awesome-multi-omics

2007 - - Parkhomenko - sparse CCA - ,

2008 - - Waaijenborg - penalized CCA / CCA-EN -

2009 - - Witten - Sparse Multi CCA - ,

2009 - - Lê Cao - sparse PLS -

2009 - - Hwang - RGSCA regularized generalized structured component analysis -

2010 - - Soneson -

2011 - - Tenenhaus - Regularized Generalized CCA and Sparse Generalized CCA - ,

2011 - - Zhang - Sparse Network-regularized Multiple Non-negative Matrix Factorization -

scca

2011 - - Lee - Sparse Canonical Covariance Analysis for High-throughput Data -

STATIS/DiSTATIS

2012 - - Abdi - structuring three-way statistical tables -

2012 - - Zhang - extension of NMF to multiple datasets -

2012 - - Li - sparse MultiBlock Partial Least Squares -

2012 - - Virtanen -

2012 - - Zhu - Reconstructing Integrative Molecular Bayesian Networks -

2013 - - Abdi - MFA: multiple factor analysis -

2013 - - Lock - joint & individual variance explained -

2013 - - Schlauch - Passing Attributes between Networks for Data Assimilation -

2014 - - Meng - MCIA: multiple co-interia analysis -

2014 - - Planell - DISCO, JIVE, & O2PLS -

2014 - - Ray -

2014 - - Khan - group factor analysis sparse ,

2015 - - Gao (3rd paper first author is Chen) - , ,

2015 - - Klami - Bayesian Canonical Correlation Analysis and Group Factor Analysis - ,

2016 - - Klami - collective matrix factorization -

2016 - - Meng - multi-omics gene set analysis -

iNMF

2016 - - Yang - integrative NMF -

BASS

2016 - - Zhao - Bayesian group factor analysis -

2016 - in - Voillet - multiple imputation for multiple factor analysis (MI-MFA) -

PLSCA

2016 - - Beaton - Partial Least Square Correspondence Analysis -

2017 - - Rohart - various methods - ,

mixedCCA

2017 - - Yoon - sparse CCA for data of mixed types -

SLIDE

2017 - - Gaynanova - Structural Learning and Integrative Decomposition of Multi-View Data -

fCCAC

2017 - - Madrigal - functional canonical correlation analysis to evaluate covariance -

TSKCCA

2017 - - Yoshida - Sparse kernel canonical correlation analysis -

2017 - - Kawaguchi - Supervised multiblock sparse multivariable analysis -

AJIVE

2018 - - Feng - angle-based JIVE -

MOFA

2018 - - Argelaguet - multi-omics factor analysis - , ,

PCA+CCA

2018 - - Brown -

JACA

2018 - - Zhang - Joint Association and Classification Analysis -

2018 - - Tang - Integrated Principal Components Analysis -

2018 - - Min - penalized COI -

2018 - - Safo - structured sparse CCA -

2018 - - Min - Sparse Weighted CCA -

OmicsPLS

2018 - - Bouhaddani - O2PLS implemented in R, with an alternative cross-validation scheme -

SCCA-BC

2018 - - Pimentel - Biclustering by sparse canonical correlation analysis -

2018 - - Mariette - kernel method for unsupervised multi-omics integration - ,

WON-PARAFAC

2019 - - Kim - weighted orthogonal nonnegative parallel factor analysis -

BIDIFAC

2019 - - Park - bidimensional integrative factorization - ,

2019 - - Shi - sparse multiple canonical correlation network analysis -

msPLS

2020 - - Csala - multiset sparse partial least squares path modeling -

2020 - - Fan - network-based multi-omic data integration for biomarker discovery -

D-CCA

2020 - - Shu - Decomposition-based Canonical Correlation Analysis -

2020 - - Hawinkel - Compositional Omics Model-Based Integration -

DPCCA

2020 - - Gundersen - Deep Probabilistic CCA -

2020 - - Velten - spatial or temporal relationships -

MultiPower

2020 - - Tarazona - Sample size in multi-omic experiments -

2020 - - Yoon - Sparse semiparametric CCA for data of mixed types -

2020 - - Min - Sparse (structured sparse) multiple co-Inertia analysis -

MuVI

2023 - - Qoku - Integrate noisy feature sets -

1994 - - Doledec - Co‐inertia analysis -

2007 - - Dray - Implementing the Duality Diagram for Ecologists -

1987 - - Wold - Multi‐way principal components‐and PLS‐analysis -

1996 - - Wold - Hierarchical multiblock PLS -

2003 - - Trygg - O2‐PLS, a two‐block (X–Y) latent variable regression (LVR) -

2011 - - Hanafi - Connections between multiple COI and consensus PCA -

THEME

2015 - - Verron - THEmatic Model Exploration -

2013 - DISCO SCA - Schouteden - distinctive and common components with simultaneous-component analysis - ,

2009 - - Shen -

2011 - - Yuan - Data fusion by Bayesian nonparametric Dirichlet modeling - ,

2012 - - Kirk - ,

2013 - - Mo -

BCC

2013 - - Lock - Bayesian consensus clustering -

iBAG

2013 - - Wang - Integrative Bayesian Analysis of Genomics -

2014 - - Wang -

2015 - moCluster - Meng - Derivative of iClusterPlus -

2017 - - Gabasova -

2017 - PFA - Shi - Pattern Fussion analysis -

2019 - - Wong -

2019 - - John -

NEMO

2019 - - Rappoport - Similarity-based Clustering -

2020 - - Chierici and Bussola -

ClustOmics

2021 - - Brière - Consensus clustering -

MOGONET

2021 - - Tongxin Wang - Multi-Omics Graph cOnvolutional NETworks -

maui

2019 - - Ronen - Stacked VAE + clustering predictive of survival -

IntegrativeVAEs

2019 - - Simidjievski - Variational autoencoders + classification -

OmiVAE

2019 - - Xiaoyu Zhang - Integrated Multi-omics Analysis Using Variational Autoencoders -

DeepProg

2021 - - Poirion - DL and ML ensemble + survival prediction -

2021 - - Wissel - Supervised Hierarchical Autoencoder + survival prediction -

MolTi-DREAM

2018 - - Didier - identifying communities from multiplex networks, and annotated the obtained clusters

NetICS

2018 - Christos Dimitrakopoulos - Network-based integration of multi-omics data for prioritizing cancer genes -

RWR-MH

2019 - - Valdeolivas - Random walk with restart on multiplex and heterogeneous biological networks

2020 - - Novoa-del-toro - A multi-objective genetic algorithm to find active modules in multiplex biological networks

RWRF

2021 - - Wen - Random Walk with Restart for multi-dimensional data Fusion

cardelino

2018 - - - gene expression states to clones (SNVs from scRNA-seq + bulk exome data) -

clonealign

2018 - - Campbell - gene expression states to clones (scRNA-seq + scDNA-seq (CNV)) -

2020 - - Kim - CITE-seq data analysis

2021 - - Wang - infer dynamics by integrating state and lineage information -

MSFA

2016 - - De Vito - multi-study factor analysis: same features, different samples -

2016 - - Chalise - methylation, gene expression and protein expression -

2019 - - Martinez-Mira - RNA-seq, ATAC-seq (DNase-seq), ChIP-seq, small RNA-seq and Methyl-seq. -

2019 - - Chung - DNA, CNV, WGBS, RNAseq, Protein expression -

2008 - Holmes -

2014 - Kohl -

2016 - Josse -

2016 - Ebrahim -

2016 - Meng -

2016 - Li -

2017 - Huang -

2017 - Hasin -

2017 - Allen -

2018 - Rappoport -

2018 - Bougeard -

2018 - Karczewski -

2018 - Yan -

2019 - Misra -

2019 - Chauvel -

2019 - McCabe - -

2019 - Pierre-Jean -

2019 - Pinu -

2019 - Wu -

2019 - Sankaran - -

2020 - Lee -

2020 - Herrmann - -

2020 - Nguyen -

2020 - Eicher -

2020 - Cantini -

2020 - Subramanian -

2020 - Krassowski - -

2021 - Espinosa -

2022 - Jiang -

2022 - Cai -

2007 - Fagan -

2011 - De la Cruz - -

2014 - Tomescu -

2014 - Costello (NCI/DREAM) -

2015 - Wang -

2016 - Wan - -

2017 - Butler -

2018 - Skelly - -

2018 - Stuart -

2018 - Ash -

2019 - Xu -

2019 - Ghaemi - Multi-omics in pregnancy using stacked generalization

2017 - - Ramos - Software for the integration of multi-omics experiments in Bioconductor -

muon

2021 - - Bredikhin -

MultiBaC

2020 - - Ugidos - and

2020 - - - June 14-19, 2020 in Banff, Canada