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Items: 14

1.

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.

2.

CellProfiler Analyst: interactive data exploration, analysis and classification of large biological image sets.

Dao D, Fraser AN, Hung J, Ljosa V, Singh S, Carpenter AE.

Bioinformatics. 2016 Oct 15;32(20):3210-3212. Epub 2016 Jun 26.

3.

Morphological Profiles of RNAi-Induced Gene Knockdown Are Highly Reproducible but Dominated by Seed Effects.

Singh S, Wu X, Ljosa V, Bray MA, Piccioni F, Root DE, Doench JG, Boehm JS, Carpenter AE.

PLoS One. 2015 Jul 21;10(7):e0131370. doi: 10.1371/journal.pone.0131370. eCollection 2015.

4.

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.

5.

Multiplex cytological profiling assay to measure diverse cellular states.

Gustafsdottir SM, Ljosa V, Sokolnicki KL, Anthony Wilson J, Walpita D, Kemp MM, Petri Seiler K, Carrel HA, Golub TR, Schreiber SL, Clemons PA, Carpenter AE, Shamji AF.

PLoS One. 2013 Dec 2;8(12):e80999. doi: 10.1371/journal.pone.0080999. eCollection 2013.

6.

Comparison of methods for image-based profiling of cellular morphological responses to small-molecule treatment.

Ljosa V, Caie PD, Ter Horst R, Sokolnicki KL, Jenkins EL, Daya S, Roberts ME, Jones TR, Singh S, Genovesio A, Clemons PA, Carragher NO, Carpenter AE.

J Biomol Screen. 2013 Dec;18(10):1321-9. doi: 10.1177/1087057113503553. Epub 2013 Sep 17.

7.

Annotated high-throughput microscopy image sets for validation.

Ljosa V, Sokolnicki KL, Carpenter AE.

Nat Methods. 2012 Jun 28;9(7):637. doi: 10.1038/nmeth.2083. No abstract available. Erratum in: Nat Methods. 2013 May;10(5):445.

8.

An image analysis toolbox for high-throughput C. elegans assays.

Wählby C, Kamentsky L, Liu ZH, Riklin-Raviv T, Conery AL, O'Rourke EJ, Sokolnicki KL, Visvikis O, Ljosa V, Irazoqui JE, Golland P, Ruvkun G, Ausubel FM, Carpenter AE.

Nat Methods. 2012 Apr 22;9(7):714-6. doi: 10.1038/nmeth.1984.

9.

RESOLVING CLUSTERED WORMS VIA PROBABILISTIC SHAPE MODELS.

Wählby C, Riklin-Raviv T, Ljosa V, Conery AL, Golland P, Ausubel FM, Carpenter AE.

Proc IEEE Int Symp Biomed Imaging. 2010 Jun 21;2010(14-17 April 2010):552-555.

10.

Improved structure, function and compatibility for CellProfiler: modular high-throughput image analysis software.

Kamentsky L, Jones TR, Fraser A, Bray MA, Logan DJ, Madden KL, Ljosa V, Rueden C, Eliceiri KW, Carpenter AE.

Bioinformatics. 2011 Apr 15;27(8):1179-80. doi: 10.1093/bioinformatics/btr095. Epub 2011 Feb 23.

11.

Morphology-guided graph search for untangling objects: C. elegans analysis.

Raviv TR, Ljosa V, Conery AL, Ausubel FM, Carpenter AE, Golland P, Wählby C.

Med Image Comput Comput Assist Interv. 2010;13(Pt 3):634-41.

12.

Introduction to the quantitative analysis of two-dimensional fluorescence microscopy images for cell-based screening.

Ljosa V, Carpenter AE.

PLoS Comput Biol. 2009 Dec;5(12):e1000603. doi: 10.1371/journal.pcbi.1000603. Epub 2009 Dec 24. No abstract available.

13.

High-throughput screens for fluorescent dye discovery.

Ljosa V, Carpenter AE.

Trends Biotechnol. 2008 Oct;26(10):527-30. doi: 10.1016/j.tibtech.2008.06.008. Epub 2008 Aug 14.

PMID:
18706725
14.

Speeding up whole-genome alignment by indexing frequency vectors.

Kahveci T, Ljosa V, Singh AK.

Bioinformatics. 2004 Sep 1;20(13):2122-34. Epub 2004 Apr 8.

PMID:
15073002

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