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Items: 42

1.

Genetic and transcriptional evolution alters cancer cell line drug response.

Ben-David U, Siranosian B, Ha G, Tang H, Oren Y, Hinohara K, Strathdee CA, Dempster J, Lyons NJ, Burns R, Nag A, Kugener G, Cimini B, Tsvetkov P, Maruvka YE, O'Rourke R, Garrity A, Tubelli AA, Bandopadhayay P, Tsherniak A, Vazquez F, Wong B, Birger C, Ghandi M, Thorner AR, Bittker JA, Meyerson M, Getz G, Beroukhim R, Golub TR.

Nature. 2018 Aug;560(7718):325-330. doi: 10.1038/s41586-018-0409-3. Epub 2018 Aug 8.

2.

High Throughput Screen Identifies Interferon γ-Dependent Inhibitors of Toxoplasma gondii Growth.

Radke JB, Carey KL, Shaw S, Metkar SR, Mulrooney C, Gale JP, Bittker JA, Hilgraf R, Comer E, Schreiber SL, Virgin HW, Perez JR, Sibley LD.

ACS Infect Dis. 2018 Oct 12;4(10):1499-1507. doi: 10.1021/acsinfecdis.8b00135. Epub 2018 Aug 28.

PMID:
30058798
3.

High-Throughput Screens To Identify Autophagy Inducers That Function by Disrupting Beclin 1/Bcl-2 Binding.

Chiang WC, Wei Y, Kuo YC, Wei S, Zhou A, Zou Z, Yehl J, Ranaghan MJ, Skepner A, Bittker JA, Perez JR, Posner BA, Levine B.

ACS Chem Biol. 2018 Aug 17;13(8):2247-2260. doi: 10.1021/acschembio.8b00421. Epub 2018 Jun 21.

4.

GDC-0879, a BRAFV600E Inhibitor, Protects Kidney Podocytes from Death.

Sieber J, Wieder N, Clark A, Reitberger M, Matan S, Schoenfelder J, Zhang J, Mandinova A, Bittker JA, Gutierrez J, Aygün O, Udeshi N, Carr S, Mundel P, Jehle AW, Greka A.

Cell Chem Biol. 2018 Feb 15;25(2):175-184.e4. doi: 10.1016/j.chembiol.2017.11.006. Epub 2017 Dec 14.

5.

A Next Generation Connectivity Map: L1000 Platform and the First 1,000,000 Profiles.

Subramanian A, Narayan R, Corsello SM, Peck DD, Natoli TE, Lu X, Gould J, Davis JF, Tubelli AA, Asiedu JK, Lahr DL, Hirschman JE, Liu Z, Donahue M, Julian B, Khan M, Wadden D, Smith IC, Lam D, Liberzon A, Toder C, Bagul M, Orzechowski M, Enache OM, Piccioni F, Johnson SA, Lyons NJ, Berger AH, Shamji AF, Brooks AN, Vrcic A, Flynn C, Rosains J, Takeda DY, Hu R, Davison D, Lamb J, Ardlie K, Hogstrom L, Greenside P, Gray NS, Clemons PA, Silver S, Wu X, Zhao WN, Read-Button W, Wu X, Haggarty SJ, Ronco LV, Boehm JS, Schreiber SL, Doench JG, Bittker JA, Root DE, Wong B, Golub TR.

Cell. 2017 Nov 30;171(6):1437-1452.e17. doi: 10.1016/j.cell.2017.10.049.

6.

Small-molecule inhibitors directly target CARD9 and mimic its protective variant in inflammatory bowel disease.

Leshchiner ES, Rush JS, Durney MA, Cao Z, Dančík V, Chittick B, Wu H, Petrone A, Bittker JA, Phillips A, Perez JR, Shamji AF, Kaushik VK, Daly MJ, Graham DB, Schreiber SL, Xavier RJ.

Proc Natl Acad Sci U S A. 2017 Oct 24;114(43):11392-11397. doi: 10.1073/pnas.1705748114. Epub 2017 Oct 9.

7.

The Drug Repurposing Hub: a next-generation drug library and information resource.

Corsello SM, Bittker JA, Liu Z, Gould J, McCarren P, Hirschman JE, Johnston SE, Vrcic A, Wong B, Khan M, Asiedu J, Narayan R, Mader CC, Subramanian A, Golub TR.

Nat Med. 2017 Apr 7;23(4):405-408. doi: 10.1038/nm.4306. No abstract available.

8.

Selective Chemical Inhibition of PGC-1α Gluconeogenic Activity Ameliorates Type 2 Diabetes.

Sharabi K, Lin H, Tavares CDJ, Dominy JE, Camporez JP, Perry RJ, Schilling R, Rines AK, Lee J, Hickey M, Bennion M, Palmer M, Nag PP, Bittker JA, Perez J, Jedrychowski MP, Ozcan U, Gygi SP, Kamenecka TM, Shulman GI, Schreiber SL, Griffin PR, Puigserver P.

Cell. 2017 Mar 23;169(1):148-160.e15. doi: 10.1016/j.cell.2017.03.001.

9.

A dataset of images and morphological profiles of 30 000 small-molecule treatments using the Cell Painting assay.

Bray MA, Gustafsdottir SM, Rohban MH, Singh S, Ljosa V, Sokolnicki KL, Bittker JA, Bodycombe NE, Dancík V, Hasaka TP, Hon CS, Kemp MM, Li K, Walpita D, Wawer MJ, Golub TR, Schreiber SL, Clemons PA, Shamji AF, Carpenter AE.

Gigascience. 2017 Dec 1;6(12):1-5. doi: 10.1093/gigascience/giw014.

10.

Identification of Highly Specific Diversity-Oriented Synthesis-Derived Inhibitors of Clostridium difficile.

Duvall JR, Bedard L, Naylor-Olsen AM, Manson AL, Bittker JA, Sun W, Fitzgerald ME, He Z, Lee MD 4th, Marie JC, Muncipinto G, Rush D, Xu D, Xu H, Zhang M, Earl AM, Palmer MA, Foley MA, Vacca JP, Scherer CA.

ACS Infect Dis. 2017 May 12;3(5):349-359. doi: 10.1021/acsinfecdis.6b00206. Epub 2017 Mar 7.

11.

Diversity-oriented synthesis yields novel multistage antimalarial inhibitors.

Kato N, Comer E, Sakata-Kato T, Sharma A, Sharma M, Maetani M, Bastien J, Brancucci NM, Bittker JA, Corey V, Clarke D, Derbyshire ER, Dornan GL, Duffy S, Eckley S, Itoe MA, Koolen KM, Lewis TA, Lui PS, Lukens AK, Lund E, March S, Meibalan E, Meier BC, McPhail JA, Mitasev B, Moss EL, Sayes M, Van Gessel Y, Wawer MJ, Yoshinaga T, Zeeman AM, Avery VM, Bhatia SN, Burke JE, Catteruccia F, Clardy JC, Clemons PA, Dechering KJ, Duvall JR, Foley MA, Gusovsky F, Kocken CH, Marti M, Morningstar ML, Munoz B, Neafsey DE, Sharma A, Winzeler EA, Wirth DF, Scherer CA, Schreiber SL.

Nature. 2016 Oct 20;538(7625):344-349. doi: 10.1038/nature19804. Epub 2016 Sep 7.

12.

Correlating chemical sensitivity and basal gene expression reveals mechanism of action.

Rees MG, Seashore-Ludlow B, Cheah JH, Adams DJ, Price EV, Gill S, Javaid S, Coletti ME, Jones VL, Bodycombe NE, Soule CK, Alexander B, Li A, Montgomery P, Kotz JD, Hon CS, Munoz B, Liefeld T, Dančík V, Haber DA, Clish CB, Bittker JA, Palmer M, Wagner BK, Clemons PA, Shamji AF, Schreiber SL.

Nat Chem Biol. 2016 Feb;12(2):109-16. doi: 10.1038/nchembio.1986. Epub 2015 Dec 14.

13.

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.

14.

Advancing Biological Understanding and Therapeutics Discovery with Small-Molecule Probes.

Schreiber SL, Kotz JD, Li M, Aubé J, Austin CP, Reed JC, Rosen H, White EL, Sklar LA, Lindsley CW, Alexander BR, Bittker JA, Clemons PA, de Souza A, Foley MA, Palmer M, Shamji AF, Wawer MJ, McManus O, Wu M, Zou B, Yu H, Golden JE, Schoenen FJ, Simeonov A, Jadhav A, Jackson MR, Pinkerton AB, Chung TD, Griffin PR, Cravatt BF, Hodder PS, Roush WR, Roberts E, Chung DH, Jonsson CB, Noah JW, Severson WE, Ananthan S, Edwards B, Oprea TI, Conn PJ, Hopkins CR, Wood MR, Stauffer SR, Emmitte KA; NIH Molecular Libraries Project Team.

Cell. 2015 Jun 4;161(6):1252-65. doi: 10.1016/j.cell.2015.05.023. Review.

15.

Discovery of small molecule probe that shows anti-tubercular activity via Mtb bioA (DAPA synthase) enzyme inhibition.

Casalena D, Nag PP, Park SW, Wilson D, Edwankar R, Johnston S, Le H, Schilling R, Bittker JA, Dandapani S, Munoz B, Dai R, Finzel BC, Schnappinger D, Aldrich C, Schreiber SL, Palmer M.

Probe Reports from the NIH Molecular Libraries Program [Internet]. Bethesda (MD): National Center for Biotechnology Information (US); 2010-.
2014 Apr 15 [updated 2015 Jan 16].

16.

Identification of a chemically validated target in replicating and non-replicating Mycobacterium tuberculosis with the aid of a small molecule probe.

Nag PP, Grant SS, Lewis TA, Gordon K, Kawate T, Fitzgerald M, Nietupski R, Gomez J, White EL, Maddox C, Nebane NM, Tower NA, McKellip S, Sosa M, Rasmussen L, Johnston S, Bittker JA, Dandapani S, Perez J, Munoz B, Palmer M, Schreiber SL, Hung DT.

Probe Reports from the NIH Molecular Libraries Program [Internet]. Bethesda (MD): National Center for Biotechnology Information (US); 2010-.
2014 Apr 15 [updated 2015 Jan 16].

17.

Target-based identification of whole-cell active inhibitors of biotin biosynthesis in Mycobacterium tuberculosis.

Park SW, Casalena DE, Wilson DJ, Dai R, Nag PP, Liu F, Boyce JP, Bittker JA, Schreiber SL, Finzel BC, Schnappinger D, Aldrich CC.

Chem Biol. 2015 Jan 22;22(1):76-86. doi: 10.1016/j.chembiol.2014.11.012. Epub 2014 Dec 31.

18.

BioAssay Research Database (BARD): chemical biology and probe-development enabled by structured metadata and result types.

Howe EA, de Souza A, Lahr DL, Chatwin S, Montgomery P, Alexander BR, Nguyen DT, Cruz Y, Stonich DA, Walzer G, Rose JT, Picard SC, Liu Z, Rose JN, Xiang X, Asiedu J, Durkin D, Levine J, Yang JJ, Schürer SC, Braisted JC, Southall N, Southern MR, Chung TD, Brudz S, Tanega C, Schreiber SL, Bittker JA, Guha R, Clemons PA.

Nucleic Acids Res. 2015 Jan;43(Database issue):D1163-70. doi: 10.1093/nar/gku1244. Epub 2014 Dec 4.

19.

Evolving BioAssay Ontology (BAO): modularization, integration and applications.

Abeyruwan S, Vempati UD, Küçük-McGinty H, Visser U, Koleti A, Mir A, Sakurai K, Chung C, Bittker JA, Clemons PA, Brudz S, Siripala A, Morales AJ, Romacker M, Twomey D, Bureeva S, Lemmon V, Schürer SC.

J Biomed Semantics. 2014 Jun 3;5(Suppl 1 Proceedings of the Bio-Ontologies Spec Interest G):S5. doi: 10.1186/2041-1480-5-S1-S5. eCollection 2014.

20.

Toward performance-diverse small-molecule libraries for cell-based phenotypic screening using multiplexed high-dimensional profiling.

Wawer MJ, Li K, Gustafsdottir SM, Ljosa V, Bodycombe NE, Marton MA, Sokolnicki KL, Bray MA, Kemp MM, Winchester E, Taylor B, Grant GB, Hon CS, Duvall JR, Wilson JA, Bittker JA, Dančík V, Narayan R, Subramanian A, Winckler W, Golub TR, Carpenter AE, Shamji AF, Schreiber SL, Clemons PA.

Proc Natl Acad Sci U S A. 2014 Jul 29;111(30):10911-6. doi: 10.1073/pnas.1410933111. Epub 2014 Jul 14.

21.

An Overview of the Challenges in Designing, Integrating, and Delivering BARD: A Public Chemical-Biology Resource and Query Portal for Multiple Organizations, Locations, and Disciplines.

de Souza A, Bittker JA, Lahr DL, Brudz S, Chatwin S, Oprea TI, Waller A, Yang JJ, Southall N, Guha R, Schürer SC, Vempati UD, Southern MR, Dawson ES, Clemons PA, Chung TD.

J Biomol Screen. 2014 Jun;19(5):614-27. doi: 10.1177/1087057113517139. Epub 2014 Jan 17. Review.

22.

Niche-based screening identifies small-molecule inhibitors of leukemia stem cells.

Hartwell KA, Miller PG, Mukherjee S, Kahn AR, Stewart AL, Logan DJ, Negri JM, Duvet M, Järås M, Puram R, Dancik V, Al-Shahrour F, Kindler T, Tothova Z, Chattopadhyay S, Hasaka T, Narayan R, Dai M, Huang C, Shterental S, Chu LP, Haydu JE, Shieh JH, Steensma DP, Munoz B, Bittker JA, Shamji AF, Clemons PA, Tolliday NJ, Carpenter AE, Gilliland DG, Stern AM, Moore MAS, Scadden DT, Schreiber SL, Ebert BL, Golub TR.

Nat Chem Biol. 2013 Dec;9(12):840-848. doi: 10.1038/nchembio.1367. Epub 2013 Oct 27.

23.

An interactive resource to identify cancer genetic and lineage dependencies targeted by small molecules.

Basu A, Bodycombe NE, Cheah JH, Price EV, Liu K, Schaefer GI, Ebright RY, Stewart ML, Ito D, Wang S, Bracha AL, Liefeld T, Wawer M, Gilbert JC, Wilson AJ, Stransky N, Kryukov GV, Dancik V, Barretina J, Garraway LA, Hon CS, Munoz B, Bittker JA, Stockwell BR, Khabele D, Stern AM, Clemons PA, Shamji AF, Schreiber SL.

Cell. 2013 Aug 29;154(5):1151-1161. doi: 10.1016/j.cell.2013.08.003.

24.

ML212: A small-molecule probe for investigating fluconazole resistance mechanisms in Candida albicans.

Youngsaye W, Hartland CL, Morgan BJ, Ting A, Nag PP, Vincent B, Mosher CA, Bittker JA, Dandapani S, Palmer M, Whitesell L, Lindquist S, Schreiber SL, Munoz B.

Beilstein J Org Chem. 2013 Jul 26;9:1501-7. doi: 10.3762/bjoc.9.171. eCollection 2013.

25.

An informatic pipeline for managing high-throughput screening experiments and analyzing data from stereochemically diverse libraries.

Mulrooney CA, Lahr DL, Quintin MJ, Youngsaye W, Moccia D, Asiedu JK, Mulligan EL, Akella LB, Marcaurelle LA, Montgomery P, Bittker JA, Clemons PA, Brudz S, Dandapani S, Duvall JR, Tolliday NJ, De Souza A.

J Comput Aided Mol Des. 2013 May;27(5):455-68. doi: 10.1007/s10822-013-9641-y. Epub 2013 Apr 13.

26.

High-Throughput RT-PCR for small-molecule screening assays.

Bittker JA.

Curr Protoc Chem Biol. 2012 Mar 1;4(1):49-63.

27.

Screen for RAS-Selective Lethal Compounds and VDAC Ligands - Probe 2.

Bittker JA, Weiwer M, Lewis T, Shimada K, Yang WS, MacPherson L, Dandapani S, Munoz B, Palmer M, Stockwell BR, Schreiber SL.

Probe Reports from the NIH Molecular Libraries Program [Internet]. Bethesda (MD): National Center for Biotechnology Information (US); 2010-.
2011 Feb 10 [updated 2011 Dec 12].

28.

Discovery of Inhibitors of Anti-Apoptotic Protein A1.

Bittker JA, Weiwer M, Wei G, Germain A, Brown E, Dandapani S, Munoz B, Palmer M, Golub T, Schreiber SL.

Probe Reports from the NIH Molecular Libraries Program [Internet]. Bethesda (MD): National Center for Biotechnology Information (US); 2010-.
2011 Mar 21 [updated 2011 Nov 21].

29.

Automatically detecting workflows in PubChem.

Calhoun BT, Browning MR, Chen BR, Bittker JA, Swamidass SJ.

J Biomol Screen. 2012 Sep;17(8):1071-9. doi: 10.1177/1087057112449054. Epub 2012 Jun 12.

PMID:
22693105
30.

Overcoming fluconazole resistance in Candida albicans clinical isolates with tetracyclic indoles.

Youngsaye W, Dockendorff C, Vincent B, Hartland CL, Bittker JA, Dandapani S, Palmer M, Whitesell L, Lindquist S, Schreiber SL, Munoz B.

Bioorg Med Chem Lett. 2012 May 1;22(9):3362-5. doi: 10.1016/j.bmcl.2012.02.035. Epub 2012 Feb 22.

31.

Development of small-molecule probes that selectively kill cells induced to express mutant RAS.

Weïwer M, Bittker JA, Lewis TA, Shimada K, Yang WS, MacPherson L, Dandapani S, Palmer M, Stockwell BR, Schreiber SL, Munoz B.

Bioorg Med Chem Lett. 2012 Feb 15;22(4):1822-6. doi: 10.1016/j.bmcl.2011.09.047. Epub 2011 Sep 28.

32.

Utility-aware screening with clique-oriented prioritization.

Swamidass SJ, Calhoun BT, Bittker JA, Bodycombe NE, Clemons PA.

J Chem Inf Model. 2012 Jan 23;52(1):29-37. doi: 10.1021/ci2003285. Epub 2011 Dec 20.

33.

Identification of small-molecule inhibitors of Trypansoma cruzi replication.

Germain AR, Carmody LC, Dockendorff C, Galan-Rodriguez C, Rodriguez A, Johnston S, Bittker JA, MacPherson L, Dandapani S, Palmer M, Schreiber SL, Munoz B.

Bioorg Med Chem Lett. 2011 Dec 1;21(23):7197-200. doi: 10.1016/j.bmcl.2011.09.057. Epub 2011 Sep 29.

PMID:
22018462
34.

Piperazinyl quinolines as chemosensitizers to increase fluconazole susceptibility of Candida albicans clinical isolates.

Youngsaye W, Vincent B, Hartland CL, Morgan BJ, Buhrlage SJ, Johnston S, Bittker JA, MacPherson L, Dandapani S, Palmer M, Whitesell L, Lindquist S, Schreiber SL, Munoz B.

Bioorg Med Chem Lett. 2011 Sep 15;21(18):5502-5. doi: 10.1016/j.bmcl.2011.06.105. Epub 2011 Jun 30.

35.

Enhancing the rate of scaffold discovery with diversity-oriented prioritization.

Swamidass SJ, Calhoun BT, Bittker JA, Bodycombe NE, Clemons PA.

Bioinformatics. 2011 Aug 15;27(16):2271-8. doi: 10.1093/bioinformatics/btr369. Epub 2011 Jun 17.

36.

Screen for RAS-Selective Lethal Compounds and VDAC Ligands - Probe 1.

Bittker JA, Weiwer M, Shimada K, Yang WS, MacPherson L, Dandapani S, Munoz B, Palmer M, Stockwell BR, Schreiber SL.

Probe Reports from the NIH Molecular Libraries Program [Internet]. Bethesda (MD): National Center for Biotechnology Information (US); 2010-.
2010 Mar 26 [updated 2011 Feb 10].

37.

Small-molecule inducers of insulin expression in pancreatic alpha-cells.

Fomina-Yadlin D, Kubicek S, Walpita D, Dancik V, Hecksher-Sørensen J, Bittker JA, Sharifnia T, Shamji A, Clemons PA, Wagner BK, Schreiber SL.

Proc Natl Acad Sci U S A. 2010 Aug 24;107(34):15099-104. doi: 10.1073/pnas.1010018107. Epub 2010 Aug 9.

38.

An economic framework to prioritize confirmatory tests after a high-throughput screen.

Swamidass SJ, Bittker JA, Bodycombe NE, Ryder SP, Clemons PA.

J Biomol Screen. 2010 Jul;15(6):680-6. doi: 10.1177/1087057110372803. Epub 2010 Jun 14.

39.
40.

Directed evolution of protein enzymes using nonhomologous random recombination.

Bittker JA, Le BV, Liu JM, Liu DR.

Proc Natl Acad Sci U S A. 2004 May 4;101(18):7011-6. Epub 2004 Apr 26.

41.

Nucleic acid evolution and minimization by nonhomologous random recombination.

Bittker JA, Le BV, Liu DR.

Nat Biotechnol. 2002 Oct;20(10):1024-9. Epub 2002 Sep 9.

42.

Recent advances in the in vitro evolution of nucleic acids.

Bittker JA, Phillips KJ, Liu DR.

Curr Opin Chem Biol. 2002 Jun;6(3):367-74. Review.

PMID:
12023118

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