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Items: 38

1.

Addendum: High-resolution specificity profiling and off-target prediction for site-specific DNA recombinases.

Bessen JL, Afeyan LK, Dančík V, Koblan LW, Thompson DB, Leichner C, Clemons PA, Liu DR.

Nat Commun. 2019 Jul 2;10(1):3003. doi: 10.1038/s41467-019-10892-9. No abstract available.

2.

A High-Throughput Platform to Identify Small-Molecule Inhibitors of CRISPR-Cas9.

Maji B, Gangopadhyay SA, Lee M, Shi M, Wu P, Heler R, Mok B, Lim D, Siriwardena SU, Paul B, Dančík V, Vetere A, Mesleh MF, Marraffini LA, Liu DR, Clemons PA, Wagner BK, Choudhary A.

Cell. 2019 May 2;177(4):1067-1079.e19. doi: 10.1016/j.cell.2019.04.009.

PMID:
31051099
3.

High-resolution specificity profiling and off-target prediction for site-specific DNA recombinases.

Bessen JL, Afeyan LK, Dančík V, Koblan LW, Thompson DB, Leichner C, Clemons PA, Liu DR.

Nat Commun. 2019 Apr 26;10(1):1937. doi: 10.1038/s41467-019-09987-0. Erratum in: Nat Commun. 2019 Jul 2;10(1):3003.

4.

A GPX4-dependent cancer cell state underlies the clear-cell morphology and confers sensitivity to ferroptosis.

Zou Y, Palte MJ, Deik AA, Li H, Eaton JK, Wang W, Tseng YY, Deasy R, Kost-Alimova M, Dančík V, Leshchiner ES, Viswanathan VS, Signoretti S, Choueiri TK, Boehm JS, Wagner BK, Doench JG, Clish CB, Clemons PA, Schreiber SL.

Nat Commun. 2019 Apr 8;10(1):1617. doi: 10.1038/s41467-019-09277-9.

5.

CTD2 Dashboard: a searchable web interface to connect validated results from the Cancer Target Discovery and Development Network.

Aksoy BA, Dancík V, Smith K, Mazerik JN, Ji Z, Gross B, Nikolova O, Jaber N, Califano A, Schreiber SL, Gerhard DS, Hermida LC, Jagu S, Sander C, Floratos A, Clemons PA.

Database (Oxford). 2017 Jan 1;2017. doi: 10.1093/database/bax054.

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.

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.

8.

A Structural and Mathematical Modeling Analysis of the Likelihood of Antibody-Dependent Enhancement in Influenza.

Ramakrishnan B, Viswanathan K, Tharakaraman K, Dančík V, Raman R, Babcock GJ, Shriver Z, Sasisekharan R.

Trends Microbiol. 2016 Dec;24(12):933-943. doi: 10.1016/j.tim.2016.09.003. Epub 2016 Oct 14. Review.

9.

DiSCoVERing Innovative Therapies for Rare Tumors: Combining Genetically Accurate Disease Models with In Silico Analysis to Identify Novel Therapeutic Targets.

Hanaford AR, Archer TC, Price A, Kahlert UD, Maciaczyk J, Nikkhah G, Kim JW, Ehrenberger T, Clemons PA, Dančík V, Seashore-Ludlow B, Viswanathan V, Stewart ML, Rees MG, Shamji A, Schreiber S, Fraenkel E, Pomeroy SL, Mesirov JP, Tamayo P, Eberhart CG, Raabe EH.

Clin Cancer Res. 2016 Aug 1;22(15):3903-14. doi: 10.1158/1078-0432.CCR-15-3011. Epub 2016 Mar 24.

10.

Inhibition of DYRK1A Stimulates Human β-Cell Proliferation.

Dirice E, Walpita D, Vetere A, Meier BC, Kahraman S, Hu J, Dančík V, Burns SM, Gilbert TJ, Olson DE, Clemons PA, Kulkarni RN, Wagner BK.

Diabetes. 2016 Jun;65(6):1660-71. doi: 10.2337/db15-1127. Epub 2016 Mar 7.

11.

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.

12.

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.

13.

Small-molecule enhancers of autophagy modulate cellular disease phenotypes suggested by human genetics.

Kuo SY, Castoreno AB, Aldrich LN, Lassen KG, Goel G, Dančík V, Kuballa P, Latorre I, Conway KL, Sarkar S, Maetzel D, Jaenisch R, Clemons PA, Schreiber SL, Shamji AF, Xavier RJ.

Proc Natl Acad Sci U S A. 2015 Aug 4;112(31):E4281-7. doi: 10.1073/pnas.1512289112. Epub 2015 Jul 20.

14.

Kinase-Independent Small-Molecule Inhibition of JAK-STAT Signaling.

Chou DH, Vetere A, Choudhary A, Scully SS, Schenone M, Tang A, Gomez R, Burns SM, Lundh M, Vital T, Comer E, Faloon PW, Dančík V, Ciarlo C, Paulk J, Dai M, Reddy C, Sun H, Young M, Donato N, Jaffe J, Clemons PA, Palmer M, Carr SA, Schreiber SL, Wagner BK.

J Am Chem Soc. 2015 Jun 24;137(24):7929-34. doi: 10.1021/jacs.5b04284. Epub 2015 Jun 15.

15.

Niche-Based Screening in Multiple Myeloma Identifies a Kinesin-5 Inhibitor with Improved Selectivity over Hematopoietic Progenitors.

Chattopadhyay S, Stewart AL, Mukherjee S, Huang C, Hartwell KA, Miller PG, Subramanian R, Carmody LC, Yusuf RZ, Sykes DB, Paulk J, Vetere A, Vallet S, Santo L, Cirstea DD, Hideshima T, Dančík V, Majireck MM, Hussain MM, Singh S, Quiroz R, Iaconelli J, Karmacharya R, Tolliday NJ, Clemons PA, Moore MAS, Stern AM, Shamji AF, Ebert BL, Golub TR, Raje NS, Scadden DT, Schreiber SL.

Cell Rep. 2015 Feb 10;10(5):755-770. doi: 10.1016/j.celrep.2015.01.017. Epub 2015 Feb 5.

16.

High-throughput luminescent reporter of insulin secretion for discovering regulators of pancreatic Beta-cell function.

Burns SM, Vetere A, Walpita D, Dančík V, Khodier C, Perez J, Clemons PA, Wagner BK, Altshuler D.

Cell Metab. 2015 Jan 6;21(1):126-37. doi: 10.1016/j.cmet.2014.12.010.

17.

Small-molecule screening identifies inhibition of salt-inducible kinases as a therapeutic strategy to enhance immunoregulatory functions of dendritic cells.

Sundberg TB, Choi HG, Song JH, Russell CN, Hussain MM, Graham DB, Khor B, Gagnon J, O'Connell DJ, Narayan K, Dančík V, Perez JR, Reinecker HC, Gray NS, Schreiber SL, Xavier RJ, Shamji AF.

Proc Natl Acad Sci U S A. 2014 Aug 26;111(34):12468-73. doi: 10.1073/pnas.1412308111. Epub 2014 Aug 11.

18.

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.

19.

Quantitative-proteomic comparison of alpha and Beta cells to uncover novel targets for lineage reprogramming.

Choudhary A, Hu He K, Mertins P, Udeshi ND, Dančík V, Fomina-Yadlin D, Kubicek S, Clemons PA, Schreiber SL, Carr SA, Wagner BK.

PLoS One. 2014 Apr 23;9(4):e95194. doi: 10.1371/journal.pone.0095194. eCollection 2014.

20.

Automated Structure-Activity Relationship Mining: Connecting Chemical Structure to Biological Profiles.

Wawer MJ, Jaramillo DE, Dančík V, Fass DM, Haggarty SJ, Shamji AF, Wagner BK, Schreiber SL, Clemons PA.

J Biomol Screen. 2014 Jun;19(5):738-48. doi: 10.1177/1087057114530783. Epub 2014 Apr 7.

21.

Connecting Small Molecules with Similar Assay Performance Profiles Leads to New Biological Hypotheses.

Dančík V, Carrel H, Bodycombe NE, Seiler KP, Fomina-Yadlin D, Kubicek ST, Hartwell K, Shamji AF, Wagner BK, Clemons PA.

J Biomol Screen. 2014 Jun;19(5):771-81. doi: 10.1177/1087057113520226. Epub 2014 Jan 24.

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.

Human genetics in rheumatoid arthritis guides a high-throughput drug screen of the CD40 signaling pathway.

Li G, Diogo D, Wu D, Spoonamore J, Dancik V, Franke L, Kurreeman F, Rossin EJ, Duclos G, Hartland C, Zhou X, Li K, Liu J, De Jager PL, Siminovitch KA, Zhernakova A, Raychaudhuri S, Bowes J, Eyre S, Padyukov L, Gregersen PK, Worthington J; Rheumatoid Arthritis Consortium International (RACI), Gupta N, Clemons PA, Stahl E, Tolliday N, Plenge RM.

PLoS Genet. 2013 May;9(5):e1003487. doi: 10.1371/journal.pgen.1003487. Epub 2013 May 16.

25.

Target identification and mechanism of action in chemical biology and drug discovery.

Schenone M, Dančík V, Wagner BK, Clemons PA.

Nat Chem Biol. 2013 Apr;9(4):232-40. doi: 10.1038/nchembio.1199. Review.

26.

Identification of regulators of polyploidization presents therapeutic targets for treatment of AMKL.

Wen Q, Goldenson B, Silver SJ, Schenone M, Dancik V, Huang Z, Wang LZ, Lewis TA, An WF, Li X, Bray MA, Thiollier C, Diebold L, Gilles L, Vokes MS, Moore CB, Bliss-Moreau M, Verplank L, Tolliday NJ, Mishra R, Vemula S, Shi J, Wei L, Kapur R, Lopez CK, Gerby B, Ballerini P, Pflumio F, Gilliland DG, Goldberg L, Birger Y, Izraeli S, Gamis AS, Smith FO, Woods WG, Taub J, Scherer CA, Bradner JE, Goh BC, Mercher T, Carpenter AE, Gould RJ, Clemons PA, Carr SA, Root DE, Schreiber SL, Stern AM, Crispino JD.

Cell. 2012 Aug 3;150(3):575-89. doi: 10.1016/j.cell.2012.06.032.

27.

Quantifying structure and performance diversity for sets of small molecules comprising small-molecule screening collections.

Clemons PA, Wilson JA, Dančík V, Muller S, Carrinski HA, Wagner BK, Koehler AN, Schreiber SL.

Proc Natl Acad Sci U S A. 2011 Apr 26;108(17):6817-22. doi: 10.1073/pnas.1015024108. Epub 2011 Apr 11.

28.

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.

29.

Distinct biological network properties between the targets of natural products and disease genes.

Dancík V, Seiler KP, Young DW, Schreiber SL, Clemons PA.

J Am Chem Soc. 2010 Jul 14;132(27):9259-61. doi: 10.1021/ja102798t.

30.

Edge-count probabilities for the identification of local protein communities and their organization.

Farutin V, Robison K, Lightcap E, Dancik V, Ruttenberg A, Letovsky S, Pradines J.

Proteins. 2006 Mar 15;62(3):800-18.

PMID:
16372355
31.

Analyzing protein lists with large networks: edge-count probabilities in random graphs with given expected degrees.

Pradines JR, Farutin V, Rowley S, Dancík V.

J Comput Biol. 2005 Mar;12(2):113-28.

PMID:
15767772
32.

Detection of activity centers in cellular pathways using transcript profiling.

Pradines J, Rudolph-Owen L, Hunter J, Leroy P, Cary M, Coopersmith R, Dancik V, Eltsefon Y, Farutin V, Leroy C, Rees J, Rose D, Rowley S, Ruttenberg A, Wieghardt P, Sander C, Reich C.

J Biopharm Stat. 2004 Aug;14(3):701-21.

PMID:
15468760
33.

Mutation-tolerant protein identification by mass spectrometry.

Pevzner PA, Dancík V, Tang CL.

J Comput Biol. 2000;7(6):777-87.

PMID:
11382361
34.

Efficiency of database search for identification of mutated and modified proteins via mass spectrometry.

Pevzner PA, Mulyukov Z, Dancik V, Tang CL.

Genome Res. 2001 Feb;11(2):290-9.

35.

De novo peptide sequencing via tandem mass spectrometry.

Dancík V, Addona TA, Clauser KR, Vath JE, Pevzner PA.

J Comput Biol. 1999 Fall-Winter;6(3-4):327-42.

PMID:
10582570
36.

Estimation for restriction sites observed by optical mapping using reversible-jump Markov Chain Monte Carlo.

Lee JK, Dancík V, Waterman MS.

J Comput Biol. 1998 Fall;5(3):505-15.

PMID:
9773346
37.

Local rules for protein folding on a triangular lattice and generalized hydrophobicity in the HP model.

Agarwala R, Batzoglou S, Dancík V, Decatur SE, Hannenhalli S, Farach M, Muthukrishnan S, Skiena S.

J Comput Biol. 1997 Fall;4(3):275-96.

PMID:
9278060
38.

Hardness of flip-cut problems from optical mapping.

Dancík V, Hannenhalli S, Muthurkrishnan S.

J Comput Biol. 1997 Summer;4(2):119-25.

PMID:
9228611

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