Longitudinal multi-omics analysis identifies early blood-based predictors of anti-TNF therapy response in inflammatory bowel disease

[1]  D. Plichta,et al.  Multi-omics reveal microbial determinants impacting responses to biologic therapies in inflammatory bowel disease. , 2021, Cell host & microbe.

[2]  Konrad U. Förstner,et al.  Longitudinal Multi-omics Analyses Identify Responses of Megakaryocytes, Erythroid Cells, and Plasmablasts as Hallmarks of Severe COVID-19 , 2020, Immunity.

[3]  P. Rosenstiel,et al.  Longitudinal multi-omics analyses identify responses of megakaryocytes, erythroid cells and plasmablasts as hallmarks of severe COVID-19 trajectories . Bernardes et al , 2020 .

[4]  O. Troyanskaya,et al.  RNA Identification of PRIME Cells Predicting Rheumatoid Arthritis Flares. , 2020, The New England journal of medicine.

[5]  L. Baglietto,et al.  Serum oncostatin M at baseline predicts mucosal healing in Crohn's disease patients treated with infliximab , 2020, Alimentary pharmacology & therapeutics.

[6]  D. Binion,et al.  Su1956 PERIPHERAL BLOOD EOSINOPHILA IS ASSOCIATED WITH LOWER INFLIXIMAB PERSISTENCE IN IBD PATIENTS: A TERTIARY CARE CENTER EXPERIENCE , 2020 .

[7]  Sven Nahnsen,et al.  The nf-core framework for community-curated bioinformatics pipelines , 2020, Nature Biotechnology.

[8]  Ash A. Alizadeh,et al.  Profiling Cell Type Abundance and Expression in Bulk Tissues with CIBERSORTx. , 2020, Methods in molecular biology.

[9]  C. Berri,et al.  Differential expression and co-expression gene network analyses reveal molecular mechanisms and candidate biomarkers involved in breast muscle myopathies in chicken , 2019, Scientific Reports.

[10]  Judy H. Cho,et al.  Blood-Derived DNA Methylation Signatures of Crohn's Disease and Severity of Intestinal Inflammation. , 2019, Gastroenterology.

[11]  Kenneth G. C. Smith,et al.  A blood-based prognostic biomarker in IBD , 2019, Gut.

[12]  Calixte Monast,et al.  I_MDS: an inflammatory bowel disease molecular activity score to classify patients with differing disease-driving pathways and therapeutic response to anti-TNF treatment , 2019, PLoS Comput. Biol..

[13]  Thomas Lengauer,et al.  RnBeads 2.0: comprehensive analysis of DNA methylation data , 2019, Genome Biology.

[14]  S. Vermeire,et al.  Low TREM1 expression in whole blood predicts anti-TNF response in inflammatory bowel disease , 2019, EBioMedicine.

[15]  S. Vermeire,et al.  Mucosal IL13RA2 expression predicts nonresponse to anti‐TNF therapy in Crohn's disease , 2019, Alimentary pharmacology & therapeutics.

[16]  S. Sridhar,et al.  Modulation of blood inflammatory markers by benralizumab in patients with eosinophilic airway diseases , 2019, Respiratory Research.

[17]  Judy H. Cho,et al.  Single-Cell Analysis of Crohn’s Disease Lesions Identifies a Pathogenic Cellular Module Associated with Resistance to Anti-TNF Therapy , 2019, Cell.

[18]  J. Silverberg,et al.  Dupilumab progressively improves systemic and cutaneous abnormalities in patients with atopic dermatitis , 2019, The Journal of allergy and clinical immunology.

[19]  Tsutomu Takeuchi,et al.  Multi-omics monitoring of drug response in rheumatoid arthritis in pursuit of molecular remission , 2018, Nature Communications.

[20]  R. Grützmann,et al.  Expansion of IL-23 receptor bearing TNFR2+ T cells is associated with molecular resistance to anti-TNF therapy in Crohn’s disease , 2018, Gut.

[21]  P. Rosenstiel,et al.  Vedolizumab is associated with changes in innate rather than adaptive immunity in patients with inflammatory bowel disease , 2018, Gut.

[22]  S. Shen-Orr,et al.  Cell-centred meta-analysis reveals baseline predictors of anti-TNFα non-response in biopsy and blood of patients with IBD , 2018, Gut.

[23]  Michael Krawczak,et al.  Increased Tryptophan Metabolism Is Associated With Activity of Inflammatory Bowel Diseases. , 2017, Gastroenterology.

[24]  M. Regueiro,et al.  Peripheral Eosinophilia in Patients With Inflammatory Bowel Disease Defines an Aggressive Disease Phenotype , 2017, The American Journal of Gastroenterology.

[25]  A. Gasbarrini,et al.  Can We Predict the Efficacy of Anti-TNF-α Agents? , 2017, International journal of molecular sciences.

[26]  G. Müller-Newen,et al.  Oncostatin M drives intestinal inflammation and predicts response to tumor necrosis factor-neutralizing therapy in patients with inflammatory bowel disease , 2017, Zeitschrift für Gastroenterologie.

[27]  Fabian J Theis,et al.  Impulse model-based differential expression analysis of time course sequencing data , 2017, bioRxiv.

[28]  R. Owens,et al.  Oncostatin M drives intestinal inflammation in mice and its abundance predicts response to tumor necrosis factor-neutralizing therapy in patients with inflammatory bowel disease , 2017, Nature Medicine.

[29]  Andreas Ziegler,et al.  ranger: A Fast Implementation of Random Forests for High Dimensional Data in C++ and R , 2015, 1508.04409.

[30]  F. Santilli,et al.  Oxidative stress and thromboxane-dependent platelet activation in inflammatory bowel disease: effects of anti-TNF-α treatment , 2016, Thrombosis and Haemostasis.

[31]  Ruigang Zhou,et al.  Integrated analysis of DNA methylation profiles and gene expression profiles to identify genes associated with pilocytic astrocytomas , 2016, Molecular medicine reports.

[32]  A. Maseri,et al.  Anti-TNFα agents curb platelet activation in patients with rheumatoid arthritis , 2016, Annals of the rheumatic diseases.

[33]  N. Ding,et al.  Systematic review: predicting and optimising response to anti‐TNF therapy in Crohn's disease – algorithm for practical management , 2016, Alimentary pharmacology & therapeutics.

[34]  Nathan C. Sheffield,et al.  LOLA: enrichment analysis for genomic region sets and regulatory elements in R and Bioconductor , 2015, Bioinform..

[35]  Jana G Hashash,et al.  Persistent or Recurrent Anemia Is Associated With Severe and Disabling Inflammatory Bowel Disease. , 2015, Clinical gastroenterology and hepatology : the official clinical practice journal of the American Gastroenterological Association.

[36]  Jana G Hashash,et al.  The Influence of Anti–tumor Necrosis Factor Agents on Hemoglobin Levels of Patients with Inflammatory Bowel Disease , 2015, Inflammatory bowel diseases.

[37]  W. Huber,et al.  Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2 , 2014, Genome Biology.

[38]  M. Greco,et al.  Anaemia from a patient perspective in inflammatory bowel disease: results from the European Federation of Crohn’s and Ulcerative Colitis Association’s online survey , 2014, European journal of gastroenterology & hepatology.

[39]  Wei Shi,et al.  featureCounts: an efficient general purpose program for assigning sequence reads to genomic features , 2013, Bioinform..

[40]  U. Kopylov,et al.  Optimizing anti-TNF treatments in inflammatory bowel disease. , 2014, Autoimmunity reviews.

[41]  Mahboob Rahman,et al.  The effect of golimumab on haemoglobin levels in patients with rheumatoid arthritis, psoriatic arthritis or ankylosing spondylitis. , 2013, Rheumatology.

[42]  B. Meskó,et al.  Peripheral blood derived gene panels predict response to infliximab in rheumatoid arthritis and Crohn's disease , 2013, Genome Medicine.

[43]  Thomas R. Gingeras,et al.  STAR: ultrafast universal RNA-seq aligner , 2013, Bioinform..

[44]  T. Down,et al.  A functional methylome map of ulcerative colitis , 2012, Genome research.

[45]  F. Massin,et al.  Plasma soluble triggering receptor expressed on myeloid cells-1 in Crohn's disease. , 2012, Digestive and Liver Disease.

[46]  P. Rosenstiel,et al.  mTNF reverse signalling induced by TNFα antagonists involves a GDF-1 dependent pathway: implications for Crohn's disease , 2012, Gut.

[47]  S. Danese New therapies for inflammatory bowel disease: from the bench to the bedside , 2011, Gut.

[48]  Miles Parkes,et al.  Gene expression profiling of CD8+ T cells predicts prognosis in patients with Crohn disease and ulcerative colitis. , 2011, The Journal of clinical investigation.

[49]  Marcel Martin Cutadapt removes adapter sequences from high-throughput sequencing reads , 2011 .

[50]  K. Van Steen,et al.  Levels of C-reactive protein are associated with response to infliximab therapy in patients with Crohn's disease. , 2011, Clinical gastroenterology and hepatology : the official clinical practice journal of the American Gastroenterological Association.

[51]  Rui Luo,et al.  Is My Network Module Preserved and Reproducible? , 2011, PLoS Comput. Biol..

[52]  Tariq Ahmad,et al.  Genome-wide meta-analysis increases to 71 the number of confirmed Crohn's disease susceptibility loci , 2010, Nature Genetics.

[53]  Alvis Brazma,et al.  A CD8 T cell transcription signature predicts prognosis in autoimmune disease , 2010, Nature Medicine.

[54]  Mahboob Rahman,et al.  Treatment with infliximab plus methotrexate improves anemia in patients with rheumatoid arthritis independent of improvement in other clinical outcome measures-a pooled analysis from three large, multicenter, double-blind, randomized clinical trials. , 2009, Seminars in arthritis and rheumatism.

[55]  G Van Assche,et al.  Mucosal gene signatures to predict response to infliximab in patients with ulcerative colitis , 2009, Gut.

[56]  Steve Horvath,et al.  WGCNA: an R package for weighted correlation network analysis , 2008, BMC Bioinformatics.

[57]  Max Kuhn,et al.  Building Predictive Models in R Using the caret Package , 2008 .

[58]  S. Horvath,et al.  Conservation and evolution of gene coexpression networks in human and chimpanzee brains , 2006, Proceedings of the National Academy of Sciences.

[59]  P. Rutgeerts,et al.  Human anti-tumor necrosis factor monoclonal antibody (adalimumab) in Crohn's disease: the CLASSIC-I trial. , 2006, Gastroenterology.

[60]  Paul Rutgeerts,et al.  Infliximab for induction and maintenance therapy for ulcerative colitis. , 2005, The New England journal of medicine.

[61]  Hilde van der Togt,et al.  Publisher's Note , 2003, J. Netw. Comput. Appl..

[62]  H. Papadaki,et al.  Anemia of chronic disease in rheumatoid arthritis is associated with increased apoptosis of bone marrow erythroid cells: improvement following anti-tumor necrosis factor-alpha antibody therapy. , 2002, Blood.

[63]  S. Hanauer,et al.  For Personal Use. Only Reproduce with Permission from the Lancet Publishing Group , 2022 .

[64]  J. Hampe,et al.  Tumour necrosis factor α and interleukin 1β in relapse of Crohn's disease , 1999, The Lancet.