Development and evaluation of a culture-free microbiota profiling platform (MYcrobiota) for clinical diagnostics

por Boers, Stefan A., Hiltemann, Saskia D., Stubbs, Andrew P., Jansen, Ruud, Hays, John P.
Publicado 2018

WeFaceNano: a user-friendly pipeline for complete ONT sequence assembly and detection of antibiotic resistance in multi-plasmid bacterial isolates

por Heikema, Astrid P., Jansen, Rick, Hiltemann, Saskia D., Hays, John P., Stubbs, Andrew P.
Publicado 2021

NetWeAvers: an R package for integrative biological network analysis with mass spectrometry data

por McClellan, Elizabeth A., Moerland, Perry D., van der Spek, Peter J., Stubbs, Andrew P.
Publicado 2013

KREAP: an automated Galaxy platform to quantify in vitro re-epithelialization kinetics

por Fernandez-Gutierrez, Marcela M, van Zessen, David B H, van Baarlen, Peter, Kleerebezem, Michiel, Stubbs, Andrew P
Publicado 2018

Galaxy mothur Toolset (GmT): a user-friendly application for 16S rRNA gene sequencing analysis using mothur

por Hiltemann, Saskia D, Boers, Stefan A, van der Spek, Peter J, Jansen, Ruud, Hays, John P, Stubbs, Andrew P
Publicado 2018

Identification, Validation, and Utilization of Immune Cells in Pancreatic Ductal Adenocarcinoma Based on Marker Genes

por de Koning, Willem, Latifi, Diba, Li, Yunlei, van Eijck, Casper H. J., Stubbs, Andrew P., Mustafa, Dana A. M.
Publicado 2021

Evaluation of the Antigen-Experienced B-Cell Receptor Repertoire in Healthy Children and Adults

por IJspeert, Hanna, van Schouwenburg, Pauline A., van Zessen, David, Pico-Knijnenburg, Ingrid, Driessen, Gertjan J., Stubbs, Andrew P., van der Burg, Mirjam
Publicado 2016

Robust deep learning model for prognostic stratification of pancreatic ductal adenocarcinoma patients

por Ju, Jie, Wismans, Leonoor V., Mustafa, Dana A.M., Reinders, Marcel J.T., van Eijck, Casper H.J., Stubbs, Andrew P., Li, Yunlei
Publicado 2021

ImmunoGlobulin galaxy (IGGalaxy) for simple determination and quantitation of immunoglobulin heavy chain rearrangements from NGS

por Moorhouse, Michael J, van Zessen, David, IJspeert, Hanna, Hiltemann, Saskia, Horsman, Sebastian, van der Spek, Peter J, van der Burg, Mirjam, Stubbs, Andrew P
Publicado 2014

Artificial Intelligence in Digital Pathology for Bladder Cancer: Hype or Hope? A Systematic Review

por Khoraminia, Farbod, Fuster, Saul, Kanwal, Neel, Olislagers, Mitchell, Engan, Kjersti, van Leenders, Geert J. L. H., Stubbs, Andrew P., Akram, Farhan, Zuiverloon, Tahlita C. M.
Publicado 2023

Automated Selection of Hotspots (ASH): enhanced automated segmentation and adaptive step finding for Ki67 hotspot detection in adrenal cortical cancer

por Lu, Hao, Papathomas, Thomas G, van Zessen, David, Palli, Ivo, de Krijger, Ronald R, van der Spek, Peter J, Dinjens, Winand NM, Stubbs, Andrew P
Publicado 2014

Antigen receptor sequencing of paired bone marrow samples shows homogeneous distribution of acute lymphoblastic leukemia subclones

por Theunissen, Prisca M.J., van Zessen, David, Stubbs, Andrew P., Faham, Malek, Zwaan, Christian M., van Dongen, Jacques J.M., Van Der Velden, Vincent H.J.
Publicado 2017

A Decentralized Kidney Transplant Biopsy Classifier for Transplant Rejection Developed Using Genes of the Banff-Human Organ Transplant Panel

por van Baardwijk, Myrthe, Cristoferi, Iacopo, Ju, Jie, Varol, Hilal, Minnee, Robert C., Reinders, Marlies E. J., Li, Yunlei, Stubbs, Andrew P., Clahsen-van Groningen, Marian C.
Publicado 2022

NanoGalaxy: Nanopore long-read sequencing data analysis in Galaxy

por de Koning, Willem, Miladi, Milad, Hiltemann, Saskia, Heikema, Astrid, Hays, John P, Flemming, Stephan, van den Beek, Marius, Mustafa, Dana A, Backofen, Rolf, Grüning, Björn, Stubbs, Andrew P
Publicado 2020

Identification of CVID Patients With Defects in Immune Repertoire Formation or Specification

por van Schouwenburg, Pauline A., IJspeert, Hanna, Pico-Knijnenburg, Ingrid, Dalm, Virgil A. S. H., van Hagen, P. Martin, van Zessen, David, Stubbs, Andrew P., Patel, Smita Y., van der Burg, Mirjam
Publicado 2018

Spatial genomics reveals a high number and specific location of B cells in the pancreatic ductal adenocarcinoma microenvironment of long-term survivors

por Aziz, Hosein M., Saida, Lawlaw, de Koning, Willem, Stubbs, Andrew P., Li, Yunlei, Sideras, Kostandinos, Palacios, Elena, Feliu, Jaime, Mendiola, Marta, van Eijck, Casper H. J., Mustafa, Dana A. M.
Publicado 2023

Strategies for B-Cell Receptor Repertoire Analysis in Primary Immunodeficiencies: From Severe Combined Immunodeficiency to Common Variable Immunodeficiency

por IJspeert, Hanna, Wentink, Marjolein, van Zessen, David, Driessen, Gertjan J., Dalm, Virgil A. S. H., van Hagen, Martin P., Pico-Knijnenburg, Ingrid, Simons, Erik J., van Dongen, Jacques J. M., Stubbs, Andrew P., van der Burg, Mirjam
Publicado 2015

Comparison of Illumina versus Nanopore 16S rRNA Gene Sequencing of the Human Nasal Microbiota

por Heikema, Astrid P., Horst-Kreft, Deborah, Boers, Stefan A., Jansen, Rick, Hiltemann, Saskia D., de Koning, Willem, Kraaij, Robert, de Ridder, Maria A. J., van Houten, Chantal B., Bont, Louis J., Stubbs, Andrew P., Hays, John P.
Publicado 2020

Deciphering imprints of impaired memory B-cell maturation in germinal centers of three patients with common variable immunodeficiency

por van Schouwenburg, Pauline, Unger, Susanne, Payne, Kathryn J., Kaiser, Fabian M. P., Pico-Knijnenburg, Ingrid, Pfeiffer, Jens, Hausmann, Oliver, Friedmann, David, Erbel, Michelle, Seidl, Maximilian, van Zessen, David, Stubbs, Andrew P., van der Burg, Mirjam, Warnatz, Klaus
Publicado 2022

Immunomodulatory Effects of Stereotactic Body Radiotherapy and Vaccination with Heat-Killed Mycobacterium Obuense (IMM-101) in Patients with Locally Advanced Pancreatic Cancer

por van ‘t Land, Freek R., Lau, Sai P., de Koning, Willem, Klaase, Larissa, Vink, Madelief, van Krimpen, Anneloes, Dumas, Jasper, Vadgama, Disha, Nuyttens, Joost J., Mustafa, Dana A. M., Stadhouders, Ralph, Willemsen, Marcella, Stubbs, Andrew P., Aerts, Joachim G., van Eijck, Casper H. J.
Publicado 2022