papers read list about biology, bioinformatics, and others
| Title | Year | Link | Code | Note |
|---|---|---|---|---|
| Profile hidden Markov models | 1998 | Bioinformatics | HMM applications review | |
| A review of UMAP in population genetics | 2021 | Journal of Human Genetics | github | UMAP application review |
| Title | Year | Link | Code | Note |
|---|---|---|---|---|
| Improved OTU-picking using long-read 16S rRNA gene amplicon sequencing and generic hierarchical clustering | 2015 | Microbiome | TGS pipeline | |
| Comparison of Methods for Picking the Operational Taxonomic Units From Amplicon Sequences | 2021 | Frontiers in Micorbiology | 4 type clustering method and 33 tools in timeline | |
| The impact of intragenomic rRNA variation on metabarcoding-derived diversity estimates: A case study from marine nematodes | 2020 | Environmental DNA | github | marine nematodes metabarcoding |
| DNA metabarcoding marker choice skews perception of marine eukaryotic biodiversity | 2021 | Environmental DNA | Evaluate marker | |
| pr2-primers: An 18S rRNA primer database for protists | 2021 | Molecular ecology resources | protist primer database | |
| Who Is Where in Marine Food Webs? A Trait-Based Analysis of Network Positions | 2021 | Frontiers in Marine Science | network | |
| Trophic level drives the host microbiome of soil invertebrates at a continental scale | 2021 | Microbiome | host microbiome | |
| Environmental DNA gives comparable results to morphology-based indices of macroinvertebrates in a large-scale ecological assessment | 2021 | Plos One | macroinvertebrates eDNA | |
| Picophytoplankton size and biomass around equatorial eastern Indian Ocean | 2021 | Microbiology Open | Eastern Indian Ocean Picophytoplankton | |
| BiomeHorizon: visualizing microbiome time series data in R | 2021 | bioRxiv | github | R package visualization |
| Strategies for sample labelling and library preparation in DNA metabarcoding studies | 2021 | Molecular Ecology Resources | Compare experimental methods | |
| SCRAPP: A tool to assess the diversity of microbial samples from phylogenetic placements | 2021 | Molecular Ecology Resources | github | diversity distribution clustering |
| Characterization of putative circular plasmids in sponge-associated bacterial communities using a selective multiply-primed rolling circle amplification | 2021 | Molecular Ecology Resources | RCA host microbiome sponge | |
| The quest for absolute abundance: The use of internal standards for DNA-based community ecology | 2021 | Molecular Ecology Resources | absolute abundance |
| Title | Year | Link | Code | Note |
|---|---|---|---|---|
| Droplet-based Single-cell Total RNA-seq Reveals Differential Non-Coding Expression and Splicing Patterns during Mouse Development | 2021 | bioRxiv | github_1 github_2 github_3 | full length scRNA-seq |
| Cells of the human intestinal tract mapped across space and time | 2021 | Nature | github_1 github_2 github_3 | gut |
| Diet-induced alteration of intestinal stem cell function underlies obesity and prediabetes in mice | 2021 | Nature Metabolism | github | gut lineage relations |
| The Specious Art of Single-Cell Genomics | 2021 | bioRxiv | github | MCML batter than t-SNE and UMAP |
| Title | Year | Link | Code | Note |
|---|---|---|---|---|
| Clock Mutants of Drosophila melanogaster | 1971 | Procedings of the National Academy of Sciences | Rhythm key gene |
| Title | Year | Link | Code | Note |
|---|---|---|---|---|
| Deep learning to analyse microscopy images | 2021 | Biochemist | github | Image segment and denoise |
| Biologically informed deep neural network for prostate cancer discovery | 2021 | Nature | github | Predict cancer state |
| Title | Year | Link | Code | Note |
|---|---|---|---|---|
| PacBio sequencing output increased through uniform and directional fivefold concatenation | 2021 | Scientific Reports | github | PacBio accuracy improve |
| Title | Year | Link | Code | Note |
|---|---|---|---|---|
| Identification of representative seamount areas in the offshore Pacific bioregion, Canada | 2021 | Canadian Science Advisory Secretariat Science Advisory Report | Northeast Pacific seamounts |
| Title | Year | Link | Code | Note |
|---|---|---|---|---|
| Interactive Effects of Hypoxia and Temperature on Coastal Pelagic Zooplankton and Fish | 2019 | Frontiers in Marine Science | Hypoxia and Temperature stress on Zooplankton and Fish |
| Title | Year | Link | Code | Note |
|---|---|---|---|---|
| Sinking enhances the degradation of organic particles by marine bacteria | 2021 | Nature Geoscience | zenodo_1 zenodo_2 | Organic particles degradation |
| Title | Year | Link | Code | Note |
|---|---|---|---|---|
| Identifying The "Core" Transcriptome of SARS-CoV-2 Infected Cells | 2021 | bioRxiv | RNA-seq |