bioconductor: CGHcall | Projects | Ecosyste.ms: Papers

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: over 15 years ago

10.1038/s41598-017-17704-4

High STAP1 expression in DUX4-rearranged cases is not suitable as therapeutic target in pediatric B-cell precursor acute lymphoblastic leukemia
Cited by: 10
Author(s): Elisabeth M. P. Steeghs, Marjolein Bakker, Alex Q. Hoogkamer, Judith M. Boer, Quirine J. Hartman, Femke Stalpers, Gabriele Escherich, Valérie de Haas, Hester A. de Groot-Kruseman, Rob Pieters, Monique L. den Boer
Software Mentions: 9
Published: over 6 years ago

10.18632/oncotarget.13492

Tyrosine kinase fusion genes in pediatric BCR-ABL1-like acute lymphoblastic leukemia
Cited by: 62
Author(s): Judith M. Boer, Elisabeth M. P. Steeghs, João R. M. Marchante, Aurélie Boeree, James J. Beaudoin, H. Berna Beverloo, Roland P. Kuiper, Gabriele Escherich, Vincent H.J. van der Velden, C. Ellen van der Schoot, Hester A. de Groot-Kruseman, Rob Pieters, Monique L. den Boer
Software Mentions: 7
Published: over 7 years ago

10.1186/s12864-021-07686-z

Evaluation of tools for identifying large copy number variations from ultra-low-coverage whole-genome sequencing data
Cited by: 6
Author(s): Johannes Smolander, Sofia Khan, Kalaimathy Singaravelu, Leni Kauko, Riikka Lund, Asta Laiho, Laura L. Elo
Software Mentions: 6
Published: about 3 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: over 6 years ago

10.1186/gm377

Digital transcriptome profiling of normal and glioblastoma-derived neural stem cells identifies genes associated with patient survival
Cited by: 47
Author(s): Pär G. Engström, Diva Tommei, Stefan H. Stricker, Christine Ender, Steven M. Pollard, Paul Bertone
Software Mentions: 5
Published: over 12 years ago

10.1084/jem.20191257

Combined deletion of Bap1, Nf2, and Cdkn2ab causes rapid onset of malignant mesothelioma in mice
Cited by: 28
Author(s): Jitendra Badhai, Gaurav Kumar Pandey, Ji‐Ying Song, Oscar Krijgsman, Rajith Bhaskaran, G. Chandrasekaran, Min-Chul Kwon, Lorenzo Bombardelli, Kim Monkhorst, Cristoforo Grasso, John Zevenhoven, Jan van der Vliet, Miranda Cozijnsen, Paul Krimpenfort, Daniel S. Peeper, Maarten van Lohuizen, Anton Berns
Software Mentions: 5
Published: over 4 years ago

10.1186/1471-2105-13-80

Matching of array CGH and gene expression microarray features for the purpose of integrative genomic analyses
Cited by: 15
Author(s): Wessel N. van Wieringen, Kristian Unger, Gwenaël G. R. Leday, Oscar Krijgsman, Renée X. de Menezes, Bauke Ylstra, Mark A. van de Wiel
Software Mentions: 4
Published: about 12 years ago

10.1186/s13014-016-0672-0

Transcriptomic analyses of the radiation response in head and neck squamous cell carcinoma subclones with different radiation sensitivity: time-course gene expression profiles and gene association networks
Cited by: 37
Author(s): Agata Michna, Ulrike Schötz, Martin Selmansberger, Horst Zitzelsberger, Kirsten Lauber, Kristian Unger, Julia Heß
Software Mentions: 3
Published: about 8 years ago

10.20892/j.issn.2095-3941.2020.0012

Patient-derived non-small cell lung cancer xenograft mirrors complex tumor heterogeneity
Cited by: 15
Author(s): Xuanming Chen, Cheng Shen, Zhe Wei, Rui Zhang, Yongsheng Wang, Lili Jiang, Ke Chen, Shuang Qiu, Yuanli Zhang, Ting Zhang, Bin Chen, Yanjun Xu, Qiyi Feng, Jen‐Wei Huang, Zhihui Zhong, Hongxia Li, Guowei Che, Kai Xiao
Software Mentions: 3
Published: over 3 years ago

10.1002/cam4.1633

Molecular heterogeneity in human papillomavirus‐dependent and ‐independent vulvar carcinogenesis
Cited by: 16
Author(s): Dorian R.A. Swarts, Quirinus J.M. Voorham, Annina P. van Splunter, Saskia M. Wilting, Daoud Sie, Divera T.M. Pronk, Marc van Beurden, Daniëlle A.M. Heideman, Peter J.F. Snijders, Chris J.L.M. Meijer, Renske D.M. Steenbergen, Maaike Bleeker
Software Mentions: 3
Published: about 6 years ago

10.1186/bcr3015

Breast tumors from CHEK2 1100delC- mutation carriers: genomic landscape and clinical implications
Cited by: 48
Author(s): Taru Muranen, Dario Greco, Rainer Fagerholm, Outi Kilpivaara, Kati Kämpjärvi, Kristiina Aittomäki, Carl Blomqvist, Päivi Heikkilä, Åke Borg, Heli Nevanlinna
Software Mentions: 3
Published: almost 13 years ago

10.1186/gb-2011-12-8-r80

Single-cell copy number variation detection
Cited by: 37
Author(s): Jun‐Hu Cheng, Evelyne Vanneste, Peter Könings, Thierry Voet, Joris Robert Vermeesch, Yves Moreau
Software Mentions: 3
Published: over 13 years ago

10.1038/s41598-017-05623-3

Association Of Plasma And Urinary Mutant DNA With Clinical Outcomes In Muscle Invasive Bladder Cancer
Cited by: 66
Author(s): Keval Patel, Kristan E. van der Vos, Christopher G. Smith, Florent Moulière, Dana W.Y. Tsui, James A. Morris, Dineika Chandrananda, Francesco Marass, Daan van den Broek, DE Neal, Vincent Gnanapragasam, Tim Forshew, Bas W. van Rhijn, Charles E. Massie, Nitzan Rosenfeld, Michiel S. van der Heijden
Software Mentions: 3
Published: about 7 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: about 9 years ago

10.12688/f1000research.9259.2

GeneBreak: detection of recurrent DNA copy number aberration-associated chromosomal breakpoints within genes
Cited by: 0
Author(s): Egon van den Broek, Stef van Lieshout, Christian Rausch, Bauke Ylstra, Mark A. van de Wiel, Gerrit A. Meijer, Remond J.A. Fijneman, Sanne Abeln
Software Mentions: 3
Published: about 7 years ago

10.1038/cddis.2015.241

IMP2/p62 induces genomic instability and an aggressive hepatocellular carcinoma phenotype
Cited by: 61
Author(s): Sonja M. Kessler, Stephan Laggai, Ahmad Barghash, Christina S. Schultheiss, Eva Lederer, Monika Artl, Volkhard Helms, Johannes Haybaeck, Alexandra K. Kiemer
Software Mentions: 3
Published: almost 9 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: almost 15 years ago

10.18632/oncotarget.24070

Differentially expressed microRNAs in lung adenocarcinoma invert effects of copy number aberrations of prognostic genes
Cited by: 8
Author(s): Tomáš Tokár, Chiara Pastrello, Varune Rohan Ramnarine, Chang-Qi Zhu, Kenneth J. Craddock, Larrisa A Pikor, Emily A. Vucic, Simon Vary, Frances A. Shepherd, Ming‐Sound Tsao, Wan L. Lam, Igor Jurišica
Software Mentions: 2
Published: over 6 years ago

10.1186/1755-8794-4-47

CNVassoc: Association analysis of CNV data using R
Cited by: 20
Author(s): Isaac Subirana, Ramón Díaz‐Uriarte, Gavin Lucas, Juan R. González
Software Mentions: 2
Published: about 13 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: over 9 years ago

10.1371/journal.pone.0155840

Analysis of Paired Primary-Metastatic Hormone-Receptor Positive Breast Tumors (HRPBC) Uncovers Potential Novel Drivers of Hormonal Resistance
Cited by: 17
Author(s): Luís Manso, Silvana Mourón, Michael L. Tress, Gonzalo Gómez‐López, Manuel Morente, Eva Ciruelos, Miriam Rubio-Camarillo, José L. Rodríguez-Peralto, Miguel Ángel Pujana, David G. Pisano, Miguel Quintela‐Fandino
Software Mentions: 2
Published: about 8 years ago

10.3390/cancers13174296

Immune-Omics Networks of CD27, PD1, and PDL1 in Non-Small Cell Lung Cancer
Cited by: 14
Author(s): Qing Ye, Salvi Singh, Peter R Qian, Nancy Lan Guo
Software Mentions: 2
Published: almost 3 years ago

10.3390/cancers11060805

Bioinformatics Analysis for Circulating Cell-Free DNA in Cancer
Cited by: 42
Author(s): Chiang-Ching Huang, Meijun Du, Liang Wang
Software Mentions: 2
Published: about 5 years ago

10.1016/j.ebiom.2016.05.029

Intra-Tumor Genetic Heterogeneity in Wilms Tumor: Clonal Evolution and Clinical Implications
Cited by: 58
Author(s): George D Cresswell, John Apps, Tasnim Chagtai, Borbála Mifsud, Christopher C. Bentley, Mariana Maschietto, Sergey Popov, Mark E. Weeks, Øystein E. Olsen, Neil J. Sebire, Kathy Pritchard‐Jones, Nicholas M. Luscombe, Richard D. Williams, William Mifsud
Software Mentions: 2
Published: about 8 years ago

10.15252/emmm.201707945

Dynamics of multiple resistance mechanisms in plasma DNA during EGFR‐targeted therapies in non‐small cell lung cancer
Cited by: 56
Author(s): Dana W.Y. Tsui, Muhammed Murtaza, Alvin Seng Cheong Wong, Oscar M. Rueda, Christopher G. Smith, Dineika Chandrananda, Ross A. Soo, Hong Liang Lim, Boon Cher Goh, Carlos Caldas, Tim Forshew, Davina Gale, Wei Liu, James A. Morris, Francesco Marass, Tim Eisen, Tan Min Chin, Nitzan Rosenfeld
Software Mentions: 2
Published: about 6 years ago

10.1186/s13059-015-0719-9

Estrogen-induced chromatin decondensation and nuclear re-organization linked to regional epigenetic regulation in breast cancer
Cited by: 42
Author(s): Sehrish Rafique, Jeremy Thomas, Duncan Sproul, Wendy A. Bickmore
Software Mentions: 2
Published: almost 9 years ago

10.1186/s13045-020-0846-y

Combination of PI3K and MEK inhibitors yields durable remission in PDX models of PIK3CA-mutated metaplastic breast cancers
Cited by: 28
Author(s): Florence Coussy, Rania El Botty, Marion Lavigne, Céline Gu, Laetitia Fuhrmann, Adrien Briaux, Leanne de Koning, Ahmed Dahmani, Élodie Montaudon, Ludivine Morisset, Léa Huguet, Laura Sourd, Pierre Painsec, Sophie Château-Joubert, Thibaut Larcher, Sophie Vacher, Samia Melaabi, Anne Vincent‐Salomon, Elisabetta Marangoni, Ivan Bièche
Software Mentions: 2
Published: over 4 years ago

10.7554/eLife.08711

Inactivation of the ATMIN/ATM pathway protects against glioblastoma formation
Cited by: 16
Author(s): Sophia M. Blake, Stefan H. Stricker, Hanna Halavach, Anna R. Poetsch, George D Cresswell, Gavin Kelly, Nnennaya Kanu, Silvia Marino, Nicholas M. Luscombe, Steven M. Pollard, Axel Behrens
Software Mentions: 2
Published: over 8 years ago

10.18632/oncotarget.12510

Genomic profiling of stage II and III colon cancers reveals APC mutations to be associated with survival in stage III colon cancer patients
Cited by: 9
Author(s): Egon van den Broek, Oscar Krijgsman, Daoud Sie, Marianne Tijssen, Sandra Mongera, Mark A. van de Wiel, Eric Belt, Sjoerd H. den Uil, Herman Bril, H. B. A. C. Stockmann, Bauke Ylstra, Beatriz Carvalho, Gerrit A. Meijer, Remond J.A. Fijneman
Software Mentions: 2
Published: almost 8 years ago

10.1186/1471-2105-11-331

CGHpower: exploring sample size calculations for chromosomal copy number experiments
Cited by: 6
Author(s): Ilari Scheinin, José A. Ferreira, Sakari Knuutila, Gerrit A. Meijer, Mark A. van de Wiel, Bauke Ylstra
Software Mentions: 1
Published: about 14 years ago

10.1186/1471-2164-10-499

Anti-proliferative action of vitamin D in MCF7 is still active after siRNA-VDR knock-down
Cited by: 44
Author(s): José Luís Costa, Paul P. Eijk, Mark A. van de Wiel, Derk ten Berge, Fernando Schmitt, Carmen J. Narvaez, JoEllen Welsh, Bauke Ylstra
Software Mentions: 1
Published: over 15 years ago

10.3390/ijms20153619

Coexisting Molecular Determinants of Acquired Oxaliplatin Resistance in Human Colorectal and Ovarian Cancer Cell Lines
Cited by: 17
Author(s): Paul Noordhuis, A.C. Laan, Kasper van de Born, Richard J. Honeywell, Godefridus J. Peters
Software Mentions: 1
Published: about 5 years ago

10.3389/fphys.2015.00010

A genomic approach to study down syndrome and cancer inverse comorbidity: untangling the chromosome 21
Cited by: 14
Author(s): Jaume Forés-Martos, Raimundo Cervera, Enrique Chirivella, Alberto Ramos-Jarero, Joan Climent
Software Mentions: 1
Published: over 9 years ago

10.1371/journal.pone.0086833

Chromosomal Copy Number Aberrations in Colorectal Metastases Resemble Their Primary Counterparts and Differences Are Typically Non-Recurrent
Cited by: 21
Author(s): L. Mekenkamp, Josien Haan, Daniëlle Israeli, Hendrik F. B. van Essen, Jeroen R. Dijkstra, Patricia van Cleef, Cornelis J.A. Punt, Gerrit A. Meijer, Irıs D. Nagtegaal, Bauke Ylstra
Software Mentions: 1
Published: over 10 years ago

10.1186/1755-8166-7-46

Single cell segmental aneuploidy detection is compromised by S phase
Cited by: 23
Author(s): Eftychia Dimitriadou, Niels van der Aa, Jun‐Hu Cheng, Thierry Voet, Joris Robert Vermeesch
Software Mentions: 1
Published: about 10 years ago

Ecosyste.ms: Papers

Projects: bioconductor: CGHcall

Papers Mentioning CGHcall 37