SAMQA: error classification and validation of high-throughput sequenced read data

by Bressler Ryan, Killcoyne Sarah, Robinson Thomas, Boyle John
Published 2011-08-01

Methods for visual mining of genomic and proteomic data atlases

by Boyle John, Kreisberg Richard, Bressler Ryan, Killcoyne Sarah
Published 2012-04-01

Systems biology driven software design for the research enterprise

by Killcoyne Sarah, Cavnor Christopher, Boyle John, Shmulevich Ilya
Published 2008-06-01

Adaptable data management for systems biology investigations

by Burdick David, Cavnor Chris, Rovira Hector, Boyle John, Killcoyne Sarah, Shmulevich Ilya
Published 2009-03-01

Hydra: a scalable proteomic search engine which utilizes the Hadoop distributed computing framework

by Lewis Steven, Csordas Attila, Killcoyne Sarah, Hermjakob Henning, Hoopmann Michael R, Moritz Robert L, Deutsch Eric W, Boyle John
Published 2012-12-01

SEQADAPT: an adaptable system for the tracking, storage and analysis of high throughput sequencing experiments

by Rovira Hector, Ramsey Stephen A, Marzolf Bruz, Lin Jake, Killcoyne Sarah, Handcock Jeremy, Cavnor Chris C, Burdick David B, Bressler Ryan, Shmulevich Ilya, Boyle John
Published 2010-07-01

Practical early cancer detection: distinguishing stable from unstable genomes in pre-cancerous tissues.

by Killcoyne, Sarah, Fitzgerald, Rebecca C
Published 2021

Genomic instability signals offer diagnostic possibility in early cancer detection

by Killcoyne, Sarah, Yusuf, Aisha, Fitzgerald, Rebecca C
Published 2021

Genomic copy number predicts esophageal cancer years before transformation

by Fitzgerald, Rebecca, Killcoyne, Sarah, Gregson, Eleanor, Wedge, David C, Woodcock, Dan J, Eldridge, Matthew, De La Rue, Rachel, Miremadi, Ahmed, Abbas, Sujath, Blasko, Adrienn, Kosmidou, Cassandra, Januszewicz, Wladyslaw, Jenkins, Aikaterini, Gerstung, Moritz
Published 2020

Rearrangement processes and structural variations show evidence of selection in oesophageal adenocarcinomas.

by Ng, Alvin Wei Tian, Contino, Gianmarco, Killcoyne, Sarah, Devonshire, Ginny, Hsu, Ray, Abbas, Sujath, Su, Jing, Redmond, Aisling M, Weaver, Jamie MJ, Eldridge, Matthew D, Tavaré, Simon, Oesophageal Cancer Clinical and Molecular Stratification (OCCAMS) Consortium, Edwards, Paul AW, Fitzgerald, Rebecca C
Published 2022

Rearrangement processes and structural variations show evidence of selection in oesophageal adenocarcinomas.

by Ng, Alvin Wei Tian, Contino, Gianmarco, Killcoyne, Sarah, Devonshire, Ginny, Hsu, Ray, Abbas, Sujath, Su, Jing, Redmond, Aisling M, Weaver, Jamie MJ, Eldridge, Matthew, Tavaré, Simon, Oesophageal Cancer Clinical and Molecular Stratification (OCCAMS) Consortium, Edwards, Paul AW, Fitzgerald, Rebecca
Published 2022

Identification of prognostic phenotypes of esophageal adenocarcinoma in two independent cohorts.

by Sawas, Tarek, Killcoyne, Sarah, Iyer, Prasad G, Wang, Kenneth K, Smyrk, Thomas C, Kisiel, John B, Qin, Yi, Ahlquist, David A, Rustgi, Anil K, OCCAMS Consortium, Costa, Rui J, Gerstung, Moritz, Fitzgerald, Rebecca C, Katzka, David A
Published 2018

The landscape of selection in 551 esophageal adenocarcinomas defines genomic biomarkers for the clinic.

by Frankell, Alexander M, Jammula, SriGanesh, Li, Xiaodun, Contino, Gianmarco, Killcoyne, Sarah, Abbas, Sujath, Perner, Juliane, Bower, Lawrence, Devonshire, Ginny, Ococks, Emma, Grehan, Nicola, Mok, James, O'Donovan, Maria, MacRae, Shona, Eldridge, Matthew D, Tavaré, Simon, Oesophageal Cancer Clinical and Molecular Stratification (OCCAMS) Consortium, Fitzgerald, Rebecca C
Published 2019

Aneuploidy in targeted endoscopic biopsies outperforms other tissue biomarkers in the prediction of histologic progression of Barrett's oesophagus: A multi-centre prospective cohor...

by Hadjinicolaou, Andreas V, van Munster, Sanne N, Achilleos, Achilleas, Santiago Garcia, Jose, Killcoyne, Sarah, Ragunath, Krish, Bergman, Jacques JGHM, Fitzgerald, Rebecca C, di Pietro, Massimiliano
Published 2020

Identification of Subtypes of Barrett's Esophagus and Esophageal Adenocarcinoma Based on DNA Methylation Profiles and Integration of Transcriptome and Genome Data.

by Jammula, SriGanesh, Katz-Summercorn, Annalise C, Li, Xiaodun, Linossi, Constanza, Smyth, Elizabeth, Killcoyne, Sarah, Biasci, Daniele, Subash, Vinod V, Abbas, Sujath, Blasko, Adrienn, Devonshire, Ginny, Grantham, Amber, Wronowski, Filip, O'Donovan, Maria, Grehan, Nicola, Eldridge, Matthew D, Tavaré, Simon, Oesophageal Cancer Clinical and Molecular Stratification (OCCAMS) consortium, Fitzgerald, Rebecca C
Published 2020