Explanipedia

Detection of heterogeneous resistance mechanisms to tyrosine kinase inhibitors from cell-free DNA Open

Heather A. Parsons, Conor Messer, Katheryn Santos, David J. Merrell, Brian P. Danysh , et al. · 2025

Though there has been substantial progress in the development of anti-human epidermal growth factor receptor 2 (HER2) therapies to treat HER2-positive metastatic breast cancer (MBC) within the past two decades, most patients still experien…

Genomic landscape of multiple myeloma and its precursor conditions Open

Jean-Baptiste Alberge, Ankit K. Dutta, Andrea Poletti, Tim Coorens, Elizabeth D. Lightbody , et al. · 2025

SVelfie: A method for discovering cancer drivers based on enrichment of likely functional structural variants Open

Xavi Loinaz, Judith Dagan, Jean-Baptiste Alberge, Antonia Kowalewski, Mendy Miller , et al. · 2025

Structural variants (SVs) can drive tumorigenesis, yet discovering SV cancer drivers remains challenging 1 . Here, we present SVelfie ( S tructural V ariants e nriched with l ikely f unctional/ i mpactful e vents), a statistical method to …

Genomic mechanisms of resistance to tyrosine kinase inhibitors in HER2 amplified breast cancer Open

Heather A. Parsons, Conor Messer, Katheryn Santos, Jakob Weiß, David J. Merrell , et al. · 2024

Though there has been substantial progress in the development of anti-HER2 therapies to treat HER2-positive metastatic breast cancer (MBC) within the past two decades, most patients still experience disease progression and cancer-related d…

Author Correction: Comprehensive analysis of chromothripsis in 2,658 human cancers using whole-genome sequencing Open

Isidro Cortés‐Ciriano, Jake June-Koo Lee, Ruibin Xi, Dhawal Jain, Youngsook L. Jung , et al. · 2023

Correction to: Nature Genetics, published online 05 February 2020. In the published version of this paper, the members of the Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium were listed in the Supplementary Information; however, th…

Author Correction: Pan-cancer analysis of whole genomes identifies driver rearrangements promoted by LINE-1 retrotransposition Open

Bernardo Rodríguez–Martín, Eva G. Álvarez, Adrian Baez‐Ortega, Jorge Zamora, Fran Supek , et al. · 2023

Correction to: Nature Genetics, published online 05 February 2020. In the published version of this paper, the members of the Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium were listed in the Supplementary Information; however, th…

Author Correction: Disruption of chromatin folding domains by somatic genomic rearrangements in human cancer Open

Kadir C. Akdemir, Victoria T. Le, Sahaana Chandran, Yilong Li, Roel G.W. Verhaak , et al. · 2023

Author Correction: Butler enables rapid cloud-based analysis of thousands of human genomes Open

Sergei Yakneen, Sebastian M. Waszak, Brice Aminou, Javier Bartolome, Keith A. Boroevich , et al. · 2023

Combined PD-1, BRAF and MEK inhibition in BRAFV600E colorectal cancer: a phase 2 trial Open

Jun Tian, Jonathan Chen, Sherry Chao, Karin Pelka, Marios Giannakis , et al. · 2023

While BRAF inhibitor combinations with EGFR and/or MEK inhibitors have improved clinical efficacy in BRAF V600E colorectal cancer (CRC), response rates remain low and lack durability. Preclinical data suggest that BRAF/MAPK pathway inhibit…

Author Correction: Patterns of somatic structural variation in human cancer genomes Open

Yilong Li, Nicola D. Roberts, Jeremiah A. Wala, Ofer Shapira, Steven E. Schumacher , et al. · 2023

Author Correction: Analyses of non-coding somatic drivers in 2,658 cancer whole genomes Open

Esther Rheinbay, Morten Muhlig Nielsen, Federico Abascal, Jeremiah A. Wala, Ofer Shapira , et al. · 2023

Evolutionary history of transformation from chronic lymphocytic leukemia to Richter syndrome Open

Erin M. Parry, Ignaty Leshchiner, Romain Guièze, Connor Johnson, Eugen Tausch , et al. · 2023

Author Correction: Integrative pathway enrichment analysis of multivariate omics data Open

Marta Paczkowska, Jonathan Barenboim, Nardnisa Sintupisut, Natalie S. Fox, Helen Zhu , et al. · 2022

Author Correction: Genomic footprints of activated telomere maintenance mechanisms in cancer Open

Lina Sieverling, Chen Hong, Sandra D. Koser, Philip Ginsbach, Kortine Kleinheinz , et al. · 2022

Author Correction: Combined burden and functional impact tests for cancer driver discovery using DriverPower Open

Shimin Shuai, Federico Abascal, Samirkumar B. Amin, Gary D. Bader, Pratiti Bandopadhayay , et al. · 2022

Author Correction: Cancer LncRNA Census reveals evidence for deep functional conservation of long noncoding RNAs in tumorigenesis Open

Joana Carlevaro-Fita, Andrés Lanzós, Lars Feuerbach, Chen Hong, David Mas-Ponte , et al. · 2022

Author Correction: Pathway and network analysis of more than 2500 whole cancer genomes Open

Matthew A. Reyna, David Haan, Marta Paczkowska, Lieven P. C. Verbeke, Miguél Vázquez , et al. · 2022

The Four mRNA Bases Have Quite Different (Un)folding Free Energies, Applications to RNA Splicing and Translation Initiation with BindOligoNet Open

Julian M. Hess, William Jannen, Daniel P. Aalberts · 2022

Expression of mRNA is often regulated by the binding of a small RNA (miRNA, snoRNA, siRNA). While the pairing contribution to the net free energy is well parameterized and can be computed in O(N) time, the cost of removing pre-existing mRN…

Author Correction: Retrospective evaluation of whole exome and genome mutation calls in 746 cancer samples Open

Matthew H. Bailey, William U. Meyerson, Lewis Jonathan Dursi, Liang-Bo Wang, Guanlan Dong , et al. · 2020

Retrospective evaluation of whole exome and genome mutation calls in 746 cancer samples Open

Matthew H. Bailey, William U. Meyerson, Lewis Jonathan Dursi, Liang-Bo Wang, Guanlan Dong , et al. · 2020

Author Correction: Cas9 activates the p53 pathway and selects for p53-inactivating mutations Open

Oana M. Enache, Verónica Rendo, Mai Abdusamad, Daniel D. Lam, Desiree Davison , et al. · 2020

Cas9 activates the p53 pathway and selects for p53-inactivating mutations Open

Oana M. Enache, Verónica Rendo, Mai Abdusamad, Daniel D. Lam, Desiree Davison , et al. · 2020

Publisher Correction: Comprehensive analysis of chromothripsis in 2,658 human cancers using whole-genome sequencing Open

Isidro Cortés‐Ciriano, Jake June-Koo Lee, Ruibin Xi, Dhawal Jain, Youngsook L. Jung , et al. · 2020

Integrative Genomic Analysis of Cholangiocarcinoma Identifies Distinct IDH -Mutant Molecular Profiles Open

Farshad Farshidfar, Siyuan Zheng, Marie‐Claude Gingras, Yulia Newton, Juliann Shih , et al. · 2020

Cholangiocarcinoma (CCA) is an aggressive malignancy of the bile ducts, with poor prognosis and limited treatment options. Here, we describe the integrated analysis of somatic mutations, RNA expression, copy number, and DNA methylation by …

Integrated Molecular Characterization of Uterine Carcinosarcoma Open

Andrew D. Cherniack, Hui Shen, Vonn Walter, Chip Stewart, Bradley A. Murray , et al. · 2020

SummaryWe performed genomic, epigenomic, transcriptomic, and proteomic characterizations of uterine carcinosarcomas (UCSs). Cohort samples had extensive copy-number alterations and highly recurrent somatic mutations. Frequent mutations wer…

Publisher Correction: Butler enables rapid cloud-based analysis of thousands of human genomes Open

Sergei Yakneen, Sebastian M. Waszak, Sergei Yakneen, Brice Aminou, Javier Bartolome , et al. · 2020

Analyses of non-coding somatic drivers in 2,658 cancer whole genomes Open

Esther Rheinbay, Morten Muhlig Nielsen, Federico Abascal, Jeremiah A. Wala, Ofer Shapira , et al. · 2020

Integrative pathway enrichment analysis of multivariate omics data Open

Marta Paczkowska, Jonathan Barenboim, Nardnisa Sintupisut, Natalie S. Fox, Helen Zhu , et al. · 2020

Comprehensive analysis of chromothripsis in 2,658 human cancers using whole-genome sequencing Open

Isidro Cortés‐Ciriano, Jake June-Koo Lee, Ruibin Xi, Dhawal Jain, Youngsook L. Jung , et al. · 2020

Cancer LncRNA Census reveals evidence for deep functional conservation of long noncoding RNAs in tumorigenesis Open

Joana Carlevaro-Fita, Andrés Lanzós, Lars Feuerbach, Chen Hong, David Mas-Ponte , et al. · 2020

Long non-coding RNAs (lncRNAs) are a growing focus of cancer genomics studies, creating the need for a resource of lncRNAs with validated cancer roles. Furthermore, it remains debated whether mutated lncRNAs can drive tumorigenesis, and wh…

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