bioconductor: QDNAseq | Projects | Ecosyste.ms: Papers

10.1186/s13058-021-01451-6

Transcriptome and genome evolution during HER2-amplified breast neoplasia
Cited by: 3
Author(s): Peipei Lu, Joseph W. Foley, Chunfang Zhu, Katherine McNamara, Korsuk Sirinukunwattana, Sujay Vennam, Sushama Varma, Hamid Fehri, Arunima Srivastava, Shirley Zhu, Jens Rittscher, Parag Mallick, Christina Curtis, Robert B. West
Software Mentions: 11
Published: about 3 years ago

10.1371/journal.ppat.1006668

Merkel cell polyomavirus recruits MYCL to the EP400 complex to promote oncogenesis
Cited by: 78
Author(s): Jingwei Cheng, Donglim Esther Park, Christian Berrios, Elizabeth White, Reety Arora, Rosa Yoon, Timothy Branigan, Tengfei Xiao, Thomas Westerling, Alexander Federation, Rhamy Zeid, Benjamin J. Strober, Selene K. Swanson, Laurence Florens, James E. Bradner, Myles Brown, Peter M. Howley, Megha Padi, Michael P. Washburn, James A. DeCaprio
Software Mentions: 6
Published: almost 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: over 3 years ago

10.1126/sciadv.abh0534

Cell-free DNA TAPS provides multimodal information for early cancer detection
Cited by: 36
Author(s): Paulina Siejka-Zielińska, Jingfei Cheng, Felix Jackson, Yibin Liu, Zahir Soonawalla, Srikanth Reddy, Michael Silva, Luminita Puta, Misti McCain, Emma L. Culver, Noor Bekkali, Benjamin Schuster-Böckler, Pier Francesco Palamara, Derek A. Mann, Helen L. Reeves, Eleanor Barnes, Shivan Sivakumar, Chun-Xiao Song
Software Mentions: 5
Published: about 3 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: about 3 years ago

10.1186/s12859-018-2288-x

HiCcompare: an R-package for joint normalization and comparison of HI-C datasets
Cited by: 94
Author(s): John C. Stansfield, Kellen Garrison Cresswell, Vladimir I. Vladimirov, Mikhail G. Dozmorov
Software Mentions: 4
Published: about 6 years ago

10.1186/s13073-021-00922-x

High-grade serous tubo-ovarian cancer refined with single-cell RNA sequencing: specific cell subtypes influence survival and determine molecular subtype classification
Cited by: 52
Author(s): Siel Olbrecht, Pieter Busschaert, Jun Qian, Adriaan Vanderstichele, Liselore Loverix, Toon Van Gorp, Els Van Nieuwenhuysen, Sileny Han, Annick Van den Broeck, An Coosemans, Anne‐Sophie Van Rompuy, Diether Lambrechts, Ignace Vergote
Software Mentions: 4
Published: about 3 years ago

10.1371/journal.pgen.1007285

Global characterization of copy number variants in epilepsy patients from whole genome sequencing
Cited by: 42
Author(s): Jean Monlong, Simon L. Girard, Caroline Meloche, Maxime Cadieux-Dion, Danielle M. Andrade, Ron G. Lafrenière, Micheline Gravel, Dan Spiegelman, Alexandre Dionne‐Laporte, Cyrus Boelman, Fadi F. Hamdan, Jacques L. Michaud, Guy A. Rouleau, Berge A. Minassian, Guillaume Bourque, Patrick Cossette
Software Mentions: 3
Published: over 6 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

10.12688/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: over 7 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

10.3390/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: over 5 years ago

10.3390/diagnostics11020337

D-karyo—A New Prenatal Rapid Screening Test Detecting Submicroscopic CNVs and Mosaicism
Cited by: 1
Author(s): Osamu Shimokawa, Masayoshi Takeda, Ohashi Hiroyasu, Akemi Shono-Ota, Michio Kumagai, Risa Matsushika, Chika Masuda, K. Uenishi, Ritsuko K. Pooh
Software Mentions: 2
Published: over 3 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: over 6 years ago

10.1038/s41598-021-83436-1

Low-coverage whole-genome sequencing of extracellular vesicle-associated DNA in patients with metastatic cancer
Cited by: 6
Author(s): Bella Nguyen, Nicholas C. Wong, Timothy Semple, Michael E. Clark, Stephen Q. Wong, Connull Leslie, Bob Mirzai, Michael Millward, Katie Meehan, Annette Lim
Software Mentions: 2
Published: over 3 years ago

10.1038/s41598-021-95985-6

Liquid biopsy uncovers distinct patterns of DNA methylation and copy number changes in NSCLC patients with different EGFR-TKI resistant mutations
Cited by: 15
Author(s): Hoai-Nghia Nguyen, Ngoc-Phuong Thi Cao, Thien-Chi Van Nguyen, Khang Nguyen Duy Le, Dat Nguyen, Quynh-Tho Thi Nguyen, Thai-Hoa Thi Nguyen, Chu Van Nguyen, Ha Thi Hai Le, Mai-Lan Thi Nguyen, Trieu Vu Nguyen, Vu Uyen Tran, Bac An Luong, Linh-Thy Le, Quoc Ho, Hong-Anh Thi Pham, Binh Thanh Vo, Luan Thanh Nguyen, Anh-Thu Huynh Dang, Sinh Duy Nguyen, Minh Duc, Thanh-Thuy Thi, Anh Vu Hoang, Kiet Truong Dinh, Minh-Duy Phan, Hoa Giang, Le Son Tran
Software Mentions: 2
Published: about 3 years ago

10.1016/j.yexmp.2018.03.006

Shallow whole genome sequencing for robust copy number profiling of formalin-fixed paraffin-embedded breast cancers
Cited by: 24
Author(s): Suet-Feung Chin, Ángela Santonja, Marta Grzelak, Soomin Ahn, Stephen‐John Sammut, Harry Clifford, Oscar M. Rueda, Michelle Pugh, Mae A. Goldgraben, Helen Bardwell, Eun Yoon Cho, Elena Provenzano, Federico Rojo, Emilio Alba, Carlos Caldas
Software Mentions: 2
Published: over 6 years ago

10.1002/path.4540

Uncovering the genomic heterogeneity of multifocal breast cancer
Cited by: 69
Author(s): Christine Desmedt, Debora Fumagalli, Elisabetta Pietri, Gabriele Zoppoli, David Brown, Serena Nik-Zainal, Gunes Gundem, Françoise Rothé, Samira Majjaj, Anna Garuti, Enrico Carminati, Sherene Loi, Thomas Van Brussel, Bram Boeckx, Marion Maetens, Laura Mudie, Delphine Vincent, Naïma Kheddoumi, Luigi Serra, Oriana Nanni, Alberto Ballestrero, Dino Amadori, Roberto Salgado, Alexandre de Wind, Diether Lambrechts, Martine Piccart, Denis Larsimont, Peter J. Campbell, Christos Sotiriou
Software Mentions: 1
Published: over 9 years ago

10.1371/journal.pone.0168153

The In Vitro Stability of Circulating Tumour DNA
Cited by: 17
Author(s): Emanuela Henao Diaz, Jeffrey Yachnin, Henrik Grönberg, Johan Lindberg
Software Mentions: 1
Published: almost 8 years ago

10.1371/journal.pone.0180467

DNA isolation protocol effects on nuclear DNA analysis by microarrays, droplet digital PCR, and whole genome sequencing, and on mitochondrial DNA copy number estimation
Cited by: 27
Author(s): E. Nacheva, Katya Mokretar, Aynur Soenmez, Alan Pittman, Colin Grace, Roberto Valli, Ayesha Ejaz, Selina Vattathil, Emanuela Maserati, Henry Houlden, Jan‐Willem Taanman, Anthony H.V. Schapira, Christos Proukakis
Software Mentions: 1
Published: over 7 years ago

10.1016/j.dib.2021.107349

Replicate whole-genome next-generation sequencing data derived from Caucasian donor saliva samples
Cited by: 0
Author(s): Mette Halskov Hansen, Charlotte Guldborg Nyvold
Software Mentions: 1
Published: about 3 years ago

10.15252/emmm.201809323

Detection of cell‐free <scp>DNA</scp> fragmentation and copy number alterations in cerebrospinal fluid from glioma patients
Cited by: 118
Author(s): Florent Moulière, Richard Mair, Dineika Chandrananda, Francesco Marass, Christopher G. Smith, Jing Su, James A. Morris, Colin Watts, Kevin M. Brindle, Nitzan Rosenfeld
Software Mentions: 1
Published: almost 6 years ago

10.1186/s13059-014-0471-6

Spatial and temporal evolution of distal 10q deletion, a prognostically unfavorable event in diffuse low-grade gliomas
Cited by: 28
Author(s): Hinke F. van Thuijl, Ilari Scheinin, Daoud Sie, Agustí Alentorn, Hendrik F. van Essen, Martijn Cordes, Ruth Fleischeuer, Anja Gijtenbeek, Guus Beute, W. A. van den Brink, Gerrit A. Meijer, Miek G. Havenith, Ahmed Idbaïh, Khê Hoang‐Xuan, Karima Mokhtari, Roel G.W. Verhaak, Paul van der Valk, Mark A. van de Wiel, Jan J. Heimans, Eleonora Aronica, Jaap C. Reijneveld, Pieter Wesseling, Bauke Ylstra
Software Mentions: 1
Published: about 10 years ago

10.1186/s13059-017-1253-8

Hi-C as a tool for precise detection and characterisation of chromosomal rearrangements and copy number variation in human tumours
Cited by: 129
Author(s): Louise Harewood, Kamal Kishore, Matthew Eldridge, Steven W. Wingett, Danita M. Pearson, Stefan Schoenfelder, V. Peter Collins, Peter Fraser
Software Mentions: 1
Published: over 7 years ago

10.1186/s13073-020-00723-8

Comprehensive characterization of cell-free tumor DNA in plasma and urine of patients with renal tumors
Cited by: 57
Author(s): Christopher G. Smith, Tina Moser, Florent Moulière, Johanna Field-Rayner, Matthew Eldridge, Anja Lisa Riediger, Dineika Chandrananda, Katrin Heider, Jonathan C. M. Wan, Anne Y. Warren, James A. Morris, Irena Hudecova, Wendy N. Cooper, Thomas J. Mitchell, Davina Gale, Andrea Ruiz-Valdepeñas, Tobias Klatte, Stephan Ursprung, Evis Sala, Antony C. P. Riddick, Tevita Aho, James Armitage, Samantha Perakis, Martin Pichler, Maximilian Seles, Gabriel Wcisło, Sarah J. Welsh, Athena Matakidou, Tim Eisen, Charles E. Massie, Nitzan Rosenfeld, Ellen Heitzer, Grant D. Stewart
Software Mentions: 1
Published: over 4 years ago

10.1038/srep31825

Performance of a TthPrimPol-based whole genome amplification kit for copy number alteration detection using massively parallel sequencing
Cited by: 14
Author(s): Lieselot Deleye, Dieter De Coninck, Annelies Dheedene, Petra De Sutter, Björn Menten, Dieter Deforce, Filip Van Nieuwerburgh
Software Mentions: 1
Published: about 8 years ago

10.1038/s41598-017-03711-y

Performance of four modern whole genome amplification methods for copy number variant detection in single cells
Cited by: 50
Author(s): Lieselot Deleye, Laurentijn Tilleman, Ann-Sophie Vander Plaetsen, Senne Cornelis, Dieter Deforce, Filip Van Nieuwerburgh
Software Mentions: 1
Published: over 7 years ago

10.1038/s41598-017-17525-5

STR profiling and Copy Number Variation analysis on single, preserved cells using current Whole Genome Amplification methods
Cited by: 8
Author(s): Ann-Sophie Vander Plaetsen, Lieselot Deleye, Senne Cornelis, Laurentijn Tilleman, Filip Van Nieuwerburgh, Dieter Deforce
Software Mentions: 1
Published: almost 7 years ago

10.1038/s41598-018-32900-6

Urinary Exosomal and cell-free DNA Detects Somatic Mutation and Copy Number Alteration in Urothelial Carcinoma of Bladder
Cited by: 40
Author(s): Dong Hoon Lee, Hana Yoon, Sanghui Park, Jeong Seon Kim, Young Ho Ahn, Kihwan Kwon, Donghwan Lee, Kwang Hyun Kim
Software Mentions: 1
Published: about 6 years ago

10.1002/jev2.12121

Extracellular vesicle miRNA predict FDG‐PET status in patients with classical Hodgkin Lymphoma
Cited by: 14
Author(s): Esther E.E. Drees, Margaretha G.M. Roemer, Nils J. Groenewegen, Jennifer Pérez-Boza, Monique A.J. van Eijndhoven, Leah I. Prins, Sandra A.W.M. Verkuijlen, Xuan Mai Tran, Julia Driessen, Gerben J.C. Zwezerijnen, Phylicia Stathi, Kevin Mol, Joey J. J. P. Karregat, Aikaterini Kalantidou, Andrea Vallés‐Martí, Tessa J. Molenaar, Ernesto Aparicio‐Puerta, Erik van Dijk, Bauke Ylstra, Catharina Gerarda Maria Groothuis-Oudshoorn, Michael Hackenberg, Daphne de Jong, Josée M. Zijlstra, D. Michiel Pegtel
Software Mentions: 1
Published: over 3 years ago

Ecosyste.ms: Papers

Projects: bioconductor: QDNAseq

Papers Mentioning QDNAseq 31