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

Network Biology Systems Genetics

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

Genomics

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

Maternal and Child Health Clinical Research

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

Bioinformatics Genomics

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

Metabolic Modelling Microbiome

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

Maternal and Child Health Machine Learning

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

Maternal and Child Health Machine Learning

2023

REVIEW: Role of genetic architecture in phenotypic plasticity

Kovuri P, Yadav A, Sinha H*

Trends in Genetics (2023) 39: 703

Maternal and Child Health Machine Learning

2021

REVIEW: Synthetic biology beyond borders

Raman K*, Sinha H*, Vickers CE*, Nikel PI*

Microbial Biotechnology (2021) 14: 2254

Synthetic Biology

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

Maternal and Child Health Clinical Research

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

Network Biology

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

Network Biology

REVIEW: Evolutionary design principles in metabolism

Sambamoorthy G, Sinha H, Raman K*

Proceedings of the Royal Society B: Biological Sciences (2019) 286: 20190098

Synthetic Biology

REVIEW: Gene-gene and gene environment interactions in complex traits in yeast

Yadav A, Sinha H*

Yeast (2018) 35: 403

Systems Genetics

Fundamental principles governing sporulation efficiency: A network theory approach

Sarkar C, Gupta S, Sinha H, Jalan S*

Canadian Journal of Biotechnology (2017) 1: 46

Network Biology

The modular adaptive ribosome

Yadav A, Radhakrishnan A, Panda A, Singh A, Sinha H*, Bhanot G*

PLOS ONE (2016) 11: e0166021

Systems Genetics

Genetic regulation of phenotypic plasticity and canalisation in yeast growth

Yadav A*, Dhole K, Sinha H*

PLOS ONE (2016) 11: e0162326

Systems Genetics

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

Systems Genetics

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

Systems Genetics

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

Systems Genetics

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

Systems Genetics

REVIEW: Conservation of PHO pathway in yeasts and role of Pho84

Tomar P, Sinha H*

Journal of Biosciences (2014) 39: 1

Systems Genetics

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

Systems Genetics

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

Systems Genetics

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

Systems Genetics

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

Systems Genetics

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

Systems Genetics

Complex genetic interactions in a quantitative trait locus

Sinha H, Nicholson BP, Steinmetz LM, McCusker JH*

PLOS Genetics (2006) 2: e13

Systems Genetics

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

Systems Genetics

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

Systems Genetics

Analysis of the role of recA in phenotypic switching of Pseudomonas tolaasii

Sinha H, Pain A, Johnstone K*

Journal of Bacteriology (2000) 182: 6532

Synthetic Biology

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

Fungal Genetics