cran: COBRA | Projects | Ecosyste.ms: Papers

10.3390/genes6041140

COBRA-Seq: Sensitive and Quantitative Methylome Profiling
Cited by: 9
Author(s): Hilal Varinli, Aaron L. Statham, Susan J. Clark, Peter L. Molloy, Jason P. Ross
Software Mentions: 3
Published: about 9 years ago

10.15252/msb.20198982

Personalized whole‐body models integrate metabolism, physiology, and the gut microbiome
Cited by: 98
Author(s): Ines Thiele, Swagatika Sahoo, Almut Heinken, Johannes Hertel, Laurent Heirendt, Maike Kathrin Aurich, Ronan M. T. Fleming
Software Mentions: 3
Published: over 4 years ago

10.1371/journal.pone.0019464

Heterochromatic Genes Undergo Epigenetic Changes and Escape Silencing in Immunodeficiency, Centromeric Instability, Facial Anomalies (ICF) Syndrome
Cited by: 30
Author(s): Marie-Elisabeth Brun, Erica Lana, Isabelle Rivals, Gérard Lefranc, Pierre Sarda, Mireille Claustres, André Mégarbané, Albertina De Sario
Software Mentions: 3
Published: over 13 years ago

10.1016/j.jbc.2021.100285

Decreases in different Dnmt3b activities drive distinct development of hematologic malignancies in mice
Cited by: 4
Author(s): Katarína Lopušná, Paweł Nowialis, Jana Opavska, Ajay Abraham, Alberto Riva, Staci L. Haney, René Opavský
Software Mentions: 3
Published: almost 4 years ago

10.1186/1752-0509-7-102

Antibacterial mechanisms identified through structural systems pharmacology
Cited by: 23
Author(s): Roger L. Chang, Lei Xie, Philip E. Bourne, Bernhard Ø. Palsson
Software Mentions: 3
Published: about 11 years ago

10.1017/S2045796020000566

Minimum clinically important differences for the Functioning Assessment Short Test and a battery of neuropsychological tests in bipolar disorders: results from the FACE-BD cohort
Cited by: 6
Author(s): Paul Roux, Éric Brunet-Gouet, Mickaël Ehrminger, Bruno Aouizerate, V. Aubin, Jean‐Michel Azorin, Frank Bellivier, Thierry Bougerol, P. Courtet, Caroline Dubertret, Jean‐Pierre Kahn, Marion Leboyer, Émilie Olié, Bruno Étain, Christine Passerieux
Software Mentions: 3
Published: almost 5 years ago

10.1186/s12864-017-4350-x

Isogenic mice exhibit sexually-dimorphic DNA methylation patterns across multiple tissues
Cited by: 26
Author(s): Helen McCormick, Paul E. Young, Suzy S J Hur, Keith Booher, Hunter Chung, Jennifer E. Cropley, Eleni Giannoulatou, Catherine M. Suter
Software Mentions: 2
Published: almost 7 years ago

10.3389/fphys.2014.00091

Membrane transporters in a human genome-scale metabolic knowledgebase and their implications for disease
Cited by: 72
Author(s): Swagatika Sahoo, Maike Kathrin Aurich, Jón J. Jónsson, Ines Thiele
Software Mentions: 2
Published: over 10 years ago

10.3389/fmicb.2016.00673

Metabolic Network Modeling of Microbial Interactions in Natural and Engineered Environmental Systems
Cited by: 96
Author(s): Octavio Perez-Garcia, Gavin Lear, Naresh Singhal
Software Mentions: 2
Published: over 8 years ago

10.1186/1471-2164-11-481

DNA methylation status of nuclear-encoded mitochondrial genes underlies the tissue-dependent mitochondrial functions
Cited by: 43
Author(s): Masaki Takasugi, Shusuke Yagi, Keiji Hirabayashi, Kunio Shiota
Software Mentions: 2
Published: over 14 years ago

10.3389/fmicb.2017.02599

Low Concentrations of Vitamin C Reduce the Synthesis of Extracellular Polymers and Destabilize Bacterial Biofilms
Cited by: 61
Author(s): Santosh Pandit, Vaishnavi Ravikumar, Alyaa M. Abdel-Haleem, Abderahmane Derouiche, Venkata Raghavendra Subrahmanya Sar Mokkapati, Carina Sihlbom, Katsuhiko Mineta, Takashi Gojobori, Xin Gao, Fredrik Westerlund, Ivan Mijaković
Software Mentions: 2
Published: almost 7 years ago

10.3389/fphys.2013.00237

The evolution of genome-scale models of cancer metabolism
Cited by: 65
Author(s): Nathan E. Lewis, Alyaa M. Abdel-Haleem
Software Mentions: 2
Published: almost 12 years ago

10.1186/1752-0509-5-167

A computational exploration of bacterial metabolic diversity identifying metabolic interactions and growth-efficient strain communities
Cited by: 41
Author(s): Eleftheria Tzamali, Panayiota Poirazi, Ioannis G. Tollis, Martin Reczko
Software Mentions: 2
Published: almost 14 years ago

10.1186/1471-2164-11-202

Metabolic modeling and analysis of the metabolic switch in Streptomyces coelicolor
Cited by: 85
Author(s): Mohammad Tauqeer Alam, Maria Elena Merlo, David A. Hodgson, E. M. H. Wellington, Eriko Takano, Rainer Breitling
Software Mentions: 2
Published: over 14 years ago

10.3389/fgene.2019.00633

FindTargetsWEB: A User-Friendly Tool for Identification of Potential Therapeutic Targets in Metabolic Networks of Bacteria
Cited by: 4
Author(s): Thiago Castanheira Merigueti, Marcia W. Carneiro, Ana Paula D'Allincourt Carvalho-Assef, Floriano Paes Silva, Fabrício Alves Barbosa Silva
Software Mentions: 2
Published: over 5 years ago

10.3389/fgene.2017.00097

Simultaneous Methylation-Level Assessment of Hundreds of CpG Sites by Targeted Bisulfite PCR Sequencing (TBPseq)
Cited by: 6
Author(s): Kyuheum Jeon, Byungkuk Min, Jung Sun Park, Yong‐Kook Kang
Software Mentions: 2
Published: over 7 years ago

10.1186/s12864-016-3311-0

Modelling microbial metabolic rewiring during growth in a complex medium
Cited by: 12
Author(s): Marco Fondi, Emanuele Bosi, Luana Presta, Diletta Natoli, Renato Fani
Software Mentions: 2
Published: almost 8 years ago

10.1186/s12918-014-0123-1

CBFA: phenotype prediction integrating metabolic models with constraints derived from experimental data
Cited by: 8
Author(s): Rafael Carreira, Pedro Evangelista, Paulo Maia, Paulo Vilaça, Marcellinus Pont, Jean-François Tomb, Isabel Rocha, Miguel Rocha
Software Mentions: 2
Published: almost 10 years ago

10.3389/fpls.2014.00491

Generalized framework for context-specific metabolic model extraction methods
Cited by: 54
Author(s): Semidán Robaina-Estévez, Zoran Nikoloski
Software Mentions: 2
Published: about 10 years ago

10.1186/1752-0509-6-55

Yeast 5 – an expanded reconstruction of the Saccharomyces cerevisiae metabolic network
Cited by: 131
Author(s): Benjamin D. Heavner, Kieran Smallbone, Brandon Barker, Pedro Mendes, Larry P. Walker
Software Mentions: 2
Published: over 12 years ago

10.1186/s12859-019-2756-y

Leveraging the effects of chloroquine on resistant malaria parasites for combination therapies
Cited by: 5
Author(s): Ana M. Untaroiu, Maureen A. Carey, Jennifer L. Guler, Jason A. Papin
Software Mentions: 2
Published: over 5 years ago

10.3389/fmicb.2013.00200

Metabolic analyses elucidate non-trivial gene targets for amplifying dihydroartemisinic acid production in yeast
Cited by: 11
Author(s): Ashok Misra, Matthew F. Conway, Joseph Johnnie, Tabish M. Qureshi, Bao Lige, Anne M. Derrick, Eddy Chukwura Agbo, Ganesh Sriram
Software Mentions: 2
Published: almost 12 years ago

10.1186/s12918-018-0607-5

Escher-FBA: a web application for interactive flux balance analysis
Cited by: 30
Author(s): Elliot Gordon Rowe, Bernhard Ø. Palsson, Zachary A. King
Software Mentions: 2
Published: about 6 years ago

10.1002/2211-5463.13231

Optimization of a modeling platform to predict oncogenes from genome‐scale metabolic networks of non‐small‐cell lung cancers
Cited by: 10
Author(s): You-Tyun Wang, Min-Ru Lin, Wei-Chen Chen, Wu‐Hsiung Wu, Feng‐Sheng Wang
Software Mentions: 2
Published: over 3 years ago

10.1186/s12918-016-0335-7

Identifying model error in metabolic flux analysis – a generalized least squares approach
Cited by: 2
Author(s): Stanislav Sokolenko, Marco Quattrociocchi, Marc G. Aucoin
Software Mentions: 2
Published: about 8 years ago

10.3389/fphys.2018.00749

A Constraint-Based Model Analysis of Enterocyte Mitochondrial Adaptation to Dietary Interventions of Lipid Type and Lipid Load
Cited by: 3
Author(s): Neeraj Sinha, María Suárez-Diez, Guido Hooiveld, Jaap Keijer, Vitor Martin dos Santos, Evert M. van Schothorst
Software Mentions: 2
Published: over 6 years ago

10.1186/s12918-017-0515-0

OptPipe - a pipeline for optimizing metabolic engineering targets
Cited by: 13
Author(s): András Hartmann, Ana Vila-Santa, Nicolai Kallscheuer, Michael Vogt, Alice Julien-Laferrière, Marie‐France Sagot, Jan Marienhagen, Susana Vinga
Software Mentions: 2
Published: almost 7 years ago

10.3389/fbioe.2014.00066

Synthetic Biology Outside the Cell: Linking Computational Tools to Cell-Free Systems
Cited by: 12
Author(s): Daniel D. Lewis, Fernando Villarreal, Fan Wu, Cheemeng Tan
Software Mentions: 2
Published: almost 10 years ago

10.3390/e22101101

A Multi-Scale Approach to Modeling E. coli Chemotaxis
Cited by: 7
Author(s): Eran Agmon, Ryan Spangler
Software Mentions: 2
Published: about 4 years ago

10.1186/s12859-020-3377-1

MOMO - multi-objective metabolic mixed integer optimization: application to yeast strain engineering
Cited by: 8
Author(s): Ricardo Andrade, Mahdi Doostmohammadi, João Santos, Marie‐France Sagot, Nuno P. Mira, Susana Vinga
Software Mentions: 2
Published: over 4 years ago

10.1002/ece3.2626

Gauging megadiversity with optimized and standardized sampling protocols: A case for tropical forest spiders
Cited by: 24
Author(s): Jagoba Malumbres‐Olarte, Nikolaj Scharff, Thomas Pape, Jonathan A. Coddington, Pedro Cardoso
Software Mentions: 2
Published: almost 8 years ago

10.1186/s12862-016-0733-x

Metabolic modelling in a dynamic evolutionary framework predicts adaptive diversification of bacteria in a long-term evolution experiment
Cited by: 61
Author(s): Tobias Großkopf, Jessika Consuegra, Joël Gaffé, John C. Willison, Richard E. Lenski, Orkun S. Soyer, Dominique Schneider
Software Mentions: 2
Published: over 8 years ago

10.1186/s12918-018-0557-y

Updated and standardized genome-scale reconstruction of Mycobacterium tuberculosis H37Rv, iEK1011, simulates flux states indicative of physiological conditions
Cited by: 53
Author(s): Erol Kavvas, Yara Seif, James T. Yurkovich, Charles J. Norsigian, Saugat Poudel, William W. Greenwald, Sankha Ghatak, Jonathan M. Monk
Software Mentions: 2
Published: over 6 years ago

10.1186/s13148-016-0291-5

Aberrant DNA hypermethylation-silenced SOX21-AS1 gene expression and its clinical importance in oral cancer
Cited by: 53
Author(s): Chung‐Yi Yang, Tsung-Han Wang, Hung-Chih Chen, Sung‐Chou Li, Ming-Chien Lee, Horng-Huei Liou, Pei‐Feng Liu, Yu‐Kai Tseng, Yow‐Ling Shiue, Luo‐Ping Ger, Kuo‐Wang Tsai
Software Mentions: 2
Published: almost 8 years ago

10.1186/s12918-018-0677-4

Modelling overflow metabolism in Escherichia coli with flux balance analysis incorporating differential proteomic efficiencies of energy pathways
Cited by: 29
Author(s): Hong Zeng, Aidong Yang
Software Mentions: 2
Published: almost 6 years ago

10.1186/1471-2105-12-28

FASIMU: flexible software for flux-balance computation series in large metabolic networks
Cited by: 57
Author(s): Andreas Hoppe, Sabrina Hoffmann, Andreas Gerasch, Christoph Gille, Hermann−Georg Holzhütter
Software Mentions: 2
Published: almost 14 years ago

10.1186/s13148-016-0269-3

MSP-HTPrimer: a high-throughput primer design tool to improve assay design for DNA methylation analysis in epigenetics
Cited by: 10
Author(s): Ram Vinay Pandey, Walter Pulverer, Rainer Kallmeyer, Gabriel Beikircher, Stephan Pabinger, Albert Kriegner, Andreas Weinhäusel
Software Mentions: 2
Published: about 8 years ago

10.1016/j.csbj.2021.06.009

Guided extraction of genome-scale metabolic models for the integration and analysis of omics data
Cited by: 10
Author(s): Andrew Walakira, Damjana Rozman, Tadeja Režen, Miha Mraz, Miha Moškon
Software Mentions: 2
Published: almost 4 years ago

10.1186/1752-0509-5-120

Systems biology of bacterial nitrogen fixation: High-throughput technology and its integrative description with constraint-based modeling
Cited by: 44
Author(s): Osbaldo Resendis‐Antonio, Magdalena Hernández, Emmanuel Salazar, Sandra Contreras, Gabriel Martínez Batallar, Yolanda Mora, Sergio Encarnación
Software Mentions: 2
Published: almost 14 years ago

10.1007/s11306-014-0721-3

Prediction of intracellular metabolic states from extracellular metabolomic data
Cited by: 55
Author(s): Maike Kathrin Aurich, Giuseppe Paglia, Óttar Rolfsson, Sigrún Hrafnsdóttir, Manuela Magnúsdóttir, Madgalena K. Stefaniak, Bernhard Ø. Palsson, Ronan M. T. Fleming, Ines Thiele
Software Mentions: 2
Published: over 10 years ago

10.1186/1471-2407-14-46

A comprehensive look at transcription factor gene expression changes in colorectal adenomas
Cited by: 20
Author(s): Janine Vonlanthen, Michał Okoniewski, Mirco Menigatti, Elisa Cattaneo, Daniela Pellegrini-Ochsner, Ritva Haider, Josef Jiricny, Teresa Staiano, Federico Buffoli, Giancarlo Marra
Software Mentions: 2
Published: almost 11 years ago

10.1186/s12918-015-0190-y

Genome-scale metabolic model of Rhodococcus jostii RHA1 (iMT1174) to study the accumulation of storage compounds during nitrogen-limited condition
Cited by: 24
Author(s): Mohammad Tajparast, Dominic Frigon
Software Mentions: 2
Published: over 9 years ago

10.3390/cancers11121976

RASSF10 Is a TGFβ-Target That Regulates ASPP2 and E-Cadherin Expression and Acts as Tumor Suppressor That Is Epigenetically Downregulated in Advanced Cancer
Cited by: 8
Author(s): Antje Richter, Miriam M. Küster, Michelle L. Woods, Sara K. Walesch, Mira Y. Gökyildirim, Marcus Krueger, Reinhard Dammann
Software Mentions: 2
Published: almost 5 years ago

10.1371/journal.pone.0126966

Retrotransposon-Derived Promoter of Mammalian Aebp2
Cited by: 1
Author(s): Hana Kim, Arundhati Bakshi, Joomyeong Kim
Software Mentions: 2
Published: over 9 years ago

10.1016/j.cell.2019.10.030

Genome-Scale Identification of Essential Metabolic Processes for Targeting the Plasmodium Liver Stage
Cited by: 82
Author(s): Rebecca R. Stanway, Ellen Bushell, Anush Chiappino-Pepe, Magali Roques, Theo Sanderson, Blandine Franke-Fayard, Reto Caldelari, Murielle Golomingi, Mary Nyonda, Vikash Pandey, Frank Schwach, Séverine Chevalley, Jai Ramesar, Tom Metcalf, Colin Herd, Paul‐Christian Burda, Julian C. Rayner, Dominique Soldati‐Favre, Chris J. Janse, Vassily Hatzimanikatis, Oliver Billker, Volker Heussler
Software Mentions: 2
Published: about 5 years ago

10.5936/csbj.201210016

EMERGING ENGINEERING PRINCIPLES FOR YIELD IMPROVEMENT IN MICROBIAL CELL DESIGN
Cited by: 9
Author(s): Santiago Comba, Ana Arabolaza, Hugo Gramajo
Software Mentions: 2
Published: about 12 years ago

10.3389/fpls.2020.00944

Systematic Multi-Omics Integration (MOI) Approach in Plant Systems Biology
Cited by: 81
Author(s): Ili Nadhirah Jamil, Juwairiah Remali, Kamalrul Azlan Azizan, Nor Azlan Nor Muhammad, Masanori Arita, Hoe-Han Goh, Wan Mohd Aizat
Software Mentions: 2
Published: over 4 years ago

10.1186/s12918-018-0574-x

Transcriptomic and metabolic flux analyses reveal shift of metabolic patterns during rice grain development
Cited by: 7
Author(s): Fangzhou Shen, Xueting Wu, Luoxi Shi, Hang Zhang, Yangmin Chen, Xiaoquan Qi, Zhuo Wang, Xuan Li
Software Mentions: 2
Published: over 6 years ago

10.1371/journal.pone.0227977

Reconstruction of a regulated two-cell metabolic model to study biohydrogen production in a diazotrophic cyanobacterium Anabaena variabilis ATCC 29413
Cited by: 14
Author(s): Ali Malek Shahkouhi, Ehsan Motamedian
Software Mentions: 2
Published: almost 5 years ago

10.1186/s12859-015-0476-5

Sampling with poling-based flux balance analysis: optimal versus sub-optimal flux space analysis of Actinobacillus succinogenes
Cited by: 12
Author(s): Michael Binns, Pedro de Atauri, Anestis Vlysidis, Marta Cascante, Constantinos Theodoropoulos
Software Mentions: 2
Published: almost 10 years ago

10.3390/metabo11080491

Modelling hCDKL5 Heterologous Expression in Bacteria
Cited by: 5
Author(s): Marco Fondi, Stefano Gonzi, Mikołaj Dziurzyński, Paola Turano, Veronica Ghini, Marzia Calvanese, Andrea Colarusso, Concetta Lauro, Ermenegilda Parrilli, Maria Luisa Tutino
Software Mentions: 2
Published: over 3 years ago

10.1186/1752-0509-4-45

OptFlux: an open-source software platform for in silico metabolic engineering
Cited by: 324
Author(s): Isabel Rocha, Paulo Maia, Pedro Evangelista, Paulo Vilaça, Simão Soares, José P. Pinto, Jens Nielsen, Kiran Raosaheb Patil, Eugénio C. Ferreira, Miguel Rocha
Software Mentions: 2
Published: over 14 years ago

10.1371/journal.pone.0253983

Persuasive linguistic tricks in social media marketing communication—The memetic approach
Cited by: 0
Author(s): Krzysztof Stepaniuk, Katarzyna Jarosz
Software Mentions: 2
Published: over 3 years ago

10.1371/journal.pone.0027550

In Vitro Grown Sheep Preantral Follicles Yield Oocytes with Normal Nuclear-Epigenetic Maturation
Cited by: 35
Author(s): Barbara Barboni, Valentina Russo, Sandra Cecconi, Valentina Curini, Alessia Colosimo, Maria Luigia A. Garofalo, Giulia Capacchietti, Oriana Di Giacinto, Mauro Mattioli
Software Mentions: 2
Published: about 13 years ago

10.1371/journal.pone.0027316

Genome-Scale Consequences of Cofactor Balancing in Engineered Pentose Utilization Pathways in Saccharomyces cerevisiae
Cited by: 54
Author(s): Amit Ghosh, Huimin Zhao, Nathan D. Price
Software Mentions: 2
Published: about 13 years ago

10.1371/journal.pone.0148031

Integration and Validation of the Genome-Scale Metabolic Models of Pichia pastoris: A Comprehensive Update of Protein Glycosylation Pathways, Lipid and Energy Metabolism
Cited by: 52
Author(s): Màrius Tomàs-Gamisans, Pau Ferrer, Joan Albiol
Software Mentions: 2
Published: almost 9 years ago

10.1371/journal.pone.0021554

Spherical Harmonics Coefficients for Ligand-Based Virtual Screening of Cyclooxygenase Inhibitors
Cited by: 8
Author(s): Wang Quan, Kerstin Birod, Carlo Angioni, Sabine Grösch, Tim Geppert, Petra Schneider, Matthias Rupp
Software Mentions: 2
Published: over 13 years ago

10.1371/journal.pone.0044858

Gamma Irradiation Does Not Induce Detectable Changes in DNA Methylation Directly following Exposure of Human Cells
Cited by: 32
Author(s): Christoph Lahtz, Steven Bates, Yong Jiang, Arthur X. Li, Xiwei Wu, Maria A. Hahn, Gerd P. Pfeifer
Software Mentions: 2
Published: about 12 years ago

10.1371/journal.pone.0210008

Constraints-based analysis identifies NAD+ recycling through metabolic reprogramming in antibiotic resistant Chromobacterium violaceum
Cited by: 10
Author(s): Deepanwita Banerjee, Anu Raghunathan
Software Mentions: 2
Published: almost 6 years ago

10.1371/journal.pone.0112524

Prediction of Metabolic Flux Distribution from Gene Expression Data Based on the Flux Minimization Principle
Cited by: 42
Author(s): Hyun‐Seob Song, Jaques Reifman, Anders Wallqvist
Software Mentions: 2
Published: about 10 years ago

10.1371/journal.pone.0055137

Construction and Analysis of the Model of Energy Metabolism in E. coli
Cited by: 4
Author(s): Zixiang Xu, Xiao Sun, Jibin Sun
Software Mentions: 2
Published: almost 12 years ago

10.1186/1471-2407-11-223

SIP1 is downregulated in hepatocellular carcinoma by promoter hypermethylation
Cited by: 30
Author(s): Tolga Acun, Emin Öztaş, Tamer Yağcı, Mustafa Cengiz Yakıcıer
Software Mentions: 2
Published: over 13 years ago

10.1371/journal.pone.0049978

Contextualization Procedure and Modeling of Monocyte Specific TLR Signaling
Cited by: 5
Author(s): Maike Kathrin Aurich, Ines Thiele
Software Mentions: 2
Published: almost 12 years ago

10.1371/journal.pgen.1006334

Dnmt3a Is a Haploinsufficient Tumor Suppressor in CD8+ Peripheral T Cell Lymphoma
Cited by: 28
Author(s): Staci L. Haney, G. Michael Upchurch, Jana Opavska, David Klinkebiel, Ryan A. Hlady, Sohini Roy, Samikshan Dutta, Kaustubh Datta, René Opavský
Software Mentions: 2
Published: about 8 years ago

10.1371/journal.pone.0018844

Relationship between Gene Body DNA Methylation and Intragenic H3K9me3 and H3K36me3 Chromatin Marks
Cited by: 127
Author(s): Maria A. Hahn, Xiwei Wu, Arthur X. Li, Torsten Hahn, Gerd P. Pfeifer
Software Mentions: 2
Published: over 13 years ago

10.1371/journal.pgen.1000329

Why Is the Correlation between Gene Importance and Gene Evolutionary Rate So Weak?
Cited by: 76
Author(s): Zhi Wang, Jianzhi Zhang
Software Mentions: 2
Published: almost 16 years ago

10.1186/s12859-016-1240-1

solveME: fast and reliable solution of nonlinear ME models
Cited by: 41
Author(s): Laurence T. Yang, Ding Ma, Ali Ebrahim, Colton J. Lloyd, Michael A. Saunders, Bernhard Ø. Palsson
Software Mentions: 2
Published: about 8 years ago

10.1371/journal.pgen.1003617

Bacterial Adaptation through Loss of Function
Cited by: 192
Author(s): Alison K. Hottes, Peter L. Freddolino, Anupama Khare, Zachary N. Donnell, Julia Liu, Saeed Tavazoie
Software Mentions: 2
Published: over 11 years ago

10.1371/journal.pone.0028730

Quantitative Analysis of miRNA Expression in Seven Human Foetal and Adult Organs
Cited by: 25
Author(s): Yanping Tang, Dong Liu, Lijie Zhang, Sigurður Ingvarsson, Huiping Chen
Software Mentions: 2
Published: almost 13 years ago

10.26508/lsa.202000954

Integrated human/SARS-CoV-2 metabolic models present novel treatment strategies against COVID-19
Cited by: 13
Author(s): Bridget P. Bannerman, Jorge Júlvez, Alexandru Oarga, Tom L. Blundell, Pablo Moreno, Andres Floto
Software Mentions: 2
Published: over 3 years ago

10.1186/1475-2867-5-29

Epigenetic inactivation and aberrant transcription of CSMD1 in squamous cell carcinoma cell lines
Cited by: 29
Author(s): Toni M. Richter, Benton D. Tong, Steven B. Scholnick
Software Mentions: 2
Published: about 19 years ago

10.1371/journal.pone.0013017

Defining Hypo-Methylated Regions of Stem Cell-Specific Promoters in Human iPS Cells Derived from Extra-Embryonic Amnions and Lung Fibroblasts
Cited by: 51
Author(s): Koichiro Nishino, Masashi Toyoda, Mayu Yamazaki-Inoue, Hidenari Makino, Yoshihiro Fukawatase, Emi Chikazawa, Yoriko Takahashi, Yoshitaka Miyagawa, Hajime Okita, Nobutaka Kiyokawa, Hidenori Akutsu, Akihiro Umezawa
Software Mentions: 2
Published: about 14 years ago

10.1186/1752-0509-8-41

Genome-scale metabolic reconstructions of Bifidobacterium adolescentis L2-32 and Faecalibacterium prausnitzii A2-165 and their interaction
Cited by: 82
Author(s): Ibrahim E. Elsemman, Fredrik Karlsson, Saeed Shoaie, Intawat Nookaew, Taysir Hassan A. Soliman, Jens Nielsen
Software Mentions: 2
Published: over 10 years ago

10.3390/md14120225

Algal Cell Factories: Approaches, Applications, and Potentials
Cited by: 61
Author(s): Weiqi Fu, Amphun Chaiboonchoe, Basel Khraiwesh, David R. Nelson, Dina Al-Khairy, Alexandra Mystikou, Amnah Alzahmi, Kourosh Salehi‐Ashtiani
Software Mentions: 2
Published: almost 8 years ago

10.1186/s12885-016-2087-6

The dual specificity phosphatase 2 gene is hypermethylated in human cancer and regulated by epigenetic mechanisms
Cited by: 19
Author(s): Tanja Haag, Antje Richter, Martin Schneider, Adriana P. Jiménez, Reinhard Dammann
Software Mentions: 2
Published: almost 9 years ago

10.1093/bib/bbv100

Towards improved genome-scale metabolic network reconstructions: unification, transcript specificity and beyond
Cited by: 14
Author(s): Thomas Pfau, Maria Pires Pacheco, Thomas Sauter
Software Mentions: 2
Published: almost 9 years ago

10.1186/s12918-017-0427-z

A scalable metabolite supplementation strategy against antibiotic resistant pathogen Chromobacterium violaceum induced by NAD+/NADH+ imbalance
Cited by: 17
Author(s): Deepanwita Banerjee, Dharmeshkumar Parmar, Nivedita Bhattacharya, Avinash D. Ghanate, Venkateswarlu Panchagnula, Anu Raghunathan
Software Mentions: 2
Published: over 7 years ago

10.1186/bcr2233

Methylation of homeobox genes is a frequent and early epigenetic event in breast cancer
Cited by: 133
Author(s): Stefania Tommasi, Deborah L Karm, Xiwei Wu, Yun Yen, Gerd P. Pfeifer
Software Mentions: 2
Published: over 15 years ago

10.1371/journal.pcbi.1003126

Reconstruction and Validation of a Genome-Scale Metabolic Model for the Filamentous Fungus Neurospora crassa Using FARM
Cited by: 57
Author(s): Jonathan M. Dreyfuss, Jeremy Zucker, Heather M. Hood, Linda R. Ocasio, Matthew S. Sachs, James E. Galagan
Software Mentions: 2
Published: over 11 years ago

10.1186/1752-0509-6-71

i AK692: A genome-scale metabolic model of Spirulina platensis C1
Cited by: 35
Author(s): Amornpan Klanchui, Chiraphan Khannapho, Atchara Phodee, Supapon Cheevadhanarak, Asawin Meechai
Software Mentions: 2
Published: over 12 years ago

10.1371/journal.pcbi.1007185

Assessing key decisions for transcriptomic data integration in biochemical networks
Cited by: 48
Author(s): Anne Richelle, Chintan Joshi, Nathan E. Lewis
Software Mentions: 2
Published: over 5 years ago

10.1371/journal.pcbi.1004363

A Method to Constrain Genome-Scale Models with 13C Labeling Data
Cited by: 51
Author(s): Héctor García Martín, Vinay Satish Kumar, Daniel Weaver, Amit Ghosh, Victor Chubukov, Aindrila Mukhopadhyay, Adam P. Arkin, Jay D. Keasling
Software Mentions: 2
Published: about 9 years ago

10.1371/journal.pcbi.1005895

Functional interrogation of Plasmodium genus metabolism identifies species- and stage-specific differences in nutrient essentiality and drug targeting
Cited by: 24
Author(s): Alyaa M. Abdel-Haleem, Hooman Hefzi, Katsuhiko Mineta, Xin Gao, Takashi Gojobori, Jaehyung Kim, Nathan E. Lewis, Neema Jamshidi
Software Mentions: 2
Published: almost 7 years ago

10.1371/journal.pone.0154216

Phylogenetic and Epigenetic Footprinting of the Putative Enhancers of the Peg3 Domain
Cited by: 6
Author(s): Joomyeong Kim, An Ye
Software Mentions: 2
Published: over 8 years ago

10.3390/metabo8040084

An Improved Genome-Scale Metabolic Model of Arthrospira platensis C1 (iAK888) and Its Application in Glycogen Overproduction
Cited by: 12
Author(s): Amornpan Klanchui, Sudarat Dulsawat, Kullapat Chaloemngam, Supapon Cheevadhanarak, Peerada Prommeenate, Asawin Meechai
Software Mentions: 2
Published: almost 6 years ago

10.1186/1752-0509-6-94

MicrobesFlux: a web platform for drafting metabolic models from the KEGG database
Cited by: 48
Author(s): Xueyang Feng, Yingcheng Xu, Yixin Chen, Yinjie J. Tang
Software Mentions: 2
Published: almost 13 years ago

10.1371/journal.pcbi.1004924

EGFR Signal-Network Reconstruction Demonstrates Metabolic Crosstalk in EMT
Cited by: 40
Author(s): Kumari Sonal Choudhary, Neha Rohatgi, Skarphéđinn Halldórsson, Eiríkur Briem, Thorarinn Gudjonsson, Steinn Guðmundsson, Óttar Rolfsson
Software Mentions: 2
Published: over 8 years ago

10.1186/s12896-021-00675-w

Genome-scale model reconstruction of the methylotrophic yeast Ogataea polymorpha
Cited by: 3
Author(s): Ulf W. Liebal, Brigida A. Fabry, Aarthi Ravikrishnan, Constantin V. l. Schedel, Simone Schmitz, Lars M. Blank, Birgitta E. Ebert
Software Mentions: 2
Published: over 3 years ago

10.1371/journal.pcbi.1000312

Genome-Scale Reconstruction of Escherichia coli's Transcriptional and Translational Machinery: A Knowledge Base, Its Mathematical Formulation, and Its Functional Characterization
Cited by: 167
Author(s): Ines Thiele, Neema Jamshidi, Ronan M. T. Fleming, Bernhard Ø. Palsson
Software Mentions: 2
Published: over 15 years ago

10.1371/journal.pcbi.1007646

Providing new insights on the biphasic lifestyle of the predatory bacterium Bdellovibrio bacteriovorus through genome-scale metabolic modeling
Cited by: 8
Author(s): Cristina Herencias, S. Salgado-Briegas, María Auxiliadora Prieto, Juan Nogales
Software Mentions: 2
Published: about 4 years ago

10.1155/2019/8304260

Human Systems Biology and Metabolic Modelling: A Review—From Disease Metabolism to Precision Medicine
Cited by: 53
Author(s): Claudio Angione
Software Mentions: 2
Published: over 5 years ago

10.1186/s12915-019-0669-x

Studying metabolic flux adaptations in cancer through integrated experimental-computational approaches
Cited by: 18
Author(s): Shoval Lagziel, Won Dong Lee, Tomer Shlomi
Software Mentions: 2
Published: over 5 years ago

10.1371/journal.pcbi.1007694

Physicochemical and metabolic constraints for thermodynamics-based stoichiometric modelling under mesophilic growth conditions
Cited by: 5
Author(s): Claudio Tomi-Andrino, Rupert Norman, Thomas Millat, Philippe Soucaille, Klaus Winzer, David A. Barrett, John R. King, Dong-Hyun Kim
Software Mentions: 2
Published: almost 4 years ago

10.1371/journal.pone.0102319

Multi-Tissue Computational Modeling Analyzes Pathophysiology of Type 2 Diabetes in MKR Mice
Cited by: 15
Author(s): Amit Kumar, Thomas F. Harrelson, Nathan E. Lewis, Emily J. Gallagher, Joseph Shiloach, Michael J. Betenbaugh
Software Mentions: 2
Published: over 10 years ago

10.1186/s12859-014-0420-0

An integrated network visualization framework towards metabolic engineering applications
Cited by: 6
Author(s): Alberto Noronha, Paulo Vilaça, Miguel Rocha
Software Mentions: 2
Published: almost 10 years ago

10.1111/1751-7915.13612

Are synthetic biology standards applicable in everyday research practice?
Cited by: 8
Author(s): Hüseyin Tas, Adam Amara, Miguel Cueva, Nadine Bongaerts, Alicia Calvo‐Villamañán, Samir Hamadache, Konstantinos Vavitsas
Software Mentions: 2
Published: over 4 years ago

10.1111/1751-7915.12871

Fine‐tuning the <i>P. pastoris</i> iMT1026 genome‐scale metabolic model for improved prediction of growth on methanol or glycerol as sole carbon sources
Cited by: 46
Author(s): Màrius Tomàs-Gamisans, Pau Ferrer, Joan Albiol
Software Mentions: 2
Published: about 7 years ago

10.1186/s12934-018-1052-2

Integration of enzymatic data in Bacillus subtilis genome-scale metabolic model improves phenotype predictions and enables in silico design of poly-γ-glutamic acid production strains
Cited by: 51
Author(s): Ilaria Massaiu, Lorenzo Pasotti, Nikolaus Sonnenschein, Erlinda Rama, Matteo Cavaletti, Paolo Magni, Cinzia Calvio, Markus J. Herrgård
Software Mentions: 2
Published: almost 6 years ago

10.1186/s12918-015-0159-x

Genome-scale resources for Thermoanaerobacterium saccharolyticum
Cited by: 22
Author(s): Devin H. Currie, Babu Raman, Christopher M. Gowen, Timothy J. Tschaplinski, Miriam Land, Steven D. Brown, Sean F. Covalla, Dawn M. Klingeman, Zamin K. Yang, Nancy L. Engle, C. M. Johnson, Miguel Rodríguez, Aubie Shaw, William R. Kenealy, Lee R. Lynd, Stephen S. Fong, Jonathan R. Mielenz, Brian H. Davison, David A. Hogsett, Christopher D. Herring
Software Mentions: 2
Published: over 9 years ago

10.1186/s13223-017-0198-5

Abstracts from the 10th C1-inhibitor deficiency workshop
Cited by: 5
Author(s): Alvin H. Schmaier, Marco Cicardi, Avner Reshef, Dumitru Moldovan, Attila Mócsai, Margarita López‐Trascasa, Alberto López-Lera, Nancy J. Brown, Anastasios E. Germenis, Rafael Filippelli-Silva, Diego Andreazzi Duarte, Renan Paulo Martin, Camila Lopes Veronez, Michel Bouvier, Michael Bäder, Claudio M. Costa‐Neto, João Bosco Pesquero, Xavier Charest‐Morin, François Marceau, GeorgesE. Rivard, Arnaud Bonnefoy, Éric Wagner, Márta L. Debreczeni, Zsuzsanna Németh, Erika Kajdácsi, Endre Schwaner, László Cervenák, Gábor Oroszlán, András Szilágyi, Ráhel Dani, Péter Závodszky, Péter Gál, József Dobó, Jacques Hébert, Matthieu Robert de Saint Vincent, Jean-Nicolas Boursiquot, Hugo Chapdeleine, Marylin Desjardins, Benoît Laramée, Rémi Gagnon, Nancy Payette, Oleksandra Lepeshkina, Delphine Charignon, Arije Ghannam, D. Ponard, Christian Drouet, Kusumam Joseph, Baby G. Tholanikunnel, Daniel J. Sexton, Allen P. Kaplan, Stefania Loffredo, María Bova, Anne Lise Ferrara, Angelica Petraroli, Chiara Suffritti, Nóra Veszeli, Andrea Zanichelli, Henriette Farkas, Gianni Marone, Samuel Luyasu, Bertrand Favier, Ludovic Martin, Kinga Viktória Kőhalmi, György Temesszentandrási, Katalin Várnai, Bruce L. Zuraw, Annette Feussner, Michael A. Tortorici, Dipti Pawaskar, Huamin Henry Li, John A. Anderson, Jonathan A. Bernstein, Ying Zhang, Ingo Pragst, Emel Aygören‐Pürsün, Kraig W. Jacobson, J. Fischer Christensen, Arthur Van Leerberghe, Yi Wang, Jennifer Schranz, Inmaculada Martinez‐Saguer, D. Soteres, Urs Steiner, Vesna Grivcheva Panovska, William Rae, Werner Aberer, Aarnoud Huissoon, Anette Bygum, Markus Magerl, Jochen Graff, Hilary Longhurst, Ramón Lleonart, Lei Fang, Melanie Cornpropst, D. Clemons, Amanda Mathis, Phil Collis, Sylvia Dobo, William Sheridan, Marcus Maurer, Marc A. Riedl, Timothy J. Craig, Aleena Banerji, Mustafa M. Shennak, William H. Yang, Jovanna Baptista, Paula J. Busse, Ira N. Kalfus, Andrew McDonald, Shawn Qian, Anthony Roberts, Con Panousis, Tim Green, Andreas Gille, Μαρία Ζαμανάκου, Gedeon Loules, Fotis Psarros, Faidra Parsopoulou, Matthaios Speletas, Davide Firinu, Tiziana Maria Angela De Pasquale, Alessandra Zoli, Anna Radice, Stefano Pizzimenti, E. Manoussakis, George N. Konstantinou, Valeria Bafunno, Vincenzo Montinaro, Mauro Cancian, Maurizio Margaglione, Konrad Bork, K. Wulff, Guenther Witzke, Jochen Hardt, Laurence Bouillet, Teresa Caballero, Anete Sevciovic Grumach, Christelle Pommie, Irmgard Andresen, Carmen Escuriola Ettingshausen, Zeynep Gutowski, K. Andritschke, R. Linde, Noémi Andrási, T Szilágyi, Iris Leibovich‐Nassi, Christine Symons, John Dempster, Isabelle Boccon‐Gibod, Anne Pagnier, Audrey Lehmann, Kristian Buur Kreiberg, Sandra A. Nieto, Raquel Martins, Renata Martins, Alejandra Menendez, Solange Oliveira Rodrigues Valle, Margarita Olivares, Maria E. Hernandez-Landeros, Elma Nievas, Natalia Lorena Fili, Olga M Barrera, René Bailleau, Ana Maria Gallardo-Olivos, Masumi Grau, Julian Rodriguez-Galindo, Marlon J. O. Carabantes, Edison Zapata-Venegas, Mario Martinez Alfonso, Maria Rosario-Grauert, Manuel Ratti, Daniel Vaszquez, Dario Josviack, Luis Fernando Landivar-Salinas, Oscar M. E. Calderón-Llosa, Rolando Campilay-Sarmiento, Pablo Raby, J E Fabiani, William R. Lumry, Henrike Feuersenger, Douglas J. Watson, Thomas Machnig, Donatella Lamacchia, Adriana Hernanz, Ana Alvez, Mariana Lluncor, María Pedrosa, Rosario Cabañas, Nieves Prior, Patrik Nordenfelt, Mats Nilsson, Anders Lindfors, Carl-Fredrik Wahlgren, Janne Björkander, Roman Hakl, Pavel Kuklı́nek, Irena Krčmová, Jana Hanzlı́ková, Martina Vachová, Radana Zachová, Marta Sobotková, Jana Strenková, Jiří Litzman, Maria Palasopoulou, Gerasimina Tsinti, Panagiota Gianni, Maria Kompoti, Sofía Garrido, Wojciech Dyga, Anna Bogdali, Aleksander Obtułowicz, Mikolajczyk Tomasz, Ewa Czarnobilska, Krystyna Obtułowicz, Teofila Książek, Anna Koncz, Dominik Gulyás, Maria Staevska, Miloš Jeseňák, K Hrubiskovã, L. Bellizzi, Anukampa Relan, Maddalena Alessandra Wu, Antonio Castelli, Riccardo Colombo, Gianmarco Podda, Marta Del Medico, E Catena, Francesco Casella, Francesca Perego, Nada Afifi Afifi, Eleonora Tobaldini, Nicola Montano, Marta Sánchez‐Jareño, Marcin Stobiecki, Irina Guryanova, Ekaterina Polyakova, Viktar Lebedz, А. П. Саливончик, Svetlana Aleshkevich, Mikhail Belevtsev, Melanie Nordmann-Kleiner, Susanne Trainotti, Janina Hahn, Jens Greve, Liudmyla Zabrodska, Maria Luiza Oliva Alonso, Rosângela Prendin Tórtora, Alfeu Tavares França, Márcia Gonçalves Ribeiro, Lisa Fu, Amin Kanani, Gina Lacuesta, Susan Waserman, Stephen Betschel, Melissa I. Espinosa, Francisco A. Contreras, M Hrubiško, Ľudmila Vavrová, Peter Bánovčin, Maryam Ayazi, Mohammad Reza Fazlollahi, Shiva Saghafi, Sajedeh Mohammadian, Susan Nabilou Deshiry, Kiana Bidad, Raheleh Shokouhi Shoormasti, Iraj Mohammadzadeh, Mohammad Hassan Bemanian, Seyed Alireza Mahdaviani, Zahra Pourpak, Anna Valerieva, Mariela Vasileva, Tsvetelina Velikova, Elena Petkova, Vasil Dimitrov, Ruggero Di Maulo, Raz Somech, Hava Golander, Erika J. Sifuentes, C. Mansard, Anne Gompel, Bernard Floccard, Claire Blanchard-Delaunay, David Launay, Olivier Fain, Alain Sobel, S. Gayet, S. Amarger, G. Armengol, Yann Ollivier, Ariane Zélinsky-Gurung, Pierre-Yves Jeandel, G. Kanny, B. Coppéré, Marie Dubrel, F. Pelletier, Aurélie Du‐Thanh, Sébastien Trouiller, J. Laurent, Claire de Moreuil, C. Pajot, Alexandre Belot, Ana Rodríguez, Dasha Roa, Alicia Prieto, M.L. Baeza, Borislava Krusheva, Stephanie K. A. Almeida, Rosemeire Navickas Constantino-Silva, Nyla Melo, Joanna Araujo Simoes, Sandra Palma, Jane da Silva, Bruna Franca Azevedo, Eli Mansour, Teresa González-Quevedo, Carmen Marcos, T Lobera, B. Sáenz de San Pedro, Ernie Avilla, Jacquie Badiou, Karen Binkley, Rozita Borici-Mazi, Linda Howlett, Paul K. Keith, Anne Rowe, Peter D. Waite, Aurore Billebeau, Isabelle Boccon-Gibbod, Kristina Lis, Yael Laitman, Eitan Friedman, Nihal Mete Gökmen, Okan Gülbahar, Hüseyin Önay, Zeynep Koç, Aytül Sin
Software Mentions: 2
Published: over 7 years ago

Projects: cran: COBRA

Papers Mentioning COBRA 629