bioconductor: DNAcopy | Projects | Ecosyste.ms: Papers

10.15252/emmm.201809443

<scp>PDX</scp> models recapitulate the genetic and epigenetic landscape of pediatric T‐cell leukemia
Cited by: 35
Author(s): Paulina Richter-Pechańska, Joachim Kunz, Beat Bornhäuser, Caroline Von Knebel Doeberitz, Tobias Rausch, Büşra Erarslan-Uysal, Yassen Assenov, Viktoras Frismantas, Blerim Marovca, Sebastian M. Waszak, Martin Zimmermann, Julia Seemann, Margit Happich, Martin Stanulla, Martin Schrappe, Gunnar Cario, Gabriele Escherich, Kseniya Bakharevich, Renate Kirschner-Schwabe, Cornelia Eckert, Martina U. Muckenthaler, Jan O. Korbel, Jean‐Pierre Bourquin, Andreas E. Kulozik
Software Mentions: 12
Published: about 6 years ago

10.1007/s00401-020-02226-7

Patient-derived organoids and orthotopic xenografts of primary and recurrent gliomas represent relevant patient avatars for precision oncology
Cited by: 69
Author(s): Anna Golebiewska, Ann-Christin Hau, Anaïs Oudin, Daniel Stieber, Yahaya A Yabo, Virginie Baus, Vanessa Barthelemy, Eliane Klein, Sébastien Bougnaud, Olivier Keunen, May Wantz, Alessandro Michelucci, Virginie Neirinckx, Arnaud Muller, Tony Kaoma, Petr V. Nazarov, Francisco Azuaje, Alfonso De Falco, Ben Flies, Lorraine Richart, Suresh Poovathingal, Thaís Arns, Kamil Grzyb, Andreas Möck, Christel Herold‐Mende, Anne Steinø, Dennis Brown, Patrick May, Hrvoje Miletić, Tathiane M. Malta, Houtan Noushmehr, Yong-Jun Kwon, Winnie Jahn, Barbara Klink, Georgette Tanner, Lucy F. Stead, Michel Mittelbronn, Alexander Skupin, Frank Hutter, Rolf Bjerkvig, Simone P. Niclou
Software Mentions: 12
Published: about 4 years ago

10.1016/j.ccell.2017.08.017

Integrated Molecular Meta-Analysis of 1,000 Pediatric High-Grade and Diffuse Intrinsic Pontine Glioma
Cited by: 662
Author(s): Alan Mackay, Anna Burford, Diana Carvalho, Elisa Izquierdo, Janat Fazal-Salom, Kathryn R. Taylor, Lynn Bjerke, Matthew Clarke, Maria Vinci, Meera Nandhabalan, Sara Temelso, Sergey Popov, Valeria Molinari, Pichai Raman, Angela J. Waanders, Harry Han, Saumya Gupta, Lynley V. Marshall, Stergios Zacharoulis, Sucheta Vaidya, Henry Mandeville, Leslie Bridges, Andrew Martin, Safa Al‐Sarraj, Christopher Chandler, Ho Keung Ng, Xingang Li, Kun Mu, Saoussen Trabelsi, Dorra H’mida-Ben Brahim, Alexei N. Kisljakov, Д. М. Коновалов, Andrew S. Moore, Ángel M. Carcaboso, Mariona Suñol, Carmen de Torres, Ofelia Cruz, Jaume Mora, Л. И. Шац, João N. Stávale, Lucas Tadeu Bidinotto, Rui Manuel Reis, Natacha Entz‐Werlé, Michael Farrell, Jane Cryan, Darach Crimmins, John Caird, Jane Pears, Michelle Monje, Marie‐Anne Debily, David Castel, Jacques Grill, Cynthia Hawkins, Hamid Nikbakht, Nada Jabado, Suzanne J. Baker, Stefan M. Pfister, David Jones, Maryam Fouladi, André O. von Bueren, Michael Baudis, Adam Resnick, Chris Jones
Software Mentions: 11
Published: about 7 years ago

10.1155/2009/201325

Analysis of Array-CGH Data Using the R and Bioconductor Software Suite
Cited by: 8
Author(s): Winfried Hofmann, Anja Weigmann, Marcel Tauscher, Britta Skawran, Tim Focken, R Buurman, Luzie U. Wingen, Brigitte Schlegelberger, Doris Steinemann
Software Mentions: 11
Published: almost 16 years ago

10.1155/2014/910390

biomvRhsmm:Genomic Segmentation with Hidden Semi-Markov Model
Cited by: 4
Author(s): Yang Du, Eduard Muráni, Siriluck Ponsuksili, Klaus Wimmers
Software Mentions: 10
Published: almost 11 years ago

10.1186/s13058-018-1022-y

Clonal relatedness in tumour pairs of breast cancer patients
Cited by: 14
Author(s): Jana Biermann, Toshima Z. Parris, Szilárd Nemes, Anna Danielsson, Hanna Engqvist, Elisabeth Werner Rönnerman, Eva Forssell-Aronsson, Anikó Kovács, Per Karlsson, Khalil Helou
Software Mentions: 8
Published: over 6 years ago

10.1371/journal.pone.0164292

Upregulation of HLA Expression in Primary Uveal Melanoma by Infiltrating Leukocytes
Cited by: 55
Author(s): T. Huibertus van Essen, Sake I. van Pelt, Inge H. G. Bronkhorst, Mieke Versluis, Fariba Némati, Cécile Laurent, Gregorius P M Luyten, Thorbald van Hall, Peter J. van den Elsen, Pieter A. van der Velden, Didier Decaudin, Martine J. Jager
Software Mentions: 8
Published: about 8 years ago

10.1371/journal.pone.0000737

ADaCGH: A Parallelized Web-Based Application and R Package for the Analysis of aCGH Data
Cited by: 26
Author(s): Ramón Díaz‐Uriarte, Oscar M. Rueda
Software Mentions: 8
Published: over 17 years ago

10.1186/s13062-016-0110-0

Altools: a user friendly NGS data analyser
Cited by: 5
Author(s): Salvatore Camiolo, Gaurav Sablok, Andrea Porceddu
Software Mentions: 7
Published: almost 9 years ago

10.1186/s12859-018-2140-3

iSeg: an efficient algorithm for segmentation of genomic and epigenomic data
Cited by: 9
Author(s): Senthil Balaji Girimurugan, Yuhang Liu, Pei-Yau Lung, Daniel Vera, Jane A Dennis, Hank W. Bass, Jinfeng Zhang
Software Mentions: 7
Published: over 6 years ago

10.1186/1471-2105-12-267

SeqGene: a comprehensive software solution for mining exome- and transcriptome- sequencing data
Cited by: 39
Author(s): Xutao Deng
Software Mentions: 7
Published: over 13 years ago

10.1155/2012/876976

A High-Throughput Computational Framework for Identifying Significant Copy Number Aberrations from Array Comparative Genomic Hybridisation Data
Cited by: 1
Author(s): Ian Roberts, Stephanie A. Carter, Cinzia G. Scarpini, Konstantina Karagavriilidou, Jenny Barna, M. Calleja, Nicholas Coleman
Software Mentions: 7
Published: over 12 years ago

10.1534/g3.117.300489

DrosophilaLarval Brain Neoplasms Present Tumour-Type Dependent Genome Instability
Cited by: 4
Author(s): Fabrizio Rossi, Camille Stephan‐Otto Attolini, José Luis Mosquera, Cayetano González
Software Mentions: 6
Published: almost 7 years ago

10.1186/1471-2105-14-164

Learning smoothing models of copy number profiles using breakpoint annotations
Cited by: 44
Author(s): Toby Dylan Hocking, Gudrun Schleiermacher, Isabelle Janoueix‐Lerosey, Valentina Boeva, Julie Cappo, Olivier Delattre, Francis Bach, Jean-Philippe Vert
Software Mentions: 6
Published: over 11 years ago

10.1371/journal.pone.0205406

Examining the contribution of smoking and HPV towards the etiology of oral cavity squamous cell carcinoma using high-throughput sequencing: A prospective observational study
Cited by: 10
Author(s): Andrew P Zammit, Rohit Anthony Sinha, Caroline Cooper, Christopher Perry, Ian H. Frazer, Zewen Kelvin Tuong
Software Mentions: 6
Published: about 6 years ago

10.1186/s13073-021-00931-w

Multi-site tumor sampling highlights molecular intra-tumor heterogeneity in malignant pleural mesothelioma
Cited by: 25
Author(s): Clément Meiller, François Montagne, Théo Z. Hirsch, Stefano Caruso, Julien De Wolf, Quentin Bayard, Jean-Baptiste Assié, Léa Meunier, Yuna Blum, Lisa Quetel, Laure Gibault, Ecaterina Pintilie, Cécile Badoual, Sarah Humez, Françoise Galateau-Sallé, Marie‐Christine Copin, Éric Letouzé, Arnaud Scherpereel, Jessica Zucman–Rossi, Françoise Le Pimpec‐Barthes, Marie-Claude Jaurand, Didier Jean
Software Mentions: 6
Published: over 3 years ago

10.1371/journal.pone.0086272

Robust Regression Analysis of Copy Number Variation Data based on a Univariate Score
Cited by: 4
Author(s): Glen A. Satten, Andrew S. Allen, Morna Ikeda, Jennifer G. Mullé, Stephen T. Warren
Software Mentions: 5
Published: almost 11 years ago

10.1371/journal.pone.0014077

Analyses of Copy Number Variation of GK Rat Reveal New Putative Type 2 Diabetes Susceptibility Loci
Cited by: 10
Author(s): Zhiqiang Ye, Shen Niu, Yang Yu, Hui Yu, Bao Hong Liu, Rong Xia Li, Hua Xiao, Rong Zeng, Yi Xue Li, Jia Wu, Yuan Yuan Li
Software Mentions: 5
Published: about 14 years ago

10.1186/1471-2105-14-S11-S1

Computational tools for copy number variation (CNV) detection using next-generation sequencing data: features and perspectives
Cited by: 426
Author(s): Min Zhao, Qingguo Wang, Quan Wang, Peilin Jia, Zhongming Zhao
Software Mentions: 5
Published: over 11 years ago

10.1038/s42003-019-0401-y

High-throughput single-cell whole-genome amplification through centrifugal emulsification and eMDA
Cited by: 33
Author(s): Yusi Fu, Fangli Zhang, Xiannian Zhang, Junlong Yin, Meijie Du, Mi Jiang, Lu Liu, Jie Li, Yanyi Huang, Jianbin Wang
Software Mentions: 5
Published: over 5 years ago

10.1371/journal.pcbi.1008012

Assessing the performance of methods for copy number aberration detection from single-cell DNA sequencing data
Cited by: 24
Author(s): Xian Mallory, Mohammadamin Edrisi, Nicholas E. Navin, Luay Nakhleh
Software Mentions: 5
Published: over 4 years ago

10.18632/oncotarget.25329

Genome-wide multi-omics profiling of the 8p11-p12 amplicon in breast carcinoma
Cited by: 13
Author(s): Toshima Z. Parris, Elisabeth Werner Rönnerman, Hanna Engqvist, Jana Biermann, Katarina Truvé, Szilárd Nemes, Eva Forssell-Aronsson, Giovanni Solinas, Anikó Kovács, Per Karlsson, Khalil Helou
Software Mentions: 5
Published: over 6 years ago

10.1186/1471-2105-8-145

A forward-backward fragment assembling algorithm for the identification of genomic amplification and deletion breakpoints using high-density single nucleotide polymorphism (SNP) array
Cited by: 24
Author(s): Tianwei Yu, Hui Ye, Wei Sun, Ker Chau Li, Zugen Chen, Sharoni Jacobs, Dione K. Bailey, David T. Wong, Xiaofeng Zhou
Software Mentions: 5
Published: over 17 years ago

10.1007/s00401-017-1743-5

Same-day genomic and epigenomic diagnosis of brain tumors using real-time nanopore sequencing
Cited by: 120
Author(s): Philipp Euskirchen, Franck Bielle, Karim Labreche, Wigard P. Kloosterman, Shai Rosenberg, Maïlys Daniau, Charlotte Schmitt, Julien Masliah‐Planchon, Franck Bourdeaut, Caroline Dehais, Yannick Marie, Jean‐Yves Delattre, Ahmed Idbaïh
Software Mentions: 4
Published: over 7 years ago

10.1186/1471-2407-10-78

Selective regain of egfr gene copies in CD44+/CD24-/lowbreast cancer cellular model MDA-MB-468
Cited by: 20
Author(s): Konstantin Agelopoulos, Burkhard Greve, Hartmut Schmidt, Heike Pospisil, Stefan Kurtz, Kai Bartkowiak, Antje Andreas, Marek Wieczorek, Eberhard Korsching, Horst Buerger, Burkhard Brandt
Software Mentions: 4
Published: almost 15 years ago

10.1186/1471-2164-11-441

Array comparative genomic hybridization analysis of Trichoderma reesei strains with enhanced cellulase production properties
Cited by: 80
Author(s): Marika Vitikainen, Mikko Arvas, Tiina Pakula, Merja Oja, Merja Penttilä, Markku Saloheimo
Software Mentions: 4
Published: almost 15 years ago

10.1155/2013/270362

A Case Report and Genetic Characterization of a Massive Acinic Cell Carcinoma of the Parotid with Delayed Distant Metastases
Cited by: 5
Author(s): Anthony C. Nichols, Michelle Chan-Seng-Yue, John Yoo, Sumit Agrawal, Maud H.W. Starmans, Daryl Waggott, Nicholas J. Harding, Samuel Dowthwaite, David A. Palma, Kevin Fung, Bret Wehrli, Danielle MacNeil, Philippe Lambin, Eric Winquist, James Koropatnick, Joe S. Mymryk, Paul C. Boutros, John W. Barrett
Software Mentions: 4
Published: almost 12 years ago

10.1371/journal.pone.0003916

A Snapshot of CNVs in the Pig Genome
Cited by: 110
Author(s): João Fadista, Marianne Nygaard, Lars‐Erik Holm, Bo Thomsen, Christian Berthou
Software Mentions: 4
Published: about 16 years ago

10.1371/journal.pone.0078143

SomatiCA: Identifying, Characterizing and Quantifying Somatic Copy Number Aberrations from Cancer Genome Sequencing Data
Cited by: 28
Author(s): Mengjie Chen, Murat Günel, Hongyu Zhao
Software Mentions: 4
Published: about 11 years ago

10.1371/journal.pone.0195334

iCopyDAV: Integrated platform for copy number variations—Detection, annotation and visualization
Cited by: 38
Author(s): Prashanthi Dharanipragada, Sriharsha Vogeti, Nita Parekh
Software Mentions: 4
Published: over 6 years ago

10.1371/journal.pone.0239966

Analysis of mutational and proteomic heterogeneity of gastric cancer suggests an effective pipeline to monitor post-treatment tumor burden using circulating tumor DNA
Cited by: 2
Author(s): Noriyuki Sasaki, Takeshi Iwaya, Tadatoshi Chiba, Masashi Fujita, Ju Zhang, Fumitaka Endo, Mizunori Yaegashi, Tsuyoshi Hachiya, Ryo Sugimoto, Tamotsu Sugai, Doris R. Siwak, Lance A. Liotta, Yiling Lu, Gordon B. Mills, Hidewaki Nakagawa, Satoshi Nishizuka
Software Mentions: 4
Published: about 4 years ago

10.1371/journal.pone.0145176

Mutational Landscapes of Sequential Prostate Metastases and Matched Patient Derived Xenografts during Enzalutamide Therapy
Cited by: 26
Author(s): Manish Kohli, Liguo Wang, Fang Xie, Hugues Sicotte, Ping Yin, Scott M. Dehm, Steven N. Hart, Peter T. Vedell, Poulami Barman, Rui Qin, Douglas W. Mahoney, Rachel E. Carlson, Jeanette E. Eckel‐Passow, Thomas D. Atwell, Patrick W. Eiken, Brendan P. McMenomy, Eric D. Wieben, Gautam Jha, Rafael E. Jimenez, Richard M. Weinshilboum, Liewei M Wang
Software Mentions: 4
Published: about 9 years ago

10.3390/cancers13051126

Transformed Canine and Murine Mesenchymal Stem Cells as a Model for Sarcoma with Complex Genomics
Cited by: 5
Author(s): Natasja Franceschini, Bas Verbruggen, Marianna A. Tryfonidou, Alwine B. Kruisselbrink, Hans J. Baelde, Karin E. de Visser, Károly Szuhai, Anne‐Marie Cleton‐Jansen, Judith V.M.G. Bovée
Software Mentions: 4
Published: almost 4 years ago

10.1038/cr.2017.82

Single-cell multi-omics sequencing of mouse early embryos and embryonic stem cells
Cited by: 262
Author(s): Fan Guo, Lin Li, Jingyun Li, Xinglong Wu, Boqiang Hu, Ping Zhu, Lu Wen, Fuchou Tang
Software Mentions: 4
Published: over 7 years ago

10.1186/s13148-020-00877-7

Methylome profiling of young adults with depression supports a link with immune response and psoriasis
Cited by: 10
Author(s): Coral Lapsley, Rachelle E Irwin, Margaret McLafferty, Sara Jayne Thursby, Siobhan O’Neill, Anthony J. Bjourson, Colum P. Walsh, Elaine Murray
Software Mentions: 4
Published: over 4 years ago

10.2174/138920209787581244

Using Free and Open-Source Bioconductor Packages to Analyze Array Comparative Genomics Hybridization (aCGH) Data
Cited by: 2
Author(s): Simon Lin, Pan Du, Nadereh Jafari, Toru Ouchi
Software Mentions: 4
Published: almost 16 years ago

10.1186/s13059-016-0945-9

Application of single-cell RNA sequencing in optimizing a combinatorial therapeutic strategy in metastatic renal cell carcinoma
Cited by: 163
Author(s): Kyu‐Tae Kim, Hye Won Lee, Hae‐Ock Lee, Hye Jin Song, Da Eun Jeong, Sang Hyun Shin, Hyunho Kim, Yoojin Shin, Do‐Hyun Nam, Byong Chang Jeong, David G. Kirsch, Kyeung Min Joo, Woong-Yang Park
Software Mentions: 4
Published: over 8 years ago

10.1016/j.isci.2021.102889

LiquidCNA: Tracking subclonal evolution from longitudinal liquid biopsies using somatic copy number alterations
Cited by: 5
Author(s): Eszter Lakatos, Helen Hockings, Maximilian Mossner, Weini Huang, Michelle Lockley, Trevor A. Graham
Software Mentions: 4
Published: over 3 years ago

10.1186/s13059-020-02092-2

PiggyBac mutagenesis and exome sequencing identify genetic driver landscapes and potential therapeutic targets of EGFR-mutant gliomas
Cited by: 16
Author(s): Imran Noorani, Jorge de la Rosa, Yoon Ha Choi, Alexander Strong, Hannes Ponstingl, M. Vijayabaskar, Jusung Lee, Eunmin Lee, Angela Richard-Londt, M. Friedrich, Federica Furlanetto, Rocío Aller de la Fuente, Ruby Banerjee, Fengtang Yang, Frances Law, Colin Watts, Roland Rad, George S. Vassiliou, Jong Kim, Thomas Santarius, Sebastian Brandner, Allan Bradley
Software Mentions: 3
Published: over 4 years ago

10.18632/oncotarget.22804

Gene amplification in mesenchymal stem cells and during differentiation towards adipocytes or osteoblasts
Cited by: 7
Author(s): Nora Corinna Altmayer, Valentina Galata, Nadine Warschburger, Andreas Keller, Eckart Meese, Ulrike Fischer
Software Mentions: 3
Published: about 7 years ago

10.1186/s13059-014-0443-x

SubcloneSeeker: a computational framework for reconstructing tumor clone structure for cancer variant interpretation and prioritization
Cited by: 58
Author(s): Yi Qiao, Aaron R. Quinlan, Amir A. Jazaeri, Roeland Verhaak, David A. Wheeler, Gábor Marth
Software Mentions: 3
Published: over 10 years ago

10.1371/journal.pgen.1004290

Copy Number Variation Is a Fundamental Aspect of the Placental Genome
Cited by: 55
Author(s): Roberta L. Hannibal, Edward B. Chuong, Juan Carlos Rivera-Mulia, David M. Gilbert, Anton Valouev, Julie C. Baker
Software Mentions: 3
Published: over 10 years ago

10.1186/s12920-021-00978-z

Genome-wide copy number variations in a large cohort of bantu African children
Cited by: 4
Author(s): Feyza Yilmaz, Megan Null, David P. Astling, J. C. Yu, Joanne B. Cole, Stephanie A. Santorico, Benedikt Hallgrímsson, Mange Manyama, Richard A. Spritz, Audrey E. Hendricks, Tamim H. Shaikh
Software Mentions: 3
Published: over 3 years ago

10.1186/1471-2105-11-297

A classification model for distinguishing copy number variants from cancer-related alterations
Cited by: 12
Author(s): Irina Ostrovnaya, Gouri J. Nanjangud, Adam B. Olshen
Software Mentions: 3
Published: over 14 years ago

10.12688/f1000research.16338.1

An accessible GenePattern notebook for the copy number variation analysis of Illumina Infinium DNA methylation arrays
Cited by: 4
Author(s): Clarence K. Mah, Jill P. Mesirov, Lukas Chávez
Software Mentions: 3
Published: about 6 years ago

10.1186/s12885-020-06719-2

Construction of an integrated human osteosarcoma database, HOsDb, based on literature mining, microarray analysis, and database retrieval
Cited by: 2
Author(s): Yun-Yu Sun, Lishan Wang, Changkuan Li, Rui Gu, Weidong Zang, Wei Song, Peng Xia
Software Mentions: 3
Published: over 4 years ago

10.1186/s12859-016-1239-7

nbCNV: a multi-constrained optimization model for discovering copy number variants in single-cell sequencing data
Cited by: 16
Author(s): Changsheng Zhang, Hongming Cai, Jingying Huang, Yan Song
Software Mentions: 3
Published: over 8 years ago

10.1186/s12885-019-5681-6

Probabilistic modeling of personalized drug combinations from integrated chemical screen and molecular data in sarcoma
Cited by: 11
Author(s): Noah Berlow, Rikhi Rikhi, Mathew Geltzeiler, Jinu Abraham, Matthew N. Svalina, Lara E. Davis, Erin Wise, Maria Mancini, Jonathan Noujaim, Atiya Mansoor, Michael J. Quist, Kevin Matlock, Martin Goros, Brian Hernandez, Yee Cheen Doung, Khin Thway, Tomohide Tsukahara, Jun Nishio, Elaine Huang, Susan D. Airhart, Carol J. Bult, Regina Gandour‐Edwards, Robert G. Maki, Robin L. Jones, Joel E. Michalek, Milan Milovancev, Souparno Ghosh, Ranadip Pal, Charles Keller
Software Mentions: 3
Published: over 5 years ago

10.1093/bioinformatics/btu436

Multi-factor data normalization enables the detection of copy number aberrations in amplicon sequencing data
Cited by: 95
Author(s): Valentina Boeva, Tatiana Popova, Maxime Lienard, Sébastien Toffoli, Maud Kamal, Christophe Le Tourneau, David Gentien, Nicolas Servant, Pierre Gestraud, Thomas Rio Frio, Philippe Hupé, Emmanuel Barillot, Jean-François Laes
Software Mentions: 3
Published: over 10 years ago

10.1186/1471-2164-10-401

CGHnormaliter: an iterative strategy to enhance normalization of array CGH data with imbalanced aberrations
Cited by: 17
Author(s): Bart P.P. van Houte, Thomas W. Binsl, Hannes Hettling, Walter Pirovano, Jaap Heringa
Software Mentions: 3
Published: over 15 years ago

10.1371/journal.pone.0165089

Chromosomal Instability Estimation Based on Next Generation Sequencing and Single Cell Genome Wide Copy Number Variation Analysis
Cited by: 29
Author(s): Stephanie Greene, Angel E. Dago, Laura Leitz, Yipeng Wang, Jerry Lee, Shannon L. Werner, Steven Gendreau, Premal H. Patel, Shidong Jia, Liangxuan Zhang, Eric Tucker, Michael Malchiodi, Ryon P. Graf, Ryan Dittamore, Dena Marrinucci, Mark Landers
Software Mentions: 3
Published: about 8 years ago

10.15252/msb.20167159

Recurrent patterns of DNA copy number alterations in tumors reflect metabolic selection pressures
Cited by: 60
Author(s): Nicholas A. Graham, Aspram Minasyan, Anastasia Lomova, Ashley Cass, Nikolas G. Balanis, Michael Friedman, Shawna T. Chan, Sophie R. Zhao, Adrián Delgado, James Go, L. P. Beck, Christian Hurtz, Carina Ng, Rong Qiao, Johanna ten Hoeve, Nicolaos Palaskas, Hong Wu, Markus Müschen, Asha S. Multani, Elisa Port, Steven M. Larson, Nikolaus Schultz, Daniel Braas, Heather R. Christofk, Ingo K. Mellinghoff, Thomas G. Graeber
Software Mentions: 3
Published: almost 8 years ago

10.1038/tp.2017.181

Differential DNA methylation at birth associated with mental disorder in individuals with 22q11.2 deletion syndrome
Cited by: 21
Author(s): Anna Starnawska, Christine Søholm Hansen, Thomas Sparsø, Wiktor Mazin, Line Olsen, Marcelo Bertalan, Alfonso Buil, Jonas Bybjerg‐Grauholm, Marie Bækvad-Hansen, David M. Hougaard, Preben Bo Mortensen, Carsten Bøcker Pedersen, Mette Nyegaard, Thomas Werge, Shantel Weinsheimer
Software Mentions: 3
Published: over 7 years ago

10.1371/journal.pone.0056274

Headbobber: A Combined Morphogenetic and Cochleosaccular Mouse Model to Study 10qter Deletions in Human Deafness
Cited by: 7
Author(s): Annalisa Buniello, Rachel E. Hardisty-Hughes, Johanna Pass, Eva Bober, Richard J.H. Smith, Karen P. Steel
Software Mentions: 3
Published: almost 12 years ago

10.1371/journal.pone.0031333

Cancer Gene Prioritization for Targeted Resequencing Using FitSNP Scores
Cited by: 3
Author(s): Annelies Fieuw, Bram De Wilde, Franki Speleman, Jo Vandesompele, Katleen De Preter
Software Mentions: 3
Published: almost 13 years ago

10.1371/journal.pone.0009983

Identification of Candidate Growth Promoting Genes in Ovarian Cancer through Integrated Copy Number and Expression Analysis
Cited by: 100
Author(s): Manasa Ramakrishna, Lauren Williams, Samantha E. Boyle, Jennifer L. Bearfoot, Anita Sridhar, Terence P. Speed, Kylie L. Gorringe, Ian Campbell
Software Mentions: 3
Published: over 14 years ago

10.1186/s12864-015-1450-3

The UBC-40 Urothelial Bladder Cancer cell line index: a genomic resource for functional studies
Cited by: 80
Author(s): Julie Earl, Daniel Rico, Enrique Carrillo de Santa Pau, Benjamín Rodríguez-Santiago, Marinela Méndez-Pertuz, Herbert Auer, Gonzalo Vázquez Gómez, H. Barton Grossman, David G. Pisano, Wolfgang A. Schulz, Luís A. Pérez-Jurado, Alfredo Carrato, Dan Theodorescu, Stephen J. Chanock, Alfonso Valencia, Francisco X. Real
Software Mentions: 3
Published: over 9 years ago

10.1111/pbi.12691

Reduction of heterozygosity (ROH) as a method to detect mosaic structural variation
Cited by: 9
Author(s): Fabio Marroni, Davide Scaglione, Sara Pinosio, Alberto Policriti, Mara Miculan, Gabriele Di Gaspero, Michèle Morgante
Software Mentions: 3
Published: almost 8 years ago

10.1186/s13336-014-0015-z

Copy number variation analysis based on AluScan sequences
Cited by: 10
Author(s): Jian Feng Yang, Xueliang Ding, Lei Chen, Wai Kin Mat, Michelle Zhi Xu, Jin Fei Chen, Jian-Min Wang, Lin Xu, Wai Sang Poon, Ava Kwong, Gilberto Ka Kit Leung, Tze-Ching Tan, Chi Hung Yu, Yue Bin Ke, Xin Xu, Xiaoyan Ke, Rong Ma, Juliana C.N. Chan, Wei Qing Wan, Li Wei Zhang, Yogesh Kumar, Suk Ying Tsang, Shao Li, Hong Yang Wang, Hong Xue
Software Mentions: 3
Published: about 10 years ago

10.1002/cam4.3975

Genetic alterations associated with multiple primary malignancies
Cited by: 6
Author(s): Jenny Nyqvist, Anikó Kovács, Zakaria Einbeigi, Per Karlsson, Eva Forssell‐Aronsson, Khalil Helou, Toshima Z. Parris
Software Mentions: 3
Published: over 3 years ago

10.1186/1756-0500-3-298

KC-SMARTR: An R package for detection of statistically significant aberrations in multi-experiment aCGH data
Cited by: 22
Author(s): Jorma J. de Ronde, Christiaan Klijn, Arno Velds, Henne Holstege, Marcel J. T. Reinders, Jos Jonkers, Lodewyk Wessels
Software Mentions: 3
Published: about 14 years ago

10.1093/bioinformatics/btu072

SegAnnDB: interactive Web-based genomic segmentation
Cited by: 17
Author(s): Toby Dylan Hocking, Valentina Boeva, Guillem Rigaill, Gudrun Schleiermacher, Isabelle Janoueix‐Lerosey, Olivier Delattre, Wilfrid Richer, Franck Bourdeaut, Miyuki Suguro, Masao Seto, Francis Bach, Jean-Philippe Vert
Software Mentions: 3
Published: almost 11 years ago

10.1371/journal.pcbi.0030122

Flexible and Accurate Detection of Genomic Copy-Number Changes from aCGH
Cited by: 52
Author(s): Oscar M. Rueda, Ramón Dı́az-Uriarte
Software Mentions: 3
Published: over 17 years ago

10.1172/jci.insight.132852

Neoadjuvant pazopanib and molecular analysis of tissue response in renal cell carcinoma
Cited by: 10
Author(s): Christopher G. Wood, James E. Ferguson, Joel S. Parker, Dominic T. Moore, Jennifer G. Whisenant, Susan J. Maygarden, Eric Wallen, William Y. Kim, Mathew I. Milowsky, Kathryn E. Beckermann, Nancy B. Davis, Scott M. Haake, Jose A. Karam, Dante S. Bortone, Benjamin G. Vincent, Thomas Powles, W. Kimryn Rathmell
Software Mentions: 3
Published: about 4 years ago

10.1038/s41416-021-01266-4

Frequent post-operative monitoring of colorectal cancer using individualised ctDNA validated by multiregional molecular profiling
Cited by: 6
Author(s): Mizunori Yaegashi, Takeshi Iwaya, Noriyuki Sasaki, Masashi Fujita, Ju Zhang, Doris R. Siwak, Tsuyoshi Hachiya, Kei Sato, Fumitaka Endo, Toshimoto Kimura, Koki Otsuka, Ryo Sugimoto, Tamotsu Sugai, Lance A. Liotta, Yiling Lu, Gordon B. Mills, Hidewaki Nakagawa, Satoshi Nishizuka
Software Mentions: 3
Published: almost 4 years ago

10.1093/bioinformatics/bty677

Detection of de novo copy number deletions from targeted sequencing of trios
Cited by: 2
Author(s): Jack Fu, Elizabeth J. Leslie, Alan F. Scott, Jeffrey C. Murray, Mary L. Marazita, Terri H. Beaty, Robert B. Scharpf, Ingo Ruczinski
Software Mentions: 2
Published: over 6 years ago

10.1155/2015/902419

Combined Analysis of SNP Array Data Identifies Novel CNV Candidates and Pathways in Ependymoma and Mesothelioma
Cited by: 3
Author(s): Gabriel Wajnberg, Benilton Carvalho, Carlos Gil Ferreira, Fábio Passetti
Software Mentions: 2
Published: almost 10 years ago

10.1186/bcr2334

Genomic profiling of breast tumours in relation to BRCAabnormalities and phenotypes
Cited by: 131
Author(s): Olafur A. Stefansson, Jón G. Jonasson, Óskar Þór Jóhannsson, Katrín Ólafsdóttir, Margrét Steinarsdóttir, Sigrı́dur Valgeirsdóttir, Jórunn E. Eyfjörd
Software Mentions: 2
Published: over 15 years ago

10.1186/s12885-017-3382-6

Whole exome sequencing of an asbestos-induced wild-type murine model of malignant mesothelioma
Cited by: 28
Author(s): Sophie Sneddon, Ann Marie Patch, Ian M. Dick, Stephen H. Kazakoff, John V. Pearson, Nicola Waddell, Richard J. N. Allcock, Robert A. Holt, Bruce Robinson, Jenette Creaney
Software Mentions: 2
Published: over 7 years ago

10.26508/lsa.202000774

Mapping the micro-proteome of the nuclear lamina and lamina-associated domains
Cited by: 20
Author(s): Xianrong Wong, Jevon Cutler, Victoria E. Hoskins, Molly R. Gordon, Anil K. Madugundu, Karen Reddy
Software Mentions: 2
Published: almost 4 years ago

10.1016/j.ymeth.2018.11.005

Optimization of DamID for use in primary cultures of mouse hepatocytes
Cited by: 5
Author(s): Leonardo Gatticchi, Jose I. de las Heras, Rita Roberti, Eric C. Schirmer
Software Mentions: 2
Published: almost 6 years ago

10.1186/s13039-019-0435-3

Genome reorganization in different cancer types: detection of cancer specific breakpoint regions
Cited by: 3
Author(s): Christoph Standfuß, Jonas Parczyk, Jérôme Ruhnau, Andreas Klein
Software Mentions: 2
Published: over 5 years ago

10.1186/s13039-021-00565-y

A rare familial rearrangement of chromosomes 9 and 15 associated with intellectual disability: a clinical and molecular study
Cited by: 0
Author(s): Natalya A. Lemskaya, Svetlana A. Romanenko, Mariia A Rezakova, Elena Filimonova, Dmitry Prokopov, Alexander A. Dolskiy, Polina L. Perelman, Yulia V. Maksimova, Asia R. Shorina, Dmitry V. Yudkin
Software Mentions: 2
Published: about 3 years ago

10.1002/mgg3.237

A potential founder variant inCARMIL2/RLTPRin three Norwegian families with warts, molluscum contagiosum, and T-cell dysfunction
Cited by: 52
Author(s): Hanne Sørmo Sorte, Liv Osnes, Børre Fevang, Pål Aukrust, Hans Christian Erichsen, Paul Hoff Backe, Tore G. Abrahamsen, Ole Bjørn Kittang, Torstein Øverland, Shalini N. Jhangiani, Donna M. Muzny, Magnus Dehli Vigeland, Pubudu Samarakoon, Tomasz Gambin, Zeynep H. Coban Akdemir, Richard A. Gibbs, Olaug K. Rødningen, Robert Lyle, James R. Lupski, Asbjørg Stray-Pedersen
Software Mentions: 2
Published: over 8 years ago

10.1371/journal.pbio.0060245

Global Reorganization of Replication Domains During Embryonic Stem Cell Differentiation
Cited by: 490
Author(s): Ichiro Hiratani, Tyrone Ryba, Mari Itoh, Tomoki Yokochi, Michaela Schwaiger, Chia‐Wei Chang, Yung Lyou, Tim M. Townes, Dirk Schübeler, David M. Gilbert
Software Mentions: 2
Published: about 16 years ago

10.1371/journal.pbio.3000464

Repair of multiple simultaneous double-strand breaks causes bursts of genome-wide clustered hypermutation
Cited by: 33
Author(s): Cynthia J. Sakofsky, Natalie Saini, Leszek J. Klimczak, Kin Chan, Ewa Malc, Piotr A. Mieczkowski, Adam Burkholder, David C. Fargo, Dmitry A. Gordenin
Software Mentions: 2
Published: over 5 years ago

10.1186/1471-2407-12-380

SNP microarray analyses reveal copy number alterations and progressive genome reorganization during tumor development in SVT/t driven mice breast cancer
Cited by: 6
Author(s): Christoph Standfuß, Heike Pospisil, Andreas Klein
Software Mentions: 2
Published: over 12 years ago

10.1371/journal.pgen.1006404

Multiple Origins of the Pathogenic Yeast Candida orthopsilosis by Separate Hybridizations between Two Parental Species
Cited by: 66
Author(s): Markus S. Schröder, Kontxi Martinez de San Vicente, Tâmara Heloísa Rocha Prandini, Stephen Hammel, Desmond G. Higgins, Eduardo Bagagli, Kenneth H. Wolfe, Geraldine Butler
Software Mentions: 2
Published: about 8 years ago

10.1371/journal.pgen.1006385

The Impact of Environmental and Endogenous Damage on Somatic Mutation Load in Human Skin Fibroblasts
Cited by: 80
Author(s): Natalie Saini, Steven A. Roberts, Leszek J. Klimczak, Kin Chan, Sara A. Grimm, Shuang-Shuang Dai, David C. Fargo, Jayne C. Boyer, William K. Kaufmann, Jack A. Taylor, Eunjung Lee, Isidro Cortés-Ciriano, Peter J. Park, Shepherd H. Schurman, Ewa Malc, Piotr A. Mieczkowski, Dmitry A. Gordenin
Software Mentions: 2
Published: about 8 years ago

10.1371/journal.pone.0248791

The copy number variation and stroke (CaNVAS) risk and outcome study
Cited by: 1
Author(s): John W. Cole, Taiwo Adigun, Rufus Akinyemi, Onoja Matthew Akpa, Steven Bell, Bowang Chen, Jordi Jiménez Conde, Uxue Lazcano, Israel Fernandez, Myriam Fornage, Cristina Gallego-Fábrega, Christina Jern, Michael Krawczak, Arne Lindgren, Hugh S. Markus, Olle Melander, Mayowa Owolabi, Kristina Schlicht, Martin Söderholm, Vinodh Srinivasasainagendra, Carolina Soriano-Tárraga, Martin Stenman, Hemant K. Tiwari, Margaret Corasaniti, Natalie Fecteau, Beth Guizzardi, Haley Lopez, Kevin A. Nguyen, Brady Gaynor, Timothy D. O’Connor, O. Colin Stine, Steven J. Kittner, Patrick F. McArdle, Braxton D. Mitchell, Huichun Xu, Caspar Grond‐Ginsbach
Software Mentions: 2
Published: over 3 years ago

10.1371/journal.pone.0109924

TP53 Mutational Status Is a Potential Marker for Risk Stratification in Wilms Tumour with Diffuse Anaplasia
Cited by: 78
Author(s): Mariana Maschietto, Richard D. Williams, Tasnim Chagtai, Sergey Popov, Neil J. Sebire, Gordan Vujanić, Elizabeth J. Perlman, James R. Anderson, Paul E. Grundy, Jeffrey S. Dome, Kathy Pritchard‐Jones
Software Mentions: 2
Published: about 10 years ago

10.1038/s41598-019-50891-w

Distinctive mutational spectrum and karyotype disruption in long-term cisplatin-treated urothelial carcinoma cell lines
Cited by: 8
Author(s): Margaretha A. Skowron, Patrick Petzsch, Karin Hardt, Nicholas Wagner, Manfred Beier, Stefanie Stepanow, Matthias Drechsler, Harald Rieder, Karl Köhrer, Günter Niegisch, Michéle J. Hoffmann, Wolfgang A. Schulz
Software Mentions: 2
Published: about 5 years ago

10.1371/journal.pone.0057356

Clinical and Biological Relevance of Genomic Heterogeneity in Chronic Lymphocytic Leukemia
Cited by: 4
Author(s): Daphne R. Friedman, Joseph E. Lucas, J. Brice Weinberg
Software Mentions: 2
Published: almost 12 years ago

10.1186/1471-2105-6-85

Cited by: 99
Author(s): Wei Chen, Fikret Erdogan, Hans‐Hilger Ropers, Steffen Lenzner, Reinhard Ullmann
Software Mentions: 2
Published: almost 20 years ago

10.1038/s41598-019-51314-6

Uncovering low-level mosaicism in human embryonic stem cells using high throughput single cell shallow sequencing
Cited by: 11
Author(s): Alexander Keller, Laurentijn Tilleman, Dominika Dziedzicka, Filippo Zambelli, Karen Sermon, Filip Van Nieuwerburgh, Claudia Spits, Mieke Geens
Software Mentions: 2
Published: about 5 years ago

10.1371/journal.pone.0113278

Differential In Vivo Tumorigenicity of Distinct Subpopulations from a Luminal-Like Breast Cancer Xenograft
Cited by: 8
Author(s): Nirma Skrbo, Geir Olav Hjortland, Alexander Kristian, Ruth Holm, Silje Nord, Lina Prasmickaite, Olav Engebraaten, Gunhild Mari Mælandsmo, Thérese Sørlie, Kristin Andersen
Software Mentions: 2
Published: about 10 years ago

10.1371/journal.pone.0203007

Genomic region detection via Spatial Convex Clustering
Cited by: 2
Author(s): John Nagorski, Genevera I. Allen
Software Mentions: 2
Published: over 6 years ago

10.1016/j.celrep.2014.07.043

Single-Cell, Genome-wide Sequencing Identifies Clonal Somatic Copy-Number Variation in the Human Brain
Cited by: 252
Author(s): Xinjiang Cai, Gilad D. Evrony, Hillel S. Lehmann, Princess C. Elhosary, Bhaven K. Mehta, Annapurna Poduri, Christopher A. Walsh
Software Mentions: 2
Published: over 10 years ago

10.18632/oncotarget.7391

Characterization of novel low passage primary and metastatic colorectal cancer cell lines
Cited by: 11
Author(s): Arnoud Boot, Jaap van Eendenburg, Stijn Crobach, Dina Ruano, Frank M. Speetjens, J.J. Calame, Jan Oosting, Hans Morreau, Tom van Wezel
Software Mentions: 2
Published: almost 9 years ago

10.18632/oncotarget.18502

Comparative analysis of primary versus relapse/refractory DLBCL identifies shifts in mutation spectrum
Cited by: 19
Author(s): Danielle M. Greenawalt, Winnie S. Liang, Sakina Saif, Justin Johnson, Petar Todorov, Austin Dulak, Daniel Enríquez, Rebecca F. Halperin, Ambar Ahmed, Vladislav Saveliev, John D. Carpten, David W. Craig, J. Carl Barrett, Brian Dougherty, Michael Zinda, Stephen E. Fawell, Jonathan R. Dry, Kate Byth
Software Mentions: 2
Published: over 7 years ago

10.18632/oncotarget.22867

Genomic landscape of colitis-associated cancer indicates the impact of chronic inflammation and its stratification by mutations in the Wnt signaling
Cited by: 32
Author(s): Masashi Fujita, Nagahide Matsubara, Ikuo Matsuda, Kazuhiro Maejima, Ayako Oosawa, Tomoki Yamano, Akihiro Fujimoto, Mayuko Furuta, Kaoru Nakano, Aya Oku‐Sasaki, Hiroko Tanaka, Yuichi Shiraishi, Raúl Nicolás Mateos, Kenta Nakai, Satoru Miyano, Naohiro Tomita, Seiichi Hirota, Hiroki Ikeuchi, Hidewaki Nakagawa
Software Mentions: 2
Published: about 7 years ago

10.1186/1756-8935-6-42

Murine esBAF chromatin remodeling complex subunits BAF250a and Brg1 are necessary to maintain and reprogram pluripotency-specific replication timing of select replication domains
Cited by: 28
Author(s): Shin‐ichiro Takebayashi, Ienglam Lei, Tyrone Ryba, Takayo Sasaki, Vishnu Dileep, Dana Battaglia, Xiaolin Gao, Fang Peng, Yong Fan, Miguel A. Esteban, Jianfeng Tang, Robert H. Crabtree, Zhong Wang, David M. Gilbert
Software Mentions: 2
Published: about 11 years ago

10.3389/fcell.2021.713499

Copy Number Signatures and Clinical Outcomes in Upper Tract Urothelial Carcinoma
Cited by: 5
Author(s): Bao Guan, Liang Yuan, Huan Lü, Zhengzheng Xu, Yue Shi, Juan Li, Wenwen Kong, Chuanyu Tian, Yezhen Tan, Yanqing Gong, Jin Liu, Dong Fang, Qi Shen, Shiming He, Muhammad Shakeel, Zhongyuan Zhang, Qun He, Xuesong Li, Weimin Ci, Liqun Zhou
Software Mentions: 2
Published: over 3 years ago

10.3389/fpls.2015.00308

Minimal evidence for consistent changes in maize DNA methylation patterns following environmental stress
Cited by: 75
Author(s): Steven R. Eichten, Nathan M. Springer
Software Mentions: 2
Published: over 9 years ago

10.3390/genes11040374

Complex Structure of Lasiopodomys mandarinus vinogradovi Sex Chromosomes, Sex Determination, and Intraspecific Autosomal Polymorphism
Cited by: 8
Author(s): Svetlana A. Romanenko, Antonina V. Smorkatcheva, Yulia M. Kovalskaya, Dmitry Prokopov, Natalya A. Lemskaya, Olga L. Gladkikh, Ivan A Polikarpov, Natalia A. Serdyukova, Vladimir A. Trifonov, Anna S. Molodtseva, Patrícia C. M. O’Brien, Fedor N. Golenishchev, Malcolm A. Ferguson‐Smith, Alexander S. Graphodatsky
Software Mentions: 2
Published: almost 5 years ago

10.1016/j.gdata.2014.04.006

A definitive haplotype map of structural variations determined by microarray analysis of duplicated haploid genomes
Cited by: 1
Author(s): Tomoko Tahira, Koji Yahara, Yoji Kukita, Koichiro Higasa, Kiyoko Kato, Norio Wake, Kenshi Hayashi
Software Mentions: 2
Published: about 10 years ago

10.1186/gm486

BAIT: Organizing genomes and mapping rearrangements in single cells
Cited by: 31
Author(s): Matthew J. Hills, Kieran O’Neill, Ester Falconer, Ryan R. Brinkman, Peter M. Lansdorp
Software Mentions: 2
Published: almost 12 years ago

10.1093/bioinformatics/btv298

Interactive analysis of large cancer copy number studies with Copy Number Explorer
Cited by: 5
Author(s): Scott Newman
Software Mentions: 2
Published: over 9 years ago

10.1371/journal.pone.0103177

Lack of Genomic Heterogeneity at High-Resolution aCGH between Primary Breast Cancers and Their Paired Lymph Node Metastases
Cited by: 9
Author(s): Marieke A. Vollebergh, Christiaan Klijn, Philip C. Schouten, Jelle Wesseling, Daniëlle Israeli, Bauke Ylstra, Lodewyk Wessels, Jos Jonkers, Sabine C. Linn
Software Mentions: 1
Published: over 10 years ago

10.1371/journal.pone.0108089

Population Structure and Comparative Genome Hybridization of European Flor Yeast Reveal a Unique Group of Saccharomyces cerevisiae Strains with Few Gene Duplications in Their Genome
Cited by: 38
Author(s): Jean Luc Legras, Claude Erny, Claudine Charpentier
Software Mentions: 1
Published: about 10 years ago

Projects: bioconductor: DNAcopy

Papers Mentioning DNAcopy 154