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Items: 1 to 50 of 95

1.

Extensive rewiring of the EGFR network in colorectal cancer cells expressing transforming levels of KRASG13D.

Kennedy SA, Jarboui MA, Srihari S, Raso C, Bryan K, Dernayka L, Charitou T, Bernal-Llinares M, Herrera-Montavez C, Krstic A, Matallanas D, Kotlyar M, Jurisica I, Curak J, Wong V, Stagljar I, LeBihan T, Imrie L, Pillai P, Lynn MA, Fasterius E, Al-Khalili Szigyarto C, Breen J, Kiel C, Serrano L, Rauch N, Rukhlenko O, Kholodenko BN, Iglesias-Martinez LF, Ryan CJ, Pilkington R, Cammareri P, Sansom O, Shave S, Auer M, Horn N, Klose F, Ueffing M, Boldt K, Lynn DJ, Kolch W.

Nat Commun. 2020 Jan 24;11(1):499. doi: 10.1038/s41467-019-14224-9.

PMID:
31980649
2.

Changes in the Composition of the Gut Microbiota and the Blood Transcriptome in Preterm Infants at Less than 29 Weeks Gestation Diagnosed with Bronchopulmonary Dysplasia.

Ryan FJ, Drew DP, Douglas C, Leong LEX, Moldovan M, Lynn M, Fink N, Sribnaia A, Penttila I, McPhee AJ, Collins CT, Makrides M, Gibson RA, Rogers GB, Lynn DJ.

mSystems. 2019 Oct 29;4(5). pii: e00484-19. doi: 10.1128/mSystems.00484-19.

3.

Transcriptional and metabolic rewiring of colorectal cancer cells expressing the oncogenic KRASG13D mutation.

Charitou T, Srihari S, Lynn MA, Jarboui MA, Fasterius E, Moldovan M, Shirasawa S, Tsunoda T, Ueffing M, Xie J, Xin J, Wang X, Proud CG, Boldt K, Al-Khalili Szigyarto C, Kolch W, Lynn DJ.

Br J Cancer. 2019 Jul;121(1):37-50. doi: 10.1038/s41416-019-0477-7. Epub 2019 May 28.

4.

Analysis and Visualization of Dynamic Networks Using the DyNet App for Cytoscape.

Salamon J, Goenawan IH, Lynn DJ.

Curr Protoc Bioinformatics. 2018 Sep;63(1):e55. doi: 10.1002/cpbi.55. Epub 2018 Aug 31.

PMID:
30168906
5.

Genome-wide association study of intraocular pressure uncovers new pathways to glaucoma.

MacGregor S, Ong JS, An J, Han X, Zhou T, Siggs OM, Law MH, Souzeau E, Sharma S, Lynn DJ, Beesley J, Sheldrick B, Mills RA, Landers J, Ruddle JB, Graham SL, Healey PR, White AJR, Casson RJ, Best S, Grigg JR, Goldberg I, Powell JE, Whiteman DC, Radford-Smith GL, Martin NG, Montgomery GW, Burdon KP, Mackey DA, Gharahkhani P, Craig JE, Hewitt AW.

Nat Genet. 2018 Aug;50(8):1067-1071. doi: 10.1038/s41588-018-0176-y. Epub 2018 Jul 27.

PMID:
30054594
6.

Network Visualization and Analysis of Spatially Aware Gene Expression Data with InsituNet.

Salamon J, Qian X, Nilsson M, Lynn DJ.

Cell Syst. 2018 May 23;6(5):626-630.e3. doi: 10.1016/j.cels.2018.03.010. Epub 2018 May 9.

7.

Early-Life Antibiotic-Driven Dysbiosis Leads to Dysregulated Vaccine Immune Responses in Mice.

Lynn MA, Tumes DJ, Choo JM, Sribnaia A, Blake SJ, Leong LEX, Young GP, Marshall HS, Wesselingh SL, Rogers GB, Lynn DJ.

Cell Host Microbe. 2018 May 9;23(5):653-660.e5. doi: 10.1016/j.chom.2018.04.009.

8.

Encompassing new use cases - level 3.0 of the HUPO-PSI format for molecular interactions.

Sivade Dumousseau M, Alonso-López D, Ammari M, Bradley G, Campbell NH, Ceol A, Cesareni G, Combe C, De Las Rivas J, Del-Toro N, Heimbach J, Hermjakob H, Jurisica I, Koch M, Licata L, Lovering RC, Lynn DJ, Meldal BHM, Micklem G, Panni S, Porras P, Ricard-Blum S, Roechert B, Salwinski L, Shrivastava A, Sullivan J, Thierry-Mieg N, Yehudi Y, Van Roey K, Orchard S.

BMC Bioinformatics. 2018 Apr 11;19(1):134. doi: 10.1186/s12859-018-2118-1.

9.

Identification of Novel Response and Predictive Biomarkers to Hsp90 Inhibitors Through Proteomic Profiling of Patient-derived Prostate Tumor Explants.

Nguyen EV, Centenera MM, Moldovan M, Das R, Irani S, Vincent AD, Chan H, Horvath LG, Lynn DJ, Daly RJ, Butler LM.

Mol Cell Proteomics. 2018 Aug;17(8):1470-1486. doi: 10.1074/mcp.RA118.000633. Epub 2018 Apr 9.

10.

Dysregulated fibronectin trafficking by Hsp90 inhibition restricts prostate cancer cell invasion.

Armstrong HK, Gillis JL, Johnson IRD, Nassar ZD, Moldovan M, Levrier C, Sadowski MC, Chin MY, Tomlinson Guns ES, Tarulli G, Lynn DJ, Brooks DA, Selth LA, Centenera MM, Butler LM.

Sci Rep. 2018 Feb 1;8(1):2090. doi: 10.1038/s41598-018-19871-4.

11.

Using the Contextual Hub Analysis Tool (CHAT) in Cytoscape to Identify Contextually Relevant Network Hubs.

Muetze T, Lynn DJ.

Curr Protoc Bioinformatics. 2017 Sep 13;59:8.24.1-8.24.13. doi: 10.1002/cpbi.35.

PMID:
28902399
12.

The potential of the microbiota to influence vaccine responses.

Lynn DJ, Pulendran B.

J Leukoc Biol. 2018 Feb;103(2):225-231. doi: 10.1189/jlb.5MR0617-216R. Epub 2017 Dec 28. Review.

13.

Retinal Pigment Epithelial Cells are a Potential Reservoir for Ebola Virus in the Human Eye.

Smith JR, Todd S, Ashander LM, Charitou T, Ma Y, Yeh S, Crozier I, Michael MZ, Appukuttan B, Williams KA, Lynn DJ, Marsh GA.

Transl Vis Sci Technol. 2017 Jul 14;6(4):12. doi: 10.1167/tvst.6.4.12. eCollection 2017 Jul.

14.

Whole exome sequencing implicates eye development, the unfolded protein response and plasma membrane homeostasis in primary open-angle glaucoma.

Zhou T, Souzeau E, Sharma S, Landers J, Mills R, Goldberg I, Healey PR, Graham S, Hewitt AW, Mackey DA, Galanopoulos A, Casson RJ, Ruddle JB, Ellis J, Leo P, Brown MA, MacGregor S, Lynn DJ, Burdon KP, Craig JE.

PLoS One. 2017 Mar 6;12(3):e0172427. doi: 10.1371/journal.pone.0172427. eCollection 2017.

15.

Contextual Hub Analysis Tool (CHAT): A Cytoscape app for identifying contextually relevant hubs in biological networks.

Muetze T, Goenawan IH, Wiencko HL, Bernal-Llinares M, Bryan K, Lynn DJ.

Version 2. F1000Res. 2016 Jul 19 [revised 2016 Jan 1];5:1745. eCollection 2016.

16.

Interferon-driven alterations of the host's amino acid metabolism in the pathogenesis of typhoid fever.

Blohmke CJ, Darton TC, Jones C, Suarez NM, Waddington CS, Angus B, Zhou L, Hill J, Clare S, Kane L, Mukhopadhyay S, Schreiber F, Duque-Correa MA, Wright JC, Roumeliotis TI, Yu L, Choudhary JS, Mejias A, Ramilo O, Shanyinde M, Sztein MB, Kingsley RA, Lockhart S, Levine MM, Lynn DJ, Dougan G, Pollard AJ.

J Exp Med. 2016 May 30;213(6):1061-77. doi: 10.1084/jem.20151025. Epub 2016 May 23.

17.

DyNet: visualization and analysis of dynamic molecular interaction networks.

Goenawan IH, Bryan K, Lynn DJ.

Bioinformatics. 2016 Sep 1;32(17):2713-5. doi: 10.1093/bioinformatics/btw187. Epub 2016 May 3.

18.

HiQuant: Rapid Postquantification Analysis of Large-Scale MS-Generated Proteomics Data.

Bryan K, Jarboui MA, Raso C, Bernal-Llinares M, McCann B, Rauch J, Boldt K, Lynn DJ.

J Proteome Res. 2016 Jun 3;15(6):2072-9. doi: 10.1021/acs.jproteome.5b01008. Epub 2016 May 16.

19.

Using biological networks to integrate, visualize and analyze genomics data.

Charitou T, Bryan K, Lynn DJ.

Genet Sel Evol. 2016 Mar 31;48:27. doi: 10.1186/s12711-016-0205-1. Review.

20.

A genome-wide association study for genetic susceptibility to Mycobacterium bovis infection in dairy cattle identifies a susceptibility QTL on chromosome 23.

Richardson IW, Berry DP, Wiencko HL, Higgins IM, More SJ, McClure J, Lynn DJ, Bradley DG.

Genet Sel Evol. 2016 Mar 9;48:19. doi: 10.1186/s12711-016-0197-x.

21.

Erratum to: 'Integrated analysis of the local and systemic changes preceding the development of post-partum cytological endometritis'.

Foley C, Chapwanya A, Callanan JJ, Whiston R, Miranda-CasoLuengo R, Lu J, Meijer WG, Lynn DJ, O'Farrelly C, Meade KG.

BMC Genomics. 2015 Dec 10;16:1050. doi: 10.1186/s12864-015-2205-x. No abstract available.

22.

Whole blood gene expression profiling of neonates with confirmed bacterial sepsis.

Dickinson P, Smith CL, Forster T, Craigon M, Ross AJ, Khondoker MR, Ivens A, Lynn DJ, Orme J, Jackson A, Lacaze P, Flanagan KL, Stenson BJ, Ghazal P.

Genom Data. 2014 Nov 15;3:41-8. doi: 10.1016/j.gdata.2014.11.003. eCollection 2015 Mar.

23.

Integrated analysis of the local and systemic changes preceding the development of post-partum cytological endometritis.

Foley C, Chapwanya A, Callanan JJ, Whiston R, Miranda-CasoLuengo R, Lu J, Meijer WG, Lynn DJ, O' Farrelly C, Meade KG.

BMC Genomics. 2015 Oct 19;16:811. doi: 10.1186/s12864-015-1967-5. Erratum in: BMC Genomics. 2015;16:1050.

24.

CerebralWeb: a Cytoscape.js plug-in to visualize networks stratified by subcellular localization.

Frias S, Bryan K, Brinkman FS, Lynn DJ.

Database (Oxford). 2015 May 7;2015:bav041. doi: 10.1093/database/bav041. Print 2015.

25.

Changes in medical students' exposure to and attitudes about drug company interactions from 2003 to 2012: a multi-institutional follow-up survey.

Sierles FS, Kessler KH, Mintz M, Beck G, Starr S, Lynn DJ, Chao J, Cleary LM, Shore W, Stengel TL, Brodkey AC.

Acad Med. 2015 Aug;90(8):1137-46. doi: 10.1097/ACM.0000000000000686.

PMID:
25785675
26.

MicroRNA profiling of the bovine alveolar macrophage response to Mycobacterium bovis infection suggests pathogen survival is enhanced by microRNA regulation of endocytosis and lysosome trafficking.

Vegh P, Magee DA, Nalpas NC, Bryan K, McCabe MS, Browne JA, Conlon KM, Gordon SV, Bradley DG, MacHugh DE, Lynn DJ.

Tuberculosis (Edinb). 2015 Jan;95(1):60-7.

27.

The Role of microRNAs in Bovine Infection and Immunity.

Lawless N, Vegh P, O'Farrelly C, Lynn DJ.

Front Immunol. 2014 Nov 27;5:611. doi: 10.3389/fimmu.2014.00611. eCollection 2014. Review.

28.

Identification of a human neonatal immune-metabolic network associated with bacterial infection.

Smith CL, Dickinson P, Forster T, Craigon M, Ross A, Khondoker MR, France R, Ivens A, Lynn DJ, Orme J, Jackson A, Lacaze P, Flanagan KL, Stenson BJ, Ghazal P.

Nat Commun. 2014 Aug 14;5:4649. doi: 10.1038/ncomms5649.

29.

The miRNAome of the postpartum dairy cow liver in negative energy balance.

Fatima A, Lynn DJ, O'Boyle P, Seoighe C, Morris D.

BMC Genomics. 2014 Apr 12;15:279. doi: 10.1186/1471-2164-15-279.

30.

MicroRNA regulation of bovine monocyte inflammatory and metabolic networks in an in vivo infection model.

Lawless N, Reinhardt TA, Bryan K, Baker M, Pesch B, Zimmerman D, Zuelke K, Sonstegard T, O'Farrelly C, Lippolis JD, Lynn DJ.

G3 (Bethesda). 2014 Jan 27;4(6):957-71. doi: 10.1534/g3.113.009936.

31.

Pathway-GPS and SIGORA: identifying relevant pathways based on the over-representation of their gene-pair signatures.

Foroushani AB, Brinkman FS, Lynn DJ.

PeerJ. 2013 Dec 19;1:e229. doi: 10.7717/peerj.229. eCollection 2013 Dec 19.

32.

A genome-wide association study for somatic cell score using the Illumina high-density bovine beadchip identifies several novel QTL potentially related to mastitis susceptibility.

Meredith BK, Berry DP, Kearney F, Finlay EK, Fahey AG, Bradley DG, Lynn DJ.

Front Genet. 2013 Nov 6;4:229. doi: 10.3389/fgene.2013.00229. eCollection 2013.

33.

Profiling microRNA expression in bovine alveolar macrophages using RNA-seq.

Vegh P, Foroushani AB, Magee DA, McCabe MS, Browne JA, Nalpas NC, Conlon KM, Gordon SV, Bradley DG, MacHugh DE, Lynn DJ.

Vet Immunol Immunopathol. 2013 Oct 1;155(4):238-44. doi: 10.1016/j.vetimm.2013.08.004. Epub 2013 Aug 24.

PMID:
24021155
34.

Next generation sequencing reveals the expression of a unique miRNA profile in response to a gram-positive bacterial infection.

Lawless N, Foroushani AB, McCabe MS, O'Farrelly C, Lynn DJ.

PLoS One. 2013;8(3):e57543. doi: 10.1371/journal.pone.0057543. Epub 2013 Mar 5.

35.

Messenger RNA sequence rather than protein sequence determines the level of self-synthesis and antigen presentation of the EBV-encoded antigen, EBNA1.

Tellam JT, Lekieffre L, Zhong J, Lynn DJ, Khanna R.

PLoS Pathog. 2012 Dec;8(12):e1003112. doi: 10.1371/journal.ppat.1003112. Epub 2012 Dec 27.

36.

InnateDB: systems biology of innate immunity and beyond--recent updates and continuing curation.

Breuer K, Foroushani AK, Laird MR, Chen C, Sribnaia A, Lo R, Winsor GL, Hancock RE, Brinkman FS, Lynn DJ.

Nucleic Acids Res. 2013 Jan;41(Database issue):D1228-33. doi: 10.1093/nar/gks1147. Epub 2012 Nov 24.

37.

Transcriptomic analysis of the stress response to weaning at housing in bovine leukocytes using RNA-seq technology.

O'Loughlin A, Lynn DJ, McGee M, Doyle S, McCabe M, Earley B.

BMC Genomics. 2012 Jun 18;13:250. doi: 10.1186/1471-2164-13-250.

38.

Effective adjunctive therapy by an innate defense regulatory peptide in a preclinical model of severe malaria.

Achtman AH, Pilat S, Law CW, Lynn DJ, Janot L, Mayer ML, Ma S, Kindrachuk J, Finlay BB, Brinkman FS, Smyth GK, Hancock RE, Schofield L.

Sci Transl Med. 2012 May 23;4(135):135ra64. doi: 10.1126/scitranslmed.3003515.

39.

Protein interaction data curation: the International Molecular Exchange (IMEx) consortium.

Orchard S, Kerrien S, Abbani S, Aranda B, Bhate J, Bidwell S, Bridge A, Briganti L, Brinkman FS, Cesareni G, Chatr-aryamontri A, Chautard E, Chen C, Dumousseau M, Goll J, Hancock RE, Hannick LI, Jurisica I, Khadake J, Lynn DJ, Mahadevan U, Perfetto L, Raghunath A, Ricard-Blum S, Roechert B, Salwinski L, Stümpflen V, Tyers M, Uetz P, Xenarios I, Hermjakob H.

Nat Methods. 2012 Apr;9(4):345-50. doi: 10.1038/nmeth.1931. Erratum in: Nat Methods. 2012 Jun;9(6):626. Brinkman, Fiona [corrected to Brinkman, Fiona S L]; Hancock, Robert [corrected to Hancock, Robert E W].

40.

Genome-wide associations for milk production and somatic cell score in Holstein-Friesian cattle in Ireland.

Meredith BK, Kearney FJ, Finlay EK, Bradley DG, Fahey AG, Berry DP, Lynn DJ.

BMC Genet. 2012 Mar 26;13:21. doi: 10.1186/1471-2156-13-21.

41.

Global gene expression and systems biology analysis of bovine monocyte-derived macrophages in response to in vitro challenge with Mycobacterium bovis.

Magee DA, Taraktsoglou M, Killick KE, Nalpas NC, Browne JA, Park SD, Conlon KM, Lynn DJ, Hokamp K, Gordon SV, Gormley E, MacHugh DE.

PLoS One. 2012;7(2):e32034. doi: 10.1371/journal.pone.0032034. Epub 2012 Feb 22.

42.

Efficacy and safety of an extended nevirapine regimen in infant children of breastfeeding mothers with HIV-1 infection for prevention of postnatal HIV-1 transmission (HPTN 046): a randomised, double-blind, placebo-controlled trial.

Coovadia HM, Brown ER, Fowler MG, Chipato T, Moodley D, Manji K, Musoke P, Stranix-Chibanda L, Chetty V, Fawzi W, Nakabiito C, Msweli L, Kisenge R, Guay L, Mwatha A, Lynn DJ, Eshleman SH, Richardson P, George K, Andrew P, Mofenson LM, Zwerski S, Maldonado Y; HPTN 046 protocol team.

Lancet. 2012 Jan 21;379(9812):221-8. doi: 10.1016/S0140-6736(11)61653-X. Epub 2011 Dec 22.

43.

The human transcriptome during nontyphoid Salmonella and HIV coinfection reveals attenuated NFkappaB-mediated inflammation and persistent cell cycle disruption.

Schreiber F, Lynn DJ, Houston A, Peters J, Mwafulirwa G, Finlay BB, Brinkman FS, Hancock RE, Heyderman RS, Dougan G, Gordon MA.

J Infect Dis. 2011 Oct 15;204(8):1237-45. doi: 10.1093/infdis/jir512.

44.

PSICQUIC and PSISCORE: accessing and scoring molecular interactions.

Aranda B, Blankenburg H, Kerrien S, Brinkman FS, Ceol A, Chautard E, Dana JM, De Las Rivas J, Dumousseau M, Galeota E, Gaulton A, Goll J, Hancock RE, Isserlin R, Jimenez RC, Kerssemakers J, Khadake J, Lynn DJ, Michaut M, O'Kelly G, Ono K, Orchard S, Prieto C, Razick S, Rigina O, Salwinski L, Simonovic M, Velankar S, Winter A, Wu G, Bader GD, Cesareni G, Donaldson IM, Eisenberg D, Kleywegt GJ, Overington J, Ricard-Blum S, Tyers M, Albrecht M, Hermjakob H.

Nat Methods. 2011 Jun 29;8(7):528-9. doi: 10.1038/nmeth.1637. No abstract available.

45.

Bovine proteins containing poly-glutamine repeats are often polymorphic and enriched for components of transcriptional regulatory complexes.

Whan V, Hobbs M, McWilliam S, Lynn DJ, Lutzow YS, Khatkar M, Barendse W, Raadsma H, Tellam RL.

BMC Genomics. 2010 Nov 23;11:654. doi: 10.1186/1471-2164-11-654.

46.

The early whole-blood transcriptional signature of dengue virus and features associated with progression to dengue shock syndrome in Vietnamese children and young adults.

Hoang LT, Lynn DJ, Henn M, Birren BW, Lennon NJ, Le PT, Duong KT, Nguyen TT, Mai LN, Farrar JJ, Hibberd ML, Simmons CP.

J Virol. 2010 Dec;84(24):12982-94. doi: 10.1128/JVI.01224-10. Epub 2010 Oct 13.

47.

The impact of a peer-designed and -led USMLE Step 1 review course: improvement in preparation and scores.

Alcamo AM, Davids AR, Way DP, Lynn DJ, Vandre DD.

Acad Med. 2010 Oct;85(10 Suppl):S45-8. doi: 10.1097/ACM.0b013e3181ed1cb9.

PMID:
20881702
48.

Curating the innate immunity interactome.

Lynn DJ, Chan C, Naseer M, Yau M, Lo R, Sribnaia A, Ring G, Que J, Wee K, Winsor GL, Laird MR, Breuer K, Foroushani AK, Brinkman FS, Hancock RE.

BMC Syst Biol. 2010 Aug 20;4:117. doi: 10.1186/1752-0509-4-117.

49.

The imprinted retrotransposon-like gene PEG11 (RTL1) is expressed as a full-length protein in skeletal muscle from Callipyge sheep.

Byrne K, Colgrave ML, Vuocolo T, Pearson R, Bidwell CA, Cockett NE, Lynn DJ, Fleming-Waddell JN, Tellam RL.

PLoS One. 2010 Jan 8;5(1):e8638. doi: 10.1371/journal.pone.0008638.

50.

Psychotherapy training for residents: reconciling requirements with evidence-based, competency-focused practice.

Weerasekera P, Manring J, Lynn DJ.

Acad Psychiatry. 2010 Jan-Feb;34(1):5-12. doi: 10.1176/appi.ap.34.1.5. Review.

PMID:
20071717

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