MycoMobilome: a community-focused non-redundant database of transposable element consensus sequences for the fungal kingdom [0.03%]
我的Mobilome：一个针对社区的非冗余转座元件共识序列数据库（真菌界）
Tobias Baril,Daniel Croll
Tobias Baril
Transposable elements (TEs) are found in nearly all eukaryotic genomes. Despite significant advances in the sequencing of genomes, TE resources remain sparse, leading to a lack of traceability, reproducibility, and duplication of effort whe...
Interpreting artificial neural networks to detect genome-wide association signals for complex traits [0.03%]
解释人工神经网络以检测复杂性状的全基因组关联信号
Burak Yelmen,Maris Alver,Merve Nur Güler;Estonian Biobank Research Team;Flora Jay et al.
Burak Yelmen et al.
Investigating the genetic architecture of complex diseases is challenging due to the multifactorial interplay of genomic and environmental influences. Although GWAS have identified thousands of variants for multiple complex traits, conventi...
Sequence-based modeling of low-affinity transcription factor-DNA binding through deep learning [0.03%]
基于深度学习的低亲和力转录因子-DNA结合的序列模型预测
Yingfei Wang,Jinsen Li,Tsu-Pei Chiu et al.
Yingfei Wang et al.
Multiple layers of molecular determinants and mechanisms affect binding specificity between transcription factors (TFs) and DNA. DNA sequence-based deep learning models using convolutional neural networks (CNNs) and self-attention (SA) tran...
Mixing features of transcription factors and genes enable accurate prediction of gene regulation relationships for unknown transcription factors [0.03%]
转录因子和基因的混合特征能够使未知转录因子的基因调控关系预测更准确
Risa Okubo,Takashi Morikura,Yusuke Hiki et al.
Risa Okubo et al.
Identifying regulatory relationships between transcription factors (TFs) and genes is essential to understand diverse biological phenomena related to gene expression. Recently, deep learning-based models to predict TFs that bind to genes fr...
Maahil Arshad,Matthew Uchmanowicz,Vanshika Rana et al.
Maahil Arshad et al.
Although the genetic code is degenerate, codon selection is nonrandom and reflects significant functional constraints. Codon-usage bias (CUB) acts as a layer of post-transcriptional regulation, influencing messenger RNA (mRNA) stability, tr...
Recurrence plot reconstruction reveals chromosomal reorganization before territory formation [0.03%]
递归图重建揭示了染色体在形成之前的空间重组
Yuki Kitanishi,Hiroki Sugishita,Yukiko Gotoh et al.
Yuki Kitanishi et al.
Chromatin conformation capture methods such as Hi-C have improved understanding of nuclear architecture. However, reconstruction from single-cell Hi-C (scHi-C) data is challenging due to limited DNA contacts per cell. We have previously dev...
Unraveling IGK locus in dog breeds: IMGT® new insights into canine immunogenetics [0.03%]
犬品种IGH基因座的解析：IMGT在犬免疫遗传学的新进展
Taismara Kustro Garnica,Ariadni Papadaki,Maria Georga et al.
Taismara Kustro Garnica et al.
Over thousands of years, selective breeding of domestic dogs (Canis lupus familiaris) has led to extensive genetic diversity, underscoring the need for refined genomic and immunogenetic investigations. This study presents a comprehensive an...
DoBSeqWF: a framework for sensitive detection of individual genetic variation in pooled sequencing data [0.03%]
pooling测序数据中个体遗传变异的敏感检测框架
Mads Cort Nielsen,Christian Munch Hagen,Ulrik Kristoffer Stoltze et al.
Mads Cort Nielsen et al.
Population screening for rare genetic diseases has the potential to increase early diagnosis and treatment, but the high cost of next-generation sequencing limits widespread implementation. Double-batched sequencing (DoBSeq) is a cost-effec...
FragmentFinder-a user-friendly, Windows-based tool for identifying and characterizing short RNAs excised from any noncoding RNA [0.03%]
片段寻找者-一个用户友好的基于Windows操作系统的鉴定和表征从任何非编码RNA中切割的短RNA的工具
Jeffrey D DeMeis,Courtlyn M Breaux,Allison H Powell et al.
Jeffrey D DeMeis et al.
Noncoding RNAs
DEprot: a comprehensive R-package for the analysis of label-free quantitation mass spectrometry data [0.03%]
DEprot：一个用于分析无标签定量质谱数据的全面R包
Nils Eickhoff,Liesbeth Hoekman,Onno Bleijerveld et al.
Nils Eickhoff et al.
In recent years, studies investigating protein-protein interactions on a proteome-wide scale have increased exponentially. These developments were achieved through implementation of new techniques, as well as improvements in mass spectromet...