On the public citation graph

Carnelian: alignment-free functional binning and abundance estimation of metagenomic reads

0 signed · 67 inferred · view as graph

Inferred edges come from two machine sources: sweeps of open repository metadata (mostly SSRN and Zenodo), and a bulk OpenAlex citation snapshot. Every row below is labelled with the one it came from. Neither is a complete citation index — absence here is not evidence of absence.

Is this your work? Sign in with ORCID and put your name on the claims that are yours.

Claim with ORCID

Reference health. See whether every reference in this work resolves to a known work and none has been retracted — and get a dated CiteStamped badge you can embed.

See reference health

What this work says

Outgoing claims: the papers this work cites, builds on, or argues with.

inferredcites →https://doi.org/10.1002/cpe.2938openalex-snapshot

Answering biological questions by querying k‐mer databases

inferredcites →https://doi.org/10.1002/mds.26069openalex-snapshot

Gut microbiota are related to Parkinson's disease and clinical phenotype

inferredcites →https://doi.org/10.1007/978-0-387-77240-0_14openalex-snapshot

Hypergeometric Testing Used for Gene Set Enrichment Analysis

inferredcites →https://doi.org/10.1007/978-1-4939-3167-5_2openalex-snapshot

UniProtKB/Swiss-Prot, the Manually Annotated Section of the UniProt KnowledgeBase: How to Use the Entry View

inferredcites →https://doi.org/10.1016/j.cell.2006.02.017openalex-snapshot

Ecological and Evolutionary Forces Shaping Microbial Diversity in the Human Intestine

inferredcites →https://doi.org/10.1016/j.cels.2015.08.004openalex-snapshot

Entropy-Scaling Search of Massive Biological Data

inferredcites →https://doi.org/10.1016/j.eng.2017.01.008openalex-snapshot

The Human Microbiota in Health and Disease

inferredcites →https://doi.org/10.1016/j.freeradbiomed.2013.05.001openalex-snapshot

Glutathione metabolism and Parkinson's disease

inferredcites →https://doi.org/10.1016/j.gdata.2016.11.004openalex-snapshot

Metagenomic investigation of the microbial diversity in a chrysotile asbestos mine pit pond, Lowell, Vermont, USA

inferredcites →https://doi.org/10.1016/j.jns.2011.07.021openalex-snapshot

Altered tryptophan metabolism in Parkinson's disease: A possible novel therapeutic approach

inferredcites →https://doi.org/10.1016/j.neurobiolaging.2013.11.001openalex-snapshot

Dysregulation of glucose metabolism is an early event in sporadic Parkinson's disease

inferredcites →https://doi.org/10.1016/j.plipres.2010.05.004openalex-snapshot

Alpha-synuclein, lipids and Parkinson’s disease

inferredcites →https://doi.org/10.1016/s0022-2836(05)80360-2openalex-snapshot

Basic Local Alignment Search Tool

inferredcites →https://doi.org/10.1016/s0168-9525(00)02024-2openalex-snapshot

EMBOSS: The European Molecular Biology Open Software Suite

inferredcites →https://doi.org/10.1038/ismej.2011.109openalex-snapshot

Structural segregation of gut microbiota between colorectal cancer patients and healthy volunteers

inferredcites →https://doi.org/10.1038/ismej.2012.8openalex-snapshot

Ultra-high-throughput microbial community analysis on the Illumina HiSeq and MiSeq platforms

inferredcites →https://doi.org/10.1038/nature11450openalex-snapshot

A metagenome-wide association study of gut microbiota in type 2 diabetes

inferredcites →https://doi.org/10.1038/nature12198openalex-snapshot

Gut metagenome in European women with normal, impaired and diabetic glucose control

inferredcites →https://doi.org/10.1038/nbt.2942openalex-snapshot

An integrated catalog of reference genes in the human gut microbiome

inferredcites →https://doi.org/10.1038/nbt.3511openalex-snapshot

Compressive mapping for next-generation sequencing

inferredcites →https://doi.org/10.1038/nbt.3519openalex-snapshot

Near-optimal probabilistic RNA-seq quantification

inferredcites →https://doi.org/10.1038/nmeth.3176openalex-snapshot

Fast and sensitive protein alignment using DIAMOND

inferredcites →https://doi.org/10.1038/nmeth0311-191openalex-snapshot

Taxonomic metagenome sequence assignment with structured output models

inferredcites →https://doi.org/10.1038/s41467-017-01973-8openalex-snapshot

Meta-analysis of gut microbiome studies identifies disease-specific and shared responses

inferredcites →https://doi.org/10.1093/bioinformatics/btp616openalex-snapshot

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

inferredcites →https://doi.org/10.1093/bioinformatics/btp692openalex-snapshot

RNA-Seq gene expression estimation with read mapping uncertainty

inferredcites →https://doi.org/10.1093/bioinformatics/btu170openalex-snapshot

Trimmomatic: a flexible trimmer for Illumina sequence data

inferredcites →https://doi.org/10.1093/bioinformatics/btv683openalex-snapshot

Large-scale machine learning for metagenomics sequence classification

inferredcites →https://doi.org/10.1093/bioinformatics/btw183openalex-snapshot

MOCAT2: a metagenomic assembly, annotation and profiling framework

inferredcites →https://doi.org/10.1093/bioinformatics/btx106openalex-snapshot

Pseudoalignment for metagenomic read assignment

inferredcites →https://doi.org/10.1093/bioinformatics/bty611openalex-snapshot

Metagenomic binning through low-density hashing

inferredcites →https://doi.org/10.1093/nar/gkh131openalex-snapshot

UniProt: the Universal Protein knowledgebase

inferredcites →https://doi.org/10.1093/nar/gkt963openalex-snapshot

IMG 4 version of the integrated microbial genomes comparative analysis system

inferredcites →https://doi.org/10.1093/nar/gkv007openalex-snapshot

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

inferredcites →https://doi.org/10.1093/nar/gkw1092openalex-snapshot

KEGG: new perspectives on genomes, pathways, diseases and drugs

inferredcites →https://doi.org/10.1093/nar/gkw1099openalex-snapshot

UniProt: the universal protein knowledgebase

inferredcites →https://doi.org/10.1093/nar/gkx1209openalex-snapshot

Functional sequencing read annotation for high precision microbiome analysis

inferredcites →https://doi.org/10.1101/gr.120618.111openalex-snapshot

Integrative analysis of environmental sequences using MEGAN4

inferredcites →https://doi.org/10.1109/tit.1962.1057683openalex-snapshot

Low-density parity-check codes

inferredcites →https://doi.org/10.1113/jphysiol.2009.174136openalex-snapshot

The core gut microbiome, energy balance and obesity

inferredcites →https://doi.org/10.1152/ajpendo.90921.2008openalex-snapshot

Dysregulated glutathione metabolism links to impaired insulin action in adipocytes

inferredcites →https://doi.org/10.1155/2016/2108909openalex-snapshot

Tyrosine Is Associated with Insulin Resistance in Longitudinal Metabolomic Profiling of Obese Children

inferredcites →https://doi.org/10.1172/jci44736openalex-snapshot

Parkin is a lipid-responsive regulator of fat uptake in mice and mutant human cells

inferredcites →https://doi.org/10.1186/1471-2105-9-386openalex-snapshot

The metagenomics RAST server – a public resource for the automatic phylogenetic and functional analysis of metagenomes

inferredcites →https://doi.org/10.1186/1471-2164-9-75openalex-snapshot

The RAST Server: Rapid Annotations using Subsystems Technology

inferredcites →https://doi.org/10.1186/gb-2014-15-2-r29openalex-snapshot

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

inferredcites →https://doi.org/10.1186/gb-2014-15-3-r46openalex-snapshot

Kraken: ultrafast metagenomic sequence classification using exact alignments

inferredcites →https://doi.org/10.1186/s12864-015-1419-2openalex-snapshot

CLARK: fast and accurate classification of metagenomic and genomic sequences using discriminative k-mers

inferredcites →https://doi.org/10.1186/s13059-016-0997-xopenalex-snapshot

Mash: fast genome and metagenome distance estimation using MinHash

inferredcites →https://doi.org/10.1186/s13059-016-1084-zopenalex-snapshot

Integrative analysis of genetic data sets reveals a shared innate immune component in autism spectrum disorder and its co-morbidities

inferredcites →https://doi.org/10.1186/s13073-017-0428-yopenalex-snapshot

Functional implications of microbial and viral gut metagenome changes in early stage L-DOPA-naïve Parkinson’s disease patients

inferredcites →https://doi.org/10.1186/s13742-015-0078-1openalex-snapshot

Tentacle: distributed quantification of genes in metagenomes

inferredcites →https://doi.org/10.1186/s40168-017-0242-1openalex-snapshot

New evidences on the altered gut microbiota in autism spectrum disorders

inferredcites →https://doi.org/10.1371/journal.pcbi.1003706openalex-snapshot

Metagenomic Data Utilization and Analysis (MEDUSA) and Construction of a Global Gut Microbial Gene Catalogue

inferredcites →https://doi.org/10.1371/journal.pone.0017288openalex-snapshot

Fast Identification and Removal of Sequence Contamination from Genomic and Metagenomic Datasets

inferredcites →https://doi.org/10.1371/journal.pone.0017299openalex-snapshot

Lipid Pathway Alterations in Parkinson's Disease Primary Visual Cortex

inferredcites →https://doi.org/10.1371/journal.pone.0049138openalex-snapshot

Integrated Metagenomics/Metaproteomics Reveals Human Host-Microbiota Signatures of Crohn's Disease

inferredcites →https://doi.org/10.1371/journal.pone.0063983openalex-snapshot

Effect of Lipopolysaccharide on Inflammation and Insulin Action in Human Muscle

inferredcites →https://doi.org/10.1371/journal.pone.0137725openalex-snapshot

Comparison of Fecal Microbiota in Children with Autism Spectrum Disorders and Neurotypical Siblings in the Simons Simplex Collection

inferredcites →https://doi.org/10.2174/1871530314666141111103217openalex-snapshot

Vitamins and Type 2 Diabetes Mellitus

inferredcites →https://doi.org/10.2337/db08-1637openalex-snapshot

Butyrate Improves Insulin Sensitivity and Increases Energy Expenditure in Mice

inferredcites →https://doi.org/10.2337/db12-1770openalex-snapshot

Diabetes Induces Lysine Acetylation of Intermediary Metabolism Enzymes in the Kidney

inferredcites →https://doi.org/10.3390/metabo7030042openalex-snapshot

Biomarker Research in Parkinson’s Disease Using Metabolite Profiling

inferredcites →https://doi.org/10.3390/nu7042930openalex-snapshot

The Role of Microbial Amino Acid Metabolism in Host Metabolism

inferredcites →https://doi.org/10.3929/ethz-b-000191807openalex-snapshot

Erratum to: Functional implications of microbial and viral gut metagenome changes in early stage L-DOPA-naive Parkinson's disease patients (vol 9, pg 39, 2017)

inferredcites →https://doi.org/10.5607/en.2013.22.1.11openalex-snapshot

Role of Oxidative Stress in Parkinson's Disease

What points at this work

Incoming claims: where this work appears in other papers’ reference lists and arguments.

inferred← citeshttps://doi.org/10.53846/goediss-9762openalex-snapshot

Alignment-free Phylogenetic Placement and its Applications

Editorial review for independent work. ICSAC — the Institute for Complexity Science and Advanced Computing — runs a structured editorial panel for researchers publishing outside journals, and publishes on CiteStamp rails. Submission is free and goes through ORCID: icsacinstitute.org/submit.