Ecosyste.ms: Papers
An open API service providing mapping between scientific papers and software projects that are mentioned in them.
All mentions data is based on the CZI Software Mentions dataset.
Projects: bioconductor: QDNAseq
https://packages.ecosyste.ms/registries/bioconductor.org/packages/QDNAseq
Quantitative DNA Sequencing for Chromosomal Aberrations
1 version
Latest release: about 1 year ago
3 dependent packages
42,879 downloads total
Papers Mentioning QDNAseq 31
10.1186/s13058-021-01451-6
Transcriptome and genome evolution during HER2-amplified breast neoplasiaCited 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: over 3 years ago
10.1371/journal.ppat.1006668
Merkel cell polyomavirus recruits MYCL to the EP400 complex to promote oncogenesisCited 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: about 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 dataCited 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 detectionCited 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 alterationsCited 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/s12859-018-2288-x
HiCcompare: an R-package for joint normalization and comparison of HI-C datasetsCited by: 94
Author(s): John C. Stansfield, Kellen Garrison Cresswell, Vladimir I. Vladimirov, Mikhail G. Dozmorov
Software Mentions: 4
Published: over 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 classificationCited 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: over 3 years ago
10.1371/journal.pgen.1007285
Global characterization of copy number variants in epilepsy patients from whole genome sequencingCited 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 carcinogenesisCited 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: over 6 years ago
10.12688/f1000research.9259.2
GeneBreak: detection of recurrent DNA copy number aberration-associated chromosomal breakpoints within genesCited 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 CancerCited 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: over 7 years ago
10.3390/cancers11060805
Bioinformatics Analysis for Circulating Cell-Free DNA in CancerCited 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 MosaicismCited 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 cancerCited 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 cancerCited 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 mutationsCited 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 cancersCited 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 cancerCited 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 DNACited 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 estimationCited 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 samplesCited 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 patientsCited 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: about 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 gliomasCited 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 tumoursCited 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 tumorsCited 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 sequencingCited 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 cellsCited 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 methodsCited 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 BladderCited 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 LymphomaCited 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