Pan-cancer analyses reveal cancer-type-specific fungal ecologies and bacteriome interactions

Fungal mycobiome drives IL-33 secretion and type 2 immunity in pancreatic cancer

(2022) Aftab Alam et al.   CANCER CELL

Hallmarks of Cancer: New Dimensions

(2022) Douglas Hanahan   Cancer Discovery

Multi-kingdom microbiota analyses identify bacterial–fungal interactions and biomarkers of colorectal cancer across cohorts

(2022) Ning-Ning Liu et al.   Nature Microbiology

Cancer's second genome: Microbial cancer diagnostics and redefining clonal evolution as a multispecies process

(2022) Gregory D. Sepich‐Poore et al.   BIOESSAYS

Phylogeny-Aware Analysis of Metagenome Community Ecology Based on Matched Reference Genomes while Bypassing Taxonomy

(2022) Qiyun Zhu et al.   mSystems

The Mycobiome: Cancer Pathogenesis, Diagnosis, and Therapy

(2022) Ahmed Gamal et al.   Cancers

Zebra: Static and Dynamic Genome Cover Thresholds with Overlapping References

(2022) Daniel Hakim et al.   mSystems

Debaryomyces is enriched in Crohn’s disease intestinal tissue and impairs healing in mice

(2021) Umang Jain et al.   SCIENCE

Accurate and sensitive detection of microbial eukaryotes from whole metagenome shotgun sequencing

(2021) Abigail L. Lind et al.   Microbiome

Identification of bacteria-derived HLA-bound peptides in melanoma

(2021) Shelly Kalaora et al.   NATURE

The microbiome and human cancer

(2021) Gregory D. Sepich-Poore et al.   SCIENCE

Epigenetics, fragmentomics, and topology of cell-free DNA in liquid biopsies

(2021) Y. M. Dennis Lo et al.   SCIENCE

Commensal bacteria and fungi differentially regulate tumor responses to radiation therapy

(2021) Stephen L. Shiao et al.   CANCER CELL

Adaptive immunity induces mutualism between commensal eukaryotes

(2021) Kyla S. Ost et al.   NATURE

Prognostic correlations with the microbiome of breast cancer subtypes

(2021) Sagarika Banerjee et al.   Cell Death & Disease

Intermittent Hypoxia and Hypercapnia Alter Diurnal Rhythms of Luminal Gut Microbiome and Metabolome

(2021) Celeste Allaband et al.   mSystems

Intratumoral accumulation of gut microbiota facilitates CD47-based immunotherapy via STING signaling

(2020) Yaoyao Shi et al.   JOURNAL OF EXPERIMENTAL MEDICINE

Pan-cancer analysis of whole genomes

(2020)   NATURE

The landscape of viral associations in human cancers

(2020) Marc Zapatka et al.   NATURE GENETICS

SciPy 1.0: fundamental algorithms for scientific computing in Python

(2020) Pauli Virtanen et al.   NATURE METHODS

Microbiome analyses of blood and tissues suggest cancer diagnostic approach

(2020) Gregory D. Poore et al.   NATURE

PICRUSt2 for prediction of metagenome functions

(2020) Gavin M. Douglas et al.   NATURE BIOTECHNOLOGY

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

(2020) Deborah Nejman et al.   SCIENCE

The gut mycobiome: The overlooked constituent of clinical outcomes and treatment complications in patients with cancer and other immunosuppressive conditions

(2020) Jessica R. Galloway-Peña et al.   PLoS Pathogens

Breast cancer colonization by Fusobacterium nucleatum accelerates tumor growth and metastatic progression

(2020) Lishay Parhi et al.   Nature Communications

Analysis of compositions of microbiomes with bias correction

(2020) Huang Lin et al.   Nature Communications

ASTRAL-Pro: Quartet-Based Species-Tree Inference despite Paralogy

(2020) Chao Zhang et al.   MOLECULAR BIOLOGY AND EVOLUTION

Antibiotics create a shift from mutualism to competition in human gut communities with a longer-lasting impact on fungi than bacteria

(2020) Bastian Seelbinder et al.   Microbiome

Defining HPV-specific B cell responses in patients with head and neck cancer

(2020) Andreas Wieland et al.   NATURE

ClipKIT: A multiple sequence alignment trimming software for accurate phylogenomic inference

(2020) Jacob L. Steenwyk et al.   PLOS BIOLOGY

A Novel Sparse Compositional Technique Reveals Microbial Perturbations

(2019) Cameron Martino et al.   mSystems

Microbiome signatures in prostate cancer

(2019) Sagarika Banerjee et al.   CARCINOGENESIS

Genome-wide cell-free DNA fragmentation in patients with cancer

(2019) Stephen Cristiano et al.   NATURE

The Tumor Microenvironment Innately Modulates Cancer Progression

(2019) Dominique C. Hinshaw et al.   CANCER RESEARCH

Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2

(2019) Evan Bolyen et al.   NATURE BIOTECHNOLOGY

Establishing microbial composition measurement standards with reference frames

(2019) James T. Morton et al.   Nature Communications

MetaBAT 2: an adaptive binning algorithm for robust and efficient genome reconstruction from metagenome assemblies

(2019) Dongwan D. Kang et al.   PeerJ

Tumor Microbiome Diversity and Composition Influence Pancreatic Cancer Outcomes

(2019) Erick Riquelme et al.   CELL

The fungal mycobiome promotes pancreatic oncogenesis via activation of MBL

(2019) Berk Aykut et al.   NATURE

Learning representations of microbe–metabolite interactions

(2019) James T. Morton et al.   NATURE METHODS

Fungal-bacterial diversity and microbiome complexity predict ecosystem functioning

(2019) Cameron Wagg et al.   Nature Communications

Minimap2: pairwise alignment for nucleotide sequences

(2018) Heng Li   BIOINFORMATICS

OUP accepted manuscript

(2018)   BIOINFORMATICS

Cell-of-Origin Patterns Dominate the Molecular Classification of 10,000 Tumors from 33 Types of Cancer

(2018) Katherine A. Hoadley et al.   CELL

Genome-reconstruction for eukaryotes from complex natural microbial communities

(2018) Patrick T. West et al.   GENOME RESEARCH

The Immune Landscape of Cancer

(2018) Vésteinn Thorsson et al.   IMMUNITY

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

(2018) Smruti Pushalkar et al.   Cancer Discovery

Distinct Microbial Signatures Associated With Different Breast Cancer Types

(2018) Sagarika Banerjee et al.   Frontiers in Microbiology

Qiita: rapid, web-enabled microbiome meta-analysis

(2018) Antonio Gonzalez et al.   NATURE METHODS

Modulation of Pulmonary Microbiota by Antibiotic or Probiotic Aerosol Therapy: A Strategy to Promote Immunosurveillance against Lung Metastases

(2018) Valentino Le Noci et al.   Cell Reports

Topography of cancer-associated immune cells in human solid tumors

(2018) Jakob Nikolas Kather et al.   eLife

MetaWRAP—a flexible pipeline for genome-resolved metagenomic data analysis

(2018) Gherman V. Uritskiy et al.   Microbiome

The UNITE database for molecular identification of fungi: handling dark taxa and parallel taxonomic classifications

(2018) Rolf Henrik Nilsson et al.   NUCLEIC ACIDS RESEARCH

Simple statistical identification and removal of contaminant sequences in marker-gene and metagenomics data

(2018) Nicole M. Davis et al.   Microbiome

metaSPAdes: a new versatile metagenomic assembler

(2017) Sergey Nurk et al.   GENOME RESEARCH

Assessment of variation in microbial community amplicon sequencing by the Microbiome Quality Control (MBQC) project consortium

(2017) Rashmi Sinha et al.   NATURE BIOTECHNOLOGY

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

(2017) Leore T. Geller et al.   SCIENCE

Bacteriome and mycobiome associations in oral tongue cancer

(2017) Pranab K. Mukherjee et al.   Oncotarget

The ovarian cancer oncobiome

(2017) Sagarika Banerjee et al.   Oncotarget

A dysbiotic mycobiome dominated by Candida albicans is identified within oral squamous-cell carcinomas

(2017) Manosha Perera et al.   Journal of Oral Microbiology

The gut mycobiome of the Human Microbiome Project healthy cohort

(2017) Andrea K. Nash et al.   Microbiome

Multiple Approaches Detect the Presence of Fungi in Human Breastmilk Samples from Healthy Mothers

(2017) Alba Boix-Amorós et al.   Scientific Reports

MaxBin 2.0: an automated binning algorithm to recover genomes from multiple metagenomic datasets

(2015) Yu-Wei Wu et al.   BIOINFORMATICS

PRROC: computing and visualizing precision-recall and receiver operating characteristic curves in R

(2015) Jan Grau et al.   BIOINFORMATICS

BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs

(2015) Felipe A. Simão et al.   BIOINFORMATICS

CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes

(2015) Donovan H. Parks et al.   GENOME RESEARCH

Robust enumeration of cell subsets from tissue expression profiles

(2015) Aaron M Newman et al.   NATURE METHODS

Distinct microbiological signatures associated with triple negative breast cancer

(2015) Sagarika Banerjee et al.   Scientific Reports

Dysbiosis of Fungal Microbiota in the Intestinal Mucosa of Patients with Colorectal Adenomas

(2015) Chunguang Luan et al.   Scientific Reports

Fusobacterium nucleatumand T Cells in Colorectal Carcinoma

(2015) Kosuke Mima et al.   JAMA Oncology

Pairwise measures of species co-occurrence for choosing indicator species and quantifying overlap

(2014) Thomas M. Neeson et al.   ECOLOGICAL INDICATORS

US Incidence of Breast Cancer Subtypes Defined by Joint Hormone Receptor and HER2 Status

(2014) Nadia Howlader et al.   JNCI-Journal of the National Cancer Institute

Binning metagenomic contigs by coverage and composition

(2014) Johannes Alneberg et al.   NATURE METHODS

The Spectrum of Fungi That Infects Humans

(2014) J. R. Kohler et al.   Cold Spring Harbor Perspectives in Medicine

voom: precision weights unlock linear model analysis tools for RNA-seq read counts

(2014) Charity W Law et al.   GENOME BIOLOGY

PEAR: a fast and accurate Illumina Paired-End reAd mergeR

(2013) J. Zhang et al.   BIOINFORMATICS

Topographic diversity of fungal and bacterial communities in human skin

(2013) Keisha Findley et al.   NATURE

phyloseq: An R Package for Reproducible Interactive Analysis and Graphics of Microbiome Census Data

(2013) Paul J. McMurdie et al.   PLoS One

EMPeror: a tool for visualizing high-throughput microbial community data

(2013) Yoshiki Vázquez-Baeza et al.   GigaScience

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Interactions Between Commensal Fungi and the C-Type Lectin Receptor Dectin-1 Influence Colitis

(2012) I. D. Iliev et al.   SCIENCE

Bacterial-Fungal Interactions: Hyphens between Agricultural, Clinical, Environmental, and Food Microbiologists

(2011) P. Frey-Klett et al.   MICROBIOLOGY AND MOLECULAR BIOLOGY REVIEWS

Accelerated Profile HMM Searches

(2011) Sean R. Eddy   PLoS Computational Biology

Supervised normalization of microarrays

(2010) Brigham H. Mecham et al.   BIOINFORMATICS

Medically important bacterial–fungal interactions

(2010) Anton Y. Peleg et al.   NATURE REVIEWS MICROBIOLOGY

FastTree 2 – Approximately Maximum-Likelihood Trees for Large Alignments

(2010) Morgan N. Price et al.   PLoS One

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS