Publications

  1. Palanikumar I, Sinha H, Raman K* (2023) Panera: A novel framework for surmounting uncertainty in microbial community modelling using Pan-genera metabolic models. bioRxiv 
  2. Sasikumar S, Kumar P, Bhatt N, Sinha H* (2023) Multi-SNP combination genome-scale metabolic models identify molecular mechanisms determining genetic interactions in a quantitative trait. bioRxiv 
  3. Venkatesh K, Sinha H* (2023) SCI-VCF: A cross-platform application to summarise, compare and design interactive visualisations of the variant call format. bioRxiv 
  4. Chaithanya KV, Sinha H* (2023) MKT1 alleles regulate stress responses through post-transcriptional modulation of Puf3 targets in budding yeast. Yeast 
  5. Golob JL, Oskotsky TT, Tang AS, Roldan A, Chung V, Ha CWY, Wong RJ, Flynn KJ, Parraga-Leo A, Wibrand C, Minot SS, Andreoletti G, Kosti I, Bletz J, Nelson A, Gas J, Wei Z, Chen G, Tang Z-Z, Novielli P, Romano D, Pantaleo E, Amoroso N, Monaco A, Vacca M, De Angelis M, Bellotti R, Tangaro S, Kuntzleman A, Bigcraft I, Techtmann S, Bae D, Kim E, Jean J, Joe S, The Preterm Birth DREAM Community, Theis KR, Ng S, Lee YS, Li L, Diaz-Gimeno P, Bennett PR, MacIntyre DA, Stolovitzky G, Lunch SV, Albrecht J, Gomez-Lopez N, Romero R, Stevenson DK, Aghaeepour N, Tarca AL, Costello JC, Sirota M (2023) Microbiome Preterm Birth DREAM Challenge: Crowdsourcing Machine Learning Approaches to Advance Preterm Birth Research. medRxiv 
  6. Gadekar VP#, Damaraju N#, Xavier A, Thankur 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* (2023) Development and external validation of Indian population-specific Garbhini-GA2 model for estimating gestational age in second and third trimesters. medRxiv 
  7. Kovuri P, Yadav A, Sinha H* (2023) Role of genetic architecture in phenotypic plasticity. Trends in Genetics
  8. 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 
  9. Raman K*, Sinha H*, Vickers CE*, Nikel PI* (2021) Synthetic biology beyond borders. Microbial Biotechnology 14: 2254
  10. 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
  11. 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
  12. 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
  13. Sambamoorthy G, Sinha H*, Raman K* (2019) Evolutionary design principles in metabolism. Proceedings of the Royal Society B: Biological Sciences 286: 20190098
  14. Sarkar C, Gupta S, Sinha H*, Jalan S* (2018) A network theory approach identifies nodes and edges defining yeast sporulation efficiency variation. bioRxiv
  15. Yadav A, Sinha H* (2018) Gene-gene and gene environment interactions in complex traits in yeast. Yeast 35: 403
  16. 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
  17. Yadav A, Radhakrishnan A, Panda A, Singh A, Sinha H*, Bhanot G* (2016) The modular adaptive ribosome. PLOS ONE 11: e0166021
  18. Yadav A*, Dhole K, Sinha H* (2016) Genetic regulation of phenotypic plasticity and canalisation in yeast growth. PLOS ONE 11: e0162326
  19. 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
  20. 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
  21. 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
  22. Singh R, Sinha H* (2015) Tiled ChrI RHS collection: a pilot high-throughput screening tool for identification of allelic variants. Yeast 32: 335
  23. Tomar P, Sinha H* (2014) Conservation of PHO pathway in yeasts and role of Pho84. Journal of Biosciences 39: 1
  24. 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
  25. 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
  26. 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
  27. 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
  28. Sinha H, David L, Pascon RC, Clauder-M√ľnster 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
  29. Sinha H, Nicholson BP, Steinmetz LM, McCusker JH (2006) Complex genetic interactions in a quantitative trait locus. PLOS Genetics 2: e13
  30. 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
  31. 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
  32. Sinha H, Pain A, Johnstone K (2000) Analysis of the role of recA in phenotypic switching of Pseudomonas tolaasii. Journal of Bacteriology 182: 6532
  33. 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