Adam Kowalczyk

Exploring effective approaches for haplotype block phasing.

Ziad Al Bkhetan, Justin Zobel, Adam Kowalczyk, Karin Verspoor, Benjamin Goudey

Journal article  |  2019  |  BMC Bioinformatics

BACKGROUND: Knowledge of phase, the specific allele sequence on each copy of homologous chromosomes, is increasingly recognized as..

Effect of outpatient antibiotics for urinary tract infections on antimicrobial resistance among commensal Enterobacteriaceae: a multinational prospective cohort study

AJ Stewardson, J Vervoort, N Adriaenssens, S Coenen, M Godycki-Cwirko, A Kowalczyk, BD Huttner, C Lammens, S Malhotra-Kumar, H Goossens, S Harbarth

Journal article  |  2018  |  Clinical Microbiology and Infection

Interactions within the MHC contribute to the genetic architecture of celiac disease

Benjamin Goudey, Gad Abraham, Eder Kikianty, Qiao Wang, Dave Rawlinson, Fan Shi, Izhak Haviv, Linda Stern, Adam Kowalczyk, Michael Inouye

Journal article  |  2017  |  PLOS ONE

Standardized ETDRS charts for mobile devices

E Kędzierska, K Petelczyc, K Kakarenko, M Bieda, A Kowalczyk, A Byszewska, A Kolodziejczyk

Journal article  |  2017  |  Photonics Letters of Poland

Charts displayed on mobile devices was verified in comparison to standardized ETDRS charts. Such method of visual acuity assessmen..

Use of a Novel Nonparametric Version of DEPTH to Identify Genomic Regions Associated with Prostate Cancer Risk

Robert J MacInnis, Daniel F Schmidt, Enes Makalic, Gianluca Severi, Liesel M FitzGerald, Matthias Reumann, Miroslaw K Kapuscinski, Adam Kowalczyk, Zeyu Zhou, Benjamin Goudey, Guoqi Qian, Quang M Bui, Daniel J Park, Adam Freeman, Melissa C Southey, Ali Amin Al Olama, Zsofia Kote-Jarai, Rosalind A Eeles, John L Hopper, Graham G Giles

Journal article  |  2016  |  Cancer Epidemiology Biomarkers & Prevention

A urinary microRNA signature can predict the presence of bladder urothelial carcinoma in patients undergoing surveillance

Nikhil Sapre, Geoff Macintyre, Michael Clarkson, Haroon Naeem, Marek Cmero, Adam Kowalczyk, Paul D Anderson, Anthony J Costello, Niall M Corcoran, Christopher M Hovens

Journal article  |  2016  |  British Journal of Cancer

Development and validation of a gene expression tumour classifier for cancer of unknown primary

Richard W Tothill, Fan Shi, Lisa Paiman, Justin Bedo, Adam Kowalczyk, Linda Mileshkin, Evangeline Buela, Robert Klupacs, David Bowtell, Keith Byron

Journal article  |  2015  |  Pathology

Curated MicroRNAs in Urine and Blood Fail to Validate as Predictive Biomarkers for High-Risk Prostate Cancer

Nikhil Sapre, Matthew KH Hong, Geoff Macintyre, Heather Lewis, Adam Kowalczyk, Anthony J Costello, Niall M Corcoran, Christopher M Hovens

Journal article  |  2014  |  PLoS ONE

Accurate and Robust Genomic Prediction of Celiac Disease Using Statistical Learning

Gad Abraham, Jason A Tye-Din, Oneil G Bhalala, Adam Kowalczyk, Justin Zobel, Michael Inouye

Journal article  |  2014  |  PLoS Genetics

GWIS(FI): a Universal GPU Interface for Exhaustive Search of Pairwise Interactions in Case-Control GWAS in Minutes

Qiao Wang, Fan Shi, Andrew Kowalczyk, Richard M Campbell, Benjamin Goudey, David Rawlinson, Aaron Harwood, Herman Ferra, Adam Kowalczyk

Conference Proceedings  |  2014  |  2014 IEEE International Conference on Bioinformatics and Biomedicine (BIBM)

Supplementary Information to 'GWISFI: a Univeral GPU Interface for Exhaustive Search of Pairwise Interactions in Case-Control GWAS in Minutes'

Q Wang, F Shi, A Kowalczyk, RM Campbell, B Goudey, D Rawlinson, A Harwood, H Ferra, A Kowalczyk

Software / Code  |  2014

Massively-parallel sequencing assists the diagnosis and guided treatment of cancers of unknown primary

Richard W Tothill, Jason Li, Linda Mileshkin, Ken Doig, Terence Siganakis, Prue Cowin, Andrew Fellowes, Timothy Semple, Stephen Fox, Keith Byron, Adam Kowalczyk, David Thomas, Penelope Schofield, David D Bowtell

Journal article  |  2013  |  Journal of Pathology

Plasma lipid profiling in a large population-based cohort

Jacquelyn M Weir, Gerard Wong, Christopher K Barlow, Melissa A Greeve, Adam Kowalczyk, Laura Almasy, Anthony G Comuzzie, Michael C Mahaney, Jeremy BM Jowett, Jonathan Shaw, Joanne E Curran, John Blangero, Peter J Meikle

Journal article  |  2013  |  Journal of Lipid Research

Plasma Lipid Profiling Shows Similar Associations with Prediabetes and Type 2 Diabetes

Peter J Meikle, Gerard Wong, Christopher K Barlow, Jacquelyn M Weir, Melissa A Greeve, Gemma L MacIntosh, Laura Almasy, Anthony G Comuzzie, Michael C Mahaney, Adam Kowalczyk, Izhac Haviv, Narelle Grantham, Dianna J Magliano, Jeremy BM Jowett, Paul Zimmet, Joanne E Curran, John Blangero, Jonathan Shaw

Journal article  |  2013  |  PLoS One

Molecular Profiling of Human Mammary Gland Links Breast Cancer Risk to a p27( ) Cell Population with Progenitor Characteristics

Sibgat Choudhury, Vanessa Almendro, Vanessa F Merino, Zhenhua Wu, Reo Maruyama, Ying Su, Filipe C Martins, Mary Jo Fackler, Marina Bessarabova, Adam Kowalczyk, Thomas Conway, Bryan Beresford-Smith, Geoff Macintyre, Yu-Kang Cheng, Zoila Lopez-Bujanda, Antony Kaspi, Rong Hu, Judith Robens, Tatiana Nikolskaya, Vilde D Haakensen, et al.

Journal article  |  2013  |  Cell Stem Cell

GWIS - model-free, fast and exhaustive search for epistatic interactions in case-control GWAS

Benjamin Goudey, David Rawlinson, Qiao Wang, Fan Shi, Herman Ferra, Richard M Campbell, Linda Stern, Michael T Inouye, Cheng Soon Ong, Adam Kowalczyk

Journal article  |  2013  |  BMC Genomics

Performance and Robustness of Penalized and Unpenalized Methods for Genetic Prediction of Complex Human Disease

Gad Abraham, Adam Kowalczyk, Justin Zobel, Michael Inouye

Journal article  |  2013  |  Genetic Epidemiology

A distinct DNA methylation signature defines pediatric pre-B cell acute lymphoblastic leukemia

Nicholas C Wong, David Ashley, Zac Chatterton, Mandy Parkinson-Bates, Hong Kiat Ng, Minhee S Halemba, Adam Kowalczyk, Justin Bedo, Qiao Wang, Katrina Bell, Elizabeth Algar, Jeffrey M Craig, Richard Saffery

Journal article  |  2012  |  Epigenetics

SparSNP: Fast and memory-efficient analysis of all SNPs for phenotype prediction

Gad Abraham, Adam Kowalczyk, Justin Zobel, Michael Inouye

Journal article  |  2012  |  BMC Bioinformatics

FSR: feature set reduction for scalable and accurate multi-class cancer subtype classification based on copy number

Gerard Wong, Christopher Leckie, Adam Kowalczyk

Journal article  |  2012  |  Bioinformatics

Plasma Lipidomic Analysis of Stable and Unstable Coronary Artery Disease

Peter J Meikle, Gerard Wong, Despina Tsorotes, Christopher K Barlow, Jacquelyn M Weir, Michael J Christopher, Gemma L MacIntosh, Benjamin Goudey, Linda Stern, Adam Kowalczyk, Izhak Haviv, Anthony J White, Anthony M Dart, Stephen J Duffy, Garry L Jennings, Bronwyn A Kingwell

Journal article  |  2011  |  Arteriosclerosis Thrombosis and Vascular Biology

Genome-wide analysis distinguishes hyperglycemia regulated epigenetic signatures of primary vascular cells

Luciano Pirola, Aneta Balcerczyk, Richard W Tothill, Izhak Haviv, Antony Kaspi, Sebastian Lunke, Mark Ziemann, Tom Karagiannis, Stephen Tonna, Adam Kowalczyk, Bryan Beresford-Smith, Geoff Macintyre, Kelong Ma, Hongyu Zhang, Jingde Zhu, Assam El-Osta

Journal article  |  2011  |  Genome Research

Genome annotation test with validation on transcription start site and ChIP-Seq for Pol-II binding data

Justin Bedo, Adam Kowalczyk

Journal article  |  2011  |  Bioinformatics

Epigenetic Regulation of Cell Type-Specific Expression Patterns in the Human Mammary Epithelium

Reo Maruyama, Sibgat Choudhury, Adam Kowalczyk, Marina Bessarabova, Bryan Beresford-Smith, Thomas Conway, Antony Kaspi, Zhenhua Wu, Tatiana Nikolskaya, Vanessa F Merino, Pang-Kuo Lo, X Shirley Liu, Yuri Nikolsky, Saraswati Sukumar, Izhak Haviv, Kornelia Polyak

Journal article  |  2011  |  PLoS Genetics

Meta-analysis of gene expression microarrays with missing replicates

Fan Shi, Gad Abraham, Christopher Leckie, Izhak Haviv, Adam Kowalczyk

Journal article  |  2011  |  BMC Bioinformatics

The Poisson Margin Test for Normalization-Free Significance Analysis of NGS Data

Adam Kowalczyk, Justin Bedo, Thomas Conway, Bryan Beresford-Smith

Journal article  |  2011  |  Journal of Computational Biology

Precision Medicine: Dawn of Supercomputing in ‘omics Research

M Reumann, KE Holt, M Inouye, T Stinear, B Goudey, G Abraham, Q WANG, F Shi, A Kowalczyk, A Pearce, A Isaac, BJ Pope, H Butzkueven, J Wagner, S Moore, M Downton, PC Church, SJ Turner, J Field, M Southey, et al.

Conference Proceedings  |  2011

Using Gene Ontology annotations in exploratory microarray clustering to understand cancer etiology

Geoff Macintyre, James Bailey, Daniel Gustafsson, Izhak Haviv, Adam Kowalczyk

Journal article  |  2010  |  Pattern Recognition Letters

A bi-ordering approach to linking gene expression with clinical annotations in gastric cancer

Fan Shi, Christopher Leckie, Geoff MacIntyre, Izhak Haviv, Alex Boussioutas, Adam Kowalczyk

Conference Proceedings  |  2010  |  Proceedings of the 2nd International Workshop on Machine Learning in Systems Biology 2008

is-rSNP: a novel technique for in silico regulatory SNP detection

Geoff Macintyre, James Bailey, Izhak Haviv, Adam Kowalczyk

Journal article  |  2010  |  Bioinformatics

Prediction of breast cancer prognosis using gene set statistics provides signature stability and biological context

Gad Abraham, Adam Kowalczyk, Sherene Loi, Izhak Haviv, Justin Zobel

Journal article  |  2010  |  BMC Bioinformatics

Exploiting sequence similarity to validate the sensitivity of SNP arrays in detecting fine-scaled copy number variations

Gerard Wong, Christopher Leckie, Kylie L Gorringe, Izhak Haviv, Ian G Campbell, Adam Kowalczyk

Journal article  |  2010  |  Bioinformatics

A bi-ordering approach to linking gene expression with clinical annotations in gastric cancer

F SHI, CAL Leckie, GJM Macintyre, I Haviv, A Boussioutas, AK Kowalczyk

Journal article  |  2010  |  BMC Bioinformatics

Optical performance monitoring based on asynchronous delay-tap sampling

Trevor B Anderson, Sarah D Dods, Adam Kowalczyk, Ken Clarke, Don Hewitt, Jonathan C Li

Book Chapter  |  2010

Multi Impairment Monitoring for Optical Networks

Trevor B Anderson, Adam Kowalczyk, Ken Clarke, Sarah D Dods, Don Hewitt, Jonathan C Li

Journal article  |  2009  |  Journal of Lightwave Technology

Precision-mapping and statistical validation of quantitative trait loci by machine learning

Justin Bedo, Peter Wenzl, Adam Kowalczyk, Andrzej Kilian

Journal article  |  2008  |  BMC Genetics

Gene Ontology Assisted Exploratory Microarray Clustering and Its Application to Cancer

Geoff Macintyre, James Bailey, Daniel Gustafsson, Alex Boussioutas, Izhak Haviv, Adam Kowalczyk

Conference Proceedings  |  2008  |  Pattern Recognition in Bioinformatics (Lecture Notes in Computer Science) 2008

Pretreatment gene expression profiles can be used to predict response to neoadjuvant chemoradiotherapy in esophageal cancer

Cuong Duong, Danielle M Greenawalt, Adam Kowalczyk, Marianne L Ciavarella, Garvesh Raskutti, William K Murray, Wayne A Phillips, Robert JS Thomas

Journal article  |  2007  |  Annals of Surgical Oncology

Asynchronous sampling for optical performance monitoring

SD Dods, TB Anderson, K Clarke, M Bakaul, A Kowalczyk

Conference Proceedings  |  2007  |  OFC/NFOEC 2007

Multi-impairment monitoring for photonic networks

TB Anderson, SD Dods, K Clarke, J Bedo, A Kowalczyk

Conference Proceedings  |  2007  |  33rd European Conference and Exhibition on Optical Communication