[Research] Key molecular pathways of canine mammary tumor development
Graim K. et al. (2020) Modeling molecular development of breast cancer in canine mammary tumors. ...
Tag
- dog 6
- biotech 5
- nf-core 5
- genome 4
- pipeline 4
- nextflow 4
- tumor 3
- spatial 3
- public data 3
- data processing 3
- proteomics 3
- reference 2
- dataset 2
- community 2
- tool 2
- ucsc 2
- NGS 2
- website 2
- epigenome 2
- aging 1
- methylome 1
- career 1
- cancer 1
- analysis 1
- luminary 1
- linux 1
- windows 1
- ssh 1
- vpn 1
- canine 1
- ngs 1
- sequencing 1
- troubleshooting 1
- ENCODE 1
- singularity 1
- genomic 1
- encode 1
- annotation 1
- lab 1
- cloud 1
- index 1
- method 1
- container 1
dog
[Resource] Canine mammary gland tumor dataset (WES and RNA-seq)
Kim K. et al. (2019) Whole-exome and whole-transcriptome sequencing of canine mammary gland tumor...
[Report] Comparing human and canine aging through methylome profiling
Wang T. et al. (2020) Quantitative translation of dog-to-human aging by conserved remodeling of t...
[Review] Dog10K consortium - Large-scale Dog GWAS
Ostrander E.A. et al. (2019) Dog10K: an international sequencing effort to advance studies of can...
[Highlight] The new canine reference genome - canFam4
Neff E.P. (2019) Whole genome sequencing has gone to the dogs. labanimal
[Research] New canine reference genome - canFam4
Wang C. et al. (2021) A novel canine reference genome resolves genomic architecture and uncovers ...
biotech
[Review] Long-read sequencing technologies
Sedlazeck F.J. et al. (2018) Piercing the dark matter: bioinformatics of long-range sequencing an...
[Resource] Spatiotemporal transcriptomic atlas of mouse organogenesis
Chen A. et al. (2022) Spatiotemporal transcriptomic atlas of mouse organogenesis using DNA nanoba...
[Review] Applying spatial transcriptomics in cancer research
Bassiouni R. et al. (2021) Applicability of spatial transcriptional profiling to cancer research....
[Review] Spatial transcriptomics 1
Rao A. et al. (2021) Exploring tissue architecture using spatial transcriptomics. Nature
[Biotech Feature] Seven technologies to watch in 2022
Eisenstein M. (2022) Seven technologies to watch in 2022. Nature
nf-core
[DB] INSDC: How to download NGS raw data
In my previous post, I described how to specifically search for public NGS-based data and fetch m...
[BI] Downloading the Singularity images of nf-core pipeline
When running nf-core pipelines for the first time, I frequently encounter errors while pulling th...
[BI] Temporary files generated by the nf-core pipeline in root folder
Problem Description
[BI] RNA-seq data processing using nf-core pipeline
Link: nf-core rnaseq pipeline
[BI] BAM to FASTQ using nf-core pipeline
If you’ve ever downloaded public NGS data from databases like TCGA or ICDC (previous post), you k...
genome
[Research] Optimizing analysis pipelines through CNV tools comparison
Coutelier M. et al. (2021) Combining callers improves the detection of copy number variants from ...
[Review] Dog10K consortium - Large-scale Dog GWAS
Ostrander E.A. et al. (2019) Dog10K: an international sequencing effort to advance studies of can...
[Highlight] The new canine reference genome - canFam4
Neff E.P. (2019) Whole genome sequencing has gone to the dogs. labanimal
[Research] New canine reference genome - canFam4
Wang C. et al. (2021) A novel canine reference genome resolves genomic architecture and uncovers ...
pipeline
[BI] ChIP-seq preprocessing witout input control using nf-core pipeline
In ChIP-seq processing, having input control (either fragmented genomic DNA or IgG pulldown) is e...
[Review] Spatial transcriptomics 2
Liao j. et al. (2021) Uncovering an Organ’s Molecular Architecture at Single-Cell Resolution by S...
[Correspondence] The Nextflow community: nf-core
Ewels P.A. et al. (2020) The nf-core framework for community-curated bioinformatics pipelines. Na...
[Perspective] Bioinformatics workflow manager
Wratten L. et al. (2021) Reproducible, scalable, and shareable analysis pipelines with bioinforma...
nextflow
[DB] INSDC: How to download NGS raw data
In my previous post, I described how to specifically search for public NGS-based data and fetch m...
[BI] Temporary files generated by the nf-core pipeline in root folder
Problem Description
[BI] RNA-seq data processing using nf-core pipeline
Link: nf-core rnaseq pipeline
[BI] BAM to FASTQ using nf-core pipeline
If you’ve ever downloaded public NGS data from databases like TCGA or ICDC (previous post), you k...
tumor
[DB] ICDC: Navigating Canine Tumor Datasets
Integrative Canine Data Commons (ICDC)
[Research] Key molecular pathways of canine mammary tumor development
Graim K. et al. (2020) Modeling molecular development of breast cancer in canine mammary tumors. ...
[Resource] Canine mammary gland tumor dataset (WES and RNA-seq)
Kim K. et al. (2019) Whole-exome and whole-transcriptome sequencing of canine mammary gland tumor...
spatial
[Resource] Spatiotemporal transcriptomic atlas of mouse organogenesis
Chen A. et al. (2022) Spatiotemporal transcriptomic atlas of mouse organogenesis using DNA nanoba...
[Review] Applying spatial transcriptomics in cancer research
Bassiouni R. et al. (2021) Applicability of spatial transcriptional profiling to cancer research....
[Review] Spatial transcriptomics 1
Rao A. et al. (2021) Exploring tissue architecture using spatial transcriptomics. Nature
public data
[DB] INSDC: How to download NGS raw data
In my previous post, I described how to specifically search for public NGS-based data and fetch m...
[DB] INSDC: Where are the public NGS data stored?
Public databases are filled with a tremendous amount of NGS-based data that can be used for resea...
[DB] ICDC: Navigating Canine Tumor Datasets
Integrative Canine Data Commons (ICDC)
data processing
[BI] ChIP-seq data processing using ENCODE pipeline
Link: GitHub - ENCODE3 ChIP-seq pipeline & Google Docs
[BI] RNA-seq data processing using nf-core pipeline
Link: nf-core rnaseq pipeline
[BI] BAM to FASTQ using nf-core pipeline
If you’ve ever downloaded public NGS data from databases like TCGA or ICDC (previous post), you k...
proteomics
[BI] Reference epigenome map: chromatin states
Chromatin states in the field of epigenomics refer to the organization and modification of chroma...
[BI] Blacklisted regions in the genome
In this post, let’s explore what a blacklist is in the context of genomics and why certain region...
[BI] Proteomic data and nf-core pipelines
Types of Proteomic Data:
reference
[Highlight] The new canine reference genome - canFam4
Neff E.P. (2019) Whole genome sequencing has gone to the dogs. labanimal
[Research] New canine reference genome - canFam4
Wang C. et al. (2021) A novel canine reference genome resolves genomic architecture and uncovers ...
dataset
[Research] Key molecular pathways of canine mammary tumor development
Graim K. et al. (2020) Modeling molecular development of breast cancer in canine mammary tumors. ...
[Resource] Canine mammary gland tumor dataset (WES and RNA-seq)
Kim K. et al. (2019) Whole-exome and whole-transcriptome sequencing of canine mammary gland tumor...
community
[Review] Spatial transcriptomics 2
Liao j. et al. (2021) Uncovering an Organ’s Molecular Architecture at Single-Cell Resolution by S...
[Correspondence] The Nextflow community: nf-core
Ewels P.A. et al. (2020) The nf-core framework for community-curated bioinformatics pipelines. Na...
tool
[BI] Genome Mappability: How to calculate it using Umap
In my previous posts, we explored the concept of problematic regions in genomes, such as the blac...
[Research] Optimizing analysis pipelines through CNV tools comparison
Coutelier M. et al. (2021) Combining callers improves the detection of copy number variants from ...
ucsc
[DB] Diverse genome annotations in UCSC browser
In the quest to understand how genomes are regulated and function, and their implications in dise...
[BI] Problematic regions and Mappability in genomic analysis
In my previous post, we delved into the concept of Blacklist regions in genomes. Expanding on thi...
NGS
[DB] INSDC: How to download NGS raw data
In my previous post, I described how to specifically search for public NGS-based data and fetch m...
[DB] INSDC: Where are the public NGS data stored?
Public databases are filled with a tremendous amount of NGS-based data that can be used for resea...
website
[Lab Life] Crisis and new opportunities in the lab
Tuesday, April 27, 2021, 2:00 AM. I was deeply engrossed in my analysis work in my lab, listening...
[Lablife] The Lab’s digital persona: crafting an impressive website
When running a research lab, having a strong team is crucial. The people you work with can make a...
epigenome
[BI] ChIP-seq preprocessing witout input control using nf-core pipeline
In ChIP-seq processing, having input control (either fragmented genomic DNA or IgG pulldown) is e...
[Research] CDCA7: conserved hemimethylated DNA sensor
Wassing I.E. et al. (2024) CDCA7 is an evolutionarily conserved hemimethylated DNA sensor in euka...
aging
[Report] Comparing human and canine aging through methylome profiling
Wang T. et al. (2020) Quantitative translation of dog-to-human aging by conserved remodeling of t...
methylome
[Report] Comparing human and canine aging through methylome profiling
Wang T. et al. (2020) Quantitative translation of dog-to-human aging by conserved remodeling of t...
career
[Career Column] Owing, not doing
Wang Y. (2022) Owning, not doing: my transition from master’s to PhD student. Nature
cancer
[Review] Applying spatial transcriptomics in cancer research
Bassiouni R. et al. (2021) Applicability of spatial transcriptional profiling to cancer research....
analysis
[Research] Normalization of RNA-seq: Addressing TPM vs. GeTMM
While revising a manuscript, I received a comment stating, “Authors used FPKM for RNA-seq analysi...
luminary
[Luminary] Nobel Laureate - Svante Pääbo
As a child attending church for several years, I often found myself contemplating the teachings I...
linux
[CS] Remote Work: Overcoming SSH Blocks
Bridging Computers with SSH through VPN
windows
[CS] Remote Work: Overcoming SSH Blocks
Bridging Computers with SSH through VPN
ssh
[CS] Remote Work: Overcoming SSH Blocks
Bridging Computers with SSH through VPN
vpn
[CS] Remote Work: Overcoming SSH Blocks
Bridging Computers with SSH through VPN
canine
[DB] ICDC: Navigating Canine Tumor Datasets
Integrative Canine Data Commons (ICDC)
ngs
[DB] ICDC: Navigating Canine Tumor Datasets
Integrative Canine Data Commons (ICDC)
sequencing
[Review] Long-read sequencing technologies
Sedlazeck F.J. et al. (2018) Piercing the dark matter: bioinformatics of long-range sequencing an...
troubleshooting
[BI] Temporary files generated by the nf-core pipeline in root folder
Problem Description
ENCODE
[BI] ChIP-seq data processing using ENCODE pipeline
Link: GitHub - ENCODE3 ChIP-seq pipeline & Google Docs
singularity
[BI] Downloading the Singularity images of nf-core pipeline
When running nf-core pipelines for the first time, I frequently encounter errors while pulling th...
genomic
[BI] Problematic regions and Mappability in genomic analysis
In my previous post, we delved into the concept of Blacklist regions in genomes. Expanding on thi...
encode
[BI] Problematic regions and Mappability in genomic analysis
In my previous post, we delved into the concept of Blacklist regions in genomes. Expanding on thi...
annotation
[DB] Diverse genome annotations in UCSC browser
In the quest to understand how genomes are regulated and function, and their implications in dise...
lab
[Lablife] Lab and personal cloud for data management
I am currently managing two NAS (Network Attached Storage) systems, one for the lab and one perso...
cloud
[Lablife] Lab and personal cloud for data management
I am currently managing two NAS (Network Attached Storage) systems, one for the lab and one perso...
index
Journal Index
This page contains a list of papers posted under the Exploration category.
method
[BI] Genome Mappability: How to calculate it using Umap
In my previous posts, we explored the concept of problematic regions in genomes, such as the blac...
container
[CS] How to create a Singularity container
In this post, I will explain how to create a Singularity container that includes all the necessar...
