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Donna K. Slonim - Publications

Affiliations: 
Computer Science Tufts University, Boston 
Area:
Computer Science, Bioinformatics Biology, Systematic Biology
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32 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2019 Choobdar S, Ahsen ME, Crawford J, Tomasoni M, Fang T, Lamparter D, Lin J, Hescott B, Hu X, Mercer J, Natoli T, Narayan R, Subramanian A, Zhang JD, ... ... Slonim DK, et al. Assessment of network module identification across complex diseases. Nature Methods. 16: 843-852. PMID 31471613 DOI: 10.1038/S41592-019-0509-5  0.338
2019 Park J, Hescott BJ, Slonim DK. Pathway centrality in protein interaction networks identifies putative functional mediating pathways in pulmonary disease. Scientific Reports. 9: 5863. PMID 30971743 DOI: 10.1038/S41598-019-42299-3  0.312
2017 Tarui T, Kim A, Flake A, Mcclain L, Stratigis J, Fried I, Newman R, Slonim DK, Bianchi DW. Amniotic fluid transcriptomics reflects novel disease mechanisms in fetuses with myelomeningocele. American Journal of Obstetrics and Gynecology. PMID 28735706 DOI: 10.1016/J.Ajog.2017.07.022  0.338
2015 Edlow AG, Slonim DK, Wick HC, Hui L, Bianchi DW. The pathway not taken: understanding 'omics data in the perinatal context. American Journal of Obstetrics and Gynecology. 213: 59.e1-59.e172. PMID 25772209 DOI: 10.1016/J.Ajog.2015.03.023  0.36
2015 Noto K, Majidi S, Edlow AG, Wick HC, Bianchi DW, Slonim DK. CSAX: Characterizing Systematic Anomalies in eXpression Data. Journal of Computational Biology : a Journal of Computational Molecular Cell Biology. 22: 402-13. PMID 25651392 DOI: 10.1089/Cmb.2014.0155  0.387
2014 Park J, Wick HC, Kee DE, Noto K, Maron JL, Slonim DK. Finding novel molecular connections between developmental processes and disease. Plos Computational Biology. 10: e1003578. PMID 24874013 DOI: 10.1371/Journal.Pcbi.1003578  0.394
2014 Massingham LJ, Johnson KL, Scholl TM, Slonim DK, Wick HC, Bianchi DW. Amniotic fluid RNA gene expression profiling provides insights into the phenotype of Turner syndrome. Human Genetics. 133: 1075-82. PMID 24850140 DOI: 10.1007/S00439-014-1448-Y  0.41
2014 Wick HC, Drabkin H, Ngu H, Sackman M, Fournier C, Haggett J, Blake JA, Bianchi DW, Slonim DK. DFLAT: functional annotation for human development. Bmc Bioinformatics. 15: 45. PMID 24507166 DOI: 10.1186/1471-2105-15-45  0.399
2014 Edlow A, Hui L, Wick H, Slonim D, Bianchi D. 103: Amniotic fluid demonstrates wider diversity of gene expression compared to cord blood from the same fetus at term American Journal of Obstetrics and Gynecology. 210. DOI: 10.1016/J.Ajog.2013.10.136  0.331
2012 Hui L, Slonim DK, Wick HC, Johnson KL, Koide K, Bianchi DW. Novel neurodevelopmental information revealed in amniotic fluid supernatant transcripts from fetuses with trisomies 18 and 21. Human Genetics. 131: 1751-9. PMID 22752091 DOI: 10.1007/S00439-012-1195-X  0.417
2012 Pritchard S, Wick HC, Slonim DK, Johnson KL, Bianchi DW. Comprehensive analysis of genes expressed by rare microchimeric fetal cells in the maternal mouse lung. Biology of Reproduction. 87: 42. PMID 22674387 DOI: 10.1095/Biolreprod.112.101147  0.373
2011 Koide K, Slonim DK, Johnson KL, Tantravahi U, Cowan JM, Bianchi DW. Transcriptomic analysis of cell-free fetal RNA suggests a specific molecular phenotype in trisomy 18. Human Genetics. 129: 295-305. PMID 21152935 DOI: 10.1007/S00439-010-0923-3  0.438
2011 Turcan S, Vetter DE, Maron JL, Wei X, Slonim DK. Mining functionally relevant gene sets for analyzing physiologically novel clinical expression data. Pacific Symposium On Biocomputing. Pacific Symposium On Biocomputing. 50-61. PMID 21121032  0.544
2010 Hescott BJ, Leiserson MDM, Cowen LJ, Slonim DK. Evaluating between-pathway models with expression data Journal of Computational Biology. 17: 477-487. PMID 20377458 DOI: 10.1089/Cmb.2009.0178  0.38
2010 Turcan S, Slonim DK, Vetter DE. 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. PMID 20140217 DOI: 10.1371/Journal.Pone.0009058  0.308
2009 Slonim DK, Yanai I. Getting started in gene expression microarray analysis. Plos Computational Biology. 5: e1000543. PMID 19876380 DOI: 10.1371/Journal.Pcbi.1000543  0.453
2009 Slonim DK, Koide K, Johnson KL, Tantravahi U, Cowan JM, Jarrah Z, Bianchi DW. Functional genomic analysis of amniotic fluid cell-free mRNA suggests that oxidative stress is significant in Down syndrome fetuses. Proceedings of the National Academy of Sciences of the United States of America. 106: 9425-9. PMID 19474297 DOI: 10.1073/Pnas.0903909106  0.368
2008 Yanai I, Baugh LR, Smith JJ, Roehrig C, Shen-Orr SS, Claggett JM, Hill AA, Slonim DK, Hunter CP. Pairing of competitive and topologically distinct regulatory modules enhances patterned gene expression. Molecular Systems Biology. 4: 163. PMID 18277379 DOI: 10.1038/Msb.2008.6  0.384
2007 Maron JL, Johnson KL, Slonim D, Lai CQ, Ramoni M, Alterovitz G, Jarrah Z, Yang Z, Bianchi DW. Gene expression analysis in pregnant women and their infants identifies unique fetal biomarkers that circulate in maternal blood. The Journal of Clinical Investigation. 117: 3007-19. PMID 17885688 DOI: 10.1172/Jci29959  0.359
2005 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. Risk factors associated with beta-amyloid(1-42) immunotherapy in preimmunization gene expression patterns of blood cells. Archives of Neurology. 62: 1531-6. PMID 16216935 DOI: 10.1001/Archneur.62.10.1531  0.333
2005 Baugh LR, Wen JC, Hill AA, Slonim DK, Brown EL, Hunter CP. Synthetic lethal analysis of Caenorhabditis elegans posterior embryonic patterning genes identifies conserved genetic interactions. Genome Biology. 6: R45. PMID 15892873 DOI: 10.1186/Gb-2005-6-5-R45  0.358
2005 Baugh LR, Hill AA, Claggett JM, Hill-Harfe K, Wen JC, Slonim DK, Brown EL, Hunter CP. The homeodomain protein PAL-1 specifies a lineage-specific regulatory network in the C. elegans embryo. Development (Cambridge, England). 132: 1843-54. PMID 15772128 DOI: 10.1242/Dev.01782  0.386
2003 Baugh LR, Hill AA, Slonim DK, Brown EL, Hunter CP. Composition and dynamics of the Caenorhabditis elegans early embryonic transcriptome. Development (Cambridge, England). 130: 889-900. PMID 12538516 DOI: 10.1242/Dev.00302  0.36
2002 Slonim DK. From patterns to pathways: gene expression data analysis comes of age. Nature Genetics. 32: 502-8. PMID 12454645 DOI: 10.1038/Ng1033  0.375
2001 Hill AA, Brown EL, Whitley MZ, Tucker-Kellogg G, Hunter CP, Slonim DK. Evaluation of normalization procedures for oligonucleotide array data based on spiked cRNA controls. Genome Biology. 2: RESEARCH0055. PMID 11790258 DOI: 10.1186/Gb-2001-2-12-Research0055  0.312
2001 Staunton JE, Slonim DK, Coller HA, Tamayo P, Angelo MJ, Park J, Scherf U, Lee JK, Reinhold WO, Weinstein JN, Mesirov JP, Lander ES, Golub TR. Chemosensitivity prediction by transcriptional profiling. Proceedings of the National Academy of Sciences of the United States of America. 98: 10787-92. PMID 11553813 DOI: 10.1073/Pnas.191368598  0.389
2000 Butte AJ, Tamayo P, Slonim D, Golub TR, Kohane IS. Discovering functional relationships between RNA expression and chemotherapeutic susceptibility using relevance networks. Proceedings of the National Academy of Sciences of the United States of America. 97: 12182-6. PMID 11027309 DOI: 10.1073/Pnas.220392197  0.379
1999 Van Etten WJ, Steen RG, Nguyen H, Castle AB, Slonim DK, Ge B, Nusbaum C, Schuler GD, Lander ES, Hudson TJ. Radiation hybrid map of the mouse genome Nature Genetics. 22: 384-387. PMID 10431245 DOI: 10.1038/11962  0.319
1999 Tamayo P, Slonim D, Mesirov J, Zhu Q, Kitareewan S, Dmitrovsky E, Lander ES, Golub TR. Interpreting patterns of gene expression with self-organizing maps: methods and application to hematopoietic differentiation. Proceedings of the National Academy of Sciences of the United States of America. 96: 2907-12. PMID 10077610 DOI: 10.1073/Pnas.96.6.2907  0.426
1998 Deloukas P, Schuler GD, Gyapay G, Beasley EM, Soderlund C, Rodriguez-Tomé P, Hui L, Matise TC, McKusick KB, Beckmann JS, Bentolila S, Bihoreau M, Birren BB, Browne J, Butler A, ... ... Slonim DK, et al. A physical map of 30,000 human genes. Science (New York, N.Y.). 282: 744-6. PMID 9784132 DOI: 10.1126/Science.282.5389.744  0.414
1997 Slonim D, Kruglyak L, Stein L, Lander E. Building human genome maps with radiation hybrids. Journal of Computational Biology : a Journal of Computational Molecular Cell Biology. 4: 487-504. PMID 9385541 DOI: 10.1089/Cmb.1997.4.487  0.311
1996 Schuler GD, Boguski MS, Stewart EA, Stein LD, Gyapay G, Rice K, White RE, Rodriguez-Tomé P, Aggarwal A, Bajorek E, Bentolila S, Birren BB, Butler A, Castle AB, Chiannilkulchai N, ... ... Slonim DK, et al. A gene map of the human genome. Science (New York, N.Y.). 274: 540-6. PMID 8849440 DOI: 10.1126/Science.274.5287.540  0.398
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