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Items: 1 to 50 of 191

1.

A 4-gene signature from histologically normal surgical margins predicts local recurrence in patients with oral carcinoma: clinical validation.

Reis PP, Tokar T, Goswami RS, Xuan Y, Sukhai M, Seneda AL, Móz LES, Perez-Ordonez B, Simpson C, Goldstein D, Brown D, Gilbert R, Gullane P, Irish J, Jurisica I, Kamel-Reid S.

Sci Rep. 2020 Feb 3;10(1):1713. doi: 10.1038/s41598-020-58688-y.

2.

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.

3.

GSOAP: A tool for visualisation of gene set over-representation analysis.

Tokar T, Pastrello C, Jurisica I.

Bioinformatics. 2020 Jan 24. pii: btaa001. doi: 10.1093/bioinformatics/btaa001. [Epub ahead of print]

PMID:
31977031
4.

Epithelial tumor suppressor ELF3 is a lineage-specific amplified oncogene in lung adenocarcinoma.

Enfield KSS, Marshall EA, Anderson C, Ng KW, Rahmati S, Xu Z, Fuller M, Milne K, Lu D, Shi R, Rowbotham DA, Becker-Santos DD, Johnson FD, English JC, MacAulay CE, Lam S, Lockwood WW, Chari R, Karsan A, Jurisica I, Lam WL.

Nat Commun. 2019 Nov 28;10(1):5438. doi: 10.1038/s41467-019-13295-y.

5.

pathDIP 4: an extended pathway annotations and enrichment analysis resource for human, model organisms and domesticated species.

Rahmati S, Abovsky M, Pastrello C, Kotlyar M, Lu R, Cumbaa CA, Rahman P, Chandran V, Jurisica I.

Nucleic Acids Res. 2020 Jan 8;48(D1):D479-D488. doi: 10.1093/nar/gkz989.

PMID:
31733064
6.

Informed Use of Protein-Protein Interaction Data: A Focus on the Integrated Interactions Database (IID).

Pastrello C, Kotlyar M, Jurisica I.

Methods Mol Biol. 2020;2074:125-134. doi: 10.1007/978-1-4939-9873-9_10.

PMID:
31583635
7.

Why imaging data alone is not enough: AI-based integration of imaging, omics, and clinical data.

Holzinger A, Haibe-Kains B, Jurisica I.

Eur J Nucl Med Mol Imaging. 2019 Dec;46(13):2722-2730. doi: 10.1007/s00259-019-04382-9. Epub 2019 Jun 15.

PMID:
31203421
8.

Immune-enrichment of non-small cell lung cancer baseline biopsies for multiplex profiling define prognostic immune checkpoint combinations for patient stratification.

Monette A, Bergeron D, Ben Amor A, Meunier L, Caron C, Mes-Masson AM, Kchir N, Hamzaoui K, Jurisica I, Lapointe R.

J Immunother Cancer. 2019 Mar 28;7(1):86. doi: 10.1186/s40425-019-0544-x.

9.

Failed immune responses across multiple pathologies share pan-tumor and circulating lymphocytic targets.

Monette A, Morou A, Al-Banna NA, Rousseau L, Lattouf JB, Rahmati S, Tokar T, Routy JP, Cailhier JF, Kaufmann DE, Jurisica I, Lapointe R.

J Clin Invest. 2019 Mar 26;129(6):2463-2479. doi: 10.1172/JCI125301.

10.

Publisher Correction: Capturing variation impact on molecular interactions in the IMEx Consortium mutations data set.

IMEx Consortium contributing authors, Del-Toro N, Duesbury M, Koch M, Perfetto L, Shrivastava A, Ochoa D, Wagih O, Piñero J, Kotlyar M, Pastrello C, Beltrao P, Furlong LI, Jurisica I, Hermjakob H, Orchard S, Porras P.

Nat Commun. 2019 Mar 4;10(1):1098. doi: 10.1038/s41467-019-08814-w.

11.

Urine Angiotensin II Signature Proteins as Markers of Fibrosis in Kidney Transplant Recipients.

Mohammed-Ali Z, Tokar T, Batruch I, Reid S, Tavares-Brum A, Yip P, Cardinal H, Hébert MJ, Li Y, Kim SJ, Jurisica I, John R, Konvalinka A.

Transplantation. 2019 Jun;103(6):e146-e158. doi: 10.1097/TP.0000000000002676.

PMID:
30801542
12.

A stemness screen reveals C3orf54/INKA1 as a promoter of human leukemia stem cell latency.

Kaufmann KB, Garcia-Prat L, Liu Q, Ng SWK, Takayanagi SI, Mitchell A, Wienholds E, van Galen P, Cumbaa CA, Tsay MJ, Pastrello C, Wagenblast E, Krivdova G, Minden MD, Lechman ER, Zandi S, Jurisica I, Wang JCY, Xie SZ, Dick JE.

Blood. 2019 May 16;133(20):2198-2211. doi: 10.1182/blood-2018-10-881441. Epub 2019 Feb 22.

PMID:
30796022
13.

TP53 mutations in high grade serous ovarian cancer and impact on clinical outcomes: a comparison of next generation sequencing and bioinformatics analyses.

Mandilaras V, Garg S, Cabanero M, Tan Q, Pastrello C, Burnier J, Karakasis K, Wang L, Dhani NC, Butler MO, Bedard PL, Siu LL, Clarke B, Shaw PA, Stockley T, Jurisica I, Oza AM, Lheureux S.

Int J Gynecol Cancer. 2019 Jan 18. pii: ijgc-2018-000087. doi: 10.1136/ijgc-2018-000087. [Epub ahead of print]

PMID:
30659026
14.

Capturing variation impact on molecular interactions in the IMEx Consortium mutations data set.

IMEx Consortium Curators, Del-Toro N, Duesbury M, Koch M, Perfetto L, Shrivastava A, Ochoa D, Wagih O, Piñero J, Kotlyar M, Pastrello C, Beltrao P, Furlong LI, Jurisica I, Hermjakob H, Orchard S, Porras P.

Nat Commun. 2019 Jan 2;10(1):10. doi: 10.1038/s41467-018-07709-6. Erratum in: Nat Commun. 2019 Mar 4;10(1):1098.

15.

IID 2018 update: context-specific physical protein-protein interactions in human, model organisms and domesticated species.

Kotlyar M, Pastrello C, Malik Z, Jurisica I.

Nucleic Acids Res. 2019 Jan 8;47(D1):D581-D589. doi: 10.1093/nar/gky1037.

16.

Ubiquitin ligase RNF8 suppresses Notch signaling to regulate mammary development and tumorigenesis.

Li L, Guturi KKN, Gautreau B, Patel PS, Saad A, Morii M, Mateo F, Palomero L, Barbour H, Gomez A, Ng D, Kotlyar M, Pastrello C, Jackson HW, Khokha R, Jurisica I, Affar EB, Raught B, Sanchez O, Alaoui-Jamali M, Pujana MA, Hakem A, Hakem R.

J Clin Invest. 2018 Oct 1;128(10):4525-4542. doi: 10.1172/JCI120401. Epub 2018 Aug 2.

17.

The complex landscape of microRNAs in articular cartilage: biology, pathology, and therapeutic targets.

Endisha H, Rockel J, Jurisica I, Kapoor M.

JCI Insight. 2018 Sep 6;3(17). pii: 121630. doi: 10.1172/jci.insight.121630. eCollection 2018 Sep 6. Review.

18.

Therapeutic Targeting of the Premetastatic Stage in Human Lung-to-Brain Metastasis.

Singh M, Venugopal C, Tokar T, McFarlane N, Subapanditha MK, Qazi M, Bakhshinyan D, Vora P, Murty NK, Jurisica I, Singh SK.

Cancer Res. 2018 Sep 1;78(17):5124-5134. doi: 10.1158/0008-5472.CAN-18-1022. Epub 2018 Jul 9.

19.

Citrobacter rodentium alters the mouse colonic miRNome.

Wen B, Tokar T, Taibi A, Chen J, Jurisica I, Comelli EM.

Genes Immun. 2019 Mar;20(3):207-213. doi: 10.1038/s41435-018-0026-z. Epub 2018 May 1.

PMID:
29728609
20.

In silico cancer research towards 3R.

Jean-Quartier C, Jeanquartier F, Jurisica I, Holzinger A.

BMC Cancer. 2018 Apr 12;18(1):408. doi: 10.1186/s12885-018-4302-0. Review.

21.

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.

22.

Large-scale discovery of previously undetected microRNAs specific to human liver.

Minatel BC, Martinez VD, Ng KW, Sage AP, Tokar T, Marshall EA, Anderson C, Enfield KSS, Stewart GL, Reis PP, Jurisica I, Lam WL.

Hum Genomics. 2018 Mar 27;12(1):16. doi: 10.1186/s40246-018-0148-4.

23.

Differentially expressed microRNAs in lung adenocarcinoma invert effects of copy number aberrations of prognostic genes.

Tokar T, Pastrello C, Ramnarine VR, Zhu CQ, Craddock KJ, Pikor LA, Vucic EA, Vary S, Shepherd FA, Tsao MS, Lam WL, Jurisica I.

Oncotarget. 2018 Jan 8;9(10):9137-9155. doi: 10.18632/oncotarget.24070. eCollection 2018 Feb 6.

24.

The ablation of the matricellular protein EMILIN2 causes defective vascularization due to impaired EGFR-dependent IL-8 production affecting tumor growth.

Paulitti A, Andreuzzi E, Bizzotto D, Pellicani R, Tarticchio G, Marastoni S, Pastrello C, Jurisica I, Ligresti G, Bucciotti F, Doliana R, Colladel R, Braghetta P, Poletto E, Di Silvestre A, Bressan G, Colombatti A, Bonaldo P, Mongiat M.

Oncogene. 2018 Jun;37(25):3399-3414. doi: 10.1038/s41388-017-0107-x. Epub 2018 Feb 27.

PMID:
29483644
25.

Prediction of Protein-Protein Interactions.

Kotlyar M, Rossos AEM, Jurisica I.

Curr Protoc Bioinformatics. 2017 Dec 8;60:8.2.1-8.2.14. doi: 10.1002/cpbi.38. Review.

PMID:
29220074
26.

mirDIP 4.1-integrative database of human microRNA target predictions.

Tokar T, Pastrello C, Rossos AEM, Abovsky M, Hauschild AC, Tsay M, Lu R, Jurisica I.

Nucleic Acids Res. 2018 Jan 4;46(D1):D360-D370. doi: 10.1093/nar/gkx1144.

27.

RNAi screen identifies essential regulators of human brain metastasis-initiating cells.

Singh M, Venugopal C, Tokar T, Brown KR, McFarlane N, Bakhshinyan D, Vijayakumar T, Manoranjan B, Mahendram S, Vora P, Qazi M, Dhillon M, Tong A, Durrer K, Murty N, Hallet R, Hassell JA, Kaplan DR, Cutz JC, Jurisica I, Moffat J, Singh SK.

Acta Neuropathol. 2017 Dec;134(6):923-940. doi: 10.1007/s00401-017-1757-z. Epub 2017 Aug 1.

PMID:
28766011
28.

Modeling tumor progression via the comparison of stage-specific graphs.

Wong SWH, Pastrello C, Kotlyar M, Faloutsos C, Jurisica I.

Methods. 2018 Jan 1;132:34-41. doi: 10.1016/j.ymeth.2017.06.033. Epub 2017 Jul 3.

PMID:
28684340
29.

Retraction: Circulating plant miRNAs can regulate human gene expression in vitro.

Pastrello C, Tsay M, McQuaid R, Abovsky M, Pasini E, Shirdel E, Angeli M, Tokar T, Jamnik J, Kotlyar M, Jurisicova A, Kotsopoulos J, El-Sohemy A, Jurisica I.

Sci Rep. 2017 May 22;7:46826. doi: 10.1038/srep46826.

30.

HABP2 p.G534E variant in patients with family history of thyroid and breast cancer.

Pinheiro M, Drigo SA, Tonhosolo R, Andrade SCS, Marchi FA, Jurisica I, Kowalski LP, Achatz MI, Rogatto SR.

Oncotarget. 2017 Jun 20;8(25):40896-40905. doi: 10.18632/oncotarget.16639.

31.

Systematic protein-protein interaction mapping for clinically relevant human GPCRs.

Sokolina K, Kittanakom S, Snider J, Kotlyar M, Maurice P, Gandía J, Benleulmi-Chaachoua A, Tadagaki K, Oishi A, Wong V, Malty RH, Deineko V, Aoki H, Amin S, Yao Z, Morató X, Otasek D, Kobayashi H, Menendez J, Auerbach D, Angers S, Pržulj N, Bouvier M, Babu M, Ciruela F, Jockers R, Jurisica I, Stagljar I.

Mol Syst Biol. 2017 Mar 15;13(3):918. doi: 10.15252/msb.20167430.

32.

Position- and Hippo signaling-dependent plasticity during lineage segregation in the early mouse embryo.

Posfai E, Petropoulos S, de Barros FRO, Schell JP, Jurisica I, Sandberg R, Lanner F, Rossant J.

Elife. 2017 Feb 22;6. pii: e22906. doi: 10.7554/eLife.22906.

33.

An Integrated Approach Identifies Mediators of Local Recurrence in Head and Neck Squamous Carcinoma.

Citron F, Armenia J, Franchin G, Polesel J, Talamini R, D'Andrea S, Sulfaro S, Croce CM, Klement W, Otasek D, Pastrello C, Tokar T, Jurisica I, French D, Bomben R, Vaccher E, Serraino D, Belletti B, Vecchione A, Barzan L, Baldassarre G.

Clin Cancer Res. 2017 Jul 15;23(14):3769-3780. doi: 10.1158/1078-0432.CCR-16-2814. Epub 2017 Feb 7.

34.

A Global Analysis of the Receptor Tyrosine Kinase-Protein Phosphatase Interactome.

Yao Z, Darowski K, St-Denis N, Wong V, Offensperger F, Villedieu A, Amin S, Malty R, Aoki H, Guo H, Xu Y, Iorio C, Kotlyar M, Emili A, Jurisica I, Neel BG, Babu M, Gingras AC, Stagljar I.

Mol Cell. 2017 Jan 19;65(2):347-360. doi: 10.1016/j.molcel.2016.12.004. Epub 2017 Jan 5.

35.

Systematic Identification of Oncogenic EGFR Interaction Partners.

Petschnigg J, Kotlyar M, Blair L, Jurisica I, Stagljar I, Ketteler R.

J Mol Biol. 2017 Jan 20;429(2):280-294. doi: 10.1016/j.jmb.2016.12.006. Epub 2016 Dec 9.

36.

pathDIP: an annotated resource for known and predicted human gene-pathway associations and pathway enrichment analysis.

Rahmati S, Abovsky M, Pastrello C, Jurisica I.

Nucleic Acids Res. 2017 Jan 4;45(D1):D419-D426. doi: 10.1093/nar/gkw1082. Epub 2016 Nov 28.

37.

Molecular heterogeneity of non-small cell lung carcinoma patient-derived xenografts closely reflect their primary tumors.

Wang D, Pham NA, Tong J, Sakashita S, Allo G, Kim L, Yanagawa N, Raghavan V, Wei Y, To C, Trinh QM, Starmans MH, Chan-Seng-Yue MA, Chadwick D, Li L, Zhu CQ, Liu N, Li M, Lee S, Ignatchenko V, Strumpf D, Taylor P, Moghal N, Liu G, Boutros PC, Kislinger T, Pintilie M, Jurisica I, Shepherd FA, McPherson JD, Muthuswamy L, Moran MF, Tsao MS.

Int J Cancer. 2017 Feb 1;140(3):662-673. doi: 10.1002/ijc.30472. Epub 2016 Nov 7.

38.

Identification of microRNA-181a-5p and microRNA-4454 as mediators of facet cartilage degeneration.

Nakamura A, Rampersaud YR, Sharma A, Lewis SJ, Wu B, Datta P, Sundararajan K, Endisha H, Rossomacha E, Rockel JS, Jurisica I, Kapoor M.

JCI Insight. 2016 Aug 4;1(12):e86820. doi: 10.1172/jci.insight.86820.

39.

Circulating plant miRNAs can regulate human gene expression in vitro.

Pastrello C, Tsay M, McQuaid R, Abovsky M, Pasini E, Shirdel E, Angeli M, Tokar T, Jamnik J, Kotlyar M, Jurisicova A, Kotsopoulos J, El-Sohemy A, Jurisica I.

Sci Rep. 2016 Sep 8;6:32773. doi: 10.1038/srep32773. Retraction in: Sci Rep. 2017 May 22;7:46826.

40.

Reduced BRCA1 transcript levels in freshly isolated blood leukocytes from BRCA1 mutation carriers is mutation specific.

Chehade R, Pettapiece-Phillips R, Salmena L, Kotlyar M, Jurisica I, Narod SA, Akbari MR, Kotsopoulos J.

Breast Cancer Res. 2016 Aug 17;18(1):87. doi: 10.1186/s13058-016-0739-8.

41.

Quantification of angiotensin II-regulated proteins in urine of patients with polycystic and other chronic kidney diseases by selected reaction monitoring.

Konvalinka A, Batruch I, Tokar T, Dimitromanolakis A, Reid S, Song X, Pei Y, Drabovich AP, Diamandis EP, Jurisica I, Scholey JW.

Clin Proteomics. 2016 Aug 5;13:16. doi: 10.1186/s12014-016-9117-x. eCollection 2016.

42.

Fibrillin-1 (FBN-1) a new marker of germ cell neoplasia in situ.

Cierna Z, Mego M, Jurisica I, Machalekova K, Chovanec M, Miskovska V, Svetlovska D, Kalavska K, Rejlekova K, Kajo K, Mardiak J, Babal P.

BMC Cancer. 2016 Aug 4;16:597. doi: 10.1186/s12885-016-2644-z.

43.

Developmental transcription factor NFIB is a putative target of oncofetal miRNAs and is associated with tumour aggressiveness in lung adenocarcinoma.

Becker-Santos DD, Thu KL, English JC, Pikor LA, Martinez VD, Zhang M, Vucic EA, Luk MT, Carraro A, Korbelik J, Piga D, Lhomme NM, Tsay MJ, Yee J, MacAulay CE, Lam S, Lockwood WW, Robinson WP, Jurisica I, Lam WL.

J Pathol. 2016 Oct;240(2):161-72. doi: 10.1002/path.4765. Epub 2016 Sep 19.

PMID:
27357447
44.

MYC interaction with the tumor suppressive SWI/SNF complex member INI1 regulates transcription and cellular transformation.

Stojanova A, Tu WB, Ponzielli R, Kotlyar M, Chan PK, Boutros PC, Khosravi F, Jurisica I, Raught B, Penn LZ.

Cell Cycle. 2016 Jul 2;15(13):1693-705. doi: 10.1080/15384101.2016.1146836. Epub 2016 Jun 7.

45.

Identification of synovial fluid microRNA signature in knee osteoarthritis: differentiating early- and late-stage knee osteoarthritis.

Li YH, Tavallaee G, Tokar T, Nakamura A, Sundararajan K, Weston A, Sharma A, Mahomed NN, Gandhi R, Jurisica I, Kapoor M.

Osteoarthritis Cartilage. 2016 Sep;24(9):1577-86. doi: 10.1016/j.joca.2016.04.019. Epub 2016 Apr 30.

46.

Integrative transcriptome analysis identifies deregulated microRNA-transcription factor networks in lung adenocarcinoma.

Cinegaglia NC, Andrade SC, Tokar T, Pinheiro M, Severino FE, Oliveira RA, Hasimoto EN, Cataneo DC, Cataneo AJ, Defaveri J, Souza CP, Marques MM, Carvalho RF, Coutinho LL, Gross JL, Rogatto SR, Lam WL, Jurisica I, Reis PP.

Oncotarget. 2016 May 17;7(20):28920-34. doi: 10.18632/oncotarget.8713.

47.

Robust quantitative scratch assay.

Vargas A, Angeli M, Pastrello C, McQuaid R, Li H, Jurisicova A, Jurisica I.

Bioinformatics. 2016 May 1;32(9):1439-40. doi: 10.1093/bioinformatics/btv746. Epub 2015 Dec 31.

48.

Fundamentals of protein interaction network mapping.

Snider J, Kotlyar M, Saraon P, Yao Z, Jurisica I, Stagljar I.

Mol Syst Biol. 2015 Dec 17;11(12):848. doi: 10.15252/msb.20156351. Review.

49.

Uninterrupted Sedentary Behavior Downregulates BRCA1 Gene Expression.

Pettapiece-Phillips R, Kotlyar M, Chehade R, Salmena L, Narod SA, Akbari M, Jurisica I, Kotsopoulos J.

Cancer Prev Res (Phila). 2016 Jan;9(1):83-8. doi: 10.1158/1940-6207.CAPR-15-0291. Epub 2015 Nov 2.

50.

Integrated interactions database: tissue-specific view of the human and model organism interactomes.

Kotlyar M, Pastrello C, Sheahan N, Jurisica I.

Nucleic Acids Res. 2016 Jan 4;44(D1):D536-41. doi: 10.1093/nar/gkv1115. Epub 2015 Oct 29.

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