom in India
Current Science, 115(1); 228 – 233 doi: 10.18520/cs/v115/i2/228-233 (2018) - Mukherjee S, Saberwal G
Managing India’s AIDS crisis in the 2000s: Quantitative modeling had impact.
Current Science, 114(10); 2005–2006 (2018) - Siddaramappa S., Viswanathan V, Thiyagarajan S., Narjala A.
Genomewide characterisation of the genetic diversity of carotenogenesis in bacteria of the order Sphingomonadales
Microbial Genomics, 2018: 4 doi: 10.1099/mgen.0.000172 (2018) - Saberwal G
Bio-business in brief: What ails clinical trials?
Curr. Sci., 115, 1648–1652 doi: 10.18520/cs/v115/i9/1648-1652 (2018) - Panga V, Raghunathan S
A cytokine protein-protein interaction network for identifying key molecules in rheumatoid arthritis
PLoS One, 13(6):e0199530 doi: https://doi.org/10.1371/journal.pone.0199530 (2018) - Uma M, Hegde SR, Rao PP, Nagalekshmi K, Gauthami S, Kumar D, Hegde NR
A novel point mutation (L70P) inactivates poliovirus 3C protease
Acta Virol, 62(1): 68-77 (2018) - Saberwal G
Cuba: A different kind of role model for biotechnology
Curr. Sci., 115(10) 1835–1836 (2018) - Bawa PS, Ravi S, Paul S, Choudhary B, Srinivasan S
A novel molecular mechanism for a long non-coding RNA PCAT92 implicated in prostate cancer
Oncotarget, 9: 32419-32434 doi: 10.18632/oncotarget.25940 (2018) - Harshan S, Dey P, Raghunathan S
Effects of rheumatoid arthritis associated transcriptional changes on osteoclast differentiation network in the synovium
PeerJ, 6:e5743 doi: 10.7717/peerj.5743 (2018) - Siddaramappa S, Pullela K, Thimmappa B, Devkota R, Bajaj R, Manivannan B, Mahalingam N, Pradeep BE
Characterization of blaCTX-M sequences of Indian origin and thirteen uropathogenic Escherichia coli isolates resistant to multiple antibiotics
BMC Res Notes, 11:630 doi: https://doi.org/10.1186/s13104-018-3735-5 (2018) - Vartak S V et al.
Autocyclized forms of SCR7 induce cancer cell death by inhibiting nonhomologous DNA end joining in a ligase IV dependent manner.
Febs J, 285 (21) 3959-3976 doi: https://doi.org/10.1111/febs.14661 (2018) - Arjun D V, Basu P and Mukherjee S.
Anticipation: an effective evolutionary strategy for a sub-optimal population in a cyclic environment
ArXiv, 1811.09167 doi: https://doi.org/10.48550/arXiv.1811.09167 (2018) - Ramadoss M, Mahadevan V
Targeting the cancer epigenome: synergistic therapy with bromodomain inhibitors
Drug Discovery Today, 23 (1), 76 - 79 doi: 10.1016/j.drudis.2017.09.011 (2018) - Maiuthed A, Ninsontia C, Erlenbach-Wuensch K, Ndreshkjana B, Muenzner JK, Caliskan A, Ahmed P. H, Chaotham C, Hartmann A, Vial Roehe A, Mahadevan V, Chanvorachote P, Schneider-Stock R.
Cytoplasmic p21 Mediates 5-Fluorouracil Resistance by Inhibiting Pro-Apoptotic Chk2.
Cancers, 10(10):373 doi: 10.3390/cancers10100373 (2018) - Mahalakshmi R., Ahmed HP, Mahadevan V.
HDAC inhibitors show differential epigenetic regulation and cell survival strategies on p53 mutant colon cancer cells
Journal of Biomolecular Structure and Dynamics, 36:4, 938-955 doi: 10.1080/07391102.2017.1302820 (2018)
- 2017
- Shukla P, Khodade VS, SharathChandra M, Chauhan P, Mishra S, Siddaramappa S, Pradeep BE, Singh A, Chakrapani H.
"On demand" redox buffering by H 2S contributes to antibiotic resistance revealed by a bacteria-specific H 2S donor
Chem. Sci., 8, 4967-4972 doi: 10.1039/c7sc00873b (2017)
- Ananda H, Sharath Kumar KS, Nishana M, Hegde M, Srivastava M, Byregowda R, Choudhary B, Raghavan SC, Rangappa KS.
Regioselective synthesis and biological studies of novel 1-aryl-3, 5-bis (het) aryl pyrazole derivatives as potential antiproliferative agents
Mol Cell Biochem, 426, 149–160 doi: 10.1007/s11010-016-2887-7 (2017)
- Mukherjee S, Stewart D, Stewart W, Lanier LL, Das J.
Connecting the dots across time: reconstruction of single-cell signalling trajectories using time-stamped data
R. Soc. open sci., 4: 170811 doi: 10.1098/rsos.170811 (2017) - Krishnan NM, Panda B.
Comparative analyses of putative toxin gene homologs from an Old World viper, Daboia russelii
PeerJ, 5:e4104 doi: 10.7717/peerj.4104 (2017) - Hegde M, Vartak SV, Kavitha CV, Ananda H, Prasanna DS, Gopalakrishnan V, Choudhary B, Rangappa KS, Raghavan SC.
A Benzothiazole Derivative (5g) Induces DNA Damage And Potent G2/M Arrest In Cancer Cells
Scientific Repo Rts, 7: 2533 doi: 10.1038/s41598-017-02489-3 (2017)
- Sunil M, Hariharan N, Dixit S, Choudhary B, Srinivasan S.
Differential genomic arrangements in Caryophyllales through deep transcriptome sequencing of A. hypochondriacus
PLoS ONE, 12(8) doi: 10.1371/journal.pone.0180528 (2017) - Vartak SV, Iyer D, Santhoshkumar TR, Sharma S, Mishra A, Goldsmith G, Srivastava M, Srivastava S, Karki SS, Surolia A, Choudhary B, Raghavan SC.
Novel BCL2 inhibitor, Disarib induces apoptosis by disruption of BCL2-BAK interaction
Biochemical Pharmacology, 131,1 doi: 10.1016/j.bcp.2017.02.015 (2017) - Karpe SD, Dhingra S, Brockmann A, Sowdhamini R.
Computational genome-wide survey of odorant receptors from two solitary bees Dufourea novaeangliae (Hymenoptera: Halictidae) and Habropoda laboriosa (Hymenoptera: Apidae).
Sci Rep.,7(1):10823. doi: 10.1038/s41598-017-11098-z (2017) - Viswanathan V, Narjala A, Ravichandran A, Jayaprasad S, Siddaramappa S
Evolutionary Genomics of an Ancient Prophage of the Order Sphingomonadales
Genome Biol. Evol., 9(3):646–658 doi: 10.1093/gbe/evx024 (2017) - Saberwal G
Supporting start-ups (Guest Editorial)
Current Science, 113 (2); 195–196 (2017) - Ellingford, JM, Campbell, C., Barton, S. et al.
Validation of copy number variation analysis for next-generation sequencing diagnostics.
Eur J Hum Genet, 25:719-724 doi: 10.1038/ejhg.2017.42 (2017) - Shukla P , Khodade VS , Sharathchandra M, Chauhan P, Mishra S, Siddaramappa S, Pradeep BE, Singh A and Chakrapani H.
“On demand” redox buffering by H2S contributes to antibiotic resistance revealed by a bacteria-specific H2S donor
Chem. Sci., 8, 4967-4972 doi: 10.1039/C7SC00873B (2017) - VijayRaghavan, K. and Saberwal, G.
Bio-business in brief: The case for ambitious action in the public sector
Current Science, 113(10), 1841–1845 doi: 10.18520/cs/v113/i10/1841-1845 (2017) - Tammana D, Tammana TVS
Human DNA helicase, RuvBL1 and its Chlamydomonas homologue, CrRuvBL1 plays an important role in ciliogenesis.
Cytoskeleton, 74(7): 251–259 doi: 10.1002/cm.21377 (2017) - Tammana D, Tammana TVS
Chlamydomonas FAP265 is a tubulin polymerization promoting protein, essential for flagellar reassembly and hatching of daughter cells from the sporangium.
PLOS ONE, 112(9): e0185108. doi: 10.1371/journal.pone.0185108 (2017) - Narayanaswamy PB, Baral TK, Haller H, Dumler I, Acharya K and Kiyan Y
Transcriptomic pathway analysis of urokinase receptor silenced breast cancer cells: a microarray study.
Oncotarget, 8(60):101572-101590. doi: 10.18632/oncotarget.21351 (2017) - Adurthi S, Kumar MM, Vinodkumar HS, Mukherjee G, Krishnamurthy H, Acharya KK, Bafna UD, Uma DK, Abhishekh B, Krishna S, Parchure A, Murali A, Jayshree RS
Oestrogen Receptor-α binds the FOXP3 promoter and modulates regulatory T-cell function in human cervical cancer.
Sci Rep, 7, 17289 doi: doi.org/10.1038/s41598-017-17102-w (2017) - Melangath G, Sen T, Kumar R, Bawa P, Srinivasan S, Vijayraghavan U.
Functions for fission yeast splicing factors SpSlu7 and SpPrp18 in alternative splice-site choice and stress-specific regulated splicing.
PLOS ONE, 12(12): e0188159 doi: 10.1371/journal.pone.0188159 (2017) - Karthikeyan S, Bawa PS. and Srinivasan, S.
hg19K: Addressing a significant lacuna in hg19-based variant calling
Mol. Genet. Genomic Med., 5(1): 15–20 doi: 10.1002/mgg3.251 (2017) - Pandey M, Kumar S, Goldsmith G, Srivastava M, Elango S, Shameem M, Bannerjee D, Choudhary B, Karki SS, Raghavan SC
Identification and Characterization of Novel Ligase I Inhibitors.
Mol. Carcinog., 56(2): 550-566 doi: 10.1002/mc.22516 (2017)
- 2016
- Ellingford JM, Barton S, Bhaskar S, O'Sullivan J, Williams SG, Lamb JA, Panda B, Sergouniotis PI, Gillespie RL, Daiger SP, Hall G, Gale T, Lloyd IC, Bishop PN, Ramsden SC, Black GCM.
Molecular findings from 537 individuals with inherited retinal disease
J Med Genet, 53 (11):761–767 doi: 10.1136/jmedgenet-2016-103837 (2016) - Kumar G, Kajuluri LP, Gupta CM, Sahasrabuddhe AA.
A twinfilin-like protein coordinates karyokinesis by influencing mitotic spindle elongation and DNA replication in Leishmania
Molecular Microbiology, 100(1), 173–187 doi: 10.1111/mmi.13310 (2016) - Srivastava S, Somasagara RR, Hegde M, Nishana M, Tadi SK, Srivastava M, Choudhary B, Raghavan SC.
Quercetin, a Natural Flavonoid Interacts with DNA, Arrests Cell Cycle and Causes Tumor Regression by Activating Mitochondrial Pathway of Apoptosis
Scientific Reports, 6:24049 doi: 10.1038/srep24049 (2016) - Tadi SK, Sebastian R, Dahal S, Babu RK, Choudhary B, Raghavan SC.
Microhomology-mediated end joining is the principal mediator of double-strand break repair during mitochondrial DNA lesions
MBoC, 27, 223 doi: 10.1091/mbc.E15-05-0260 (2016) - Thomas E, Gopalakrishnan V, Hegde M, Kumar S, Karki SS, Raghavan SC, Choudhary B.
A Novel Resveratrol Based Tubulin Inhibitor Induces Mitotic Arrest and Activates Apoptosis in Cancer Cells
Scientific Reports, 6:34653 doi: 10.1038/srep34653 (2016)> - Bhat AR, Gupta MK, Krithivasan P, Dhas K, Nair J, Reddy RB, Sudheendra HV, Chavan S, Vardhan H, Darsi S, Balakrishnan L, Katragadda S, Kekatpure V, Suresh A, Tata P, Panda B, Kuriakose MA, Sirdeshmukh R.
Sample preparation method considerations for integrated transcriptomic and proteomic analysis of tumors
Wiley Online Library, 11, 3-4 doi: 10.1002/prca.201600100 (2016) - Krishnan NM, Jain P, Gupta S, Hariharan AK, Panda B.
An Improved Genome Assembly of Azadirachta indica A. Juss
G3 (Bethesda), 6:7, 1835–1840 doi: 10.1534/g3.116.030056 (2016)
- Thomas E, Gopalakrishnan V, Somasagara RR, Choudhary B, Raghavan SC.
Extract of Vernonia condensata,Inhibits Tumor Progression and Improves Survival of Tumor-
allograft Bearing Mouse
Scientific Reports, 6:23255 doi: 10.1038/srep23255 (2016) - Krishnan, NM, Dhas, K., Nair, J., Palve, V., Bagwan, J., Siddappa, G., Suresh, A., Kekatpure, VD, Kuriakose, MA and Panda, B.
A minimal DNA methylation signature in oral tongue squamous cell carcinoma links altered methylation with tumor attributes
Mol Cancer Res, 14(9): 805–819 doi: 10.1158/1541-7786.MCR-15-0395 (2016) - Dey, P., Panga, V. and Raghunathan, S.
A cytokine signalling network for the regulation of inducible nitric oxide synthase expression in rheumatoid arthritis.
PLOS ONE, 11(9): e0161306 doi: 10.1371/journal.pone.0161306 (2016) - Iyer, D., Vartak, SV., Mishra, A., Goldsmith, G., Kumar, S., Srivastava, M., Hegde, M., Gopalakrishnan, V., Glenn, M., Velusamy, M., Choudhary, B., Kalakonda, N., Karki, SS., Surolia, A. and Raghavan, SC.
Identification of a Novel BCL2-Specific Inhibitor that Binds Predominantly to the BH1 Domain
The FEBS Journal, 283(18):3408-37 doi: 10.1111/febs.13815 (2016) - Mehrotra, B. and Saberwal, G.
Patents protecting biologics or small molecule drugs are litigated, not others awarded to drug discovery companies.
J Intellect Prop Rights, 21, 149-156 (2016). - Kang, YS, Brame, K, Jetter, J, Bothner, BB, Wang, G, Thiyagarajan, S and McDermott, TR.
Regulatory Activities of Four ArsR Proteins in Agrobacterium tumefaciens 5A
Appl Environ Microbiol, 82(12): 3471-80. doi: 10.1128/AEM.00262-16 (2016) - Goldsmith, G, Rathinavelan, T and Yathindra, N
Selective preference of parallel DNA triplexes is due to the disruption of Hoogsteen hydrogen bonds caused by the severe nonisostericity between the G*GC and T*AT triplets
PLOS ONE, 11(3): e0152102 doi: https://doi.org/10.1371/journal.pone.0152102 (2016) - Keezhupalat, SM, Naik, A., Gupta, S., Raghunathan, S. and Saberwal, G
An analysis of sponsors/collaborators of 69,160 drug trials registered with ClinicalTrials.gov
PLOS ONE, 11(2): e0149416. doi:10.1371/journal.pone.0149416 (2016) - Padmanabhan, B., Ramu, M., Mathur, S., Unni, S. and Thiyagarajan, S
Identification of New Inhibitors for Human SIRT1: An in-silico Approach
Med Chem, 12(4):347-61. doi: 10.2174/1573406412666160107111612 (2016) - Siddaramappa S
Histophilus somni genomics and genetics
Curr Top Microbiol Immunol, 396:49-70 396:49-70. doi: 10.1007/82_2015_5009 (2016) - Kumar MM, Davuluri S, Poojar S, Mukherjee G, Bajpai AK, Bafna UD, Devi UK, Kallur PP, Kshitish AK, Jayshree RS
Role of estrogen receptor alpha in human cervical cancer-associated fibroblasts: a transcriptomic study.
Tumour Biol, 37(4):4409-20. doi: 10.1007/s13277-015-4257-6 (2016) - Saberwal, G.
India’s intellectual property-based biomedical start-ups.
Curr. Sci., 110, 167-171 doi: 10.18520/cs/v110/i2/167-171 (2016) - Kouser. K, Lavanya PG, Rangarajan L, Acharya KK
Effective Feature Selection for Classification of Promoter Sequences.
PLOS One, 11(12): e0167165 doi: https://doi.org/10.1371/journal.pone.0167165 (2016)
- Pathak, BR., Breed, AA., Apte, S., Acharya, K., Mahale, SD.
Cysteine-rich secretory protein 3 plays a role in prostate cancer cell invasion and affects expression of PSA and ANXA1.
Mol Cell Biochem, 411:11-21 doi: 10.1007/s11010-015-2564-2 (2016) - Raghavan CS, Choudhary B, Iyer D, Vartak S, Goldsmith G, Karki S, Surolia A
Novel inhibitors of antiapoptotic Bcl-2 protein Indian patent number: 201641014968
- 2015
- Mishra R, Palve V, Kannan S, Pawar S, Teni T
High expression of survivin and its splice variants survivin and survivin 2 B in oral cancers
Science Direct, 120:4, 497-507 doi: 10.1016/j.oooo.2015.06.027 (2015) - Krishnan, NM et al
Integrated analysis of oral tongue squamous cell carcinoma identifies key variants and pathways linked to risk habits, HPV, clinical parameters and tumor recurrence
F1000Research, 4: 1215 doi: 10.12688/f1000research.7302.1 (2015) - Nair J, Jain P, Chandola U, Palve V, Harsha Vardhan NR, Reddy RB, Kekatpure VD, Suresh A, Kuriakose MA, Panda B.
Gene and miRNA expression changes in squamous cell carcinoma of larynx and hypopharynx.
Genes Cancer, 6 (7-8): 328-40 doi: 10.18632/genesandcancer.69 (2015) - Srivastava, R., Kajuluri, L.P., Pathak, N., Gupta, C.M. and Sahasrabuddhe, A.A.
Oligomerization of coronin: Implication on actin filament length in Leishmania.
Cytoskeleton, 72: 621–632 doi: 10.1002/cm.21269 (2015) - Ganjiwale A, Cowsik SM.
Membrane Induced Structure of Novel Human Tachykinin Hemokinin-1 (hHK1)
Biopolymer, 103(12), 702–710. doi: 10.1002/bip.22734 (2015) - Mathew J, Jagadeesh S M, Bhat M, Udhaya Kumar S, Thiyagarajan S and Srinivasan S
Mutations in ARSB in MPS VI patients in India
Mol Genet Metab Rep, 4: 53-61 doi: 10.1016/j.ymgmr.2015.06.002 (2015) - Chandrashekar D.S., Dey P. and Acharya K.K.
GREAM: A Web Server to Short-List Potentially Important Genomic Repeat Elements Based on Over-/Under-Representation in Specific Chromosomal Locations, Such as the Gene Neighborhoods, within or across 17 Mammalian Species
PLOS ONE, 10(7): e0133647. doi: 10.1371/journal.pone.0133647 (2015) - Duley A, Gowda V., Ganjiwale A., Raghothama S. and Ramanathan G.
Effect of methylene group insertions on the structural rigidity of Aib containing helices.
Biopolymer, 104(6): 720-732 doi: 10.1002/bip.22691 (2015) - Gupta, C.M., Thiyagarajan, S. and Sahasrabuddhe, A.A.
Unconventional actins and actin-binding proteins in human protozoan parasites.
Int. J. Parasitol. , 45(7):435-447 doi: 10.1016/j.ijpara.2015.01.011 (2015) - Kouser, Rangarajan, L., Chandrashekar, D. S., Acharya, K. K. and Abraham, E. M.
Alignment free frequency based distance measures for promoter sequence comparison.
In: Bioinformatics and Biomedical Engineering Third International Conference, IWBBIO 2015, Granada, Spain, April 15-17, 2015, Proceedings, Part II; Editors: Ortuño, Francisco, Rojas, Ignacio (Eds.) pp. 183-193, Springer (2015) - Bawa, P., Zackaria, S., Verma, M., Gupta, S., Srivatsan R, Chaudhary, B. and Srinivasan, S.
Integrative analysis of normal long intergenic non-coding RNAs in prostate cancer.
PLoS One, 10(5): e0122143. doi: 10.1371/journal.pone.0122143 (2015) - Gupta S, Krishnan MN, Panda B
Survival Signature in Squamous Cell Carcinoma of Head and Neck (HNSCC) And Applications Thereof Provisional patent application, 4316/CHE (2015) - Gupta S, Krishnan MN, Panda B
Biomarkers Of Squamous Cell Carcinoma Of Head And Neck Prognostic Markers of Recurrence In Squamous Cell Carcinoma of Head And Methods Thereof Provisional patent application, 4031/CHE (2015) - Panda B
miRNA Aberration(s) In Squamous Cell Carcinoma of Head And Neck (HNSCC) And Applications Thereof Provisional patent application, 2921/CHE (2015) - Panda B, Krishnan MN
Methylation Signature in Squamous Cell Carcinoma of Head and Neck (HNSCC) And Applications Thereof Provisional patent application, 4888/CHE (2015) - Panda B
Gene Expression Changes in Squamous Cell Carcinoma of Larynx and Hypopharynx and Applications Thereof Provisional patent application, 2969/CHE (2015) - Panda B
Gene Signature in Squamous Cell Carcinoma of Head and Neck (HNSCC) And Applications Thereof Provisional patent application, 2970/CHE (2015)
- 2014
- Gupta, S, Chaudhury, S and Panda, B
MUSIC: A hybrid-computing environment for Burrows-Wheeler alignment for massive amount of short read sequence data.
2nd Middle East Conference on Biomedical Engineering, Pgs: 188-191
DOI: https://doi.org/10.1109/MECBME.2014.6783237 (2014) - Chandola, U, Das, R and Panda, B
Role of the N6-methyladenosine RNA mark in gene regulation and its implications on development and disease.
Briefings in Functional Genomics, Pgs: 169-179 DOI: https://doi.org/10.1093/bfgp/elu039 (2014) - Srivastava, M., Hegde, M., Chiruvella, K. et al.
Sapodilla Plum (Achras sapota) Induces Apoptosis in Cancer Cell Lines and Inhibits Tumor Progression in Mice
Scientific Reports 4 : 6147 DOI: https://doi.org/10.1038/srep06147 (2014) - Muherjee K, Bowman KS, Rainey FA, Siddaramappa S, Challacombe JF and Moe WM
Dehalogenimonas lykanthroporepellens BL-DC-9T simultaneously transcribes many rdhA genes during organohalide respiration with 1,2-DCA, 1,2-DCP, and 1,2,3-TCP as electron acceptors.
FEMS Microbiol Lett, 354, 111–118 DOI: https://doi.org/10.1111/1574-6968.12434 (2014) - Suravajhala P and Acharya K
Whither genome sequencing of Passer?
Eur. Chem. Bull., 3, 1086-1087 DOI: https://doi.org/10.17628/ECB.2014.3.1086 (2014) - Sunil, M., Hariharan, A.K., Nayak, S., Gupta, S., Nambisan, S., Panda, B., Choudhary, B. and Srinivasan, S.
The draft genome and transcriptome of Amaranthus hypochondriacus: A C4 dicot producing high-lysine edible pseudo-cereal.
DNA Research, 21, 585-602 DOI: https://doi.org/10.1093/dnares/dsu021 (2014) - Siddaramappa, S., Challacombe, J. F., Petersen, J. M., Pillai, S. and Fellow, C.R.K.
Comparative analyses of a putative Francisella conjugative element
Genome, 57, 137-144 DOI: https://doi.org/10.1139/gen-2013-0231 (2014) - Bhagwat, S. et al.
Acetylated alpha tubulin is reduced in individuals with poor sperm motility.
Fertility and Sterility, 101: 95-104 DOI: https://doi.org/10.1016/j.fertnstert.2013.09.016 (2014) - Sunil, M. and Jinsha, K.
Non-coding genomics. (A meeting report)
Current Science, 106, 657-658 (2014) - Pattnaik, S., Gupta, S., Rao, A A and Panda, B.
SInC: an accurate and fast error-model based simulator for SNPs, Indels and CNVs coupled with a read generator for short-read sequence data.
BMC Bioinformatics, 15: 40 DOI: https://doi.org/10.1186/1471-2105-15-40 (2014) - Saberwal, G.
On being a professional mutant
Nature Biotechnology, 32, 106-107 DOI: https://doi.org/10.1038/nbt.2796 (2014) - Jaroslawski, S. and Saberwal, G.
In eHealth in India today, the nature of work, the challenges and the finances: an interview based study.
BMC Medical Informatics and Decision Making, 14, 1 DOI: https://doi.org/10.1186/1472-6947-14-1 (2014)
- 2013
- Metri R, Jerath G, Kailas G, Gacche N, Pal A, Ramakrishnan V.
Structure-based barcoding of proteins
Protein science, 23, 117-120 doi: 10.1002/pro.2392 (2013) - Chitturi N, Balagannavar G, Chandrashekar DS, Abinaya S, Srini VS and Acharya KK
TIPMaP: a web server to establish transcript isoform profiles from reliable microarray probes.
BMC Genomics, 14, 922 DOI: https://doi.org/10.1186/1471-2164-14-922 (2013) - Ganjiwale A, Cowsik SM.
Molecular recognition of Tachykinin Receptor selective agonists: Insights from structural studies.
Mini-Reviews in Medicinal Chemistry. 13, 2036-2046 DOI: https://doi.org/10.2174/13895575113139990079 (2013). - Sundararajan, PR, Balaji, PV and Yathindra, N.
Obituary: VSR Rao (1931–2013)
Current Science, 105, 1303-1304 (2013) - Jain, P. , Krishnan, N.M. and Panda, B.
Augmenting transcriptome assembly by combining de novo and genome-guided tools.
Peer J., 1, e133 DOI: https://doi.org/10.7717/peerj.133 (2013) - Ananth, P., Goldsmith, G. and Yathindra, N.
An innate twist between Crick's wobble and Watson & Crick base pairs.
RNA, 19, 1038-1053 DOI: https://doi.org/10.1261/rna.036905.112 (2013) - Kumari, S. and Saberwal, G.
Patent maintenance by Indian pharma and bio-pharma companies.
Asian Biotechnology Development Review, 15, 69-77 (2013) - Bhagwat SR, Chandrashekar DS, Kakar R, Davuluri S, Bajpai AK, Nayak S, Bhutada S, Acharya K, Sachdeva G.
Endometrial receptivity: a revisit to functional genomics studies on human endometrium and creation of HGEx-ERdb.
PLOS One, 8(3), e58419 DOI: https://doi.org/10.1371/journal.pone.0058419 (2013) - Jaroslawski, S. and Saberwal, G.
Case studies of innovative medical device companies from India: barriers and enablers to development.
BMC Health Services Research, 13:199 DOI: https://doi.org/10.1186/1472-6963-13-199 (2013) - Saberwal, G.
Giving voice to India’s entrepreneurs.
Nature Biotechnology, 31, 104-107 DOI: https://doi.org/10.1038/nbt.2493 (2013)
- 2012
- Srivastava, M. et al.
An inhibitor of nonhomologous end-joining abrogates double-strand break repair and impedes cancer progression.
Cell, 151, 1474-1487 (2012) - Kaushik, S. Krishnarjuna, B., Raghothama, S., Aggarwal, S. Raghunathan, V. and Ganjiwale, A.
Theoretical and in vitro studies of a C-terminal peptide from PGKC of Leishmania mexicana mexicana.
Molecular and Biochemical Parasitology. 185, 27-35 (2012) - Panda. B.
Whither genomics diagnostics tests in India?
Indian J. Med. Paediatr. Oncol., 33, 250-252 (2012) - Srinivasan, S, Patil, AH, Verma, M, Bingham, JL and Srivatsan, R.
Genome-wide profiling of RNA splicing in prostate tumor from RNA-seq data using virtual microarrays.
J. Clinical Bioinformatics, 2, 21-33 (2012) - Hegde, M. et al.
Novel Levamisole derivative induces extrinsic pathway of apoptosis in cancer cells and inhibits tumor progression in mice.
PLoS One, 7(9), e43632 (2012) - Krishnan NM, Gaur P, Choudhary R, Rao AA and Panda B
COPS: A sensitive and accurate tool for detecting somatic copy number alterations using short-read sequence data from paired samples.
PLoS One, 7(10), e47812 (2012) - Saberwal, G
Translating academic discoveries
Current Science, 103, 767-769 (2012) - Krishnan NM, et al.
A draft of the genome and four transcriptomes of a medicinal and pesticidal angiosperm Azadirachta indica.
BMC Genomics, 13, 464 (2012) - Vangala, R.K., Singh, L. and Gupta, R.P.
BioParishodhana: A novel graphical interface integrating BLAST, CLUSTALW, primer3 and restriction digestion tools.
Bioinformation, 8, 639-643 (2012) - Chiruvella, K.K., Sebastian, R., Sharma, S., Karande, A.A., Choudhary, B. and Raghavan, S.C.
Time-dependent predominance of nonhomologous DNA end-joining pathways during embryonic development in mice.
J. Mol Biol., 417, 197-211 (2012) - Bajpai, A K, Davuluri, S, Chandrashekar, D S, Ilakya, S, Dinakaran, M and Acharya, K K
MGEx-Udb: A Mammalian Uterus Database for Expression-Based Cataloguing of Genes across Conditions, Including Endometriosis and Cervical Cancer.
PLoS One, 7, e36776 (2012) - Venkatachalam, S and Saberwal, G
Bio-business in brief: a case for new drugs at generic prices from India
Current Science, 102, 1375-1381 (2012) - Jaroslawski, S and Pai, M
Why are inaccurate tuberculosis serological tests widely used in the Indian private healthcare sector? A root-cause analysis
Journal of Epidemiology and Global Health, 2, 39-50 (2012) - Patil, A H et al.
From data repositories to potential biomarkers: application to prostate cancer
Current Science, 102, 1111-1116 (2012) - Soby, S, Sebastian, T and Saberwal, G
US patent holdings of Indian non-corporate entities
Asian Biotechnology and Development Review, 14, 21-33 (2012) - Soby, S, Kandasamy, M and Saberwal, G
Work outsourced to Indian biotech and pharma companies is not yet significantly innovative
Current Science, 102 , 401-404 (2012) - Pattnaik, S et al.
Customisation of the exome data analysis pipeline using a combinatorial approach
PLoS One, 7(1): e30080 (2012) - Marimuthu, G, Kumari, S, Kandasamy, M, Raghunathan, S and Saberwal, G
Maintaining patents protecting biologics or small molecule drugs
Nature Biotechnology, 30, 50-53 (2012) - Sathees C. Raghavan, Mrinal Srivastava, Subhas S Karki and Bibha Choudhary.
Compounds as Inhibitor of DNA Double-Strand Break Repair, Methods and Applications thereofRef. IP19597/VJ/ysr. Indian Patent Application Number: 2713/CHE/2012,
WO2014006518A1
- 2011
- Prakash, A., Yogeeshwari, S., Sircar, S. and Agrawal, S.
Protein domain of unknown function 3233 is a Translocation Domain of Autotransporter Secretory Mechanism in Gamma proteobacteria
PLoS One, 6(11), e255570 (2011) - Bajpai, AK et al.
In search of the right literature search engine(s)
Nature Precedings, 10.1038/npre.2011.2101.3 (2011) - Nambiar, M. et al.
Formation of a G-quadruplex at the BCL-2 major breakpoint region of the t(14;18) translocation in follicular lymphoma
Nucleic Acids Research, 39, 936-948 (2011) - Bateman, A. et al.
RNAcentral: a vision for an international database of RNA sequences
RNA, 17, 1941-1946 (2011) - Karthigeyan, D., Prasad, S.B.B., Shandilya, J., Agrawal, S. and Kundu, T.K.
Biology of Aurora A Kinase: Implications in cancer manifestation and therapy
Medicinal Research Reviews, 31, 757-793 (2011) - Krishnan, N. M. et al.
De novo sequencing and assembly of Azadirachta indica fruit transcriptome
Current Science, 101, 1553-1561 (2011) (Cover page article) - Jaroslawski, S. and Toumi, M.
Market access agreements for pharmaceuticals in Europe: diversity of approaches and underlying concepts
BMC Health Services Research, 11, 259-265 (2011) - Sebastian, T.E., Pattnayak, J.P.R., Soby, S and Saberwal, G.
Patent holdings of Indian pharmaceutical and biotechnology companies in international markets of different sizes
Asian Biotechnology Development Review, 13, 17-37 (2011) - Srinivasan, S.
Alternative splicing in eukaryotes: the norm, not an anomaly
Current Science, 100, 813-814 (2011)
- 2010
- Agrawal, S., Nishant, K. T. and Rao, M. R. S.
Analysis of meiotic recombination hotspots: A bioinformatics approach
In A Practical Guide to Bionformatics Analysis. iConcept Press, pp. 133-149 (2010) - Sebastian, A., Bender, A. and Ramakrishnan, V.
Virtual activity profiling of bioactive molecules by 1D fingerprinting.
Molecular Informatics, 29, 773-779 (2010) - Yathindra, N.
Structure of an enzyme revealed 80 years after it was crystallized – differential functional behaviour of plant and microbial ureases uncovered
Current Science, 99, 566-568 (2010) - Acharya, K. K. et al.
A novel tissue-specific meta-analysis approach for gene-expression predictions, initiated with a mammalian gene expression testis database
BMC Genomics, 11, 467-476 (2010) - Ladha, J. et al.
Glioblastoma-specific protein interaction network identifies PP1A and CSK21 as connecting molecules between cell cycle-associated genes
Cancer Research, 70, 6437-6447 (2010) - Saberwal, G.
Bio-business in brief: A bit about technology transfer
Current Science, 99, 177-180 (2010) - Kapoor, M. and Saberwal, G.
The new crossroads
Biotech News, 5, 143-145 (2010) - Saberwal, G.
Bio-business in brief: The debate over biosimilars
Current Science, 98, 1575-1578 (2010) - Saberwal, G.
Grants officers on deputation to national research laboratories
Current Science, 98, 999 (2010) - Selvi, B.R., Batta, K., Kishore, A.H., Mantelingu, K., Varier, R.A., Balasubramanyam, K., Pradhan, S.K., Dasgupta, D., Sokalingam, S., Agrawal, S. and Kundu, T.K.
Identification of a novel inhibitor of coactivator-associated arginine methyl transferase 1 (CARM-1)-mediated methylation of histone H3 Arg-17.
The Journal of Biological Chemistry, 285, 7143-7152 (2010) - Jeevitesh, M. S., Behera, N., Jose, J., Kant, K. and Dey, A.
Higher accuracy protein multiple sequence alignment by stochastic algorithm
Nature Precedings, https://doi.org/10.1038/npre.2010.4258.1 (2010)
- 2009
- Sengupta, U, Ukil, S, Dimitrova, N and Agrawal, S
Expression-based network biology identifies alteration in key regulatory pathways of Type 2 diabetes and associated risks/complications
PLoS One, 4 (12) e8100 (2009) - Saberwal, G
Drug development in India: What does the future look like?
Contemporary Perspectives: History and Sociology of South Asia.
History and Sociology of South Asia, Ed. N Tyabji, 3, 293-309 (2009) - Saberwal, G
A long march
Biotech News, IV, 68-69, 75 (2009) - Saberwal, G
Bio-business in brief: The paradox of being a drug company
Current Science, 97, 623-625 (2009) - Ravindra, K. C., Selvi, B. R., Arif, M., Reddy, B. A. A., Thanuja, G. R., Agrawal, S., Pradhan, S. K., Nagashayana, N., Dasgupta, D. and Kundu, T. K.
Inhibition of Lysine Acetyltransferase KAT3B/p300 activity by a naturally occurring hydroxynaphthoquinone, Plumbagin
The Journal of Biological Chemistry, 284, 24453-24464 (2009) - Saberwal, G
Seeding a skilled workforce
Nature Biotechnology, 27,773-775 (2009) - Acharya, K K
Book review: Career development in bioengineering and biotechnology By Madhavan, G., Oakley, B. and Kun, L. (eds) Springer Science + Business Media (New York)
Current Science, 96, 293 (2009) - Sebastian, T. E., Yerram, C. B. and Saberwal, G.
Patent holdings of US biotherapeutic companies in major markets
Drug Discovery Today, 14, 442-445 (2009) - Saberwal, G
The proposed 4-year B.S. programme
Current Science, 96, 445-446 (2009) - Sundaramoorthy, S., Yerram, C. B. , Mehdiratta, R. and Saberwal, G.
The US patent holdings of homegrown Indian biotech and pharma companies
Current Science, 96, 252-259 (2009) - Arif, M, Pradhan, S K, Thanuja G R, Vedamurthy, B M, Agrawal, S, Dasgupta, D and Kundu, T K
Mechanism of p300 specific histone acetyltransferase inhibition by small molecules
Journal of Medicinal Chemistry, 52, 267-277 (2009)
- 2008
- Acharya, K., Kasliwal, G. and Haridas, H.
How do you choose your literature search tool(s)?
Nat Prec, doi: 10.1038/npre.2008.2101.2 (2008)
- Alva, V, Syamala Devi, D P and Sowdhamini, R
COILCHECK: an interactive server for the analysis of interface regions in coiled coils
Protein and Peptide Letters, 15, 33-38 (2008) - Ramakrishnan, N and Bhalla, U S
Memory switches in chemical reaction space
PLoS Computational Biology, 4: e1000122 (2008) - Agrawal, S., Dimitrova, N., Nathan, P., Udaykumar, K., Sailakshmi, S, Sriram, S, Manjusha, N. and Sengupta, U.
T2D-Db: An integrated platform to study the molecular basis of Type 2 diabetes
BMC Genomics, 9, 320-331 (2008) - Parida, D K, Mehdiratta, R and Saberwal, G
How many patents does a biopharmaceutical company need?
Nature Biotechnology, 26, 763-766 (2008) - Devaguptapu, S, Mehdiratta, R and Saberwal, G
Bio-business in brief: The case of Cytokinetics Inc.
Current Science, 94, 1576-1581 (2008) - Kishore H A, Vedamurthy BM, Mantelingu K, Agrawal, S, Reddy BAA, Roy S, Rangappa K S and Kundu TK.
Specific small-molecule activator of Aurora kinase A induces autophosphorylation in a cell-free system.
Journal of Medicinal Chemistry, 51, 792-797(2008)
- 2007
- Sai Lakshmi, S and Agrawal, S
piRNABank: A web resource on classified and clustered piwi interacting RNAs
Nucleic Acids Research, 36, D173-D177 (2007) - Mehdiratta, R, Parida, D K and Saberwal, G
Bio-business in brief: The challenges of clinical trials
Current Science, 93, 1367-1375 (2007) - Mehdiratta, R and Saberwal, G
Bio-business in brief: Many a monoclonal
Current Science, 93, 789-796 (2007) - Mehdiratta, R and Saberwal, G
Bio-business in brief: The case of conotoxins
Current Science, 92, 39-45 (2007)
- 2006
- Rathinavelan, T and Yathindra, N
Base triplet nonisomorphism strongly influences DNA triplex conformation: Effect of nonisomorphic G*GC and A*AT triplets and bending of DNA triplexes.
Biopolymers, 82, 443-461 (2006) - Acharya K K
The biotech-bioinfo interface in the context of education and growth of the biotechnology industry in India today
Biovistas, 1, 7-13 (2006) - Saberwal, G
New pharma-biotech company formation in India
Nature Biotechnology, 24, 499-501 (2006)
- 2005
- Yathindra, N
M. Sundaralingam (1931-2004): distinguished nucleic acid researcher
Acta Cryst., D61, 845-849 doi: 10.1107/S0907444905014964 (2005)
- Rathinavelan, T and Yathindra, N
Molecular dynamics structures of peptide nucleic acid DNA hybrid in the wild-type and mutated alleles of Ki-ras proto-oncogene
FEBS Journal, 272, 4055-4070 (2005) - Rajalalitha, P and Vali, S
Molecular pathogenesis of oral submucos fibrosis – a collagen metabolic disorder
Journal of Oral Pathology Medicine, 34, 321-328 (2005) - Saberwal, G
English composition as a professional skill
Current Science, 88, 848 (2005) - Kant, R
Sweet proteins – Potential replacement for artificial low calorie sweeteners
Nutrition Journal, 4, 5 (2005) - Sandhu, K S and Acharya, K K
ExPrimer: To design primers from exon-exon junctions
Bioinformatics, 21, 2091-2092 (2005) - Kant, R, Rajasekaran, M B and Suryanarayanarao, R
Sweet and taste modifying proteins – Comparative modeling and docking studies of curculin, mabinlin, miraculin with the T1R2-T1R3 receptor
Internet Electronic Journal of Molecular Design, 4, 106-123 (2005) - Venkatesh, S and Bansal, M
Role of informatics in biodiversity conservation: overview of available resources. In Biodiversity: Status and Prospects (Eds. P. Tandon, M. Sharma and R. Swarup)
Narosa Publishing House, New Delhi, 134-145 (2005) - Rekha, N, Machado, S M, Narayanan, C, Krupa, A and Srinivasan, N
Interaction interfaces of protein domains are not topologically equivalent across families within superfamilies: Implications for metabolic and signalling pathways
Proteins, 58, 339-353 (2005)
- 2004
- Saberwal, G
Biotechnology incubation in India
Business incubation: Initiatives in India‘ Ed. R. K. Lagu brought out by NSTEDB, DST, Pages 16-18 (2004) - Kanhere, A and Bansal, M
DNA bending and curvature: A turning point in DNA function
Proc. Indian Natl. Sci. Acad., B70, 239-254 (2004) - Venkatesh, S and Bansal, M
Role of informatics in food biotechnology and safety
Indian Food Industry, 23, 32-36 (2004)
- 2003
- Bansal, M
DNA structure: Revisiting the Watson-Crick double helix
Current Science, 85, 1556-1563 (2003) - Madhumalar, A and Bansal, M
Sequence dependent structural features of A3T3 vs(AT)3 from molecular dynamics study
Recent Trends in Biophysical Research (ed. N. Maiti), Calcutta, pp. 10-16 (2003) - Madhumalar, A and Bansal, M
Structural insights into the effect of hydration and ions on A-tract DNA: A molecular dynamics study
Biophysics Journal, 85, 1805-1816 (2003) - Venkatesh, S and Bansal, M
Role of informatics in biodiversity conservation: overview of available resources
Proceedings of the 72nd Annual Session & National Symposium on
Biodiversity (2003) - Kanhere, A and Bansal, M
An assessment of three dinucleotide parameters to predict DNA curvature by quantitative comparison with experimental data
Nucleic Acids Research, 31, 2647-2658 (2003) - Ghosh, A and Bansal, M
A glossary of DNA structures from A to Z
Acta Crystallographica, D59, 620-626 (2003) - Behera, N
Book Review: Molecular Systematics and Evolution: Theory and Practice. R. DeSalle,
G. Giribet and W. Wheeler (eds)
Birkhauser Verlag, P.O. Box 133, CH-4010 Basel, Switzerland
Current Science, 84, 99-100 (2003)
- 2002
Saberwal, G
Institute of Bioinformatics and Applied Biotechnology: Bioinformatics training with a
difference
Current Science, 83, 794 (2002)