Update project descriptions

zellerlab · Mar 18, 2024 · 68faf27 · 68faf27
1 parent b87a39c
commit 68faf27
Show file tree

Hide file tree

Showing 4 changed files with 6 additions and 4 deletions.
diff --git a/tools/_posts/2013-10-02-motus.md b/tools/_posts/2013-10-02-motus.md
@@ -27,7 +27,7 @@ For many years, we have been developing mOTUs jointly with [Shinichi Sunagawa’
 
 ![mOTUs](/assets/images/tools/2022-12-09-mOTUs_picture_modified.png)
 
-## mOTUS has been used in the following publications:
+### mOTUS has been used in the following publications:
 
 1. [Meta-analysis of fecal metagenomes reveals global microbial signatures that are specific for colorectal cancer](https://www.nature.com/articles/s41591-019-0406-6)  
 2. [Removal of false positives in metagenomics-based taxonomy profiling via targeting Type IIB restriction sites](https://www.nature.com/articles/s41467-023-41099-8)  

diff --git a/tools/_posts/2021-03-30-siamcat.md b/tools/_posts/2021-03-30-siamcat.md
@@ -27,7 +27,8 @@ The human microbiome has been shown to exhibit distinct differences in many host
 
 SIAMCAT is distributed under the [GPL-3](https://www.gnu.org/licenses/gpl-3.0.en.html) license.  
 
-## SIAMCAT has been used in the following publications highlighting its broad applicability:
+### SIAMCAT has been used in the following publications:
+
 1. [Cross-cohort gut microbiome associations with immune checkpoint inhibitor response in advanced melanoma](https://www.nature.com/articles/s41591-022-01695-5)
 2. [A faecal microbiota signature with high specificity for pancreatic cancer](https://gut.bmj.com/content/71/7/1359)
 3. [MGnify: the microbiome sequence data analysis resource in 2023](https://academic.oup.com/nar/article/51/D1/D753/6880769)

diff --git a/tools/_posts/2021-05-04-gecco.md b/tools/_posts/2021-05-04-gecco.md
@@ -30,7 +30,8 @@ The GECCO software is implemented in [Python](https://www.python.org/), supports
 
 Graphical depiction of the biosynthetic gene cluster (BGC) identification and classification approach implemented in GECCO. Briefly, GECCO identifies open reading frames (ORFs) in an assembled prokaryotic (meta)genome (Step 1). Protein domains are annotated in the resulting ORFs using profile hidden Markov models (pHMMs; Step 2). The resulting ordered domain vectors serve as features for a conditional random field (CRF) that is trained to predict whether a stretch of contiguous genes belong to a BGC or not (Step 3). Predicted BGCs are classified into one of six major biosynthetic classes as defined in the Minimum Information about a Biosynthetic Gene cluster (MIBiG) database using a Random Forest classifier (Step 4).
 
-## GECCO has been used in the following publications:
+### GECCO has been cited in the following publications:
+
 1. [MIBiG 3.0: a community-driven effort to annotate experimentally validated biosynthetic gene clusters](https://academic.oup.com/nar/article/51/D1/D603/6833236)
 2. [Artificial intelligence for natural product drug discovery](https://www.nature.com/articles/s41573-023-00774-7)
 3. [proGenomes3: approaching one million accurately and consistently annotated high-quality prokaryotic genomes](https://academic.oup.com/nar/article/51/D1/D760/6835361)

diff --git a/tools/_posts/2023-05-04-pyhmmer.md b/tools/_posts/2023-05-04-pyhmmer.md
@@ -32,7 +32,7 @@ statistics like uncorrected P-values. A new parallelization model greatly
 improves performance when running multithreaded searches, while producing the
 exact same results as HMMER.
 
-## PyHMMER has been used in the following publications:
+### PyHMMER has been used in the following publications:
 
 1. [Accurate de novo identification of biosynthetic gene clusters with GECCO (preprint)](https://www.biorxiv.org/content/10.1101/2021.05.03.442509v1).
 2. [Identification of microbial metabolic functional guilds from large genomic datasets](https://www.frontiersin.org/articles/10.3389/fmicb.2023.1197329/full).