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Items: 1 to 50 of 74

1.

Using consumer-wearable technology for remote assessment of physiological response to stress in the naturalistic environment.

Pakhomov SVS, Thuras PD, Finzel R, Eppel J, Kotlyar M.

PLoS One. 2020 Mar 25;15(3):e0229942. doi: 10.1371/journal.pone.0229942. eCollection 2020.

2.

Relationships between the Nicotine Metabolite Ratio and a Panel of Exposure and Effect Biomarkers: Findings from Two Studies of U.S. Commercial Cigarette Smokers.

Carroll DM, Murphy SE, Benowitz NL, Strasser AA, Kotlyar M, Hecht SS, Carmella SG, McClernon FJ, Pacek LR, Dermody SS, Vandrey RG, Donny EC, Hatsukami DK.

Cancer Epidemiol Biomarkers Prev. 2020 Apr;29(4):871-879. doi: 10.1158/1055-9965.EPI-19-0644. Epub 2020 Feb 12.

PMID:
32051195
3.

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.

4.

Effects of Very Low Nicotine Content Cigarettes on Smoking Behavior and Biomarkers of Exposure in Menthol and Non-menthol Smokers.

Denlinger-Apte RL, Kotlyar M, Koopmeiners JS, Tidey JW, Luo X, Benowitz NL, Jensen JA, Ikuemonisan JO, Pacek LR, Smith TT, Vandrey R, Donny EC, Hatsukami DK.

Nicotine Tob Res. 2019 Dec 23;21(Suppl 1):S63-S72. doi: 10.1093/ntr/ntz160.

5.

Effect of nicotine lozenge use prior to smoking cue presentation on craving and withdrawal symptom severity.

Kotlyar M, Vogel RI, Dufresne SR, Mills AM, Vuchetich JP.

Drug Alcohol Depend. 2020 Jan 1;206:107706. doi: 10.1016/j.drugalcdep.2019.107706. Epub 2019 Nov 2.

PMID:
31757519
6.

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
7.

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
8.

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.

9.

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.

10.

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.

11.

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.

12.

Effects of smoking and paroxetine on stress-induced craving and withdrawal symptoms.

Kotlyar M, Chau HT, Thuras P.

J Subst Use. 2018;23(6):655-659. doi: 10.1080/14659891.2018.1489008. Epub 2018 Jul 6.

13.

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
14.

Tight focusing of laser light using a chromium Fresnel zone plate.

Kotlyar VV, Stafeev SS, Nalimov AG, Kotlyar MV, O'Faolain L, Kozlova ES.

Opt Express. 2017 Aug 21;25(17):19662-19671. doi: 10.1364/OE.25.019662.

PMID:
29041654
15.

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
16.

Sex differences in physiological response to the combination of stress and smoking.

Kotlyar M, Thuras P, Hatsukami DK, al'Absi M.

Int J Psychophysiol. 2017 Aug;118:27-31. doi: 10.1016/j.ijpsycho.2017.05.008. Epub 2017 May 23.

17.

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.

18.

Thin high numerical aperture metalens.

Kotlyar VV, Nalimov AG, Stafeev SS, Hu C, O'Faolain L, Kotlyar MV, Gibson D, Song S.

Opt Express. 2017 Apr 3;25(7):8158-8167. doi: 10.1364/OE.25.008158.

PMID:
28380931
19.

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.

20.

Timing of nicotine lozenge administration to minimize trigger induced craving and withdrawal symptoms.

Kotlyar M, Lindgren BR, Vuchetich JP, Le C, Mills AM, Amiot E, Hatsukami DK.

Addict Behav. 2017 Aug;71:18-24. doi: 10.1016/j.addbeh.2017.02.018. Epub 2017 Feb 10.

21.

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.

22.

Microlens-aided focusing of linearly and azimuthally polarized laser light.

Stafeev SS, Nalimov AG, Kotlyar MV, Gibson D, Song S, O'Faolain L, Kotlyar VV.

Opt Express. 2016 Dec 26;24(26):29800-29813. doi: 10.1364/OE.24.029800.

PMID:
28059366
23.

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.

24.

Use of an automated mobile application to assess effects of nicotine withdrawal on verbal fluency: A pilot study.

Pakhomov SV, Teeple W, Mills AM, Kotlyar M.

Exp Clin Psychopharmacol. 2016 Oct;24(5):341-347. Epub 2016 Aug 15.

25.

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.

26.

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.

27.

Subwavelength micropolarizer in a gold film for visible light.

Kotlyar VV, Stafeev SS, Kotlyar MV, Nalimov AG, Faolain LO.

Appl Opt. 2016 Jul 1;55(19):5025-32. doi: 10.1364/AO.55.005025.

PMID:
27409186
28.

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.

29.

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.

30.

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.

31.

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.

32.

Prioritizing therapeutics for lung cancer: an integrative meta-analysis of cancer gene signatures and chemogenomic data.

Fortney K, Griesman J, Kotlyar M, Pastrello C, Angeli M, Sound-Tsao M, Jurisica I.

PLoS Comput Biol. 2015 Mar 18;11(3):e1004068. doi: 10.1371/journal.pcbi.1004068. eCollection 2015 Mar.

33.

In silico prediction of physical protein interactions and characterization of interactome orphans.

Kotlyar M, Pastrello C, Pivetta F, Lo Sardo A, Cumbaa C, Li H, Naranian T, Niu Y, Ding Z, Vafaee F, Broackes-Carter F, Petschnigg J, Mills GB, Jurisicova A, Stagljar I, Maestro R, Jurisica I.

Nat Methods. 2015 Jan;12(1):79-84. doi: 10.1038/nmeth.3178. Epub 2014 Nov 17.

PMID:
25402006
34.

The mammalian-membrane two-hybrid assay (MaMTH) for probing membrane-protein interactions in human cells.

Petschnigg J, Groisman B, Kotlyar M, Taipale M, Zheng Y, Kurat CF, Sayad A, Sierra JR, Mattiazzi Usaj M, Snider J, Nachman A, Krykbaeva I, Tsao MS, Moffat J, Pawson T, Lindquist S, Jurisica I, Stagljar I.

Nat Methods. 2014 May;11(5):585-92. doi: 10.1038/nmeth.2895. Epub 2014 Mar 23.

PMID:
24658140
35.

CHIP-MYTH: a novel interactive proteomics method for the assessment of agonist-dependent interactions of the human β₂-adrenergic receptor.

Kittanakom S, Barrios-Rodiles M, Petschnigg J, Arnoldo A, Wong V, Kotlyar M, Heisler LE, Jurisica I, Wrana JL, Nislow C, Stagljar I.

Biochem Biophys Res Commun. 2014 Mar 21;445(4):746-56. doi: 10.1016/j.bbrc.2014.02.033. Epub 2014 Feb 19.

PMID:
24561123
36.

Integration, visualization and analysis of human interactome.

Pastrello C, Pasini E, Kotlyar M, Otasek D, Wong S, Sangrar W, Rahmati S, Jurisica I.

Biochem Biophys Res Commun. 2014 Mar 21;445(4):757-73. doi: 10.1016/j.bbrc.2014.01.151. Epub 2014 Feb 1. Review.

PMID:
24491561
37.

Effect of paroxetine on physiological response to stress and smoking.

Kotlyar M, al'Absi M, Thuras P, Vuchetich JP, Adson DE, Nowack AL, Hatsukami DK.

Psychosom Med. 2013 Apr;75(3):236-43. doi: 10.1097/PSY.0b013e3182898f6d. Epub 2013 Mar 15.

38.

NetwoRx: connecting drugs to networks and phenotypes in Saccharomyces cerevisiae.

Fortney K, Xie W, Kotlyar M, Griesman J, Kotseruba Y, Jurisica I.

Nucleic Acids Res. 2013 Jan;41(Database issue):D720-7. doi: 10.1093/nar/gks1106. Epub 2012 Nov 29.

39.

Menstrual phase and depressive symptoms differences in physiological response to nicotine following acute smoking abstinence.

Allen SS, Allen AM, Kotlyar M, Lunos S, Al'absi M, Hatsukami D.

Nicotine Tob Res. 2013 Jun;15(6):1091-8. doi: 10.1093/ntr/nts236. Epub 2012 Nov 15.

40.

Network-based characterization of drug-regulated genes, drug targets, and toxicity.

Kotlyar M, Fortney K, Jurisica I.

Methods. 2012 Aug;57(4):499-507. doi: 10.1016/j.ymeth.2012.06.003. Epub 2012 Jun 27. Review.

41.

In silico drug screen in mouse liver identifies candidate calorie restriction mimetics.

Fortney K, Morgen EK, Kotlyar M, Jurisica I.

Rejuvenation Res. 2012 Apr;15(2):148-52. doi: 10.1089/rej.2011.1263.

PMID:
22533420
42.

Effect of stress and bupropion on craving, withdrawal symptoms, and mood in smokers.

Kotlyar M, Drone D, Thuras P, Hatsukami DK, Brauer L, Adson DE, al'Absi M.

Nicotine Tob Res. 2011 Jun;13(6):492-7. doi: 10.1093/ntr/ntr011. Epub 2011 Mar 4.

43.

Effect of oral snus and medicinal nicotine in smokers on toxicant exposure and withdrawal symptoms: a feasibility study.

Kotlyar M, Hertsgaard LA, Lindgren BR, Jensen JA, Carmella SG, Stepanov I, Murphy SE, Hecht SS, Hatsukami DK.

Cancer Epidemiol Biomarkers Prev. 2011 Jan;20(1):91-100. doi: 10.1158/1055-9965.EPI-10-0349. Epub 2010 Nov 10. Erratum in: Cancer Epidemiol Biomarkers Prev. 2011 May;20(5):1048.

44.

Inferring the functions of longevity genes with modular subnetwork biomarkers of Caenorhabditis elegans aging.

Fortney K, Kotlyar M, Jurisica I.

Genome Biol. 2010;11(2):R13. doi: 10.1186/gb-2010-11-2-r13. Epub 2010 Feb 3.

45.

Reduced nicotine content cigarettes: effects on toxicant exposure, dependence and cessation.

Hatsukami DK, Kotlyar M, Hertsgaard LA, Zhang Y, Carmella SG, Jensen JA, Allen SS, Shields PG, Murphy SE, Stepanov I, Hecht SS.

Addiction. 2010 Feb;105(2):343-55. doi: 10.1111/j.1360-0443.2009.02780.x.

46.

Photonic crystal lens for coupling two waveguides.

Kotlyar MI, Triandaphilov YR, Kovalev AA, Soifer VA, Kotlyar MV, O'Faolain L.

Appl Opt. 2009 Jul 1;48(19):3722-30.

PMID:
19571929
47.

Comparative systems biology of human and mouse as a tool to guide the modeling of human placental pathology.

Cox B, Kotlyar M, Evangelou AI, Ignatchenko V, Ignatchenko A, Whiteley K, Jurisica I, Adamson SL, Rossant J, Kislinger T.

Mol Syst Biol. 2009;5:279. doi: 10.1038/msb.2009.37. Epub 2009 Jun 16.

48.

Physiological response to a speech stressor presented in a virtual reality environment.

Kotlyar M, Donahue C, Thuras P, Kushner MG, O'Gorman N, Smith EA, Adson DE.

Psychophysiology. 2008 Nov;45(6):1034-7. doi: 10.1111/j.1469-8986.2008.00690.x. Epub 2008 Sep 4.

PMID:
18778321
49.

Developing the science base for reducing tobacco harm.

Hatsukami DK, Joseph AM, Lesage M, Jensen J, Murphy SE, Pentel PR, Kotlyar M, Borgida E, Le C, Hecht SS.

Nicotine Tob Res. 2007 Nov;9 Suppl 4:S537-53. doi: 10.1080/14622200701679040. Review.

50.

Effect of selective serotonin reuptake inhibitors on cardiovascular morbidity and mortality.

Von Ruden AE, Adson DE, Kotlyar M.

J Cardiovasc Pharmacol Ther. 2008 Mar;13(1):32-40. doi: 10.1177/1074248407308467. Review.

PMID:
18287588

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