bioconductor: DNAcopy | Projects | Ecosyste.ms: Papers

10.3390/cancers12061599

Whole Exome Sequencing of Multi-Regional Biopsies from Metastatic Lesions to Evaluate Actionable Truncal Mutations Using a Single-Pass Percutaneous Technique
Cited by: 2
Author(s): Valerie Heong, Darwin Tay, Shane Goh, Bernard Wee, Tuan Zea Tan, Ross A. Soo, Brendan Pang, Diana Lim, Anil Gopinathan, Samuel G.W. Ow, Cheng Ean Chee, Boon Cher Goh, Soo‐Chin Lee, Wei Peng Yong, Andrea Li Ann Wong, Mohamed Feroz Mohd Omar, Richie Soong, David Sp Tan
Software Mentions: 1
Published: over 4 years ago

10.3390/cancers12092529

DNA FISH Diagnostic Assay on Cytological Samples of Thyroid Follicular Neoplasms
Cited by: 2
Author(s): Philippe Vielh, Zsuzsanna Balogh, Voïchita Suciu, Catherine Richon, Bastien Job, Guillaume Meurice, Alexander Valent, Ludovic Lacroix, Virginie Marty, Nelly Motté, Philippe Dessen, Bernard Caillou, Abir Al Ghuzlan, Jean Michel Bidart, Vladimir Lazar, Paul Hofman, Jean‐Yves Scoazec, Adel K. El‐Naggar, Martin Schlumberger
Software Mentions: 1
Published: about 4 years ago

10.3390/cancers11070997

In-Vitro and In-Vivo Establishment and Characterization of Bioluminescent Orthotopic Chemotherapy-Resistant Human Osteosarcoma Models in NSG Mice
Cited by: 10
Author(s): Maria Eugénia Marques Da Costa, Antonin Marchais, Anne Gomez‐Brouchet, Bastien Job, Noémie Assoun, Estelle Daudigeos-Dubus, Olivia Fromigué, Conceição Santos, Birgit Geoerger, Nathalie Gaspar
Software Mentions: 1
Published: over 5 years ago

10.1186/s40478-020-0882-4

H3F3A mutant allele specific imbalance in an aggressive subtype of diffuse midline glioma, H3 K27M-mutant
Cited by: 10
Author(s): Sachi Maeda, Fumiharu Ohka, Yusuke Okuno, Kosuke Aoki, Kazuya Motomura, Kazuhito Takeuchi, Hironao Kusakari, Nobuyuki Yanagisawa, Shinya Sato, Junya Yamaguchi, Kuniaki Tanahashi, Masaki Hashimoto, Akira Kato, Hiroyuki Shimizu, Yasushi Kitano, Shintaro Yamazaki, Shinji Yamashita, Hideo Takeshima, Keiko Shinjo, Yutaka Kondo, Toshihiko Wakabayashi, Atsushi Natsume
Software Mentions: 1
Published: almost 5 years ago

10.3390/cancers10010010

Mutations in EMT-Related Genes in ALK Positive Crizotinib Resistant Non-Small Cell Lung Cancers
Cited by: 32
Author(s): Jiacong Wei, Anthonie J. van der Wekken, Aly Saber, Miente Martijn Terpstra, Ed Schuuring, Wim Timens, T Jeroen N Hiltermann, Harry J.M. Groen, Anke van den Berg, Klaas Kok
Software Mentions: 1
Published: almost 7 years ago

10.1186/s12864-017-3531-y

Diversity and regulatory impact of copy number variation in the primate Macaca fascicularis
Cited by: 9
Author(s): Andreas R. Gschwind, Anjali Singh, Ulrich Certa, Alexandre Reymond, Tobias Heckel
Software Mentions: 1
Published: almost 8 years ago

10.1186/s12864-016-2754-7

Copy number variants in the sheep genome detected using multiple approaches
Cited by: 26
Author(s): Gemma Jenkins, Michael E. Goddard, Michael A. Black, Rüdiger Bräuning, B. Auvray, K. G. Dodds, James W. Kijas, Noelle E. Cockett, John C. McEwan
Software Mentions: 1
Published: over 8 years ago

10.15252/msb.20166951

Disentangling genetic and epigenetic determinants of ultrafast adaptation
Cited by: 9
Author(s): Arne B. Gjuvsland, Enikö Zörgö, Jeevan Karloss Antony Samy, Simon Stenberg, İbrahim Halil Demirsoy, Francisco S. Roque, Ewa Maciaszczyk‐Dziubinska, Magdalena Migocka, Elisa Alonso-Pérez, Martin Zackrisson, Robert Wysocki, Markus J. Tamás, Inge Jonassen, Stig W. Omholt, Jonas Warringer
Software Mentions: 1
Published: almost 8 years ago

10.1186/1471-2105-10-424

CHESS (CgHExpreSS): A comprehensive analysis tool for the analysis of genomic alterations and their effects on the expression profile of the genome
Cited by: 6
Author(s): Mi-Kyung Lee, Yangseok Kim
Software Mentions: 1
Published: almost 15 years ago

10.1371/journal.pone.0015661

Somatic Mutation Profiles of MSI and MSS Colorectal Cancer Identified by Whole Exome Next Generation Sequencing and Bioinformatics Analysis
Cited by: 209
Author(s): Bernd Timmermann, Martin Kerick, Christina Roehr, Axel Fischer, Melanie Isau, Stefan Boerno, Andrea Wunderlich, Christian Barmeyer, Petra Seemann, Jana Koenig, Michael Lappé, Andreas W. Kuß, Masoud Garshasbi, Lars Bertram, Kathrin Trappe, Martin Werber, Bernhard G. Herrmann, Kurt Zatloukal, Hans Lehrach, Michal R. Schweiger
Software Mentions: 1
Published: almost 14 years ago

10.1038/srep29267

Independent Tumor Origin in Two Cases of Synchronous Bilateral Clear Cell Renal Cell Carcinoma
Cited by: 7
Author(s): Zhengguo Ji, Jialu Zhao, Tian Zhao, Yong Chol Han, Yujun Zhang, Haihong Ye
Software Mentions: 1
Published: over 8 years ago

10.1186/1471-2105-9-243

MD-SeeGH: a platform for integrative analysis of multi-dimensional genomic data
Cited by: 28
Author(s): Bryan Chi, Ronald J. deLeeuw, Bradley P. Coe, Raymond T. Ng, Calum MacAulay, Wan L. Lam
Software Mentions: 1
Published: over 16 years ago

10.3390/microarrays2030171

Comparative Analysis of CNV Calling Algorithms: Literature Survey and a Case Study Using Bovine High-Density SNP Data
Cited by: 36
Author(s): Lingyang Xu, Yali Hou, Derek M. Bickhart, Jiuzhou Song, George E. Liu
Software Mentions: 1
Published: over 11 years ago

10.1371/journal.pone.0158995

Comprehensive Analysis of Genome Rearrangements in Eight Human Malignant Tumor Tissues
Cited by: 7
Author(s): Stefanie Marczok, Birgit Bortz, Chong Wang, Heike Pospisil
Software Mentions: 1
Published: over 8 years ago

10.1038/srep41268

Genomic structural variations for cardiovascular and metabolic comorbidity
Cited by: 27
Author(s): М. С. Назаренко, А. А. Слепцов, I. N. Lebedev, N. A. Skryabin, А. В. Марков, М. В. Голубенко, I A Koroleva, Anton N. Kazancev, O. L. Barbarash, V. P. Puzyrev
Software Mentions: 1
Published: almost 8 years ago

10.3389/fgene.2013.00217

Evaluation of calling algorithms for array-CGH
Cited by: 11
Author(s): Snigdha Roy, Alison A. Motsinger‐Reif
Software Mentions: 1
Published: almost 12 years ago

10.3389/fgene.2020.543528

Genomic Analysis of Korean Patient With Microcephaly
Cited by: 7
Author(s): Jiwon Lee, Jong Eun Park, Chung Lee, Ah Reum Kim, Byung Joon Kim, Woong-Yang Park, Chang‐Seok Ki, Jeehun Lee
Software Mentions: 1
Published: almost 4 years ago

10.1186/1752-0509-5-121

Inferring causal genomic alterations in breast cancer using gene expression data
Cited by: 58
Author(s): Linh M. Tran, Bin Zhang, Zhan Zhang, Chunsheng Zhang, Tao Xie, John Lamb, Hongyue Dai, Eric E. Schadt, Jun Zhu
Software Mentions: 1
Published: over 13 years ago

10.1534/g3.112.004689

A Discovery Resource of Rare Copy Number Variations in Individuals with Autism Spectrum Disorder
Cited by: 166
Author(s): Aparna Prasad, Daniele Merico, Bhooma Thiruvahindrapuram, John Wei, Anath C. Lionel, Daisuke Sato, Jessica Rickaby, Chao Lü, Péter Szatmári, Wendy Roberts, Bridget A. Fernandez, Christian R. Marshall, Eli Hatchwell, Peggy S. Eis, Stephen W. Scherer
Software Mentions: 1
Published: almost 12 years ago

10.1371/journal.pgen.1004414

ATRA-Induced Cellular Differentiation and CD38 Expression Inhibits Acquisition of BCR-ABL Mutations for CML Acquired Resistance
Cited by: 30
Author(s): Zhiqiang Wang, Zheng Liu, Xiwei Wu, Su Chu, Jinhui Wang, Hongfeng Yuan, Mendel Roth, Yate-Ching Yuan, Smita Bhatia, Wenyong Chen
Software Mentions: 1
Published: over 10 years ago

10.1186/s13040-021-00253-y

Genetic risk score for ovarian cancer based on chromosomal-scale length variation
Cited by: 3
Author(s): Christopher Toh, James P. Brody
Software Mentions: 1
Published: over 3 years ago

10.1534/genetics.116.198895

Experimental Evolution Reveals Favored Adaptive Routes to Cell Aggregation in Yeast
Cited by: 68
Author(s): Elyse A. Hope, Clara J. Amorosi, Aaron W. Miller, Kolena Dang, Caiti Smukowski Heil, Maitreya J. Dunham
Software Mentions: 1
Published: over 7 years ago

10.1186/1471-2156-12-29

Comparative analysis of copy number variation detection methods and database construction
Cited by: 20
Author(s): Atsushi Koike, Nao Nishida, Daisuke Yamashita, Katsushi Tokunaga
Software Mentions: 1
Published: almost 14 years ago

10.1186/gb-2008-9-1-r13

An improved method for detecting and delineating genomic regions with altered gene expression in cancer
Cited by: 16
Author(s): Björn Nilsson, Mikael Johansson, Anders Heyden, Sven Nelander, Thoas Fioretos
Software Mentions: 1
Published: almost 17 years ago

10.1186/gb-2009-10-11-r128

Genome Alteration Print (GAP): a tool to visualize and mine complex cancer genomic profiles obtained by SNP arrays
Cited by: 175
Author(s): Tatiana Popova, Élodie Manié, Dominique Stoppa‐Lyonnet, Guillem Rigaill, Emmanuel Barillot, Marc‐Henri Stern
Software Mentions: 1
Published: almost 16 years ago

10.1186/gb-2012-13-8-r73

Novel origins of copy number variation in the dog genome
Cited by: 69
Author(s): J. Andrew Berglund, Elisa Nevalainen, Anna-Maja Molin, Michele Perloski, Catherine André, Michael C. Zody, Ted Sharpe, Christophe Hitte, Kerstin Lindblad‐Toh, Hannes Lohi, Matthew T. Webster
Software Mentions: 1
Published: almost 13 years ago

10.1186/gb-2013-14-3-r24

Patchwork: allele-specific copy number analysis of whole-genome sequenced tumor tissue
Cited by: 66
Author(s): Markus Mayrhofer, Sebastian DiLorenzo, Anders Isaksson
Software Mentions: 1
Published: almost 12 years ago

10.1186/s13059-014-0432-0

Deep sequencing reveals clonal evolution patterns and mutation events associated with relapse in B-cell lymphomas
Cited by: 46
Author(s): Yanwen Jiang, David Redmond, Kun Nie, Ken Eng, Thomas Clozel, Peter Martin, Leonard Tan, Ari Melnick, Wayne Tam, Olivier Elemento
Software Mentions: 1
Published: over 10 years ago

10.1371/journal.pgen.1004041

Molecular Specificity, Convergence and Constraint Shape Adaptive Evolution in Nutrient-Poor Environments
Cited by: 99
Author(s): Jae‐Hee Hong, David Gresham
Software Mentions: 1
Published: almost 11 years ago

10.1371/journal.pgen.1002202

Hunger Artists: Yeast Adapted to Carbon Limitation Show Trade-Offs under Carbon Sufficiency
Cited by: 123
Author(s): Jared W. Wenger, Jeffrey S Piotrowski, Saisubramanian Nagarajan, Kami Chiotti, Gavin Sherlock, Frank Rosenzweig
Software Mentions: 1
Published: over 13 years ago

10.1186/s13059-019-1732-1

SMURF-seq: efficient copy number profiling on long-read sequencers
Cited by: 9
Author(s): Rishvanth K. Prabakar, Liya Xu, James Hicks, Andrew D. Smith
Software Mentions: 1
Published: over 5 years ago

10.1371/journal.pgen.1000734

Maize Inbreds Exhibit High Levels of Copy Number Variation (CNV) and Presence/Absence Variation (PAV) in Genome Content
Cited by: 477
Author(s): Nathan M. Springer, Kai Ying, Yan Fu, Tieming Ji, Cheng‐Ting Yeh, Yi Jia, Weiwei Wu, Todd Richmond, Jacob O. Kitzman, Heidi Rosenbaum, A. Leonardo Iniguez, W. Brad Barbazuk, Jeffrey A. Jeddeloh, Dan Nettleton, Patrick S. Schnable
Software Mentions: 1
Published: about 15 years ago

10.1155/2014/282815

An ANOCEF Genomic and Transcriptomic Microarray Study of the Response to Irinotecan and Bevacizumab in Recurrent Glioblastomas
Cited by: 7
Author(s): Julien Laffaire, Anna Luisa Di Stefano, Olivier Chinot, Ahmed Idbaïh, Jaime Gállego Pérez-Larraya, Yannick Marie, Nadia Vintonenko, Blandine Boisselier, Patrizia Farina, Jean‐Yves Delattre, Dominique Figarella‐Branger, Jérôme Honnorat, Marc Sanson, François Ducray
Software Mentions: 1
Published: almost 11 years ago

10.1186/1471-2105-10-12

Estimation of tumor heterogeneity using CGH array data
Cited by: 21
Author(s): Kai Wang, Jian Li, Shengting Li, Lars Bolund, Carsten Wiuf
Software Mentions: 1
Published: almost 16 years ago

10.1371/journal.pcbi.1004871

Fast Bayesian Inference of Copy Number Variants using Hidden Markov Models with Wavelet Compression
Cited by: 5
Author(s): John Wiedenhoeft, Eric Brugel, Alexander Schliep
Software Mentions: 1
Published: over 8 years ago

10.1200/CCI.19.00171

Integrated Computational Pipeline for Single-Cell Genomic Profiling
Cited by: 2
Author(s): Lubomir Chorbadjiev, Jude Kendall, Joan Alexander, Viacheslav Zhygulin, Junyan Song, Michael Wigler, Alexander Krasnitz
Software Mentions: 1
Published: about 4 years ago

10.1186/2043-9113-1-20

FISH Oracle: a web server for flexible visualization of DNA copy number data in a genomic context
Cited by: 13
Author(s): Malte Mäder, Ronald Simon, Sascha Steinbiss, Stefan Kurtz
Software Mentions: 1
Published: almost 14 years ago

10.1371/journal.pbio.1002155

The Fitness Consequences of Aneuploidy Are Driven by Condition-Dependent Gene Effects
Cited by: 88
Author(s): Anna B. Sunshine, Célia Payen, Giang T. Ong, Ivan Liachko, Kean Ming Tan, Maitreya J. Dunham
Software Mentions: 1
Published: over 9 years ago

10.1186/1471-2407-10-295

Establishment and characterization of a new human pancreatic adenocarcinoma cell line with high metastatic potential to the lung
Cited by: 46
Author(s): Tatyana Kalinina, Cenap Güngör, Sabrina Thieltges, Maren Möller-Krull, Eva Maria Murga Penas, Daniel Wicklein, Thomas Streichert, Udo Schumacher, Viacheslav Kalinin, Ronald Simon, Benjamin Otto, Judith Dierlamm, Heidi Schwarzenbach, Katharina E. Effenberger, Maximilian Bockhorn, Jakob R. Izbicki, Emre F. Yekebas
Software Mentions: 1
Published: over 14 years ago

10.1371/journal.pone.0005548

Genome-Wide Massively Parallel Sequencing of Formaldehyde Fixed-Paraffin Embedded (FFPE) Tumor Tissues for Copy-Number- and Mutation-Analysis
Cited by: 150
Author(s): Michal R. Schweiger, Martin Kerick, Bernd Timmermann, Marcus W. Albrecht, Tatiana Borodina, Dmitri Parkhomchuk, Kurt Zatloukal, Hans Lehrach
Software Mentions: 1
Published: over 15 years ago

10.1038/srep16106

Statistical Approach to Decreasing the Error Rate of Noninvasive Prenatal Aneuploid Detection caused by Maternal Copy Number Variation
Cited by: 13
Author(s): Han Zhang, Yangyu Zhao, Jing Song, Qiying Zhu, Hua Yang, Mingzhu Zheng, Zhaoling Xuan, Yuan Wei, Yang Chen, Pengbo Yuan, Yu Yang, Dawei Li, Junbin Liang, Fan Liu, Chongjian Chen, Jie Qiao
Software Mentions: 1
Published: about 9 years ago

10.1038/srep11334

Deep intronic GPR143 mutation in a Japanese family with ocular albinism
Cited by: 26
Author(s): Takuya Naruto, Nobuhiko Okamoto, Kiyoshi Masuda, Tamio Endo, Yoshikazu Hatsukawa, Tomohiro Kohmoto, Issei Imoto
Software Mentions: 1
Published: over 9 years ago

10.1371/journal.pone.0063219

CNVrd, a Read-Depth Algorithm for Assigning Copy-Number at the FCGR Locus: Population-Specific Tagging of Copy Number Variation at FCGR3B
Cited by: 12
Author(s): Hoang Nguyen, Tony R. Merriman, Michael A. Black
Software Mentions: 1
Published: over 11 years ago

10.1186/1471-2407-14-121

Impact of chromosomal instability on colorectal cancer progression and outcome
Cited by: 35
Author(s): Béatrice Orsetti, Janick Sèlves, Caroline Bascoul-Mollevi, Laurence Lasorsa, K. Gordien, Fréderic Bibeau, Blandine Massemin, François Paraf, Isabelle Soubeyran, Isabelle Hostein, Valérie Dapremont, Rosine Guimbaud, Christophe Cazaux, Michel Longy, Charles Theillet
Software Mentions: 1
Published: over 10 years ago

10.1371/journal.pone.0051422

Estimation of Copy Number Alterations from Exome Sequencing Data
Cited by: 20
Author(s): Rafael Valdés-Mas, Sı́lvia Beà, Diana Puente, Carlos López‐Otín, Xosé S. Puente
Software Mentions: 1
Published: almost 12 years ago

10.1038/s41598-020-80948-0

Detectable chromosome X mosaicism in males is rarely tolerated in peripheral leukocytes
Cited by: 10
Author(s): Weiyin Zhou, Shu-Hong Lin, Seema Khan, Meredith Yeager, Stephen J. Chanock, Mitchell J. Machiela
Software Mentions: 1
Published: almost 4 years ago

10.1371/journal.pone.0149162

Exome Sequencing in Classic Hairy Cell Leukaemia Reveals Widespread Variation in Acquired Somatic Mutations between Individual Tumours Apart from the Signature BRAF V(600)E Lesion
Cited by: 17
Author(s): Nicola J. Weston-Bell, William Tapper, Jane Gibson, Dean Bryant, Yurany Moreno, McCormick John, Sarah Ennis, Hanneke C. Kluin-Nelemans, Andrew Collins, Surinder S. Sahota
Software Mentions: 1
Published: almost 9 years ago

10.1186/1471-2164-8-84

A new look towards BAC-based array CGH through a comprehensive comparison with oligo-based array CGH
Cited by: 47
Author(s): Nicolas Wicker, Annaïck Carles, Ian G. Mills, Maija Wolf, Abhi Veerakumarasivam, Henrik Edgren, F. Boileau, Bohdan Wasylyk, Jack A. Schalken, David E. Neal, Olli Kallioniemi, Olivier Poch
Software Mentions: 1
Published: almost 18 years ago

10.1186/1471-2164-11-88

Whole-genome sequencing of a laboratory-evolved yeast strain
Cited by: 89
Author(s): Carlos L. Araya, Célia Payen, Maitreya J. Dunham, Stanley Fields
Software Mentions: 1
Published: almost 15 years ago

10.1186/s12859-018-2565-8

DBS: a fast and informative segmentation algorithm for DNA copy number analysis
Cited by: 83
Author(s): Jing Ruan, Zhen Liu, Ming Sun, Yue Wang, Junqiu Yue, Guoqiang Yu
Software Mentions: 1
Published: almost 6 years ago

10.1371/journal.pone.0004150

Allele-Specific Gene Expression Is Widespread Across the Genome and Biological Processes
Cited by: 52
Author(s): Ricardo Palácios, Élodie Gazave, Joaquín Goñi, Gabriel Piedrafita, Olga Fernando, Arcadi Navarro, Pablo Villoslada
Software Mentions: 1
Published: almost 16 years ago

10.1371/journal.pone.0035897

Identity by Descent Mapping of Founder Mutations in Cancer Using High-Resolution Tumor SNP Data
Cited by: 8
Author(s): Éric Letouzé, Ahmadou Bamba Sow, Fabien Petel, Roberto Rosati, Bonald C. Figueiredo, Nelly Burnichon, Anne-Paule Gimenez-Roqueplo, Enzo Lalli, Aurélien de Reyniès
Software Mentions: 1
Published: over 12 years ago

10.5402/2012/710692

Comparison of Whole Genome Amplification Methods for Analysis of DNA Extracted from Microdissected Early Breast Lesions in Formalin-Fixed Paraffin-Embedded Tissue
Cited by: 4
Author(s): Nona Arneson, Juan Antonio Moreno, Vladimir V. Iakovlev, Arezou A. Ghazani, Keisha Warren, David R. McCready, Igor Jurišica, Susan J. Done
Software Mentions: 1
Published: over 12 years ago

Projects: bioconductor: DNAcopy

Papers Mentioning DNAcopy 154