Predicting cancer prognosis and drug response from the tumor microbiome

The cancer microbiome atlas: a pan-cancer comparative analysis to distinguish tissue-resident microbiota from contaminants

(2021) Anders B. Dohlman et al.   Cell Host & Microbe

Identification of bacteria-derived HLA-bound peptides in melanoma

(2021) Shelly Kalaora et al.   NATURE

Cancer prognosis with shallow tumor RNA sequencing

(2020) Pedro Milanez-Almeida et al.   NATURE MEDICINE

Microbiome and Breast Cancer: New Role for an Ancient Population

(2020) Zahra Eslami-S et al.   Frontiers in Oncology

Microbiome analyses of blood and tissues suggest cancer diagnostic approach

(2020) Gregory D. Poore et al.   NATURE

The human tumor microbiome is composed of tumor type–specific intracellular bacteria

(2020) Deborah Nejman et al.   SCIENCE

Microbiome factors in HPV-driven carcinogenesis and cancers

(2020) Daniel Lin et al.   PLoS Pathogens

Machine learning algorithm validation with a limited sample size

(2019) Andrius Vabalas et al.   PLoS One

An Integrated TCGA Pan-Cancer Clinical Data Resource to Drive High-Quality Survival Outcome Analytics

(2018) Jianfang Liu et al.   CELL

The Pancreatic Cancer Microbiome Promotes Oncogenesis by Induction of Innate and Adaptive Immune Suppression

(2018) Smruti Pushalkar et al.   Cancer Discovery

Association between expression of random gene sets and survival is evident in multiple cancer types and may be explained by sub-classification

(2018) Yishai Shimoni   PLoS Computational Biology

Profiling the Urinary Microbiota in Male Patients With Bladder Cancer in China

(2018) Peng Wu et al.   Frontiers in Cellular and Infection Microbiology

Mucosal microbiome dysbiosis in gastric carcinogenesis

(2017) Olabisi Oluwabukola Coker et al.   GUT

Gastric microbial community profiling reveals a dysbiotic cancer-associated microbiota

(2017) Rui M Ferreira et al.   GUT

Identification of cancer genes that are independent of dominant proliferation and lineage programs

(2017) Laura M. Selfors et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Potential role of intratumor bacteria in mediating tumor resistance to the chemotherapeutic drug gemcitabine

(2017) Leore T. Geller et al.   SCIENCE

Dysbiosis of the microbiome in gastric carcinogenesis

(2017) Natalia Castaño-Rodríguez et al.   Scientific Reports

Evaluating the molecule-based prediction of clinical drug responses in cancer

(2016) Zijian Ding et al.   BIOINFORMATICS

Development of a RNA-Seq Based Prognostic Signature in Lung Adenocarcinoma

(2016) Sudhanshu Shukla et al.   JNCI-Journal of the National Cancer Institute

Chlamydia Trachomatis Infection-Associated Risk of Cervical Cancer

(2016) Haiyan Zhu et al.   MEDICINE

Toward a Shared Vision for Cancer Genomic Data

(2016) Robert L. Grossman et al.   NEW ENGLAND JOURNAL OF MEDICINE

Summary measure of discrimination in survival models based on cumulative/dynamic time-dependent ROC curves

(2016) Jérôme Lambert et al.   STATISTICAL METHODS IN MEDICAL RESEARCH

Development of a RNA-Seq Based Prognostic Signature in Lung Adenocarcinoma

(2016) Sudhanshu Shukla et al.   JNCI-Journal of the National Cancer Institute

limma powers differential expression analyses for RNA-sequencing and microarray studies

(2015) Matthew E. Ritchie et al.   NUCLEIC ACIDS RESEARCH

Implementing a Class of Permutation Tests: ThecoinPackage

(2015) Torsten Hothorn et al.   Journal of Statistical Software

Regularization Paths for Cox's Proportional Hazards Model via Coordinate Descent

(2015) Noah Simon et al.   Journal of Statistical Software

Expression Profiling of Primary and Metastatic Ovarian Tumors Reveals Differences Indicative of Aggressive Disease

(2014) Alexander S. Brodsky et al.   PLoS One

The First Korean Case ofSphingobacterium spiritivorumBacteremia in a Patient with Acute Myeloid Leukemia

(2013) Young Rae Koh et al.   Annals of Laboratory Medicine

The human gut and groundwater harbor non-photosynthetic bacteria belonging to a new candidate phylum sibling to Cyanobacteria

(2013) Sara C Di Rienzi et al.   eLife

Bacteraemia due to Cedecea davisae in a patient with sigmoid colon cancer: a case report and brief review of the literature

(2012) Karolina Akinosoglou et al.   DIAGNOSTIC MICROBIOLOGY AND INFECTIOUS DISEASE

Differential expression analysis of multifactor RNA-Seq experiments with respect to biological variation

(2012) Davis J. McCarthy et al.   NUCLEIC ACIDS RESEARCH

Bacterial Conversion of Folinic Acid Is Required for Antifolate Resistance

(2011) Sam Ogwang et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Cedecea davisae bacteremia in a neutropenic patient with acute myeloid leukemia

(2011) Getahun Abate et al.   JOURNAL OF INFECTION

Association between Epstein-Barr virus infection and chemoresistance to docetaxel in gastric carcinoma

(2011) Hee Jong Shin et al.   MOLECULES AND CELLS

Most Random Gene Expression Signatures Are Significantly Associated with Breast Cancer Outcome

(2011) David Venet et al.   PLoS Computational Biology

edgeR: a Bioconductor package for differential expression analysis of digital gene expression data

(2009) M. D. Robinson et al.   BIOINFORMATICS