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Items: 28

1.

Chemogenomic model identifies synergistic drug combinations robust to the pathogen microenvironment.

Cokol M, Li C, Chandrasekaran S.

PLoS Comput Biol. 2018 Dec 31;14(12):e1006677. doi: 10.1371/journal.pcbi.1006677. eCollection 2018 Dec.

2.

Modeling the impact of drug interactions on therapeutic selectivity.

Weinstein ZB, Kuru N, Kiriakov S, Palmer AC, Khalil AS, Clemons PA, Zaman MH, Roth FP, Cokol M.

Nat Commun. 2018 Aug 27;9(1):3452. doi: 10.1038/s41467-018-05954-3.

3.

Diagonal Method to Measure Synergy Among Any Number of Drugs.

Cokol-Cakmak M, Bakan F, Cetiner S, Cokol M.

J Vis Exp. 2018 Jun 21;(136). doi: 10.3791/57713.

4.

A Parallel Adder Coordinates Mycobacterial Cell-Cycle Progression and Cell-Size Homeostasis in the Context of Asymmetric Growth and Organization.

Logsdon MM, Ho PY, Papavinasasundaram K, Richardson K, Cokol M, Sassetti CM, Amir A, Aldridge BB.

Curr Biol. 2017 Nov 6;27(21):3367-3374.e7. doi: 10.1016/j.cub.2017.09.046. Epub 2017 Oct 26.

5.

Efficient measurement and factorization of high-order drug interactions in Mycobacterium tuberculosis.

Cokol M, Kuru N, Bicak E, Larkins-Ford J, Aldridge BB.

Sci Adv. 2017 Oct 11;3(10):e1701881. doi: 10.1126/sciadv.1701881. eCollection 2017 Oct.

6.

Synthesis and characterization of amino acid-functionalized calcium phosphate nanoparticles for siRNA delivery.

Bakan F, Kara G, Cokol Cakmak M, Cokol M, Denkbas EB.

Colloids Surf B Biointerfaces. 2017 Oct 1;158:175-181. doi: 10.1016/j.colsurfb.2017.06.028. Epub 2017 Jun 27.

PMID:
28689100
7.

Prediction of Antibiotic Interactions Using Descriptors Derived from Molecular Structure.

Mason DJ, Stott I, Ashenden S, Weinstein ZB, Karakoc I, Meral S, Kuru N, Bender A, Cokol M.

J Med Chem. 2017 May 11;60(9):3902-3912. doi: 10.1021/acs.jmedchem.7b00204. Epub 2017 Apr 27.

PMID:
28383902
8.

Synergistic activity of vorinostat combined with gefitinib but not with sorafenib in mutant KRAS human non-small cell lung cancers and hepatocarcinoma.

Jeannot V, Busser B, Vanwonterghem L, Michallet S, Ferroudj S, Cokol M, Coll JL, Ozturk M, Hurbin A.

Onco Targets Ther. 2016 Nov 9;9:6843-6855. eCollection 2016.

9.

Temporal and intrinsic factors of rifampicin tolerance in mycobacteria.

Richardson K, Bennion OT, Tan S, Hoang AN, Cokol M, Aldridge BB.

Proc Natl Acad Sci U S A. 2016 Jul 19;113(29):8302-7. doi: 10.1073/pnas.1600372113. Epub 2016 Jun 29.

10.

Chemogenomics and orthology-based design of antibiotic combination therapies.

Chandrasekaran S, Cokol-Cakmak M, Sahin N, Yilancioglu K, Kazan H, Collins JJ, Cokol M.

Mol Syst Biol. 2016 May 24;12(5):872. doi: 10.15252/msb.20156777.

11.

Harnessing Connectivity in a Large-Scale Small-Molecule Sensitivity Dataset.

Seashore-Ludlow B, Rees MG, Cheah JH, Cokol M, Price EV, Coletti ME, Jones V, Bodycombe NE, Soule CK, Gould J, Alexander B, Li A, Montgomery P, Wawer MJ, Kuru N, Kotz JD, Hon CS, Munoz B, Liefeld T, Dančík V, Bittker JA, Palmer M, Bradner JE, Shamji AF, Clemons PA, Schreiber SL.

Cancer Discov. 2015 Nov;5(11):1210-23. doi: 10.1158/2159-8290.CD-15-0235. Epub 2015 Oct 19.

12.

Modelling of compound combination effects and applications to efficacy and toxicity: state-of-the-art, challenges and perspectives.

Bulusu KC, Guha R, Mason DJ, Lewis RP, Muratov E, Kalantar Motamedi Y, Cokol M, Bender A.

Drug Discov Today. 2016 Feb;21(2):225-38. doi: 10.1016/j.drudis.2015.09.003. Epub 2015 Sep 7. Review.

13.

Target-independent prediction of drug synergies using only drug lipophilicity.

Yilancioglu K, Weinstein ZB, Meydan C, Akhmetov A, Toprak I, Durmaz A, Iossifov I, Kazan H, Roth FP, Cokol M.

J Chem Inf Model. 2014 Aug 25;54(8):2286-93. doi: 10.1021/ci500276x. Epub 2014 Aug 1.

14.

Strength of selection pressure is an important parameter contributing to the complexity of antibiotic resistance evolution.

Oz T, Guvenek A, Yildiz S, Karaboga E, Tamer YT, Mumcuyan N, Ozan VB, Senturk GH, Cokol M, Yeh P, Toprak E.

Mol Biol Evol. 2014 Sep;31(9):2387-401. doi: 10.1093/molbev/msu191. Epub 2014 Jun 24.

15.

A drug similarity network for understanding drug mechanism of action.

Karabulut NP, Akhmedov M, Cokol M.

J Bioinform Comput Biol. 2014 Apr;12(2):1441007. doi: 10.1142/S0219720014410078. Epub 2014 Mar 31.

PMID:
24712534
16.

Large-scale identification and analysis of suppressive drug interactions.

Cokol M, Weinstein ZB, Yilancioglu K, Tasan M, Doak A, Cansever D, Mutlu B, Li S, Rodriguez-Esteban R, Akhmedov M, Guvenek A, Cokol M, Cetiner S, Giaever G, Iossifov I, Nislow C, Shoichet B, Roth FP.

Chem Biol. 2014 Apr 24;21(4):541-551. doi: 10.1016/j.chembiol.2014.02.012. Epub 2014 Apr 3.

17.

Oxidative stress is a mediator for increased lipid accumulation in a newly isolated Dunaliella salina strain.

Yilancioglu K, Cokol M, Pastirmaci I, Erman B, Cetiner S.

PLoS One. 2014 Mar 20;9(3):e91957. doi: 10.1371/journal.pone.0091957. eCollection 2014.

18.

Drugs and their interactions.

Cokol M.

Curr Drug Discov Technol. 2013 Jun;10(2):106-13.

PMID:
23237673
19.

Novel anti-HER2 monoclonal antibodies: synergy and antagonism with tumor necrosis factor-α.

Ceran C, Cokol M, Cingoz S, Tasan I, Ozturk M, Yagci T.

BMC Cancer. 2012 Oct 4;12:450. doi: 10.1186/1471-2407-12-450.

20.

Systematic exploration of synergistic drug pairs.

Cokol M, Chua HN, Tasan M, Mutlu B, Weinstein ZB, Suzuki Y, Nergiz ME, Costanzo M, Baryshnikova A, Giaever G, Nislow C, Myers CL, Andrews BJ, Boone C, Roth FP.

Mol Syst Biol. 2011 Nov 8;7:544. doi: 10.1038/msb.2011.71.

21.

The genetic landscape of a cell.

Costanzo M, Baryshnikova A, Bellay J, Kim Y, Spear ED, Sevier CS, Ding H, Koh JL, Toufighi K, Mostafavi S, Prinz J, St Onge RP, VanderSluis B, Makhnevych T, Vizeacoumar FJ, Alizadeh S, Bahr S, Brost RL, Chen Y, Cokol M, Deshpande R, Li Z, Lin ZY, Liang W, Marback M, Paw J, San Luis BJ, Shuteriqi E, Tong AH, van Dyk N, Wallace IM, Whitney JA, Weirauch MT, Zhong G, Zhu H, Houry WA, Brudno M, Ragibizadeh S, Papp B, Pál C, Roth FP, Giaever G, Nislow C, Troyanskaya OG, Bussey H, Bader GD, Gingras AC, Morris QD, Kim PM, Kaiser CA, Myers CL, Andrews BJ, Boone C.

Science. 2010 Jan 22;327(5964):425-31. doi: 10.1126/science.1180823.

22.

A protein domain-based interactome network for C. elegans early embryogenesis.

Boxem M, Maliga Z, Klitgord N, Li N, Lemmens I, Mana M, de Lichtervelde L, Mul JD, van de Peut D, Devos M, Simonis N, Yildirim MA, Cokol M, Kao HL, de Smet AS, Wang H, Schlaitz AL, Hao T, Milstein S, Fan C, Tipsword M, Drew K, Galli M, Rhrissorrakrai K, Drechsel D, Koller D, Roth FP, Iakoucheva LM, Dunker AK, Bonneau R, Gunsalus KC, Hill DE, Piano F, Tavernier J, van den Heuvel S, Hyman AA, Vidal M.

Cell. 2008 Aug 8;134(3):534-45. doi: 10.1016/j.cell.2008.07.009. Erratum in: Cell. 2012 Dec 21;151(7):1633.

23.

Visualizing evolution and impact of biomedical fields.

Cokol M, Rodriguez-Esteban R.

J Biomed Inform. 2008 Dec;41(6):1050-2. doi: 10.1016/j.jbi.2008.05.002. Epub 2008 May 11.

24.

Retraction rates are on the rise.

Cokol M, Ozbay F, Rodriguez-Esteban R.

EMBO Rep. 2008 Jan;9(1):2. doi: 10.1038/sj.embor.7401143. No abstract available.

25.

A recipe for high impact.

Cokol M, Rodriguez-Esteban R, Rzhetsky A.

Genome Biol. 2007;8(5):406.

26.

How many scientific papers should be retracted?

Cokol M, Iossifov I, Rodriguez-Esteban R, Rzhetsky A.

EMBO Rep. 2007 May;8(5):422-3. No abstract available.

27.

Emergent behavior of growing knowledge about molecular interactions.

Cokol M, Iossifov I, Weinreb C, Rzhetsky A.

Nat Biotechnol. 2005 Oct;23(10):1243-7. No abstract available.

PMID:
16211067
28.

Finding nuclear localization signals.

Cokol M, Nair R, Rost B.

EMBO Rep. 2000 Nov;1(5):411-5.

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