iPiDA-LTR: Identifying piwi-interacting RNA-disease associations based on Learning to Rank

Prediction of Microbe-drug Associations based on Chemical Structures and the KATZ Measure

(2021) Lingzhi Zhu et al.   Current Bioinformatics

iCircDA-LTR: identification of circRNA-disease associations based on Learning to Rank

(2021) Hang Wei et al.   BIOINFORMATICS

Sensitive protein alignments at tree-of-life scale using DIAMOND

(2021) Benjamin Buchfink et al.   NATURE METHODS

Computational Methods and Online Resources for Identification of piRNA-Related Molecules

(2021) Yajun Liu et al.   Interdisciplinary Sciences-Computational Life Sciences

piRNA-823 Is Involved in Cancer Stem Cell Regulation Through Altering DNA Methylation in Association With Luminal Breast Cancer

(2021) Xin Ding et al.   Frontiers in Cell and Developmental Biology

An Overview of Recommendation Techniques and Their Applications in Healthcare

(2021) Wenbin Yue et al.   IEEE-CAA Journal of Automatica Sinica

Integrative machine learning framework for the identification of cell-specific enhancers from the human genome

(2021) Shaherin Basith et al.   BRIEFINGS IN BIOINFORMATICS

Deep learning methods for biomedical named entity recognition: a survey and qualitative comparison

(2021) Bosheng Song et al.   BRIEFINGS IN BIOINFORMATICS

Molecular design in drug discovery: a comprehensive review of deep generative models

(2021) Yu Cheng et al.   BRIEFINGS IN BIOINFORMATICS

Review of unsupervised pretraining strategies for molecules representation

(2021) Linhui Yu et al.   Briefings in Functional Genomics

PEPRF: Identification of Essential Proteins by Integrating Topological Features of PPI Network and Sequence-based Features via Random Forest

(2021) Chuanyan Wu et al.   Current Bioinformatics

NmRF: identification of multispecies RNA 2’-O-methylation modification sites from RNA sequences

(2021) Chunyan Ao et al.   BRIEFINGS IN BIOINFORMATICS

Toward better drug discovery with knowledge graph

(2021) Xiangxiang Zeng et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

BioSeq-BLM: a platform for analyzing DNA, RNA and protein sequences based on biological language models

(2021) Hong-Liang Li et al.   NUCLEIC ACIDS RESEARCH

Network-based prediction of drug–target interactions using an arbitrary-order proximity embedded deep forest

(2020) Xiangxiang Zeng et al.   BIOINFORMATICS

Comparisons of microRNA set enrichment analysis tools on cancer de-regulated miRNAs from TCGA expression datasets

(2020) Jianwei Li et al.   Current Bioinformatics

HPOLabeler: improving prediction of human protein-phenotype associations by learning to rank

(2020) Lizhi Liu et al.   BIOINFORMATICS

iPiDi-PUL: identifying Piwi-interacting RNA-disease associations based on positive unlabeled learning

(2020) Hang Wei et al.   BRIEFINGS IN BIOINFORMATICS

piRNAs in Gastric Cancer: A New Approach Towards Translational Research

(2020) Gleyce Fonseca Cabral et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

Detection of Hepatitis B virus-associated Hepatocellular Carcinoma Disease Using Hybrid Hierarchical k-Means Clustering and SVM Algorithm

(2020) Lailil Muflikhah et al.   Current Bioinformatics

Fusing multiple biological networks to effectively predict miRNA-disease associations

(2020) Qingqi Zhu et al.   Current Bioinformatics

Delineating characteristic sequence and structural features of precursor and mature Piwi-interacting RNAs of epithelial ovarian cancer

(2020) Garima Singh et al.   Current Bioinformatics

Repurpose Open Data to Discover Therapeutics for COVID-19 Using Deep Learning

(2020) Xiangxiang Zeng et al.   JOURNAL OF PROTEOME RESEARCH

SMI-BLAST: a novel supervised search framework based on PSI-BLAST for protein remote homology detection

(2020) Xiaopeng Jin et al.   BIOINFORMATICS

iPiDA-sHN: Identification of Piwi-interacting RNA-disease associations by selecting high quality negative samples

(2020) Hang Wei et al.   COMPUTATIONAL BIOLOGY AND CHEMISTRY

DeepYY1: a deep learning approach to identify YY1-mediated chromatin loops

(2020) Fu-Ying Dao et al.   BRIEFINGS IN BIOINFORMATICS

A new approach for predicting the exact value of gene expression: Two-way collaborative filtering

(2019) Tuncay Bayrak et al.   Current Bioinformatics

The emerging role of the piRNA/piwi complex in cancer

(2019) Yongmei Liu et al.   Molecular Cancer

BioSeq-Analysis2.0: an updated platform for analyzing DNA, RNA and protein sequences at sequence level and residue level based on machine learning approaches

(2019) Bin Liu et al.   NUCLEIC ACIDS RESEARCH

Predicting disease-associated circular RNAs using deep forests combined with positive-unlabeled learning methods

(2019) Xiangxiang Zeng et al.   BRIEFINGS IN BIOINFORMATICS

A Novel Model for Predicting LncRNA-disease Associations based on the LncRNA-MiRNA-Disease Interactive Network

(2018) Lei Wang et al.   Current Bioinformatics

Human Disease Ontology 2018 update: classification, content and workflow expansion

(2018) Lynn M Schriml et al.   NUCLEIC ACIDS RESEARCH

piRBase: a comprehensive database of piRNA sequences

(2018) Jiajia Wang et al.   NUCLEIC ACIDS RESEARCH

DNRLMF-MDA:Predicting microRNA-disease associations based on similarities of microRNAs and diseases

(2017) Cheng Yan et al.   IEEE-ACM Transactions on Computational Biology and Bioinformatics

Inferring MicroRNA-Disease Associations by Random Walk on a Heterogeneous Network with Multiple Data Sources

(2017) Yuansheng Liu et al.   IEEE-ACM Transactions on Computational Biology and Bioinformatics

A novel approach for predicting microRNA-disease associations by unbalanced bi-random walk on heterogeneous network

(2017) Jiawei Luo et al.   JOURNAL OF BIOMEDICAL INFORMATICS

Small RNA sequencing revealed dysregulated piRNAs in Alzheimer's disease and their probable role in pathogenesis

(2017) Jyoti Roy et al.   Molecular BioSystems

piRNA-mediated regulation of transposon alternative splicing in the soma and germ line

(2017) Felipe Karam Teixeira et al.   NATURE

MMseqs2 enables sensitive protein sequence searching for the analysis of massive data sets

(2017) Martin Steinegger et al.   NATURE BIOTECHNOLOGY

Transcriptome-wide piRNA profiling in human brains of Alzheimer's disease

(2017) Wenying Qiu et al.   NEUROBIOLOGY OF AGING

DrugE-Rank: improving drug–target interaction prediction of new candidate drugs or targets by ensemble learning to rank

(2016) Qingjun Yuan et al.   BIOINFORMATICS

Piwi-interacting RNAs and PIWI genes as novel prognostic markers for breast cancer

(2016) Preethi Krishnan et al.   Oncotarget

Application of learning to rank to protein remote homology detection

(2015) Bin Liu et al.   BIOINFORMATICS

An atlas of gastric PIWI-interacting RNA transcriptomes and their utility for identifying signatures of gastric cancer recurrence

(2015) Victor D. Martinez et al.   Gastric Cancer

Piwi-interacting RNAs as novel prognostic markers in clear cell renal cell carcinomas

(2015) Jonas Busch et al.   JOURNAL OF EXPERIMENTAL & CLINICAL CANCER RESEARCH

piRNA cluster database: a web resource for piRNA producing loci

(2015) David Rosenkranz   NUCLEIC ACIDS RESEARCH

The SMC5/6 Complex Is Involved in Crucial Processes During Human Spermatogenesis1

(2014) Dideke E. Verver et al.   BIOLOGY OF REPRODUCTION

piRBase: a web resource assisting piRNA functional study

(2014) Peng Zhang et al.   Database-The Journal of Biological Databases and Curation

Semi-supervised learning for potential human microRNA-disease associations inference

(2014) Xing Chen et al.   Scientific Reports

piRNA, the new non-coding RNA, is aberrantly expressed in human cancer cells

(2011) Jia Cheng et al.   CLINICA CHIMICA ACTA

A Short Introduction to Learning to Rank

(2011) Hang LI   IEICE TRANSACTIONS ON INFORMATION AND SYSTEMS

piRNAs mediate posttranscriptional retroelement silencing and localization to pi-bodies in theDrosophilagermline

(2009) Ai Khim Lim et al.   JOURNAL OF CELL BIOLOGY