4.7 Article

Protein deep profile and model predictions for identifying the causal genes of male infertility based on deep learning

Related references

Note: Only part of the references are listed.
Article Computer Science, Artificial Intelligence

Memory based fusion for multi-modal deep learning

Darshana Priyasad et al.

Summary: The proposed Memory based Attentive Fusion layer can fuse current features and long-term dependencies to enhance the model's understanding of modalities, leading to improved performance in experiments.

INFORMATION FUSION (2021)

Article Computer Science, Artificial Intelligence

Covid-19 classification by FGCNet with deep feature fusion from graph convolutional network and convolutional neural network

Shui-Hua Wang et al.

Summary: The study aims to develop an AI tool for diagnosing COVID-19 on chest CT images, and the proposed FGCNet model outperforms 15 state-of-the-art methods, showing its effectiveness in assisting radiologists in detecting COVID-19 rapidly.

INFORMATION FUSION (2021)

Article Computer Science, Artificial Intelligence

A survey on deep learning in medicine: Why, how and when?

Francesco Piccialli et al.

Summary: New technologies are revolutionizing medicine, with a key role played by data. Artificial intelligence, especially Deep Learning, is well-suited to handle the exponential growth of health-related information in the field of medicine, helping to build optimal neural networks for clinical problems as the amount of training data increases.

INFORMATION FUSION (2021)

Article Computer Science, Artificial Intelligence

Multiple graph kernel learning based on GMDH-type neural network

Lixiang Xu et al.

Summary: This study proposes a method utilizing the advantages of GMDH-NN to build MGKL, enhancing the categorization performance of graph kernel SVMs. By defining USRC and a new initial model structure, combining hybrid graph kernel and GMDH-NN, a pool of optimal graph kernels is obtained.

INFORMATION FUSION (2021)

Review Computer Science, Artificial Intelligence

Bridging deep and multiple kernel learning: A review

Tinghua Wang et al.

Summary: Kernel methods and deep learning are two prominent machine learning techniques, with the former capturing nonlinear patterns and the latter learning abstract features through multiple layers of nonlinearity. Deep kernel learning bridges the gap between the two, effectively learning complex feature representations.

INFORMATION FUSION (2021)

Article Computer Science, Artificial Intelligence

Alzheimer's disease multiclass diagnosis via multimodal neuroimaging embedding feature selection and fusion

Yuanpeng Zhang et al.

Summary: The study introduces a novel multiclass classification framework for AD based on multimodal neuroimaging with embedded feature selection and fusion. By using regularization and optimization techniques, it achieves feature selection and fusion, proving the convergence of the optimization process. Experimental results demonstrate the method's promising performance.

INFORMATION FUSION (2021)

Article Computer Science, Artificial Intelligence

A survey on machine learning for data fusion

Tong Meng et al.

INFORMATION FUSION (2020)

Article Biochemical Research Methods

ToxDL: deep learning using primary structure and domain embeddings for assessing protein toxicity

Xiaoyong Pan et al.

BIOINFORMATICS (2020)

Article Biochemistry & Molecular Biology

Predicting protein subcellular location with network embedding and enrichment features

Xiaoyong Pan et al.

BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS (2020)

Article Computer Science, Artificial Intelligence

Knowledge graph fusion for smart systems: A Survey

Hoang Long Nguyen et al.

INFORMATION FUSION (2020)

Article Computer Science, Artificial Intelligence

A smart healthcare monitoring system for heart disease prediction based on ensemble deep learning and feature fusion

Farman Ali et al.

INFORMATION FUSION (2020)

Article Computer Science, Artificial Intelligence

Machine learning for integrating data in biology and medicine: Principles, practice, and opportunities

Marinka Zitnik et al.

INFORMATION FUSION (2019)

Review Obstetrics & Gynecology

A systematic review and standardized clinical validity assessment of male infertility genes

Manon S. Oud et al.

HUMAN REPRODUCTION (2019)

Article Obstetrics & Gynecology

A new MEIOB mutation is a recurrent cause for azoospermia and testicular meiotic arrest

Moran Gershoni et al.

HUMAN REPRODUCTION (2019)

Article Cell Biology

Deficiency of TPPP2, a factor linked to oligoasthenozoospermia, causes subfertility in male mice

Feng Zhu et al.

JOURNAL OF CELLULAR AND MOLECULAR MEDICINE (2019)

Article Biochemistry & Molecular Biology

ENU-induced mutant allele of Dnah1, ferf1, causes abnormal sperm behavior and fertilization failure in mice

Jianjun Hu et al.

MOLECULAR REPRODUCTION AND DEVELOPMENT (2019)

Article Biochemistry & Molecular Biology

Dephosphorylation of protamine 2 at serine 56 is crucial for murine sperm maturation in vivo

Katsuhiko Itoh et al.

SCIENCE SIGNALING (2019)

Review Biochemical Research Methods

Deep learning for cellular image analysis

Erick Moen et al.

NATURE METHODS (2019)

Letter Reproductive Biology

RNF216 is essential for spermatogenesis and male fertility

Ashley F. Melnick et al.

BIOLOGY OF REPRODUCTION (2019)

Article Genetics & Heredity

Whole-exome sequencing identified a novel mutation of AURKC in a Chinese family with macrozoospermia

Juan Hua et al.

JOURNAL OF ASSISTED REPRODUCTION AND GENETICS (2019)

Article Medical Laboratory Technology

A novel stopgain mutation c.G992A (p.W331X) in TACR3 gene was identified in nonobstructive azoospermia by targeted next-generation sequencing

Dongfeng Geng et al.

JOURNAL OF CLINICAL LABORATORY ANALYSIS (2019)

Letter Biochemistry & Molecular Biology

Homozygous loss-of-function mutations in FSIP2 cause male infertility with asthenoteratospermia

Wangjie Liu et al.

JOURNAL OF GENETICS AND GENOMICS (2019)

Article Genetics & Heredity

Biallelic mutations of CFAP251 cause sperm flagellar defects and human male infertility

Weiyu Li et al.

JOURNAL OF HUMAN GENETICS (2019)

Article Genetics & Heredity

A primer on deep learning in genomics

James Zou et al.

NATURE GENETICS (2019)

Editorial Material Genetics & Heredity

Deep learning for genomics

[Anonymous]

NATURE GENETICS (2019)

Editorial Material Chemistry, Physical

Avoiding common pitfalls in machine learning omic data science

Andrew E. Teschendorff

NATURE MATERIALS (2019)

Article Biochemistry & Molecular Biology

A guide to deep learning in healthcare

Andre Esteva et al.

NATURE MEDICINE (2019)

Article Biochemistry & Molecular Biology

UniProt: a worldwide hub of protein knowledge

Alex Bateman et al.

NUCLEIC ACIDS RESEARCH (2019)

Article Biochemistry & Molecular Biology

The Pfam protein families database in 2019

Sara El-Gebali et al.

NUCLEIC ACIDS RESEARCH (2019)

Article Obstetrics & Gynecology

Germ cell arrest associated with a SETX mutation in ataxia oculomotor apraxia type 2

S. R. Catford et al.

REPRODUCTIVE BIOMEDICINE ONLINE (2019)

Article Genetics & Heredity

Bi-allelic Mutations in TTC21A Induce Asthenoteratospermia in Humans and Mice

Wangjie Liu et al.

AMERICAN JOURNAL OF HUMAN GENETICS (2019)

Article Andrology

Novel DPY19L2 variants in globozoospermic patients and the overcoming this male infertility

Yong-Liang Shang et al.

ASIAN JOURNAL OF ANDROLOGY (2019)

Article Biochemical Research Methods

Predicting MicroRNA-Disease Associations Based on Improved MicroRNA and Disease Similarities

Wei Lan et al.

IEEE-ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS (2018)

Article Biochemistry & Molecular Biology

Mouse Genome Database (MGD)-2018: knowledgebase for the laboratory mouse

Cynthia L. Smith et al.

NUCLEIC ACIDS RESEARCH (2018)

Article Biochemical Research Methods

Random forest versus logistic regression: a large-scale benchmark experiment

Raphael Couronne et al.

BMC BIOINFORMATICS (2018)

Review Obstetrics & Gynecology

The contribution of human sperm proteins to the development and epigenome of the preimplantation embryo

Judit Castillo et al.

HUMAN REPRODUCTION UPDATE (2018)

Article Computer Science, Information Systems

Correlation analysis of performance measures for multi-label classification

Rafael B. Pereira et al.

INFORMATION PROCESSING & MANAGEMENT (2018)

Article Computer Science, Artificial Intelligence

Graph embedding techniques, applications, and performance: A survey

Palash Goyal et al.

KNOWLEDGE-BASED SYSTEMS (2018)

Editorial Material Biochemical Research Methods

A deep (learning) dive into a cell

Kristin Branson

NATURE METHODS (2018)

Article Biochemical Research Methods

Using deep learning to model the hierarchical structure and function of a cell

Jianzhu Ma et al.

NATURE METHODS (2018)

Review Genetics & Heredity

Integrative omics for health and disease

Konrad J. Karczewski et al.

NATURE REVIEWS GENETICS (2018)

Review Urology & Nephrology

Genetics of male infertility

Csilla Krausz et al.

NATURE REVIEWS UROLOGY (2018)

Editorial Material Medicine, General & Internal

On the Prospects for a (Deep) Learning Health Care System

C. David Naylor

JAMA-JOURNAL OF THE AMERICAN MEDICAL ASSOCIATION (2018)

Review Genetics & Heredity

Genetic evaluation of patients with non-syndromic male infertility

Ozlem Okutman et al.

JOURNAL OF ASSISTED REPRODUCTION AND GENETICS (2018)

Article Biotechnology & Applied Microbiology

Deep learning in biomedicine

Michael Wainberg et al.

NATURE BIOTECHNOLOGY (2018)

Article Genetics & Heredity

Mutations in Outer Dynein Arm Heavy Chain DNAH9 Cause Motile Cilia Defects and Situs Inversus

Mahmoud R. Fassad et al.

AMERICAN JOURNAL OF HUMAN GENETICS (2018)

Article Multidisciplinary Sciences

X-linked ADGRG2 mutation and obstructive azoospermia in a large Pakistani family

Muhammad Jaseem Khan et al.

SCIENTIFIC REPORTS (2018)

Article Genetics & Heredity

Compound heterozygous mutations in CFTR causing CBAVD in Chinese pedigrees

Bin Yang et al.

MOLECULAR GENETICS & GENOMIC MEDICINE (2018)

Article Biochemical Research Methods

Unsupervised multiple kernel learning for heterogeneous data integration

Jerome Mariette et al.

BIOINFORMATICS (2018)

Article Biochemistry & Molecular Biology

MalaCards: an amalgamated human disease compendium with diverse clinical and genetic annotation and structured search

Noa Rappaport et al.

NUCLEIC ACIDS RESEARCH (2017)

Article Biochemistry & Molecular Biology

Database Resources of the National Center for Biotechnology

Richa Agarwala et al.

NUCLEIC ACIDS RESEARCH (2017)

Article Biochemical Research Methods

mixOmics: An R package for 'omics feature selection and multiple data integration

Florian Rohart et al.

PLOS COMPUTATIONAL BIOLOGY (2017)

Article Biochemical Research Methods

Predicting multicellular function through multi-layer tissue networks

Marinka Zitnik et al.

BIOINFORMATICS (2017)

Review Genetics & Heredity

10 Years of GWAS Discovery: Biology, Function, and Translation

Peter M. Visscher et al.

AMERICAN JOURNAL OF HUMAN GENETICS (2017)

Article Biochemistry & Molecular Biology

ClinVar: public archive of interpretations of clinically relevant variants

Melissa J. Landrum et al.

NUCLEIC ACIDS RESEARCH (2016)

Article Biochemical Research Methods

Jumping across biomedical contexts using compressive data fusion

Marinka Zitnik et al.

BIOINFORMATICS (2016)

Review Chemistry, Multidisciplinary

Predicting Protein-Protein Interactions from the Molecular to the Proteome Level

Ozlem Keskin et al.

CHEMICAL REVIEWS (2016)

Article Biochemical Research Methods

Improve Glioblastoma Multiforme Prognosis Prediction by Using Feature Selection and Multiple Kernel Learning

Ya Zhang et al.

IEEE-ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS (2016)

Review Biochemistry & Molecular Biology

Deep learning for computational biology

Christof Angermueller et al.

MOLECULAR SYSTEMS BIOLOGY (2016)

Article Biochemistry & Molecular Biology

KeyPathwayMinerWeb: online multi-omics network enrichment

Markus List et al.

NUCLEIC ACIDS RESEARCH (2016)

Review Engineering, Electrical & Electronic

Machine Learning in Genomic Medicine: A Review of Computational Problems and Data Sets

Michael K. K. Leung et al.

PROCEEDINGS OF THE IEEE (2016)

Article Computer Science, Artificial Intelligence

SNAP: A General-Purpose Network Analysis and Graph-Mining Library

Jure Leskovec et al.

ACM TRANSACTIONS ON INTELLIGENT SYSTEMS AND TECHNOLOGY (2016)

Article Biochemical Research Methods

Identification of causal genes for complex traits

Farhad Hormozdiari et al.

BIOINFORMATICS (2015)

Article Biochemical Research Methods

Gene network inference by fusing data from diverse distributions

Marinka Zitnik et al.

BIOINFORMATICS (2015)

Article Medicine, General & Internal

Multi-omic signature of body weight change: results from a population-based cohort study

Simone Wahl et al.

BMC MEDICINE (2015)

Article Computer Science, Artificial Intelligence

Data Fusion by Matrix Factorization

Marinka Zitnik et al.

IEEE TRANSACTIONS ON PATTERN ANALYSIS AND MACHINE INTELLIGENCE (2015)

Article Biochemical Research Methods

Integrative Data Analysis of Multi-Platform Cancer Data with a Multimodal Deep Learning Approach

Muxuan Liang et al.

IEEE-ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS (2015)

Review Multidisciplinary Sciences

Deep learning

Yann LeCun et al.

NATURE (2015)

Article Biotechnology & Applied Microbiology

Predicting the sequence specificities of DNA- and RNA-binding proteins by deep learning

Babak Alipanahi et al.

NATURE BIOTECHNOLOGY (2015)

Article Biochemical Research Methods

Predicting effects of noncoding variants with deep learning-based sequence model

Jian Zhou et al.

NATURE METHODS (2015)

Review Genetics & Heredity

Methods of integrating data to uncover genotype-phenotype interactions

Marylyn D. Ritchie et al.

NATURE REVIEWS GENETICS (2015)

Article Multidisciplinary Sciences

The Genotype-Tissue Expression (GTEx) pilot analysis: Multitissue gene regulation in humans

Kristin G. Ardlie et al.

SCIENCE (2015)

Article Biochemical Research Methods

DANN: a deep learning approach for annotating the pathogenicity of genetic variants

Daniel Quang et al.

BIOINFORMATICS (2015)

Article Biochemistry & Molecular Biology

OMIM.org: Online Mendelian Inheritance in Man (OMIM®), an online catalog of human genes and genetic disorders

Joanna S. Amberger et al.

NUCLEIC ACIDS RESEARCH (2015)

Article Biochemistry & Molecular Biology

InParanoid 8: orthology analysis between 273 proteomes, mostly eukaryotic

Erik L. L. Sonnhammer et al.

NUCLEIC ACIDS RESEARCH (2015)

Article Multidisciplinary Sciences

Continuous Distributed Representation of Biological Sequences for Deep Proteomics and Genomics

Ehsaneddin Asgari et al.

PLOS ONE (2015)

Article Biochemical Research Methods

ATHENA: the analysis tool for heritable and environmental network associations

Emily R. Holzinger et al.

BIOINFORMATICS (2014)

Article Biochemical Research Methods

Towards a piRNA prediction using multiple kernel fusion and support vector machine

Jocelyn Brayet et al.

BIOINFORMATICS (2014)

Article Genetics & Heredity

Genetic Variations and Diseases in UniProtKB/Swiss-Prot: The Ins and Outs of Expert Manual Curation

Maria Livia Famiglietti et al.

HUMAN MUTATION (2014)

Article Biochemical Research Methods

Similarity network fusion for aggregating data types on a genomic scale

Bo Wang et al.

NATURE METHODS (2014)

Review Medicine, General & Internal

Diagnostic Clinical Genome and Exome Sequencing

Leslie G. Biesecker et al.

NEW ENGLAND JOURNAL OF MEDICINE (2014)

Article Biochemistry & Molecular Biology

The NHGRI GWAS Catalog, a curated resource of SNP-trait associations

Danielle Welter et al.

NUCLEIC ACIDS RESEARCH (2014)

Article Biochemistry & Molecular Biology

Constructing module maps for integrated analysis of heterogeneous biological networks

David Amar et al.

NUCLEIC ACIDS RESEARCH (2014)

Article Biotechnology & Applied Microbiology

Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2

Michael I. Love et al.

GENOME BIOLOGY (2014)

Article Biochemical Research Methods

Bayesian consensus clustering

Eric F. Lock et al.

BIOINFORMATICS (2013)

Review Computer Science, Artificial Intelligence

Representation Learning: A Review and New Perspectives

Yoshua Bengio et al.

IEEE TRANSACTIONS ON PATTERN ANALYSIS AND MACHINE INTELLIGENCE (2013)

Editorial Material Genetics & Heredity

The Genotype-Tissue Expression (GTEx) project

John Lonsdale et al.

NATURE GENETICS (2013)

Article Biochemical Research Methods

Bayesian correlated clustering to integrate multiple datasets

Paul Kirk et al.

BIOINFORMATICS (2012)

Article Genetics & Heredity

A Bayesian Integrative Genomic Model for Pathway Analysis of Complex Traits

Brooke L. Fridley et al.

GENETIC EPIDEMIOLOGY (2012)

Article Computer Science, Interdisciplinary Applications

Synergistic effect of different levels of genomic data for cancer clinical outcome prediction

Dokyoon Kim et al.

JOURNAL OF BIOMEDICAL INFORMATICS (2012)

Article Biochemical Research Methods

Wisdom of crowds for robust gene network inference

Daniel Marbach et al.

NATURE METHODS (2012)

Article Multidisciplinary Sciences

Integrative Subtype Discovery in Glioblastoma Using iCluster

Ronglai Shen et al.

PLOS ONE (2012)

Article Multidisciplinary Sciences

Time to Recurrence and Survival in Serous Ovarian Tumors Predicted from Integrated Genomic Profiles

Parminder K. Mankoo et al.

PLOS ONE (2011)

Article Biochemical Research Methods

Genome-wide inferring gene-phenotype relationship by walking on the heterogeneous network

Yongjin Li et al.

BIOINFORMATICS (2010)

Article Biochemistry & Molecular Biology

An Integrated Approach to Uncover Drivers of Cancer

Uri David Akavia et al.

Article Computer Science, Artificial Intelligence

A Survey on Transfer Learning

Sinno Jialin Pan et al.

IEEE TRANSACTIONS ON KNOWLEDGE AND DATA ENGINEERING (2010)

Article Computer Science, Artificial Intelligence

Sensitivity Analysis of k-Fold Cross Validation in Prediction Error Estimation

Juan Diego Rodriguez et al.

IEEE TRANSACTIONS ON PATTERN ANALYSIS AND MACHINE INTELLIGENCE (2010)

Article Computer Science, Information Systems

A systematic analysis of performance measures for classification tasks

Marina Sokolova et al.

INFORMATION PROCESSING & MANAGEMENT (2009)

Article Biochemical Research Methods

Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources

Da Wei Huang et al.

NATURE PROTOCOLS (2009)

Article Biochemical Research Methods

PRINCESS, a protein interaction confidence evaluation system with multiple data sources

Dong Li et al.

MOLECULAR & CELLULAR PROTEOMICS (2008)

Article Biotechnology & Applied Microbiology

GeneMANIA: a real-time multiple association network integration algorithm for predicting gene function

Sara Mostafavi et al.

GENOME BIOLOGY (2008)

Article Biochemical Research Methods

Graph sharpening plus graph integration: a synergy that improves protein functional classification

Hyunjung Shin et al.

BIOINFORMATICS (2007)

Article Computer Science, Artificial Intelligence

ML-KNN: A lazy learning approach to multi-label leaming

Min-Ling Zhang et al.

PATTERN RECOGNITION (2007)

Article Biochemical Research Methods

Ensemble classifier for protein fold pattern recognition

Hong-Bin Shen et al.

BIOINFORMATICS (2006)

Article Geochemistry & Geophysics

Independent component analysis-based dimensionality reduction with applications in hyperspectral image analysis

Jing Wang et al.

IEEE TRANSACTIONS ON GEOSCIENCE AND REMOTE SENSING (2006)

Article Biochemistry & Molecular Biology

A human protein-protein interaction network:: A resource for annotating the proteome

U Stelzl et al.

Article Biochemical Research Methods

Fast protein classification with multiple networks

K Tsuda et al.

BIOINFORMATICS (2005)

Article Biochemical Research Methods

Protein function prediction via graph kernels

KM Borgwardt et al.

BIOINFORMATICS (2005)

Article Biochemical Research Methods

A statistical framework for genomic data fusion

GRG Lanckriet et al.

BIOINFORMATICS (2004)

Article Biochemical Research Methods

Predicting HIV drug resistance with neural networks

S Draghici et al.

BIOINFORMATICS (2003)

Article Computer Science, Artificial Intelligence

Random forests

L Breiman

MACHINE LEARNING (2001)

Article Multidisciplinary Sciences

A global geometric framework for nonlinear dimensionality reduction

JB Tenenbaum et al.

SCIENCE (2000)

Article Statistics & Probability

Additive logistic regression: A statistical view of boosting

J Friedman et al.

ANNALS OF STATISTICS (2000)