Rudiyanto Gunawan

SCREAM: Single-cell Clustering using Representation Autoencoder of Multiomics

SCREAM is a deep learning framework for integrating and clustering multi-omics single-cell data, showing superior performance in benchmarking with high ARI and NMI scores.

GlycoEnzDB: A database of enzymes involved in human glycosylation

GlycoEnzDB curates and presents human glycoenzyme data, linking enzyme functions, pathways, and expression data with external resources and AI-generated descriptions.

Transformer-based Deep Learning for Glycan Structure Inference from Tandem Mass Spectrometry

This paper introduces GlycoBERT and GlycoBART, transformer-based models for glycan structure prediction from MS/MS data, achieving high accuracy and enabling de novo structure inference.

Cell and tissue-specific glycosylation pathways informed by single-cell transcriptomics

The paper analyzes single-cell glycogene expression in human tissues to identify cell- and tissue-specific glycosylation pathways and transcription factor regulation.

CrossTx: Cross-cell line Transcriptomic Signature Predictions

CrossTx predicts drug transcriptomic signatures for unseen cell lines using reference data and correction methods, achieving accurate and efficient results.

Universality of cell differentiation trajectories revealed by a reconstruction of transcriptional uncertainty landscapes from single-cell transcriptomic data

The paper uses CALISTA to reconstruct transcriptional uncertainty landscapes from single-cell data, revealing universal patterns in cell differentiation trajectories.

GlycoEnzOnto: A GlycoEnzyme Pathway and Molecular Function Ontology

GlycoEnzOnto curates 386 human glycoEnzymes across 135 pathways and 134 molecular functions to improve glycosylation pathway analysis.

Rewiring Dynamics of Functional Connectome in Motor Cortex during Motor Skill Learning

This study examines how functional connectomes in the motor cortex of mice rewire during motor skill learning, revealing a biphasic pattern of connectivity changes that optimize performance and maintain network density.

FARCI: Fast and Robust Connectome Inference

FARCI infers neuronal connectomes from two-photon calcium imaging data, showing accuracy and efficiency across network sizes and noise levels.

ΔFBA: Predicting metabolic flux alterations using genome-scale metabolic models and differential transcriptomic data

DeltaFBA predicts metabolic flux changes between conditions using genome-scale models and gene expression data without requiring a specified cellular objective.

A systems based framework to computationally predict putative transcription factors and signaling pathways regulating glycan biosynthesis

This paper predicts tissue-specific transcription factors and signaling pathways regulating glycan biosynthesis using multi-omics data across 29 cancer types.

DeltaNeTS+: Elucidating the mechanism of drugs and diseases using gene expression and transcriptional regulatory networks

DeltaNeTS+ infers direct gene targets of drugs and diseases from gene expression data, showing effectiveness in complex organisms and time-course profiles.

Nutrient signaling pathways regulate amyloid clearance and synaptic loss in Alzheimer's disease

This study identifies nutrient signaling pathways that regulate amyloid clearance and synaptic loss in Alzheimer's disease, showing both protective and harmful effects.

CALISTA: Clustering And Lineage Inference in Single-Cell Transcriptional Analysis

CALISTA is a single-cell transcriptomic analysis tool that improves lineage reconstruction and cell ordering compared to existing methods.

Metabolic stress is a primary pathogenic event in transgenic Caenorhabditis elegans expressing neuronal human amyloid-β

This study identifies metabolic dysfunction, particularly in the TCA cycle, as an early and causative event in Alzheimer's disease using a transgenic C. elegans model.

Clonal expansion of mitochondrial DNA deletions is a private mechanism of ageing in long-lived animals

The paper identifies mtDNA deletions in ageing nematodes and finds they are rare, not age-dependent, and not clonally expanded, suggesting they are not a major driver of ageing in short-lived species.

Thermodynamic analysis of mitochondrial DNA breakpoints reveals mechanistic details of deletion mutagenesis

The paper analyzes mtDNA deletion breakpoints using thermodynamic methods to identify misalignment lengths and proposes mechanisms for DSB-induced deletions.

Network perturbation analysis of gene transcriptional profiles reveals protein targets and mechanism of action of drugs and influenza A viral infection

ProTINA infers protein targets of drugs and influenza A virus by analyzing gene expression changes, revealing accurate targets and infection mechanisms.

SINCERITIES: Inferring gene regulatory networks fromtime-stamped single cell transcriptional expression profiles

SINCERITIES infers gene regulatory networks from time-stamped single-cell expression data, showing better accuracy than existing methods in simulated and experimental datasets.

Glycosylation Flux Analysis Reveals Dynamic Changes Of Intracellular Glycosylation Flux Distribution In Chinese Hamster Ovary Fed-Batch Cultures

This study introduces glycosylation flux analysis to predict intracellular glycosylation fluxes in CHO cells, showing that galactosylation fluxes decrease over time and Mn addition increases them initially.