PUBLICATIONS — Shraddha Pai Lab

Atienza J, Benedict A, Stein LD, Pirzada K, White C, Pai S. Fourteen quick tips for crowdsourcing geographically linked data for public health advocacy (2023). PLoS Comp. Biol. 19 (9): e1011285.
Pai S, Hui S, Weber P, Narayan S, Whitley O, Li P, Labrie V, Baumbach J, Bader GD. Multi-scale systems genomics analysis predicts pathways, cell types and drug targets involved in normative variation in peri-adolescent human cognition (2023). Cerebral Cortex 33 (13): 8581-93.

Kozlowski HN, Malekjahani A, Li VYC, Lekuti AA, Perusini S, Bell NG, Voisin V, Pouyabahar D, Pai S, Bader GD, Mubareka S, Gubbay JB, Chan WCW. (2023). Genotyping SARS-CoV-2 Variants Using Ratiometric Nucleic Acid Barcode Panels. Anal. Chem. 95 (14), 5877-85.
Tupper P, Pai S, COVID Schools Canada, Colijn C. (2022) COVID-19 cluster size and transmission rates in schools from crowdsourced case reports. eLife. https://doi.org/10.7554/eLife.76174
Pai S, Weber P, Isserlin I, Kaka H, Hui S, Shah MA, Nøhr AK, Baumbach J, GD Bader. (2021) netDx: Software for building interpretable patient classifiers by multi-‘omic data integration using patient similarity networks. F1000 Research 9:1239.
Gustavsen JA, Pai S, Isserlin R, Demchak B, and AR Pico. (2019). RCy3: Network Biology using Cytoscape from within R. F1000Res. 8:1774.
Pai S, Li P, Killinger B, Marshall L, Jia P, Liao J, Petronis A, Szabó PE, Labrie V (2019). Differential methylation of enhancer at IGF2 is associated with abnormal dopamine synthesis in major psychosis. Nature Comms. 10:2046.
Pai S, Hui S, Isserlin R, Shah MA, Kaka H, Bader GD. (2019). netDx: interpretable patient classification using integrated patient similarity networks. Mol Sys Biol 15:e8497
Pai S and Bader GD. (2018). Patient Similarity Networks for Precision Medicine. Invited review. J Mol Biol. 430 (18 Pt A); 2924.
Kriukienė E, Labrie V, Khare T, Urbanavičiūtė G, Lapinaitė A, Koncevičius K, Li D, Wang T, Pai S, Ptak C, Gordevičius J, Wang SC, Petronis A, Klimašauskas S. (2013). DNA unmethylome profiling by covalent capture of CpG sites. Nature Communications. 4:2190.
Khare T*, Pai S*, Koncevicius K, Pal M, Kriukiene E, Liutkeviciute Z, Irimia M, Jia P, Ptak C, Xia M, Tice R, Tochigi M, Moréra S, Nazarians A, Belsham D, Wong AH, Blencowe BJ, Wang SC, Kapranov P, Kustra R, Labrie V, Klimasauskas S, Petronis A. (2012). 5-hmC in the brain is abundant in synaptic genes and shows differences at the exon-intron boundary. Nat Struct Mol Biol. 19 (10): 1037-43. * Co-lead author.
Labrie V*, Pai S*, Petronis A. (2012) Epigenetics of major psychosis: progress, problems and perspectives. Trends in Genetics, invited review. 28 (9): 427-35. * Co-lead author.
Kaminsky Z et al. (2012). A multi-tissue analysis identifies HLA complex group 9 gene methylation differences in bipolar disorder. Mol Psychiatry. 2012. 17 (7): 728-40.
Pai S, Erlich JC, Kopec C, Brody CD. (2011). Minimal impairment in a rat model of duration discrimination following excitotoxic lesions of primary auditory and prefrontal cortices.Front Syst Neurosci. 5:74.
Kopec CD, Bowers AC, Pai S, Brody CD. (2011). Semi-automated atlas-based analysis of brain histological sections. J Neurosci Meth. 196 (1):12-9.
Chen N, Pai S, Zhao Z, Mah A, Newbury R, Johnsen RC, Altun Z, Moerman DG, Baillie DL, Stein LD. (2005). Identification of a nematode chemosensory gene family. Proc Natl Acad Sci USA, 102 (1):146-51.
Chen N et al. (2005). WormBase: a comprehensive data resource for Caenorhabditis biology and genomics. Nucleic Acids Res. 33 (Database issue): D383-9.