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Items: 25

1.

CHEMGENIE: integration of chemogenomics data for applications in chemical biology.

Kutchukian PS, Chang C, Fox SJ, Cook E, Barnard R, Tellers D, Wang H, Pertusi D, Glick M, Sheridan RP, Wallace IM, Wassermann AM.

Drug Discov Today. 2018 Jan;23(1):151-160. doi: 10.1016/j.drudis.2017.09.004. Epub 2017 Sep 14. Review.

PMID:
28917822
2.

Open Source Drug Discovery: Highly Potent Antimalarial Compounds Derived from the Tres Cantos Arylpyrroles.

Williamson AE, Ylioja PM, Robertson MN, Antonova-Koch Y, Avery V, Baell JB, Batchu H, Batra S, Burrows JN, Bhattacharyya S, Calderon F, Charman SA, Clark J, Crespo B, Dean M, Debbert SL, Delves M, Dennis AS, Deroose F, Duffy S, Fletcher S, Giaever G, Hallyburton I, Gamo FJ, Gebbia M, Guy RK, Hungerford Z, Kirk K, Lafuente-Monasterio MJ, Lee A, Meister S, Nislow C, Overington JP, Papadatos G, Patiny L, Pham J, Ralph SA, Ruecker A, Ryan E, Southan C, Srivastava K, Swain C, Tarnowski MJ, Thomson P, Turner P, Wallace IM, Wells TN, White K, White L, Willis P, Winzeler EA, Wittlin S, Todd MH.

ACS Cent Sci. 2016 Oct 26;2(10):687-701. Epub 2016 Sep 14.

3.

Dark chemical matter as a promising starting point for drug lead discovery.

Wassermann AM, Lounkine E, Hoepfner D, Le Goff G, King FJ, Studer C, Peltier JM, Grippo ML, Prindle V, Tao J, Schuffenhauer A, Wallace IM, Chen S, Krastel P, Cobos-Correa A, Parker CN, Davies JW, Glick M.

Nat Chem Biol. 2015 Dec;11(12):958-66. doi: 10.1038/nchembio.1936. Epub 2015 Oct 19.

PMID:
26479441
4.

Is patient confidentiality compromised with the electronic health record?: a position paper.

Wallace IM.

Comput Inform Nurs. 2015 Feb;33(2):58-62; quiz E1. doi: 10.1097/CIN.0000000000000126.

PMID:
25532832
5.

Mapping the cellular response to small molecules using chemogenomic fitness signatures.

Lee AY, St Onge RP, Proctor MJ, Wallace IM, Nile AH, Spagnuolo PA, Jitkova Y, Gronda M, Wu Y, Kim MK, Cheung-Ong K, Torres NP, Spear ED, Han MK, Schlecht U, Suresh S, Duby G, Heisler LE, Surendra A, Fung E, Urbanus ML, Gebbia M, Lissina E, Miranda M, Chiang JH, Aparicio AM, Zeghouf M, Davis RW, Cherfils J, Boutry M, Kaiser CA, Cummins CL, Trimble WS, Brown GW, Schimmer AD, Bankaitis VA, Nislow C, Bader GD, Giaever G.

Science. 2014 Apr 11;344(6180):208-11. doi: 10.1126/science.1250217. Erratum in: Science. 2014 May 23;344(6186):1255771.

6.

PITPs as targets for selectively interfering with phosphoinositide signaling in cells.

Nile AH, Tripathi A, Yuan P, Mousley CJ, Suresh S, Wallace IM, Shah SD, Pohlhaus DT, Temple B, Nislow C, Giaever G, Tropsha A, Davis RW, St Onge RP, Bankaitis VA.

Nat Chem Biol. 2014 Jan;10(1):76-84. doi: 10.1038/nchembio.1389. Epub 2013 Nov 24.

7.

Target prediction for an open access set of compounds active against Mycobacterium tuberculosis.

Martínez-Jiménez F, Papadatos G, Yang L, Wallace IM, Kumar V, Pieper U, Sali A, Brown JR, Overington JP, Marti-Renom MA.

PLoS Comput Biol. 2013;9(10):e1003253. doi: 10.1371/journal.pcbi.1003253. Epub 2013 Oct 3.

8.

A phenotypic screening platform to identify small molecule modulators of Chlamydomonas reinhardtii growth, motility and photosynthesis.

Alfred SE, Surendra A, Le C, Lin K, Mok A, Wallace IM, Proctor M, Urbanus ML, Giaever G, Nislow C.

Genome Biol. 2012 Nov 18;13(11):R105. doi: 10.1186/gb-2012-13-11-r105.

9.

Dafadine inhibits DAF-9 to promote dauer formation and longevity of Caenorhabditis elegans.

Luciani GM, Magomedova L, Puckrin R, Urbanus ML, Wallace IM, Giaever G, Nislow C, Cummins CL, Roy PJ.

Nat Chem Biol. 2011 Nov 6;7(12):891-3. doi: 10.1038/nchembio.698. Erratum in: Nat Chem Biol. 2012 Mar;8(3):318.

PMID:
22057127
10.

Compound prioritization methods increase rates of chemical probe discovery in model organisms.

Wallace IM, Urbanus ML, Luciani GM, Burns AR, Han MK, Wang H, Arora K, Heisler LE, Proctor M, St Onge RP, Roemer T, Roy PJ, Cummins CL, Bader GD, Nislow C, Giaever G.

Chem Biol. 2011 Oct 28;18(10):1273-83. doi: 10.1016/j.chembiol.2011.07.018.

11.

Displaying chemical information on a biological network using Cytoscape.

Wallace IM, Bader GD, Giaever G, Nislow C.

Methods Mol Biol. 2011;781:363-76. doi: 10.1007/978-1-61779-276-2_18.

PMID:
21877291
12.

Design, synthesis and characterization of a highly effective inhibitor for analog-sensitive (as) kinases.

Klein M, Morillas M, Vendrell A, Brive L, Gebbia M, Wallace IM, Giaever G, Nislow C, Posas F, Grøtli M.

PLoS One. 2011;6(6):e20789. doi: 10.1371/journal.pone.0020789. Epub 2011 Jun 17.

13.

A predictive model for drug bioaccumulation and bioactivity in Caenorhabditis elegans.

Burns AR, Wallace IM, Wildenhain J, Tyers M, Giaever G, Bader GD, Nislow C, Cutler SR, Roy PJ.

Nat Chem Biol. 2010 Jul;6(7):549-57. doi: 10.1038/nchembio.380. Epub 2010 May 30.

PMID:
20512140
14.

Highly-multiplexed barcode sequencing: an efficient method for parallel analysis of pooled samples.

Smith AM, Heisler LE, St Onge RP, Farias-Hesson E, Wallace IM, Bodeau J, Harris AN, Perry KM, Giaever G, Pourmand N, Nislow C.

Nucleic Acids Res. 2010 Jul;38(13):e142. doi: 10.1093/nar/gkq368. Epub 2010 May 11.

15.

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.

16.

An integrated platform of genomic assays reveals small-molecule bioactivities.

Hoon S, Smith AM, Wallace IM, Suresh S, Miranda M, Fung E, Proctor M, Shokat KM, Zhang C, Davis RW, Giaever G, St Onge RP, Nislow C.

Nat Chem Biol. 2008 Aug;4(8):498-506. doi: 10.1038/nchembio.100. Epub 2008 Jul 11. Erratum in: Nat Chem Biol.2008 Oct;4(10):632.. StOnge, Robert P [corrected to St Onge,Robert P].

PMID:
18622389
17.

Fast embedding methods for clustering tens of thousands of sequences.

Blackshields G, Larkin M, Wallace IM, Wilm A, Higgins DG.

Comput Biol Chem. 2008 Aug;32(4):282-6. doi: 10.1016/j.compbiolchem.2008.03.005. Epub 2008 Mar 26.

PMID:
18450519
18.

Clustal W and Clustal X version 2.0.

Larkin MA, Blackshields G, Brown NP, Chenna R, McGettigan PA, McWilliam H, Valentin F, Wallace IM, Wilm A, Lopez R, Thompson JD, Gibson TJ, Higgins DG.

Bioinformatics. 2007 Nov 1;23(21):2947-8. Epub 2007 Sep 10.

PMID:
17846036
19.

The M-Coffee web server: a meta-method for computing multiple sequence alignments by combining alternative alignment methods.

Moretti S, Armougom F, Wallace IM, Higgins DG, Jongeneel CV, Notredame C.

Nucleic Acids Res. 2007 Jul;35(Web Server issue):W645-8. Epub 2007 May 25.

20.
21.

Analysis and comparison of benchmarks for multiple sequence alignment.

Blackshields G, Wallace IM, Larkin M, Higgins DG.

In Silico Biol. 2006;6(4):321-39.

PMID:
16922695
22.

M-Coffee: combining multiple sequence alignment methods with T-Coffee.

Wallace IM, O'Sullivan O, Higgins DG, Notredame C.

Nucleic Acids Res. 2006 Mar 23;34(6):1692-9. Print 2006.

23.

Mind the gaps: progress in progressive alignment.

Higgins DG, Blackshields G, Wallace IM.

Proc Natl Acad Sci U S A. 2005 Jul 26;102(30):10411-2. Epub 2005 Jul 18. No abstract available.

24.

Multiple sequence alignments.

Wallace IM, Blackshields G, Higgins DG.

Curr Opin Struct Biol. 2005 Jun;15(3):261-6. Review.

PMID:
15963889
25.

Evaluation of iterative alignment algorithms for multiple alignment.

Wallace IM, O'Sullivan O, Higgins DG.

Bioinformatics. 2005 Apr 15;21(8):1408-14. Epub 2004 Nov 25.

PMID:
15564300

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