Works matching AU Gunawan, Rudiyanto

Results: 47

Effects of Lithium on Age-related Decline in Mitochondrial Turnover and Function in Caenorhabditis elegans.

Published in:

2014

By:

Tam, Zhi Yang;
Gruber, Jan;
Ng, Li Fang;
Halliwell, Barry;
Gunawan, Rudiyanto

Publication type:

Journal Article

Effects of Lithium on Age-related Decline in Mitochondrial Turnover and Function in Caenorhabditis elegans.

Published in:

Journals of Gerontology Series A: Biological Sciences & Medical Sciences, 2014, v. 69, n. 7, p. 810, doi. 10.1093/gerona/glt210

By:

Tam, Zhi Yang;
Gruber, Jan;
Ng, Li Fang;
Halliwell, Barry;
Gunawan, Rudiyanto

Publication type:

Article

GlycoEnzOnto: a GlycoEnzyme pathway and molecular function ontology.

Published in:

Bioinformatics, 2022, v. 38, n. 24, p. 5413, doi. 10.1093/bioinformatics/btac704

By:

Groth, Theodore;
Diehl, Alexander D;
Gunawan, Rudiyanto;
Neelamegham, Sriram

Publication type:

Article

Maximizing signal-to-noise ratio in the random mutation capture assay.

Published in:

Nucleic Acids Research, 2012, v. 40, n. 5, p. e35, doi. 10.1093/nar/gkr1221

By:

Poovathingal, Suresh Kumar;
Gruber, Jan;
Ng, Li Fang;
Halliwell, Barry;
Gunawan, Rudiyanto

Publication type:

Article

Parallel High-Resolution Finite Volume Simulation of Particulate Processes.

Published in:

AIChE Journal, 2008, v. 54, n. 6, p. 1449, doi. 10.1002/aic.11484

By:

Gunawan, Rudiyanto;
Fusman, Irene;
Braatz, Richard D.

Publication type:

Article

High Resolution Algorithms for Multidimensional Population Balance Equations.

Published in:

AIChE Journal, 2004, v. 50, n. 11, p. 2738, doi. 10.1002/aic.10228

By:

Gunawan, Rudiyanto;
Fusman, Irene;
Braatz, Richard D.

Publication type:

Article

Divergent Learning-Related Transcriptional States of Cortical Glutamatergic Neurons.

Published in:

Journal of Neuroscience, 2024, v. 44, n. 10, p. 1, doi. 10.1523/JNEUROSCI.0302-23.2023

By:

Dunton, Katie L.;
Hedrick, Nathan G.;
Meamardoost, Saber;
Chi Ren;
Howe, James R.;
Jing Wang;
Root, Cory M.;
Gunawan, Rudiyanto;
Takaki Komiyama;
Ying Zhang;
Eun Jung Hwang

Publication type:

Article

SINCERITIES: inferring gene regulatory networks from time-stamped single cell transcriptional expression profiles.

Published in:

Bioinformatics, 2018, v. 34, n. 2, p. 258, doi. 10.1093/bioinformatics/btx575

By:

Gao, Nan Papili;
Ud-Dean, S M Minhaz;
Gandrillon, Olivier;
Gunawan, Rudiyanto

Publication type:

Article

Inferring gene targets of drugs and chemical compounds from gene expression profiles.

Published in:

Bioinformatics, 2016, v. 32, n. 14, p. 2120, doi. 10.1093/bioinformatics/btw148

By:

Noh, Heeju;
Gunawan, Rudiyanto

Publication type:

Article

Optimal design of gene knockout experiments for gene regulatory network inference.

Published in:

Bioinformatics, 2016, v. 32, n. 6, p. 875, doi. 10.1093/bioinformatics/btv672

By:

Minhaz Ud-Dean, S. M.;
Gunawan, Rudiyanto

Publication type:

Article

REDEMPTION: reduced dimension ensemble modeling and parameter estimation.

Published in:

Bioinformatics, 2015, v. 31, n. 20, p. 3387, doi. 10.1093/bioinformatics/btv365

By:

Yang Liu;
Manesso, Erica;
Gunawan, Rudiyanto

Publication type:

Article

Parameter estimation of kinetic models from metabolic profiles: two-phase dynamic decoupling method.

Published in:

Bioinformatics, 2011, v. 27, n. 14, p. 1964, doi. 10.1093/bioinformatics/btr293

By:

Jia, Gengjie;
Stephanopoulos, Gregory N.;
Gunawan, Rudiyanto

Publication type:

Article

Parameter estimation of dynamic biological network models using integrated fluxes.

Published in:

BMC Systems Biology, 2014, v. 8, n. 1, p. 127, doi. 10.1186/s12918-014-0127-x

By:

Yang Liu;
Gunawan, Rudiyanto

Publication type:

Article

Incremental parameter estimation of kinetic metabolic network models.

Published in:

BMC Systems Biology, 2012, v. 6, n. 1, p. 1, doi. 10.1186/1752-0509-6-142

By:

Jia, Gengjie;
Stephanopoulos, Gregory;
Gunawan, Rudiyanto

Publication type:

Article

Understanding dynamics using sensitivity analysis: caveat and solution.

Published in:

BMC Systems Biology, 2011, v. 5, n. 1, p. 41, doi. 10.1186/1752-0509-5-41

By:

Perumal, Thanneer M.;
Gunawan, Rudiyanto

Publication type:

Article

TRaCE+: Ensemble inference of gene regulatory networks from transcriptional expression profiles of gene knock-out experiments.

Published in:

BMC Bioinformatics, 2016, v. 17, p. 1, doi. 10.1186/s12859-016-1137-z

By:

Minhaz Ud-Dean, S. M.;
Heise, Sandra;
Klamt, Steffen;
Gunawan, Rudiyanto

Publication type:

Article

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

Published in:

PLoS Computational Biology, 2021, v. 17, n. 11, p. 1, doi. 10.1371/journal.pcbi.1009589

By:

Ravi, Sudharshan;
Gunawan, Rudiyanto

Publication type:

Article

Clonal expansion of mitochondrial DNA deletions is a private mechanism of aging in long‐lived animals.

Published in:

Aging Cell, 2018, v. 17, n. 5, p. 1, doi. 10.1111/acel.12814

By:

Lakshmanan, Lakshmi Narayanan;
Yee, Zhuangli;
Ng, Li Fang;
Gunawan, Rudiyanto;
Halliwell, Barry;
Gruber, Jan

Publication type:

Article

FARCI: Fast and Robust Connectome Inference.

Published in:

Brain Sciences (2076-3425), 2021, v. 11, n. 12, p. 1556, doi. 10.3390/brainsci11121556

By:

Meamardoost, Saber;
Bhattacharya, Mahasweta;
Hwang, Eun Jung;
Komiyama, Takaki;
Mewes, Claudia;
Wang, Linbing;
Zhang, Ying;
Gunawan, Rudiyanto

Publication type:

Article

Global parameter estimation methods forstochastic biochemical systems.

Published in:

BMC Bioinformatics, 2010, v. 11, p. 414, doi. 10.1186/1471-2105-11-414

By:

Poovathingal, Suresh Kumar;
Gunawan, Rudiyanto

Publication type:

Article

Iterative approach to model identification of biological networks.

Published in:

BMC Bioinformatics, 2005, v. 6, p. 155, doi. 10.1186/1471-2105-6-155

By:

Gadkar, Kapil G.;
Gunawan, Rudiyanto;
Doyle III, Francis J.

Publication type:

Article

Context-Dependent Role of Mitochondrial Fusion-Fission in Clonal Expansion of mtDNA Mutations.

Published in:

PLoS Computational Biology, 2015, v. 11, n. 5, p. 1, doi. 10.1371/journal.pcbi.1004183

By:

Tam, Zhi Yang;
Gruber, Jan;
Halliwell, Barry;
Gunawan, Rudiyanto

Publication type:

Article

Stochastic Drift in Mitochondrial DNA Point Mutations: A Novel Perspective Ex Silico.

Published in:

PLoS Computational Biology, 2009, v. 5, n. 11, p. 1, doi. 10.1371/journal.pcbi.1000572

By:

Poovathingal, Suresh Kumar;
Gruber, Jan;
Halliwell, Barry;
Gunawan, Rudiyanto

Publication type:

Article

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

Published in:

Nucleic Acids Research, 2018, v. 46, n. 6, p. 1, doi. 10.1093/nar/gkx1314

By:

Noh, Heeju;
Shoemaker, Jason E;
Gunawan, Rudiyanto

Publication type:

Article

Are mutagenic non D-loop direct repeat motifs in mitochondrial DNA under a negative selection pressure?

Published in:

Nucleic Acids Research, 2015, v. 43, n. 8, p. 4098, doi. 10.1093/nar/gkv299

By:

Lakshmanan, Lakshmi Narayanan;
Gruber, Jan;
Halliwell, Barry;
Gunawan, Rudiyanto

Publication type:

Article

Global genome decompaction leads to stochastic activation of gene expression as a first step toward fate commitment in human hematopoietic cells.

Published in:

PLoS Biology, 2022, v. 20, n. 10, p. 1, doi. 10.1371/journal.pbio.3001849

By:

Parmentier, Romuald;
Racine, Laëtitia;
Moussy, Alice;
Chantalat, Sophie;
Sudharshan, Ravi;
Papili Gao, Nan;
Stockholm, Daniel;
Corre, Guillaume;
Fourel, Geneviève;
Deleuze, Jean-François;
Gunawan, Rudiyanto;
Paldi, Andras

Publication type:

Article

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

Published in:

NAR Genomics & Bioinformatics, 2024, v. 6, n. 4, p. 1, doi. 10.1093/nargab/lqae169

By:

Chrysinas, Panagiotis;
Venkatesan, Shriramprasad;
Ang, Isaac;
Ghosh, Vishnu;
Chen, Changyou;
Neelamegham, Sriram;
Gunawan, Rudiyanto

Publication type:

Article

Introduction to Editorial Board Member: Professor Francis J. Doyle III.

Published in:

2017

By:

Bagheri, Neda;
Gunawan, Rudiyanto

Publication type:

Editorial

Immobilized NRG1 Accelerates Neural Crest like Cell Differentiation Toward Functional Schwann Cells Through Sustained Erk1/2 Activation and YAP/TAZ Nuclear Translocation.

Published in:

Advanced Science, 2024, v. 11, n. 33, p. 1, doi. 10.1002/advs.202402607

By:

Tseropoulos, Georgios;
Mehrotra, Pihu;
Podder, Ashis Kumer;
Wilson, Emma;
Zhang, Yali;
Wang, Jianmin;
Koontz, Alison;
Gao, Nan Papili;
Gunawan, Rudiyanto;
Liu, Song;
Feltri, Laura M.;
Bronner, Marianne E.;
Andreadis, Stelios T.

Publication type:

Article

Ensemble Inference and Inferability of Gene Regulatory Networks.

Published in:

PLoS ONE, 2014, v. 9, n. 8, p. 1, doi. 10.1371/journal.pone.0103812

By:

Ud-Dean, S. M. Minhaz;
Gunawan, Rudiyanto

Publication type:

Article

Assessment of Network Inference Methods: How to Cope with an Underdetermined Problem.

Published in:

PLoS ONE, 2014, v. 9, n. 3, p. 1, doi. 10.1371/journal.pone.0090481

By:

Siegenthaler, Caroline;
Gunawan, Rudiyanto

Publication type:

Article

Mathematical Modeling of the Role of Mitochondrial Fusion and Fission in Mitochondrial DNA Maintenance.

Published in:

PLoS ONE, 2013, v. 8, n. 10, p. 1, doi. 10.1371/journal.pone.0076230

By:

Tam, Zhi Yang;
Gruber, Jan;
Halliwell, Barry;
Gunawan, Rudiyanto

Publication type:

Article

Role of Direct Repeat and Stem-Loop Motifs in mtDNA Deletions: Cause or Coincidence?

Published in:

PLoS ONE, 2012, v. 7, n. 4, p. 1, doi. 10.1371/journal.pone.0035271

By:

Lakshmanan, Lakshmi Narayanan;
Gruber, Jan;
Halliwell, Barry;
Gunawan, Rudiyanto

Publication type:

Article

Kinetic Modeling of Mammalian Cell Culture Bioprocessing: The Quest to Advance Biomanufacturing.

Published in:

Biotechnology Journal, 2018, v. 13, n. 3, p. 1, doi. 10.1002/biot.201700229

By:

Kyriakopoulos, Sarantos;
Ang, Kok Siong;
Lakshmanan, Meiyappan;
Huang, Zhuangrong;
Yoon, Seongkyu;
Gunawan, Rudiyanto;
Lee, Dong‐Yup

Publication type:

Article

Is mitochondrial DNA turnover slower than commonly assumed?

Published in:

Biogerontology, 2012, v. 13, n. 5, p. 557, doi. 10.1007/s10522-012-9390-7

By:

Poovathingal, Suresh;
Gruber, Jan;
Lakshmanan, LakshmiNarayanan;
Halliwell, Barry;
Gunawan, Rudiyanto

Publication type:

Article

CrossTx: Cross-Cell-Line Transcriptomic Signature Predictions.

Published in:

Processes, 2024, v. 12, n. 2, p. 332, doi. 10.3390/pr12020332

By:

Chrysinas, Panagiotis;
Chen, Changyou;
Gunawan, Rudiyanto

Publication type:

Article

Special Issue on "Biological Networks".

Published in:

2018

By:

Gunawan, Rudiyanto;
Bagheri, Neda

Publication type:

Editorial

Glycosylation Flux Analysis of Immunoglobulin G in Chinese Hamster Ovary Perfusion Cell Culture.

Published in:

Processes, 2018, v. 6, n. 10, p. 176, doi. 10.3390/pr6100176

By:

Wolf, Moritz;
Lepori, Dario;
Schweigler, Thea;
Morbidelli, Massimo;
Hutter, Sandro;
Papili Gao, Nan;
Gunawan, Rudiyanto

Publication type:

Article

Elucidating Cellular Population Dynamics by Molecular Density Function Perturbations.

Published in:

Processes, 2018, v. 6, n. 2, p. 9, doi. 10.3390/pr6020009

By:

Perumal, Thanneer Malai;
Gunawan, Rudiyanto

Publication type:

Article

Multi-Objective Optimization of Experiments Using Curvature and Fisher Information Matrix.

Published in:

Processes, 2017, v. 5, n. 4, p. 63, doi. 10.3390/pr5040063

By:

Manesso, Erica;
Sridharan, Srinath;
Gunawan, Rudiyanto

Publication type:

Article

Single-Cell-Based Analysis Highlights a Surge in Cell-to-Cell Molecular Variability Preceding Irreversible Commitment in a Differentiation Process.

Published in:

PLoS Biology, 2016, v. 14, n. 12, p. 1, doi. 10.1371/journal.pbio.1002585

By:

Richard, Angélique;
Boullu, Loïs;
Herbach, Ulysse;
Bonnafoux, Arnaud;
Morin, Valérie;
Vallin, Elodie;
Guillemin, Anissa;
Papili Gao, Nan;
Gunawan, Rudiyanto;
Cosette, Jérémie;
Arnaud, Ophélie;
Kupiec, Jean-Jacques;
Espinasse, Thibault;
Gonin-Giraud, Sandrine;
Gandrillon, Olivier

Publication type:

Article

Immune-mediated regeneration of cell-free vascular grafts in an ovine model.

Published in:

NPJ Regenerative Medicine, 2025, v. 10, n. 1, p. 1, doi. 10.1038/s41536-025-00400-7

By:

Nasiri, Bita;
Das, Arundhati;
Ramachandran, Karthik;
Bhamidipati, Sai Harsha;
Wu, Yulun;
Venkatesan, Shriramprasad;
Gunawan, Rudiyanto;
Swartz, Daniel D.;
Andreadis, Stelios T.

Publication type:

Article

Phase Sensitivity Analysis of Circadian Rhythm Entrainment.

Published in:

Journal of Biological Rhythms, 2007, v. 22, n. 2, p. 180, doi. 10.1177/0748730407299194

By:

Gunawan, Rudiyanto;
Doyle III, Francis J.

Publication type:

Article

Microfluidics: Stochastic and Age‐Dependent Proteostasis Decline Underlies Heterogeneity in Heat‐Shock Response Dynamics (Small 30/2021).

Published in:

Small, 2021, v. 17, n. 30, p. 1, doi. 10.1002/smll.202170157

By:

Vertti‐Quintero, Nadia;
Berger, Simon;
Casadevall i Solvas, Xavier;
Statzer, Cyril;
Annis, Jillian;
Ruppen, Peter;
Stavrakis, Stavros;
Ewald, Collin Y.;
Gunawan, Rudiyanto;
deMello, Andrew J.

Publication type:

Article

Stochastic and Age‐Dependent Proteostasis Decline Underlies Heterogeneity in Heat‐Shock Response Dynamics.

Published in:

Small, 2021, v. 17, n. 30, p. 1, doi. 10.1002/smll.202102145

By:

Vertti‐Quintero, Nadia;
Berger, Simon;
Casadevall i Solvas, Xavier;
Statzer, Cyril;
Annis, Jillian;
Ruppen, Peter;
Stavrakis, Stavros;
Ewald, Collin Y.;
Gunawan, Rudiyanto;
deMello, Andrew J.

Publication type:

Article

Identification of Kinetic Parameters in Multidimensional Crystallization Processes.

Published in:

International Journal of Modern Physics B: Condensed Matter Physics; Statistical Physics; Applied Physics, 2002, v. 16, n. 1/2, p. 367, doi. 10.1142/S0217979202009883

By:

Gunawan, Rudiyanto;
Ma, David L.;
Fujiwara, Mitsuko;
Braatz, Richard D.

Publication type:

Article

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

Published in:

BMC Bioinformatics, 2021, v. 22, n. 1, p. 1, doi. 10.1186/s12859-021-04046-2

By:

Noh, Heeju;
Hua, Ziyi;
Chrysinas, Panagiotis;
Shoemaker, Jason E.;
Gunawan, Rudiyanto

Publication type:

Article