Recent Publications from the Slonim Lab

Research Publications Genetics


Tarui T, Kim A, Flake A, Mcclain L, Stratigis J, Fried I, Newman R, Slonim DK, Bianchi DW. 2017. Amniotic fluid transcriptomics reflects novel disease mechanisms in fetuses with myelomeningocele. Am J Obstet Gynecol. 217: 587.e1-587.e10.  books

Park J, Hescott BJ, Slonim DK. 2017. Towards a more molecular taxonomy of disease. J Biomed Semantics 8:25.  books

Yang X, Hartman MR, Harrington KT, Etson CM, Fierman MB, Slonim DK, Walt DR. 2017. Using next-generation sequencing to explore genetics and race in the high school classroom. CBE Lif Sic Educ. 16: pii: ar22. doi: 10.1187/cbe.16-09-0281. books

Hartman MR, Harrington KT, Etson CM, Fierman MB, Slonim DK, Walt DR. 2016. Personal microbiomes and next-generation sequencing for laboratory-based education. FEMS Microbiol Lett. 363(23).  books

Slonim DK. 2016. Time is money: Designing cost-effective time series experiments. Cell Syst. 3: 15-16. books

Guedj F, Pennings JL, Ferres MA, Graham LC, Wick HC, Miczek KA, Slonim DK, Bianchi DW. 2015. The fetal brain transcriptome and neonatal behavioral phenotype in the Ts1Cje mouse model of Down syndrome. Am J Med Genet A 167A: 1993-2008. books

Edlow AG, Slonim DK, Wick HC, Hui L, Bianchi DW. 2015. The pathway not taken: Understanding 'omics data in the perinatal context. Am J Obstet Gynecol. 213: 59.e1-172. books

Park J, Wick HC, Kee DE, Noto K, Maron JL, Slonim DK. 2014. Finding novel molecular connections between developmental processes and disease. PLoS Comput Biol. 10: e1003578. books

Wick HC, Drabkin H, Ngu H, Sackman M, Fournier C, Haggett J, Blake JA, Bianchi DW, Slonim DK. 2014. DFLAT: functional annotation for human development. BMC Bioinformatics 15: 45. books

Hui L, Slonim DK, Wick HC, Johnson KL, Bianchi DW. 2012. The amniotic fluid transcriptome: a source of novel information about human fetal development. Obstet Gynecol. 119: 111-118. books

Pritchard S, Wick HC, Slonim DK, Johnson KL, Bianchi DW. 2012. Comprehensive analysis of genes expressed by rare microchimeric fetal cells in the maternal mouse lung. Biol. Reprod. 87: 42. books

Hui L, Slonim DK, Wick HC, Johnson KL, Koide K, Bianchi DW. 2012. Novel neurodevelopmental information revealed in amniotic fluid supernatant transcripts from fetuses with trisomies 18 and 21. Hum Genet. 131: 1751-1759. books

Koide K, Slonim DK, Johnson KL, Tantravahi U, Cowan JM, Bianchi DW. 2011. Transcriptomic analysis of cell-free fetal RNA suggests a specific molecular phenotype in trisomy 18. Hum Genet. 129: 295-305. books

Fox AD, Hescott BJ, Blumer AC, Slonim DK. 2011. Connectedness of PPI network neighborhoods identifies regulatory hub proteins. Bioinformatics 27: 1135-1142. books

Turcan S, Vetter DE, Maron JL, Wei X, Slonim DK. 2011. Mining functionally relevant gene sets for analyzing physiologically novel clinical expression data. Pac Symp Biocomput. 2011: 50-61. books

Hescott BJ, Leiserson MD, Cowen LJ, Slonim DK. 2010. Evaluating between-pathway models with expression data. J Comput Biol. 17: 477-487. books

Turcan S, Slonim DK, Vetter DE. 2010. Lack of nAChR activity depresses cochlear maturation and up-regulates GABA system components: temporal profiling of gene expression in alpha9 null mice. PLos One 5: e9058. books

Przytycka TM, Singh M, Slonim DK. 2010. Toward the dynamic interactome: it's about time. Brief Bioinform. 11: 15-29. books

Berger-Wolf TY, Przytycka TM, Singh M, Slonim DK. 2009. Dynamics of biological networks - Session Introduction. Pac Symp Biocomput. 15: 120-122. books

Slonim DK, Yanai I. 2009. Getting started in microarray analysis. PLoS Comp Biol. 5: e1000543. books

Slonim DK, Koide K, Johnson KL, Tantravahi U, Cowan JM, Jarrah Z, Bianchi DW. 2009. Functional genomic analysis of amniotic fluid cell-free mRNA suggests that oxidative stress is significant in Down syndrome fetuses. Proc Natl Acad Sci USA 106: 9425-9429. books

Fox A, Taylor D, Slonim DK. 2009. High throughput interaction data reveals degree conservation of hub proteins. Pac Symp Biocomput. 391-402. books

Yanai I, Baugh LR, Smith JJ, Roehrig C, Shen-Orr SS, Claggett JM, Hill AA, Slonim DK, Hunter CP. 2008. Pairing of competitive and topologically distinct regulatory modules enhances patterned gene expression.  Mol Sys Biol. 4: 163. books

Maron JL, Johnson KL, Slonim D, Lai CQ, Ramoni M, Alterovitz G, Jarrah Z, Yang Z, Bianchi DW. 2007. Gene expression analysis in pregnant women and their infants identifies unique fetal biomarkers that circulate in maternal blood. J Clin Invest. 117: 3007-3019. books

O'Toole M, Janszen DB, Slonim DK, Reddy PS, Ellis DK, Legault HM, Hill AA, Whitley MZ, Mounts WM, Zuberek K, Immermann FW, Black RS, Dorner AJ. 2005. Risk factors associated with beta-amyloid(1-42) immunotherapy in preimmunization gene expression patterns of blood cells. Arch Neurol. 62: 1531-1536. books

Baugh LR, Wen JC, Hill AA, Slonim DK, Brown EL, Hunter CP. 2005. Synthetic lethal analysis of Caenorhabditis elegans posterior embryonic patterning genes identifies conserved genetic interactions. Genome Biol. 6: R45. books

Baugh LR, Hill AA, Claggett JM, Hill-Harfe K, Wen JC, Slonim DK, Brown EL, Hunter CP. 2005. The homeodomain protein PAL-1 specifies a lineage-specific regulatory network in the C. elegans embryo. Development 132: 1843-1854. books

Burczynski ME, Twine NC, Dukart G, Marshall B, Hidalgo M, Stadler WM, Logan T, Dutcher J, Hudes G, Trepicchio WL, Strahs A, Immermann F, Slonim DK, Dorner AJ. 2005. Transcriptional profiles in peripheral blood mononuclear cells prognostic of clinical outcomes in patients with advanced renal cell carcinoma. Clin Cancer Res. 11: 1181-1189. books

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