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Items: 46

1.

aTEMPO: Pathway-Specific Temporal Anomalies for Precision Therapeutics.

Pietras CM, Power L, Slonim DK.

Pac Symp Biocomput. 2020;25:683-694.

2.

A history of opioid exposure in females increases the risk of metabolic disorders in their future male offspring.

Toorie AM, Vassoler FM, Qu F, Schonhoff CM, Bradburn S, Murgatroyd CA, Slonim DK, Byrnes EM.

Addict Biol. 2019 Nov 28:e12856. doi: 10.1111/adb.12856. [Epub ahead of print]

PMID:
31782234
3.

Assessment of network module identification across complex diseases.

Choobdar S, Ahsen ME, Crawford J, Tomasoni M, Fang T, Lamparter D, Lin J, Hescott B, Hu X, Mercer J, Natoli T, Narayan R; DREAM Module Identification Challenge Consortium, Subramanian A, Zhang JD, Stolovitzky G, Kutalik Z, Lage K, Slonim DK, Saez-Rodriguez J, Cowen LJ, Bergmann S, Marbach D.

Nat Methods. 2019 Sep;16(9):843-852. doi: 10.1038/s41592-019-0509-5. Epub 2019 Aug 30.

4.

Pathway centrality in protein interaction networks identifies putative functional mediating pathways in pulmonary disease.

Park J, Hescott BJ, Slonim DK.

Sci Rep. 2019 Apr 10;9(1):5863. doi: 10.1038/s41598-019-42299-3.

5.

Towards a more molecular taxonomy of disease.

Park J, Hescott BJ, Slonim DK.

J Biomed Semantics. 2017 Jul 27;8(1):25. doi: 10.1186/s13326-017-0134-0.

6.

Amniotic fluid transcriptomics reflects novel disease mechanisms in fetuses with myelomeningocele.

Tarui T, Kim A, Flake A, McClain L, Stratigis JD, Fried I, Newman R, Slonim DK, Bianchi DW.

Am J Obstet Gynecol. 2017 Nov;217(5):587.e1-587.e10. doi: 10.1016/j.ajog.2017.07.022. Epub 2017 Jul 20.

7.

Using Next-Generation Sequencing to Explore Genetics and Race in the High School Classroom.

Yang X, Hartman MR, Harrington KT, Etson CM, Fierman MB, Slonim DK, Walt DR.

CBE Life Sci Educ. 2017 Summer;16(2). pii: ar22. doi: 10.1187/cbe.16-09-0281.

8.

Personal microbiomes and next-generation sequencing for laboratory-based education.

Hartman MR, Harrington KT, Etson CM, Fierman MB, Slonim DK, Walt DR.

FEMS Microbiol Lett. 2016 Dec;363(23). pii: fnw266. doi: 10.1093/femsle/fnw266. Epub 2016 Nov 16.

9.

Time is Money: Designing Cost-Effective Time Series Experiments.

Slonim DK.

Cell Syst. 2016 Jul;3(1):15-6. doi: 10.1016/j.cels.2016.07.008.

10.

Guest Editors’ Introduction: Selected Papers from ACM-BCB 2013.

Aluru S, Slonim DK.

IEEE/ACM Trans Comput Biol Bioinform. 2015 Jan-Feb;12(1):2-3. No abstract available.

PMID:
26605392
11.

The fetal brain transcriptome and neonatal behavioral phenotype in the Ts1Cje mouse model of Down syndrome.

Guedj F, Pennings JL, Ferres MA, Graham LC, Wick HC, Miczek KA, Slonim DK, Bianchi DW.

Am J Med Genet A. 2015 Sep;167A(9):1993-2008. doi: 10.1002/ajmg.a.37156. Epub 2015 May 14.

12.

The pathway not taken: understanding 'omics data in the perinatal context.

Edlow AG, Slonim DK, Wick HC, Hui L, Bianchi DW.

Am J Obstet Gynecol. 2015 Jul;213(1):59.e1-59.e172. doi: 10.1016/j.ajog.2015.03.023. Epub 2015 Mar 12.

13.

CSAX: Characterizing Systematic Anomalies in eXpression Data.

Noto K, Majidi S, Edlow AG, Wick HC, Bianchi DW, Slonim DK.

J Comput Biol. 2015 May;22(5):402-13. doi: 10.1089/cmb.2014.0155. Epub 2015 Feb 4.

14.

Finding novel molecular connections between developmental processes and disease.

Park J, Wick HC, Kee DE, Noto K, Maron JL, Slonim DK.

PLoS Comput Biol. 2014 May 29;10(5):e1003578. doi: 10.1371/journal.pcbi.1003578. eCollection 2014 May.

15.

Amniotic fluid RNA gene expression profiling provides insights into the phenotype of Turner syndrome.

Massingham LJ, Johnson KL, Scholl TM, Slonim DK, Wick HC, Bianchi DW.

Hum Genet. 2014 Sep;133(9):1075-82. doi: 10.1007/s00439-014-1448-y. Epub 2014 May 22.

16.

DFLAT: functional annotation for human development.

Wick HC, Drabkin H, Ngu H, Sackman M, Fournier C, Haggett J, Blake JA, Bianchi DW, Slonim DK.

BMC Bioinformatics. 2014 Feb 7;15:45. doi: 10.1186/1471-2105-15-45.

17.

Novel neurodevelopmental information revealed in amniotic fluid supernatant transcripts from fetuses with trisomies 18 and 21.

Hui L, Slonim DK, Wick HC, Johnson KL, Koide K, Bianchi DW.

Hum Genet. 2012 Nov;131(11):1751-9. doi: 10.1007/s00439-012-1195-x. Epub 2012 Jul 3.

18.

Comprehensive analysis of genes expressed by rare microchimeric fetal cells in the maternal mouse lung.

Pritchard S, Wick HC, Slonim DK, Johnson KL, Bianchi DW.

Biol Reprod. 2012 Aug 23;87(2):42. doi: 10.1095/biolreprod.112.101147. Print 2012 Aug.

19.

The amniotic fluid transcriptome: a source of novel information about human fetal development.

Hui L, Slonim DK, Wick HC, Johnson KL, Bianchi DW.

Obstet Gynecol. 2012 Jan;119(1):111-8. doi: 10.1097/AOG.0b013e31823d4150.

20.

Connectedness of PPI network neighborhoods identifies regulatory hub proteins.

Fox AD, Hescott BJ, Blumer AC, Slonim DK.

Bioinformatics. 2011 Apr 15;27(8):1135-42. doi: 10.1093/bioinformatics/btr099. Epub 2011 Mar 2.

21.

Transcriptomic analysis of cell-free fetal RNA suggests a specific molecular phenotype in trisomy 18.

Koide K, Slonim DK, Johnson KL, Tantravahi U, Cowan JM, Bianchi DW.

Hum Genet. 2011 Mar;129(3):295-305. doi: 10.1007/s00439-010-0923-3. Epub 2010 Dec 9.

22.

Mining functionally relevant gene sets for analyzing physiologically novel clinical expression data.

Turcan S, Vetter DE, Maron JL, Wei X, Slonim DK.

Pac Symp Biocomput. 2011:50-61.

23.

Evaluating between-pathway models with expression data.

Hescott BJ, Leiserson MD, Cowen LJ, Slonim DK.

J Comput Biol. 2010 Mar;17(3):477-87. doi: 10.1089/cmb.2009.0178.

24.
25.

Toward the dynamic interactome: it's about time.

Przytycka TM, Singh M, Slonim DK.

Brief Bioinform. 2010 Jan;11(1):15-29. doi: 10.1093/bib/bbp057. Epub 2010 Jan 8. Review.

26.

Getting started in gene expression microarray analysis.

Slonim DK, Yanai I.

PLoS Comput Biol. 2009 Oct;5(10):e1000543. doi: 10.1371/journal.pcbi.1000543. Epub 2009 Oct 30. Review. No abstract available.

27.

Functional genomic analysis of amniotic fluid cell-free mRNA suggests that oxidative stress is significant in Down syndrome fetuses.

Slonim DK, Koide K, Johnson KL, Tantravahi U, Cowan JM, Jarrah Z, Bianchi DW.

Proc Natl Acad Sci U S A. 2009 Jun 9;106(23):9425-9. doi: 10.1073/pnas.0903909106. Epub 2009 May 27.

28.

High throughput interaction data reveals degree conservation of hub proteins.

Fox A, Taylor D, Slonim DK.

Pac Symp Biocomput. 2009:391-402.

29.

Pairing of competitive and topologically distinct regulatory modules enhances patterned gene expression.

Yanai I, Baugh LR, Smith JJ, Roehrig C, Shen-Orr SS, Claggett JM, Hill AA, Slonim DK, Hunter CP.

Mol Syst Biol. 2008;4:163. doi: 10.1038/msb.2008.6. Epub 2008 Feb 12.

30.

Risk factors associated with beta-amyloid(1-42) immunotherapy in preimmunization gene expression patterns of blood cells.

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.

Arch Neurol. 2005 Oct;62(10):1531-6.

PMID:
16216935
31.

Synthetic lethal analysis of Caenorhabditis elegans posterior embryonic patterning genes identifies conserved genetic interactions.

Baugh LR, Wen JC, Hill AA, Slonim DK, Brown EL, Hunter CP.

Genome Biol. 2005;6(5):R45. Epub 2005 Apr 11.

32.

The homeodomain protein PAL-1 specifies a lineage-specific regulatory network in the C. elegans embryo.

Baugh LR, Hill AA, Claggett JM, Hill-Harfe K, Wen JC, Slonim DK, Brown EL, Hunter CP.

Development. 2005 Apr;132(8):1843-54. Epub 2005 Mar 16.

33.

Transcriptional profiles in peripheral blood mononuclear cells prognostic of clinical outcomes in patients with advanced renal cell carcinoma.

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.

Clin Cancer Res. 2005 Feb 1;11(3):1181-9.

34.

Disease-associated expression profiles in peripheral blood mononuclear cells from patients with advanced renal cell carcinoma.

Twine NC, Stover JA, Marshall B, Dukart G, Hidalgo M, Stadler W, Logan T, Dutcher J, Hudes G, Dorner AJ, Slonim DK, Trepicchio WL, Burczynski ME.

Cancer Res. 2003 Sep 15;63(18):6069-75.

35.

Composition and dynamics of the Caenorhabditis elegans early embryonic transcriptome.

Baugh LR, Hill AA, Slonim DK, Brown EL, Hunter CP.

Development. 2003 Mar;130(5):889-900.

36.

From patterns to pathways: gene expression data analysis comes of age.

Slonim DK.

Nat Genet. 2002 Dec;32 Suppl:502-8. Review.

PMID:
12454645
37.

Evaluation of normalization procedures for oligonucleotide array data based on spiked cRNA controls.

Hill AA, Brown EL, Whitley MZ, Tucker-Kellogg G, Hunter CP, Slonim DK.

Genome Biol. 2001;2(12):RESEARCH0055. Epub 2001 Nov 21.

38.

Chemosensitivity prediction by transcriptional profiling.

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.

Proc Natl Acad Sci U S A. 2001 Sep 11;98(19):10787-92.

39.

Transcriptional profiling in cancer: the path to clinical pharmacogenomics.

Slonim DK.

Pharmacogenomics. 2001 May;2(2):123-36. Review.

PMID:
11368751
40.

Molecular classification of cancer: class discovery and class prediction by gene expression monitoring.

Golub TR, Slonim DK, Tamayo P, Huard C, Gaasenbeek M, Mesirov JP, Coller H, Loh ML, Downing JR, Caligiuri MA, Bloomfield CD, Lander ES.

Science. 1999 Oct 15;286(5439):531-7.

41.

A YAC-based physical map of the mouse genome.

Nusbaum C, Slonim DK, Harris KL, Birren BW, Steen RG, Stein LD, Miller J, Dietrich WF, Nahf R, Wang V, Merport O, Castle AB, Husain Z, Farino G, Gray D, Anderson MO, Devine R, Horton LT Jr, Ye W, Wu X, Kouyoumjian V, Zemsteva IS, Wu Y, Collymore AJ, Courtney DF, Tam J, Cadman M, Haynes AR, Heuston C, Marsland T, Southwell A, Trickett P, Strivens MA, Ross MT, Makalowski W, Xu Y, Boguski MS, Carter NP, Denny P, Brown SD, Hudson TJ, Lander ES.

Nat Genet. 1999 Aug;22(4):388-93.

PMID:
10431246
42.

Radiation hybrid map of the mouse genome.

Van Etten WJ, Steen RG, Nguyen H, Castle AB, Slonim DK, Ge B, Nusbaum C, Schuler GD, Lander ES, Hudson TJ.

Nat Genet. 1999 Aug;22(4):384-7.

PMID:
10431245
43.

A physical map of 30,000 human genes.

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, Castle AB, Chiannilkulchai N, Clee C, Day PJ, Dehejia A, Dibling T, Drouot N, Duprat S, Fizames C, Fox S, Gelling S, Green L, Harrison P, Hocking R, Holloway E, Hunt S, Keil S, Lijnzaad P, Louis-Dit-Sully C, Ma J, Mendis A, Miller J, Morissette J, Muselet D, Nusbaum HC, Peck A, Rozen S, Simon D, Slonim DK, Staples R, Stein LD, Stewart EA, Suchard MA, Thangarajah T, Vega-Czarny N, Webber C, Wu X, Hudson J, Auffray C, Nomura N, Sikela JM, Polymeropoulos MH, James MR, Lander ES, Hudson TJ, Myers RM, Cox DR, Weissenbach J, Boguski MS, Bentley DR.

Science. 1998 Oct 23;282(5389):744-6.

44.

Genome maps 7. The human transcript map. Wall chart.

Schuler GD, Boguski MS, Hudson TJ, Hui L, Ma J, Castle AB, Wu X, Silva J, Nusbaum HC, Birren BB, Slonim DK, Rozen S, Stein LD, Page D, Lander ES, Stewart EA, Aggarwal A, Bajorek E, Brady S, Chu S, Fang N, Hadley D, Harris M, Hussain S, Hudson JR Jr, et al.

Science. 1996 Oct 25;274(5287):547-62. No abstract available.

PMID:
8928009
45.

A gene map of the human genome.

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, Chu A, Clee C, Cowles S, Day PJ, Dibling T, Drouot N, Dunham I, Duprat S, East C, Edwards C, Fan JB, Fang N, Fizames C, Garrett C, Green L, Hadley D, Harris M, Harrison P, Brady S, Hicks A, Holloway E, Hui L, Hussain S, Louis-Dit-Sully C, Ma J, MacGilvery A, Mader C, Maratukulam A, Matise TC, McKusick KB, Morissette J, Mungall A, Muselet D, Nusbaum HC, Page DC, Peck A, Perkins S, Piercy M, Qin F, Quackenbush J, Ranby S, Reif T, Rozen S, Sanders C, She X, Silva J, Slonim DK, Soderlund C, Sun WL, Tabar P, Thangarajah T, Vega-Czarny N, Vollrath D, Voyticky S, Wilmer T, Wu X, Adams MD, Auffray C, Walter NA, Brandon R, Dehejia A, Goodfellow PN, Houlgatte R, Hudson JR Jr, Ide SE, Iorio KR, Lee WY, Seki N, Nagase T, Ishikawa K, Nomura N, Phillips C, Polymeropoulos MH, Sandusky M, Schmitt K, Berry R, Swanson K, Torres R, Venter JC, Sikela JM, Beckmann JS, Weissenbach J, Myers RM, Cox DR, James MR, Bentley D, Deloukas P, Lander ES, Hudson TJ.

Science. 1996 Oct 25;274(5287):540-6. Review.

PMID:
8849440
46.

An STS-based map of the human genome.

Hudson TJ, Stein LD, Gerety SS, Ma J, Castle AB, Silva J, Slonim DK, Baptista R, Kruglyak L, Xu SH, Hu X, Colbert AM, Rosenberg C, Reeve-Daly MP, Rozen S, Hui L, Wu X, Vestergaard C, Wilson KM, Bae JS, Maitra S, Ganiatsas S, Evans CA, DeAngelis MM, Ingalls KA, Nahf RW, Horton LT Jr, Anderson MO, Collymore AJ, Ye W, Kouyoumjian V, Zemsteva IS, Tam J, Devine R, Courtney DF, Renaud MT, Nguyen H, O'Connor TJ, Fizames C, Fauré S, Gyapay G, Dib C, Morissette J, Orlin JB, Birren BW, Goodman N, Weissenbach J, Hawkins TL, Foote S, Page DC, Lander ES.

Science. 1995 Dec 22;270(5244):1945-54.

PMID:
8533086

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