Publications
Peer-reviewed research articles, reviews, and preprints from our laboratory
2025
Genome-scale metabolic modelling identifies reactions mediated by SNP-SNP interactions associated with yeast sporulation
Sasikumar S, Kumar P, Bhatt N, Sinha H*
npj Systems Biology and Applications (2025) 11: 50
Mapping genetic diversity with the GenomeIndia project
Bhattacharya C, Subramanian K, Uppili B, Biswas N, Ramdas S, Tallapaka KB, Arvind P, Rupanagudi KV, Maitra A, Nagabandi T, De T, Singh K, Sharma P, Sharma N, Raghav SK, Prasad P, Soniya EV, Jaleel A, Sathi SN, Joshi M, Joshi C, Lahiri M, Dixit S, Shashidhara LS, Kumar NS, Lalhruaitluanga H, Nundanga L, Shivakumar V, Venkatasubramanian G, Rao NP, Ganie MA, Wani IA, Jha G, Dalal A, Bashyam M, Varadwaj PK, Sanjeev BS, Simmhan Y, Jain C, Sundar D, Gupta I, Yadav P, Sinha H, Narayanan M, Raman K, Padinjat R, Sabarinathan R, GenomeIndia Consortium, Narahari Y, Ravindranath V, Kumarasamy T*, Sowpati DT*, Faruq M*, Basu A*, Kahali B*
Nature Genetics (2025) 57: 767
2024
Incidence of and risk factors for small vulnerable newborns in north India: a secondary analysis of a prospective pregnancy cohort
Thiruvengadam R, Ayushi, Murugesan DR, Desiraju BK, Misra S, Sharma D, Subbaian SS, Mehta U, Singh A, Sharma S, Khurana A, Mittal P, Chellani H, Bharti R, Tripathi R, Sopory S, Kshetrapal P, Salunke DM, Natchu UCM, Ramji S, GARBH-Ini study team, Wadhwa N, Bhatnagar S*
The Lancet Global Health (2024) 12: e1261
SCI-VCF: A cross-platform application to summarise, compare and design interactive visualisations of the variant call format
Kamaraj V, Sinha H*
NAR Genomics and Bioinformatics (2024) 6: lqae083
Panera: A novel framework for surmounting uncertainty in microbial community modelling using pan-genera metabolic models
Palanikumar I, Sinha H, Raman K*
iScience (2024) 27: 110358
Modeling multiple adverse pregnancy outcomes: Learning from diverse data sources
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*
In: Finkelstein J, Moskovitch R, Parimbelli E (eds) Artificial Intelligence in Medicine. AIME 2024. Lecture Notes in Computer Science (Springer). (2024) 14844: 293
Development and external validation of Indian population-specific Garbhini-GA2 model for estimating gestational age in second and third trimesters
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*
The Lancet Regional Health Southeast Asia (2024) 25: 100362
2023
MKT1 alleles regulate stress responses through post-transcriptional modulation of Puf3 targets in budding yeast
Chaithanya KV, Sinha H*
Yeast (2023) 40: 616
REVIEW: Role of genetic architecture in phenotypic plasticity
Kovuri P, Yadav A, Sinha H*
Trends in Genetics (2023) 39: 703
2021
REVIEW: Synthetic biology beyond borders
Raman K*, Sinha H*, Vickers CE*, Nikel PI*
Microbial Biotechnology (2021) 14: 2254
Comparison of first trimester dating methods for gestational age estimation and their implication on preterm birth classification in a North Indian cohort
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*
BMC Pregnancy and Childbirth (2021) 21: 343
Upto 2020
Assessment of network module identification across complex diseases
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*
Nature Methods (2019) 16: 843
Adapting community detection algorithms for disease module identification in heterogeneous biological networks
Tripathi B, Parthasarathy S, Sinha H, Raman K, Ravindran B*
Frontiers in Genetics (2019) 10: 164
REVIEW: Evolutionary design principles in metabolism
Sambamoorthy G, Sinha H, Raman K*
Proceedings of the Royal Society B: Biological Sciences (2019) 286: 20190098
REVIEW: Gene-gene and gene environment interactions in complex traits in yeast
Yadav A, Sinha H*
Yeast (2018) 35: 403
Fundamental principles governing sporulation efficiency: A network theory approach
Sarkar C, Gupta S, Sinha H, Jalan S*
Canadian Journal of Biotechnology (2017) 1: 46
The modular adaptive ribosome
Yadav A, Radhakrishnan A, Panda A, Singh A, Sinha H*, Bhanot G*
PLOS ONE (2016) 11: e0166021
Genetic regulation of phenotypic plasticity and canalisation in yeast growth
Yadav A*, Dhole K, Sinha H*
PLOS ONE (2016) 11: e0162326
Meiotic interactors of a mitotic gene TAO3 revealed by functional analysis of its rare variant
Gupta S, Radhakrishnan A, Nitin R, Pandu R-L, Lin G, Steinmetz LM, Gagneur J, Sinha H*
G3: Genes, Genomics, Genetics (2016) 6: 2255
Differential regulation of cryptic genetic variation shapes the genetic interactome underlying complex traits
Yadav A, Dhole K, Sinha H*
Genome Biology and Evolution (2016) 8: 3559
Temporal expression profiling identifies pathways mediating effect of causal variant on phenotype
Gupta S, Radhakrishnan A, Pandu R-L, Lin G, Steinmetz LM, Gagneur J, Sinha H*
PLOS Genetics (2015) 11: e1005195
Differential regulation of antagonistic pleiotropy in synthetic and natural populations suggests its role in adaptation
Yadav A, Radhakrishnan A, Bhanot G, Sinha H*
G3: Genes, Genomics, Genetics (2015) 5: 699
Tiled ChrI RHS collection: a pilot high-throughput screening tool for identification of allelic variants
Singh R, Sinha H*
Yeast (2015) 32: 335
REVIEW: Conservation of PHO pathway in yeasts and role of Pho84
Tomar P, Sinha H*
Journal of Biosciences (2014) 39: 1
Yeast growth plasticity is regulated by environment specific multi-QTL interactions
Bhatia A, Yadav A, Zhu C, Gagneur J, Steinmetz LM, Bhanot G, Sinha H*
G3: Genes, Genomes, Genetics (2014) 4: 769
Sporulation genes associated with sporulation efficiency in natural isolates of yeast
Tomar P, Bhatia A, Ramdas S, Diao L, Bhanot G, Sinha H*
PLOS ONE 8: (2013) e69765
Polygenic cis-regulatory adaptation in the evolution of yeast pathogenicity
Fraser HB*, Levy S, Chavan A, Shah HB, Perez JC, Zhou Y, Siegal ML, Sinha H
Genome Research (2012) 22: 1930
Genome-wide allele- and strand-specific expression profiling
Gagnuer J, Sinha H, Perocchi F, Bourgon R, Huber W, Steinmetz LM*
Molecular Systems Biology (2009) 5: 274
Sequential elimination of major-effect contributors identifies additional quantitative trait loci conditioning high-temperature growth in yeast
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*
Genetics (2008) 180: 1661
Complex genetic interactions in a quantitative trait locus
Sinha H, Nicholson BP, Steinmetz LM, McCusker JH*
PLOS Genetics (2006) 2: e13
The tRNA-Tyr gene family of Saccharomyces cerevisiae: agents of phenotypic variation and position effects on mutation frequency
Ito-Harashima S, Hartzog PE, Sinha H, McCusker JH*
Genetics (2002) 161: 1395
Dissecting the architecture of a quantitative trait locus in yeast
Steinmetz LM, Sinha H, Richards DR, Spiegelman JI, Oefner PJ, McCusker JH, Davis RW*
Nature (2002) 416: 326
Analysis of the role of recA in phenotypic switching of Pseudomonas tolaasii
Sinha H, Pain A, Johnstone K*
Journal of Bacteriology (2000) 182: 6532
Cloning and expression studies during vegetative and sexual development of Pbs1, a septin gene homologue from Pyrenopeziza brassicae
Singh G, Sinha H, Ashby AM*
Biochimica Biophysica Acta: Molecular Cell Research (2000) 1497: 168