Publications

    Preprint

  1. Kamaraj V, Gupta A, Narayanan M, Raman K, Sinha H* (2024) Unveiling genomic complexity: a framework for genome graph structural analysis and optimised variant calling workflows. bioRxiv 
  2. Sasikumar S, Kumar P, Bhatt N, Sinha H* (2024) Multi-SNP combination genome-scale metabolic models identify molecular mechanisms determining genetic interactions in a quantitative trait. bioRxiv 
  3. Venkatesan N, Xavier A, Sindhu KJ, Sinha H*, Devrajan K* (2021) Identification and validation of putative target genes regulated by miR-34 in cervical cancer. bioRxiv 

    Published

  1. Kamaraj V, Sinha H* (2024) SCI-VCF: A cross-platform application to summarise, compare and design interactive visualisations of the variant call format. NAR Genomics and Bioinformatics (accepted) 
  2. Palanikumar I, Sinha H, Raman K* (2024) Panera: A novel framework for surmounting uncertainty in microbial community modelling using pan-genera metabolic models. iScience (in press) 
  3. Mathur S, Gadekar VP, Ramola R, Wang A, Thiruvengadam R, Haas DM, Bhatnagar B, Wadhwa N, Garbhini Study Group, Radivojac P, Sinha H, Kersting K, Natarajan S* (2024) Modeling multiple adverse pregnancy outcomes: Learning from diverse data sources. 22nd International Conference on Artifical Intelligence in Medicine 2024 (accepted)
  4. Gadekar VP#, Damaraju N#, Xavier A, Thakur SS, Vijayram R, Desiraju BK, Misra S, GARBH-Ini Study Group, Wadhwa N, Khurana A, Rathore S, Abraham A, , Rengaswamy R, Benjamin S, Cherian AG, Bhatnagar S, Thiruvengadam R*, Sinha H* (2024) Development and external validation of Indian population-specific Garbhini-GA2 model for estimating gestational age in second and third trimesters. Lancet Regional Health Southeast Asia 
  5. Chaithanya KV, Sinha H* (2023) MKT1 alleles regulate stress responses through post-transcriptional modulation of Puf3 targets in budding yeast. Yeast 40: 616
  6. Kovuri P, Yadav A, Sinha H* (2023) Role of genetic architecture in phenotypic plasticity. Trends in Genetics 39: 703
  7. Raman K*, Sinha H*, Vickers CE*, Nikel PI* (2021) Synthetic biology beyond borders. Microbial Biotechnology 14: 2254
  8. Vijayram R#, Damaraju N#, Xavier A, Desiraju BK, Thiruvengadam R, Misra S, Chopra S, Khurana A, Wadhwa N, Garbh-Ini Study Group, Rengaswamy R, Sinha H*, Bhatnagar S* (2021) Comparison of first trimester dating methods for gestational age estimation and their implication on preterm birth classification in a North Indian cohort. BMC Pregnancy and Childbirth 21: 343
  9. Choobdar S, Ahsen ME, Crawford J, Tomasoni M, Lamparter D, Lin J, Hescott B, Hu X, Mercer J, Natoli T, Narayan R, The DREAM Module Identification Challenge Consortium, Subramanian A, Stolovitzky G, Kutalik Z, Lage K, Slonim DK, Saez-Rodriguez J, Cowen LJ, Bergmann S, Marbach D* (2019) Assessment of network module identification across complex diseases. Nature Methods 16: 843
  10. Tripathi B, Parthasarathy S, Sinha H, Raman K, Ravindran B* (2019) Adapting community detection algorithms for disease module identification in heterogeneous biological networks. Frontiers in Genetics 10: 164
  11. Sambamoorthy G, Sinha H*, Raman K* (2019) Evolutionary design principles in metabolism. Proceedings of the Royal Society B: Biological Sciences 286: 20190098
  12. Yadav A, Sinha H* (2018) Gene-gene and gene environment interactions in complex traits in yeast. Yeast 35: 403
  13. Sarkar C, Gupta S, Sinha H, Jalan S (2017) Fundamental principles governing sporulation efficiency: A network theory approach. Canadian Journal of Biotechnology 1: 46
  14. Yadav A, Radhakrishnan A, Panda A, Singh A, Sinha H*, Bhanot G* (2016) The modular adaptive ribosome. PLOS ONE 11: e0166021
  15. Yadav A*, Dhole K, Sinha H* (2016) Genetic regulation of phenotypic plasticity and canalisation in yeast growth. PLOS ONE 11: e0162326
  16. Gupta S, Radhakrishnan A, Nitin R, Pandu R-L, Lin G, Steinmetz LM, Gagneur J, Sinha H* (2016) Meiotic interactors of a mitotic gene TAO3 revealed by functional analysis of its rare variant. G3: Genes, Genomics, Genetics 6: 2255
  17. Gupta S, Radhakrishnan A, Pandu R-L, Lin G, Steinmetz LM, Gagneur J, Sinha H* (2015) Temporal expression profiling identifies pathways mediating effect of causal variant on phenotype. PLOS Genetics 11: e1005195
  18. Yadav A, Dhole K, Sinha H* (2016) Differential regulation of cryptic genetic variation shapes the genetic interactome underlying complex traits. Genome Biology and Evolution 8: 3559
  19. Yadav A, Radhakrishnan A, Bhanot G, Sinha H* (2015) Differential regulation of antagonistic pleiotropy in synthetic and natural populations suggests its role in adaptation. G3: Genes, Genomics, Genetics 5: 699
  20. Singh R, Sinha H* (2015) Tiled ChrI RHS collection: a pilot high-throughput screening tool for identification of allelic variants. Yeast 32: 335
  21. Tomar P, Sinha H* (2014) Conservation of PHO pathway in yeasts and role of Pho84. Journal of Biosciences 39: 1
  22. Bhatia A, Yadav A, Zhu C, Gagneur J, Steinmetz LM, Bhanot G, Sinha H* (2014) Yeast growth plasticity is regulated by environment specific multi-QTL interactions. G3: Genes, Genomes, Genetics 4: 769
  23. Tomar P, Bhatia A, Ramdas S, Diao L, Bhanot G, Sinha H* (2013) Sporulation genes associated with sporulation efficiency in natural isolates of yeast. PLOS ONE 8: e69765
  24. Fraser HB, Levy S, Chavan A, Shah HB, Perez JC, Zhou Y, Siegal ML, Sinha H (2012) Polygenic cis-regulatory adaptation in the evolution of yeast pathogenicity. Genome Research 22: 1930
  25. Gagnuer J, Sinha H, Perocchi F, Bourgon R, Huber W, Steinmetz LM (2009) Genome-wide allele- and strand-specific expression profiling. Molecular Systems Biology 5: 274
  26. Sinha H, David L, Pascon RC, Clauder-Münster S, Krishnakumar S, Nguyen M, Shi G, Dean J, Davis RW, Oefner PJ, McCusker JH, Steinmetz LM (2008) Sequential elimination of major-effect contributors identifies additional quantitative trait loci conditioning high-temperature growth in yeast. Genetics 180: 1661
  27. Sinha H, Nicholson BP, Steinmetz LM, McCusker JH (2006) Complex genetic interactions in a quantitative trait locus. PLOS Genetics 2: e13
  28. Ito-Harashima S, Hartzog PE, Sinha H, McCusker JH (2002) The tRNA-Tyr gene family of Saccharomyces cerevisiae: agents of phenotypic variation and position effects on mutation frequency. Genetics 161: 1395
  29. Steinmetz LM, Sinha H, Richards DR, Spiegelman JI, Oefner PJ, McCusker JH, Davis RW (2002) Dissecting the architecture of a quantitative trait locus in yeast. Nature 416: 326
  30. Sinha H, Pain A, Johnstone K (2000) Analysis of the role of recA in phenotypic switching of Pseudomonas tolaasii. Journal of Bacteriology 182: 6532
  31. Singh G, Sinha H, Ashby AM (2000) Cloning and expression studies during vegetative and sexual development of Pbs1, a septin gene homologue from Pyrenopeziza brassicae. Biochimica Biophysica Acta: Molecular Cell Research 1497: 168