ManiNetCluster: a novel manifold learning approach to reveal the functional links between gene networks

PrimAlign: PageRank-inspired Markovian alignment for large biological networks

(2018) Karel Kalecky et al.   BIOINFORMATICS

Alignment of single-cell trajectories to compare cellular expression dynamics

(2018) Ayelet Alpert et al.   NATURE METHODS

Evolution of Chlamydomonas reinhardtii ferredoxins and their interactions with [FeFe]-hydrogenases

(2017) Anne Sawyer et al.   PHOTOSYNTHESIS RESEARCH

Testing the manifold hypothesis

(2016) Charles Fefferman et al.   JOURNAL OF THE AMERICAN MATHEMATICAL SOCIETY

Cross-Disciplinary Network Comparison: Matchmaking between Hairballs

(2016) Koon-Kiu Yan et al.   Cell Systems

MAGNA++: Maximizing Accuracy in Global Network Alignment via both node and edge conservation

(2015) V. Vijayan et al.   BIOINFORMATICS

Recovering the number of clusters in data sets with noise features using feature rescaling factors

(2015) Renato Cordeiro de Amorim et al.   INFORMATION SCIENCES

MAGNA: Maximizing Accuracy in Global Network Alignment

(2014) Vikram Saraph et al.   BIOINFORMATICS

On the selection of appropriate distances for gene expression data clustering

(2014) Pablo A Jaskowiak et al.   BMC BIOINFORMATICS

Gene co-expression network analysis reveals common system-level properties of prognostic genes across cancer types

(2014) Yang Yang et al.   Nature Communications

OrthoClust: an orthology-based network framework for clustering data across multiple species

(2014) Koon-Kiu Yan et al.   GENOME BIOLOGY

Skeletal representations of orthogonal shapes

(2013) Jonàs Martínez et al.   GRAPHICAL MODELS

Representation Learning: A Review and New Perspectives

(2013) Y. Bengio et al.   IEEE TRANSACTIONS ON PATTERN ANALYSIS AND MACHINE INTELLIGENCE

A survey of multi-view machine learning

(2013) Shiliang Sun   NEURAL COMPUTING & APPLICATIONS

The GreenCut: re-evaluation of physiological role of previously studied proteins and potential novel protein functions

(2013) Mark L. Heinnickel et al.   PHOTOSYNTHESIS RESEARCH

The GreenCut2 Resource, a Phylogenomically Derived Inventory of Proteins Specific to the Plant Lineage

(2011) Steven J. Karpowicz et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Large-scale prediction of long non-coding RNA functions in a coding–non-coding gene co-expression network

(2011) Qi Liao et al.   NUCLEIC ACIDS RESEARCH

Assembly of the Light-Harvesting Chlorophyll Antenna in the Green Alga Chlamydomonas reinhardtii Requires Expression of the TLA2-CpFTSY Gene

(2011) H. Kirst et al.   PLANT PHYSIOLOGY

A human B-cell interactome identifies MYB and FOXM1 as master regulators of proliferation in germinal centers

(2010) Celine Lefebvre et al.   Molecular Systems Biology

Simultaneous Clustering of Multiple Gene Expression and Physical Interaction Datasets

(2010) Manikandan Narayanan et al.   PLoS Computational Biology

IsoRankN: spectral methods for global alignment of multiple protein networks

(2009) C.-S. Liao et al.   BIOINFORMATICS

Unlocking the secrets of the genome

(2009) Susan E. Celniker et al.   NATURE

A global view of genomic information – moving beyond the gene and the master regulator

(2009) John S. Mattick et al.   TRENDS IN GENETICS

WGCNA: an R package for weighted correlation network analysis

(2008) Peter Langfelder et al.   BMC BIOINFORMATICS

Global alignment of multiple protein interaction networks with application to functional orthology detection

(2008) R. Singh et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA