Literature DB >> 25168174

GoIFISH: a system for the quantification of single cell heterogeneity from IFISH images.

Anne Trinh, Inga H Rye, Vanessa Almendro, Aslaug Helland, Hege G Russnes, Florian Markowetz.   

Abstract

Molecular analysis has revealed extensive intra-tumor heterogeneity in human cancer samples, but cannot identify cell-to-cell variations within the tissue microenvironment. In contrast, in situ analysis can identify genetic aberrations in phenotypically defined cell subpopulations while preserving tissue-context specificity. GoIFISHGoIFISH is a widely applicable, user-friendly system tailored for the objective and semi-automated visualization, detection and quantification of genomic alterations and protein expression obtained from fluorescence in situ analysis. In a sample set of HER2-positive breast cancers GoIFISHGoIFISH is highly robust in visual analysis and its accuracy compares favorably to other leading image analysis methods. GoIFISHGoIFISH is freely available at www.sourceforge.net/projects/goifish/.

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Mesh：

Year:  2014        PMID： 25168174      PMCID： PMC4167144          DOI： 10.1186/s13059-014-0442-y

Source DB:  PubMed          Journal:  Genome Biol        ISSN： 1474-7596            Impact factor:   13.583


  23 in total

1.  Active contours without edges.

Authors:  T F Chan; L A Vese
Journal:  IEEE Trans Image Process       Date:  2001       Impact factor: 10.856

2.  Genetic and phenotypic diversity in breast tumor metastases.

Authors:  Vanessa Almendro; Hee Jung Kim; Yu-Kang Cheng; Mithat Gönen; Shalev Itzkovitz; Pedram Argani; Alexander van Oudenaarden; Saraswati Sukumar; Franziska Michor; Kornelia Polyak
Journal:  Cancer Res       Date:  2014-01-21       Impact factor: 12.701

3.  The life history of 21 breast cancers.

Authors:  Serena Nik-Zainal; Peter Van Loo; David C Wedge; Ludmil B Alexandrov; Christopher D Greenman; King Wai Lau; Keiran Raine; David Jones; John Marshall; Manasa Ramakrishna; Adam Shlien; Susanna L Cooke; Jonathan Hinton; Andrew Menzies; Lucy A Stebbings; Catherine Leroy; Mingming Jia; Richard Rance; Laura J Mudie; Stephen J Gamble; Philip J Stephens; Stuart McLaren; Patrick S Tarpey; Elli Papaemmanuil; Helen R Davies; Ignacio Varela; David J McBride; Graham R Bignell; Kenric Leung; Adam P Butler; Jon W Teague; Sancha Martin; Goran Jönsson; Odette Mariani; Sandrine Boyault; Penelope Miron; Aquila Fatima; Anita Langerød; Samuel A J R Aparicio; Andrew Tutt; Anieta M Sieuwerts; Åke Borg; Gilles Thomas; Anne Vincent Salomon; Andrea L Richardson; Anne-Lise Børresen-Dale; P Andrew Futreal; Michael R Stratton; Peter J Campbell
Journal:  Cell       Date:  2012-05-17       Impact factor: 41.582

4.  NIH Image to ImageJ: 25 years of image analysis.

Authors:  Caroline A Schneider; Wayne S Rasband; Kevin W Eliceiri
Journal:  Nat Methods       Date:  2012-07       Impact factor: 28.547

Review 5.  Cancer as an evolutionary and ecological process.

Authors:  Lauren M F Merlo; John W Pepper; Brian J Reid; Carlo C Maley
Journal:  Nat Rev Cancer       Date:  2006-11-16       Impact factor: 60.716

6.  Tumour evolution inferred by single-cell sequencing.

Authors:  Nicholas Navin; Jude Kendall; Jennifer Troge; Peter Andrews; Linda Rodgers; Jeanne McIndoo; Kerry Cook; Asya Stepansky; Dan Levy; Diane Esposito; Lakshmi Muthuswamy; Alex Krasnitz; W Richard McCombie; James Hicks; Michael Wigler
Journal:  Nature       Date:  2011-03-13       Impact factor: 49.962

7.  Hypoxia contributes to melanoma heterogeneity by triggering HIF1α-dependent phenotype switching.

Authors:  Daniel S Widmer; Keith S Hoek; Phil F Cheng; Ossia M Eichhoff; Thomas Biedermann; Marieke I G Raaijmakers; Silvio Hemmi; Reinhard Dummer; Mitchell P Levesque
Journal:  J Invest Dermatol       Date:  2013-03-08       Impact factor: 8.551

Review 8.  Current issues in ER and HER2 testing by IHC in breast cancer.

Authors:  Allen M Gown
Journal:  Mod Pathol       Date:  2008-05       Impact factor: 7.842

9.  Quantitative image analysis of cellular heterogeneity in breast tumors complements genomic profiling.

Authors:  Yinyin Yuan; Henrik Failmezger; Oscar M Rueda; H Raza Ali; Stefan Gräf; Suet-Feung Chin; Roland F Schwarz; Christina Curtis; Mark J Dunning; Helen Bardwell; Nicola Johnson; Sarah Doyle; Gulisa Turashvili; Elena Provenzano; Sam Aparicio; Carlos Caldas; Florian Markowetz
Journal:  Sci Transl Med       Date:  2012-10-24       Impact factor: 17.956

10.  CellProfiler: image analysis software for identifying and quantifying cell phenotypes.

Authors:  Anne E Carpenter; Thouis R Jones; Michael R Lamprecht; Colin Clarke; In Han Kang; Ola Friman; David A Guertin; Joo Han Chang; Robert A Lindquist; Jason Moffat; Polina Golland; David M Sabatini
Journal:  Genome Biol       Date:  2006-10-31       Impact factor: 13.583
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  5 in total

1.  Ellipsoid Segmentation Model for Analyzing Light-Attenuated 3D Confocal Image Stacks of Fluorescent Multi-Cellular Spheroids.

Authors:  Michaël Barbier; Steffen Jaensch; Frans Cornelissen; Suzana Vidic; Kjersti Gjerde; Ronald de Hoogt; Ralph Graeser; Emmanuel Gustin; Yolanda T Chong
Journal:  PLoS One       Date:  2016-06-15       Impact factor: 3.240

Review 2.  Cancer evolution: mathematical models and computational inference.

Authors:  Niko Beerenwinkel; Roland F Schwarz; Moritz Gerstung; Florian Markowetz
Journal:  Syst Biol       Date:  2014-10-07       Impact factor: 15.683

3.  Intratumor heterogeneity defines treatment-resistant HER2+ breast tumors.

Authors:  Inga H Rye; Anne Trinh; Anna B Saetersdal; Daniel Nebdal; Ole Christian Lingjaerde; Vanessa Almendro; Kornelia Polyak; Anne-Lise Børresen-Dale; Åslaug Helland; Florian Markowetz; Hege G Russnes
Journal:  Mol Oncol       Date:  2018-09-21       Impact factor: 6.603

4.  You Are Not Working for Me; I Am Working with You.

Authors:  Florian Markowetz
Journal:  PLoS Comput Biol       Date:  2015-09-24       Impact factor: 4.475

Review 5.  Computational Cancer Biology: An Evolutionary Perspective.

Authors:  Niko Beerenwinkel; Chris D Greenman; Jens Lagergren
Journal:  PLoS Comput Biol       Date:  2016-02-04       Impact factor: 4.475
  5 in total

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