Ecosyste.ms: Papers

An open API service providing mapping between scientific papers and software projects that are mentioned in them.
All mentions data is based on the CZI Software Mentions dataset.

Projects: cran: COBRA

https://packages.ecosyste.ms/registries/cran.r-project.org/packages/COBRA

Nonlinear Aggregation of Predictors
5 versions
Latest release: over 11 years ago
0 downloads

Papers Mentioning COBRA 629

10.1016/j.xpro.2021.100837
Protocol for hybrid flux balance, statistical, and machine learning analysis of multi-omic data from the cyanobacterium Synechococcus sp. PCC 7002
Cited by: 3
Author(s): Supreeta Vijayakumar, Claudio Angione
Software Mentions: 13
Published: almost 3 years ago
10.1186/s40425-019-0764-0
34th Annual Meeting & Pre-Conference Programs of the Society for Immunotherapy of Cancer (SITC 2019): part 2
Cited by: 28
Author(s):
Software Mentions: 12
Published: about 5 years ago
10.1038/s41598-018-33733-z
Human gut microbe co-cultures have greater potential than monocultures for food waste remediation to commodity chemicals
Cited by: 14
Author(s): Matthew Perisin, Christian Sund
Software Mentions: 9
Published: about 6 years ago
10.1038/s41598-018-29378-7
Epigenetic and transcriptional dysregulation of VWA2 associated with a MYC-driven oncogenic program in colorectal cancer
Cited by: 7
Author(s): Beatríz González, Ferran Fece de la Cruz, Johanna Samuelsson, Andreu Alibés, Sergio Alonso
Software Mentions: 8
Published: over 6 years ago
10.1371/journal.pone.0211692
The impact of bipedal mechanical loading history on longitudinal long bone growth
Cited by: 7
Author(s): A. D. Foster
Software Mentions: 7
Published: almost 6 years ago
10.1371/journal.pone.0236890
Defining the nutritional input for genome-scale metabolic models: A roadmap
Cited by: 21
Author(s): Γεώργιος Μαρίνος, Christoph Kaleta, Silvio Waschina
Software Mentions: 7
Published: over 4 years ago
10.1002/1873-3468.14180
Genome‐scale metabolic modelling of SARS‐CoV‐2 in cancer cells reveals an increased shift to glycolytic energy production
Cited by: 13
Author(s): Elisabeth Yaneske, Guido Zampieri, Loris Bertoldi, Giuseppe Benvenuto, Claudio Angione
Software Mentions: 7
Published: about 3 years ago
10.1371/journal.pone.0119016
Using Bioconductor Package BiGGR for Metabolic Flux Estimation Based on Gene Expression Changes in Brain
Cited by: 17
Author(s): Anand Gavai, Farahaniza Supandi, Hannes Hettling, Paul Murrell, Jack A. M. Leunissen, Hans van Beek
Software Mentions: 7
Published: over 9 years ago
10.3390/metabo10030088
Analysis and Simulation of Glioblastoma Cell Lines-Derived Extracellular Vesicles Metabolome
Cited by: 25
Author(s): Miroslava Čuperlović-Culf, Nam Huan Khieu, Anuradha Surendra, Melissa Hewitt, Claudie Charlebois, Jagdeep K. Sandhu
Software Mentions: 6
Published: over 4 years ago
10.1155/2014/649453
Computational Approaches for Microalgal Biofuel Optimization: A Review
Cited by: 21
Author(s): Joseph Koussa, Amphun Chaiboonchoe, Kourosh Salehi‐Ashtiani
Software Mentions: 6
Published: almost 11 years ago
10.3389/fbioe.2014.00061
Improving Collaboration by Standardization Efforts in Systems Biology
Cited by: 49
Author(s): Andreas Dräger, Bernhard Ø. Palsson
Software Mentions: 6
Published: almost 10 years ago
10.7554/eLife.50069
Metabolic stress is a primary pathogenic event in transgenic Caenorhabditis elegans expressing pan-neuronal human amyloid beta
Cited by: 49
Author(s): Emelyne Teo, Sudharshan Ravi, Diogo Barardo, Hyung-Seok Kim, Sheng Fong, Amaury Cazenave-Gassiot, Tsze Yin Tan, Jianhong Ching, Jean‐Paul Kovalik, Markus R. Wenk, Rudiyanto Gunawan, Philip K. Moore, Barry Halliwell, Nicholas S. Tolwinski, Jan Gruber
Software Mentions: 6
Published: about 5 years ago
10.1186/s40168-019-0689-3
Systematic assessment of secondary bile acid metabolism in gut microbes reveals distinct metabolic capabilities in inflammatory bowel disease
Cited by: 184
Author(s): Almut Heinken, Dmitry A. Ravcheev, Federico Baldini, Laurent Heirendt, Ronan M. T. Fleming, Ines Thiele
Software Mentions: 6
Published: over 5 years ago
10.1186/s13578-019-0334-7
The metabolic network model of primed/naive human embryonic stem cells underlines the importance of oxidation-reduction potential and tryptophan metabolism in primed pluripotency
Cited by: 6
Author(s): Meisam Yousefi, Sayed-Amir Marashi, Ali Sharifi‐Zarchi, Sara Taleahmad
Software Mentions: 6
Published: about 5 years ago
10.1186/s12859-019-2615-x
ModelExplorer - software for visual inspection and inconsistency correction of genome-scale metabolic reconstructions
Cited by: 10
Author(s): Nikolay Martyushenko, Eivind Almaas
Software Mentions: 5
Published: almost 6 years ago
10.7717/peerj.6046
In silico engineering of<i>Pseudomonas</i>metabolism reveals new biomarkers for increased biosurfactant production
Cited by: 16
Author(s): Annalisa Occhipinti, Filmon Eyassu, Thahira Rahman, Pattanathu Rahman, Claudio Angione
Software Mentions: 5
Published: almost 6 years ago
10.1371/journal.pcbi.1007786
Minimizing the number of optimizations for efficient community dynamic flux balance analysis
Cited by: 12
Author(s): James D. Brunner, Nicholas Chia
Software Mentions: 5
Published: about 4 years ago
10.3390/metabo10020066
EFMviz: A COBRA Toolbox Extension to Visualize Elementary Flux Modes in Genome-Scale Metabolic Models
Cited by: 6
Author(s): Chaitra Sarathy, Martina Kutmon, Michael Lenz, Michiel E. Adriaens, Chris T. Evelo, Ilja C. W. Arts
Software Mentions: 5
Published: almost 5 years ago
10.1093/bioinformatics/btz088
Gsmodutils: a python based framework for test-driven genome scale metabolic model development
Cited by: 2
Author(s): James P. Gilbert, Nicole Pearcy, Rupert Norman, Thomas Millat, Klaus Winzer, John R. King, Charlie Hodgman, Nigel P. Minton, Jamie Twycross
Software Mentions: 5
Published: almost 6 years ago
10.3390/metabo9020022
Metabolic Modeling of Human Gut Microbiota on a Genome Scale: An Overview
Cited by: 65
Author(s): Partho Sen, Matej Orešič
Software Mentions: 5
Published: almost 6 years ago
10.7554/eLife.04530
The long non-coding RNA Dali is an epigenetic regulator of neural differentiation
Cited by: 142
Author(s): Vladislava Chalei, Stephen N. Sansom, Lesheng Kong, Sheena Lee, Juan Montiel, Keith W. Vance, Chris P. Ponting
Software Mentions: 5
Published: about 10 years ago
10.1371/journal.pcbi.1007764
StanDep: Capturing transcriptomic variability improves context-specific metabolic models
Cited by: 19
Author(s): Chintan Joshi, Song‐Min Schinn, Anne Richelle, Isaac Shamie, Eyleen J. O’Rourke, Nathan E. Lewis
Software Mentions: 5
Published: over 4 years ago
10.1186/s12918-014-0130-2
MetaNET - a web-accessible interactive platform for biological metabolic network analysis
Cited by: 8
Author(s): Pankaj Narang, Shawez Khan, Anmol Jaywant Hemrom, Andrew M. Lynn
Software Mentions: 5
Published: almost 10 years ago
10.3390/metabo11010020
Identifying Personalized Metabolic Signatures in Breast Cancer
Cited by: 8
Author(s): Priyanka Baloni, Wikum Dinalankara, John C. Earls, Theo Knijnenburg, Donald Geman, Luigi Marchionni, Nathan D. Price
Software Mentions: 5
Published: almost 4 years ago
10.1371/journal.pcbi.1004732
PSAMM: A Portable System for the Analysis of Metabolic Models
Cited by: 35
Author(s): Jon Lund Steffensen, Keith Dufault‐Thompson, Ying Zhang
Software Mentions: 5
Published: almost 9 years ago
10.1128/mSystems.00579-19
Defining and Evaluating Microbial Contributions to Metabolite Variation in Microbiome-Metabolome Association Studies
Cited by: 48
Author(s): Cecilia Noecker, Hsuan-Chao Chiu, Christopher A. McNally, Elhanan Borenstein
Software Mentions: 5
Published: almost 5 years ago
10.1111/pbi.12926
Genome and evolution of the shade‐requiring medicinal herb <i>Panax ginseng</i>
Cited by: 120
Author(s): Nam Hoon Kim, Murukarthick Jayakodi, Sang Choon Lee, Beom Soon Choi, Woojong Jang, Junki Lee, Hyun Hee Kim, Nomar Espinosa Waminal, Meiyappan Lakshmanan, Binh van Nguyen, Yun Sun Lee, Hyun Seung Park, Hyun Jo Koo, Jee Young Park, Sampath Perumal, Ho Jun Joh, Hana Lee, Jin‐Kyung Kim, In Seo Kim, Kyung‐Hee Kim, Lokanand Koduru, Kyo Bin Kang, Sang Hyun Sung, Yeisoo Yu, Daniel Park, Doil Choi, Eun-Young Seo, Seungill Kim, Young Chang Kim, Dong Yun Hyun, Youn‐Il Park, Chang-Soo Kim, Tae Ho Lee, Hyun Uk Kim, Moon-Soo Soh, Liu Yi, Jun Gyo In, Heui-Soo Kim, Yong Min Kim, Deok Chun Yang, Rod A. Wing, Dong-Yup Lee, Andrew H. Paterson, Tae Jin Yang
Software Mentions: 5
Published: over 6 years ago
10.1111/febs.15292
Fibroblast‐specific genome‐scale modelling predicts an imbalance in amino acid metabolism in Refsum disease
Cited by: 4
Author(s): Agnieszka B. Wegrzyn, Katharina Herzog, Albert Gerding, Marcel Kwiatkowski, Justina C. Wolters, Amalia M. Dolga, A. E. M. van Lint, Ronald J. A. Wanders, Hans R. Waterham, Barbara M. Bakker
Software Mentions: 5
Published: over 4 years ago
10.1186/s13068-020-01838-1
Genome-scale metabolic modeling underscores the potential of Cutaneotrichosporon oleaginosus ATCC 20509 as a cell factory for biofuel production
Cited by: 16
Author(s): Nhung Pham, Maarten J.M.F. Reijnders, María Suárez-Diez, Bart Nijsse, Jan Springer, Gerrit Eggink, Peter J. Schaap
Software Mentions: 5
Published: almost 4 years ago
10.1186/s12859-020-03711-2
VFFVA: dynamic load balancing enables large-scale flux variability analysis
Cited by: 6
Author(s): Marouen Ben Guebila
Software Mentions: 4
Published: about 4 years ago
10.3389/fphys.2016.00327
MetaboTools: A Comprehensive Toolbox for Analysis of Genome-Scale Metabolic Models
Cited by: 37
Author(s): Maike Kathrin Aurich, Ronan M. T. Fleming, Ines Thiele
Software Mentions: 4
Published: over 8 years ago
10.3389/fmicb.2020.00393
The Computational Diet: A Review of Computational Methods Across Diet, Microbiome, and Health
Cited by: 30
Author(s): Ameen Eetemadi, Navneet Rai, Beatriz Merchel Piovesan Pereira, Minseung Kim, Harold H. Schmitz, Ilias Tagkopoulos
Software Mentions: 4
Published: over 4 years ago
10.1186/s12859-020-3410-4
FastMM: an efficient toolbox for personalized constraint-based metabolic modeling
Cited by: 6
Author(s): Gong‐Hua Li, Shao‐Xing Dai, Feifei Han, Weihua Li, Jing‐Fei Huang, Wenzhong Xiao
Software Mentions: 4
Published: over 4 years ago
10.1128/mSphere.00245-21
Collateral Sensitivity to β-Lactam Drugs in Drug-Resistant Tuberculosis Is Driven by the Transcriptional Wiring of BlaI Operon Genes
Cited by: 2
Author(s): Anna S Trigos, Benjamin Goudey, Justin Bedő, Thomas Conway, Noel Faux, Kelly L. Wyres
Software Mentions: 4
Published: over 3 years ago
10.1186/1471-2105-11-213
BiGG: a Biochemical Genetic and Genomic knowledgebase of large scale metabolic reconstructions
Cited by: 505
Author(s): Jan Schellenberger, Junyoung O. Park, Tom M Conrad, Bernhard Ø. Palsson
Software Mentions: 4
Published: over 14 years ago
10.1186/s13040-014-0028-y
Synthetic learning machines
Cited by: 22
Author(s): Hemant Ishwaran, James D. Malley
Software Mentions: 4
Published: almost 10 years ago
10.1155/2013/187509
Reconstruction and Analysis of Human Kidney-Specific Metabolic Network Based on Omics Data
Cited by: 8
Author(s): Ai-Di Zhang, Shao‐Xing Dai, Jing‐Fei Huang
Software Mentions: 4
Published: almost 12 years ago
10.1186/s12859-017-1615-y
The JBEI quantitative metabolic modeling library (jQMM): a python library for modeling microbial metabolism
Cited by: 16
Author(s): Garrett W. Birkel, Amit Ghosh, Vinay Satish Kumar, Daniel Weaver, David Ando, Tyler W. H. Backman, Adam P. Arkin, Jay D. Keasling, Héctor García Martín
Software Mentions: 4
Published: over 7 years ago
10.1186/s12915-020-00775-7
Parkinson’s disease-associated alterations of the gut microbiome predict disease-relevant changes in metabolic functions
Cited by: 114
Author(s): Federico Baldini, Johannes Hertel, Estelle Sandt, Cyrille C. Thinnes, Lorieza Neuberger-Castillo, Lukas Pavelka, Fay Betsou, Rejko Krüger, Ines Thiele
Software Mentions: 4
Published: over 4 years ago
10.1371/journal.pone.0235393
A comparison of Monte Carlo sampling methods for metabolic network models
Cited by: 28
Author(s): Shirin Fallahi, Hans J. Skaug, Guttorm Alendal
Software Mentions: 4
Published: over 4 years ago
10.1371/journal.pcbi.1005544
BacArena: Individual-based metabolic modeling of heterogeneous microbes in complex communities
Cited by: 173
Author(s): Eugen Bauer, Johannes Zimmermann, Federico Baldini, Ines Thiele, Christoph Kaleta
Software Mentions: 4
Published: over 7 years ago
10.1186/s12918-018-0542-5
Genome-scale model-driven strain design for dicarboxylic acid production in Yarrowia lipolytica
Cited by: 51
Author(s): Pramod Kumar Mishra, Na-Rae Lee, Meiyappan Lakshmanan, Minsuk Kim, Byung‐Gee Kim, Dong-Yup Lee
Software Mentions: 4
Published: over 6 years ago
10.1371/journal.pcbi.1005698
A systems approach reveals distinct metabolic strategies among the NCI-60 cancer cell lines
Cited by: 19
Author(s): Maike Kathrin Aurich, Ronan M. T. Fleming, Ines Thiele
Software Mentions: 4
Published: over 7 years ago
10.1371/journal.pcbi.1003424
Fast Reconstruction of Compact Context-Specific Metabolic Network Models
Cited by: 200
Author(s): Nikos Vlassis, Maria Pires Pacheco, Thomas Sauter
Software Mentions: 4
Published: almost 11 years ago
10.1371/journal.pcbi.1008208
MASSpy: Building, simulating, and visualizing dynamic biological models in Python using mass action kinetics
Cited by: 14
Author(s): Zachary B. Haiman, Daniel C. Zielinski, Yuko Koike, James T. Yurkovich, Jaehyung Kim
Software Mentions: 4
Published: almost 4 years ago
10.1371/journal.pcbi.1007847
Medusa: Software to build and analyze ensembles of genome-scale metabolic network reconstructions
Cited by: 18
Author(s): Gregory L. Medlock, Thomas J. Moutinho, Jason A. Papin
Software Mentions: 4
Published: over 4 years ago
10.1186/s12859-018-2472-z
Automated generation of genome-scale metabolic draft reconstructions based on KEGG
Cited by: 55
Author(s): Emil Karlsen, Christian Schulz, Eivind Almaas
Software Mentions: 4
Published: almost 6 years ago
10.1002/bit.26380
Metabolic modeling to identify engineering targets forKomagataella phaffii: The effect of biomass composition on gene target identification
Cited by: 13
Author(s): Ayca Cankorur-Cetinkaya, Duygu Dikicioglu, Stephen G. Oliver
Software Mentions: 4
Published: over 7 years ago
10.1038/s41598-020-62130-8
Genome-scale metabolic models of Microbacterium species isolated from a high altitude desert environment
Cited by: 14
Author(s): Dinka Mandaković, Ángela Cintolesi, Jonathan Maldonado, Sebastián N. Mendoza, Méziane Aïte, Alexis Gaete, Francisco Saitua, Miguel L. Allende, Verónica Cambiazo, Anne Siegel, Alejandro Maass, Maurício González, Mauricio Latorre
Software Mentions: 3
Published: over 4 years ago
10.1038/s41598-018-37442-5
Wnt/β-catenin signaling pathway safeguards epigenetic stability and homeostasis of mouse embryonic stem cells
Cited by: 28
Author(s): Ilda Theka, Francesco Sottile, Marco Cammisa, Sarah Bonnin, Marta Sánchez-Delgado, Umberto Di Vicino, Maria Victoria Neguembor, Karthik Arumugam, Francesco Aulicino, David Gabriel Monk, Andrea Riccio, María Pía Cosma
Software Mentions: 3
Published: almost 6 years ago
10.1038/s41598-020-63235-w
iMM1865: A New Reconstruction of Mouse Genome-Scale Metabolic Model
Cited by: 15
Author(s): Saeideh Khodaee, Yazdan Asgari, Mehdi Totonchi, Mohammad Hossein Karimi‐Jafari
Software Mentions: 3
Published: over 4 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
10.3390/microorganisms8111793
Genome-Scale Metabolic Modeling Reveals Metabolic Alterations of Multidrug-Resistant Acinetobacter baumannii in a Murine Bloodstream Infection Model
Cited by: 10
Author(s): Jinxin Zhao, Yan Zhu, Ji-Ru Han, Yu Wei Lin, Michael Aichem, Jiping Wang, Ke Chen, Tony Velkov, Falk Schreiber, Jian Li
Software Mentions: 3
Published: about 4 years ago
10.1128/mBio.00454-19
Metabolic Model of the <i>Phytophthora infestans</i> -Tomato Interaction Reveals Metabolic Switches during Host Colonization
Cited by: 19
Author(s): Sander Y.A. Rodenburg, Michael Seidl, Howard S. Judelson, A. L. Vu, F. Govers, Dick de Ridder
Software Mentions: 3
Published: about 5 years ago
10.3389/fmolb.2020.591406
ReCodLiver0.9: Overcoming Challenges in Genome-Scale Metabolic Reconstruction of a Non-model Species
Cited by: 9
Author(s): Eileen Marie Hanna, Xiaokang Zhang, Marta Eide, Shirin Fallahi, Tomasz Furmanek, Fekadu Yadetie, Daniel C. Zielinski, Anders Goksøyr, Inge Jonassen
Software Mentions: 3
Published: almost 4 years ago
10.3389/fgene.2020.00837
Genome-Scale Metabolic Model of Xanthomonas phaseoli pv. manihotis: An Approach to Elucidate Pathogenicity at the Metabolic Level
Cited by: 5
Author(s): David Botero, Jonathan M. Monk, María Juliana Rodríguez Cubillos, Andrés Rodríguez Cubillos, Mariana Restrepo, Vivian Bernal-Galeano, Alejandro Reyes, Andrés Barrios, Bernhard Ø. Palsson, Silvia Restrepo, Adriana Bernal
Software Mentions: 3
Published: over 4 years ago
10.3389/fgene.2021.633073
In silico Design for Systems-Based Metabolic Engineering for the Bioconversion of Valuable Compounds From Industrial By-Products
Cited by: 2
Author(s): Albert Enrique Tafur Rangel, Wendy Ríos, Daisy Mejía, Carmen Ojeda, Richard A. Carlson, Jorge M. Gómez, Andrés Fernando González Barrios
Software Mentions: 3
Published: over 3 years ago
10.3389/fgene.2014.00319
Bioremediation in marine ecosystems: a computational study combining ecological modeling and flux balance analysis
Cited by: 11
Author(s): Marianna Taffi, Nicola Paoletti, Claudio Angione, Sandra Pucciarelli, Mauro Marini, Píetro Lió
Software Mentions: 3
Published: about 10 years ago
10.1016/j.molcel.2018.01.034
NADH Shuttling Couples Cytosolic Reductive Carboxylation of Glutamine with Glycolysis in Cells with Mitochondrial Dysfunction
Cited by: 157
Author(s): Edoardo Gaude, Christina Schmidt, Payam A. Gammage, Aurélien Dugourd, Thomas S. Blacker, Sew Peak Chew, Julio Sáez-Rodríguez, John S. O’Neill, György Szabadkai, Michal Minczuk, Christian Frezza
Software Mentions: 3
Published: almost 7 years ago
10.3389/fphys.2015.00410
Benchmarking Procedures for High-Throughput Context Specific Reconstruction Algorithms
Cited by: 22
Author(s): Maria Pires Pacheco, Thomas Pfau, Thomas Sauter
Software Mentions: 3
Published: almost 9 years ago
10.3389/fcimb.2018.00264
Modeling the Metabolic State of Mycobacterium tuberculosis Upon Infection
Cited by: 16
Author(s): Rienk A. Rienksma, Peter J. Schaap, Vítor A. P. Martins dos Santos, María Suárez-Diez
Software Mentions: 3
Published: over 6 years ago
10.1038/s41598-018-37618-z
The bovine alveolar macrophage DNA methylome is resilient to infection with Mycobacterium bovis
Cited by: 9
Author(s): Alan M. O’Doherty, Kévin Rue-Albrecht, David A. Magee, Simone Ahting, Rachelle E Irwin, Thomas Jonathan Hall, John A. Browne, Nicolas C. Nalpas, Colum P. Walsh, Stephen V. Gordon, Marcin W. Wojewodzic, David E. MacHugh
Software Mentions: 3
Published: almost 6 years ago
10.3390/metabo11040221
Revealing the Metabolic Alterations during Biofilm Development of Burkholderia cenocepacia Based on Genome-Scale Metabolic Modeling
Cited by: 5
Author(s): Özlem Altay, Cheng Cheng Zhang, Hasan Türkez, Jens Nielsen, Mathias Uhlén, Adil Mardinoğlu
Software Mentions: 3
Published: over 3 years ago
10.3389/fchem.2020.593497
A Multi-Pronged Computational Pipeline for Prioritizing Drug Target Strategies for Latent Tuberculosis
Cited by: 7
Author(s): Ushashi Banerjee, Santhosh Sankar, Amit Singh, Nagasuma Chandra
Software Mentions: 3
Published: almost 4 years ago
10.1186/s12934-021-01509-2
Engineering Escherichia coli for the utilization of ethylene glycol
Cited by: 11
Author(s): Aditya Vikram Pandit, Emma Harrison, Radhakrishnan Mahadevan
Software Mentions: 3
Published: almost 4 years ago
10.1002/2211-5463.12033
Reconstruction and applications of consensus yeast metabolic network based on <scp>RNA</scp> sequencing
Cited by: 4
Author(s): Yuqi Zhao, Yanjie Wang, Lei Zou, Jing‐Fei Huang
Software Mentions: 3
Published: over 8 years ago
10.3389/fendo.2015.00021
Promoter Methylation Status of Ras-Association Domain Family Member in Pheochromocytoma
Cited by: 17
Author(s): Antje Richter, Tobias Zimmermann, Tanja Haag, Sara K. Walesch, Reinhard Dammann
Software Mentions: 3
Published: almost 10 years ago
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
10.1186/s13148-019-0760-8
The phenotypic variations of multi-locus imprinting disturbances associated with maternal-effect variants of NLRP5 range from overt imprinting disorder to apparently healthy phenotype
Cited by: 19
Author(s): Ángela Sparago, Ankit Verma, Maria Grazia Patricelli, Laura Pignata, Silvia Russo, Luciano Calzari, Naomi De Francesco, Rosita Del Prete, Orazio Palumbo, Massimo Carella, Deborah J G Mackay, Faisal I. Rezwan, Claudia Angelini, Flavia Cerrato, Maria Vittoria Cubellis, Andrea Riccio
Software Mentions: 3
Published: almost 5 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
10.1186/s41512-021-00101-x
The development and validation of a prognostic model to PREDICT Relapse of depression in adult patients in primary care: protocol for the PREDICTR study
Cited by: 3
Author(s): Andrew S. Moriarty, Lewis William Paton, Kym I E Snell, Richard D Riley, Joshua E J Buckman, Simon Gilbody, Carolyn A Chew-Graham, Shehzad Ali, Stephen Pilling, Nick Meader, Bob Phillips, Peter Coventry, Jaime Delgadillo, David Richards, Chris Salisbury, Dean McMillan
Software Mentions: 3
Published: over 3 years ago
10.1371/journal.pone.0013020
Genome-Wide DNA Methylation Maps in Follicular Lymphoma Cells Determined by Methylation-Enriched Bisulfite Sequencing
Cited by: 36
Author(s): Jeong-Hyeon Choi, Yajun Li, Jiangtao Guo, Lirong Pei, Tibor A. Rauch, Robin Kramer, Simone Macmil, Graham B. Wiley, Lynda Bennett, Jennifer Schnabel, Kristen H. Taylor, Sun Il Kim, Dong Xu, Arun Sreekumar, Gerd P. Pfeifer, Bruce A. Roe, Charles W. Caldwell, Kapil N. Bhalla, Huidong Shi
Software Mentions: 3
Published: about 14 years ago
10.1371/journal.pone.0135636
Obstructions to Sampling Qualitative Properties
Cited by: 3
Author(s): Arne C. Reimers
Software Mentions: 3
Published: over 9 years ago
10.3390/metabo9040076
Systems Biology and Multi-Omics Integration: Viewpoints from the Metabolomics Research Community
Cited by: 350
Author(s): Farhana R. Pinu, David J. Beale, Amy M. Paten, Konstantinos A. Kouremenos, Sanjay Swarup, Horst Joachim Schirra, David S. Wishart
Software Mentions: 3
Published: over 5 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
10.1371/journal.pone.0063369
Rapid Countermeasure Discovery against Francisella tularensis Based on a Metabolic Network Reconstruction
Cited by: 19
Author(s): Sidhartha Chaudhury, Mohamed Diwan M. AbdulHameed, Narender Singh, Gregory J. Tawa, Patrik D’haeseleer, Adam Zemła, Ali Navid, Carol L. Ecale Zhou, Matthew C. Franklin, Jonah Cheung, M. Rudolph, J. Love, John Graf, David A. Rozak, Jennifer L. Dankmeyer, Kei Amemiya, Simon Daefler, Anders Wallqvist
Software Mentions: 3
Published: over 11 years ago
10.1002/bit.26347
Metabolic modeling of energy balances in<i>Mycoplasma hyopneumoniae</i>shows that pyruvate addition increases growth rate
Cited by: 11
Author(s): Tjerko Kamminga, Simen Jan Slagman, Jetta J. E. Bijlsma, Vítor A. P. Martins dos Santos, María Suárez-Diez, Peter J. Schaap
Software Mentions: 3
Published: over 7 years ago
10.1371/journal.pone.0131875
Context-Specific Metabolic Model Extraction Based on Regularized Least Squares Optimization
Cited by: 41
Author(s): Semidán Robaina-Estévez, Zoran Nikoloski
Software Mentions: 3
Published: over 9 years ago
10.3390/metabo5040794
Flux Balance Analysis Inspired Bioprocess Upgrading for Lycopene Production by a Metabolically Engineered Strain of Yarrowia lipolytica
Cited by: 28
Author(s): Komi Nambou, Xingxing Jian, Xinkai Zhang, Liujing Wei, Jiajia Lou, Catherine Madzak, Qiang Hua
Software Mentions: 3
Published: almost 9 years ago
10.31557/APJCP.2020.21.12.3539
Omics Integration Analysis Unravel the Landscape of Driving Mechanisms of Colorectal Cancer
Cited by: 6
Author(s): Fatemeh Nikmanesh, Shamim Sarhadi, Mehdi Dadashpour, Yazdan Asghari
Software Mentions: 3
Published: almost 4 years ago
10.1042/EBC20180045
Genome-driven cell engineering review: <i>in vivo</i> and <i>in silico</i> metabolic and genome engineering
Cited by: 11
Author(s): Sophie Landon, Joshua Rees-Garbutt, Lucia Marucci, Claire Grierson
Software Mentions: 3
Published: over 5 years ago
10.1186/s12918-015-0155-1
Spatially-resolved metabolic cooperativity within dense bacterial colonies
Cited by: 69
Author(s): John A. Cole, Lars Köhler, Jamila Hedhli, Zaida Luthey‐Schulten
Software Mentions: 3
Published: over 9 years ago
10.1371/journal.pcbi.1005728
Population FBA predicts metabolic phenotypes in yeast
Cited by: 18
Author(s): Piyush Labhsetwar, Marcelo C.R. Melo, John A. Cole, Zaida Luthey‐Schulten
Software Mentions: 3
Published: about 7 years ago
10.3390/biom11040490
Simultaneous Integration of Gene Expression and Nutrient Availability for Studying the Metabolism of Hepatocellular Carcinoma Cell Lines
Cited by: 9
Author(s): Ewelina Węglarz-Tomczak, Thierry D.G.A. Mondeel, Diewertje G. E. Piebes, Hans V. Westerhoff
Software Mentions: 3
Published: over 3 years ago
10.1002/bit.26846
Process development for the continuous production of heterologous proteins by the industrial yeast, <i>Komagataella phaffii</i>
Cited by: 12
Author(s): Ayca Cankorur-Cetinkaya, Nathalie Narraidoo, Ceyda Kasavi, Nigel K.H. Slater, David B. Archer, Stephen G. Oliver
Software Mentions: 3
Published: about 6 years ago
10.1371/journal.pone.0004967
Filling Kinetic Gaps: Dynamic Modeling of Metabolism Where Detailed Kinetic Information Is Lacking
Cited by: 19
Author(s): Osbaldo Resendis‐Antonio
Software Mentions: 3
Published: over 15 years ago
10.1371/journal.pcbi.1006507
Reconciling high-throughput gene essentiality data with metabolic network reconstructions
Cited by: 21
Author(s): Anna S. Blazier, Jason A. Papin
Software Mentions: 3
Published: over 5 years ago
10.1371/journal.pcbi.1005276
Meneco, a Topology-Based Gap-Filling Tool Applicable to Degraded Genome-Wide Metabolic Networks
Cited by: 68
Author(s): Sylvain Prigent, Clémence Frioux, Simon M. Dittami, Sven Thiele, Abdelhalim Larhlimi, Guillaume Collet, Fabien Gutknecht, Jeanne Got, Damien Eveillard, Jérémie Bourdon, Frédéric Plewniak, Thierry Tonon, Anne Siegel
Software Mentions: 3
Published: almost 8 years ago
10.1186/1752-0509-8-79
A genome-scale metabolic flux model of Escherichia coli K–12 derived from the EcoCyc database
Cited by: 42
Author(s): Daniel Weaver, Ingrid M. Keseler, Amanda Mackie, Ian T. Paulsen, Peter D. Karp
Software Mentions: 3
Published: almost 11 years ago
10.1186/1752-0509-7-129
MC3: a steady-state model and constraint consistency checker for biochemical networks
Cited by: 11
Author(s): Mona Yousofshahi, Ehsan Ullah, Russell Stern, Soha Hassoun
Software Mentions: 3
Published: about 11 years ago
10.1371/journal.pcbi.1008730
DEXOM: Diversity-based enumeration of optimal context-specific metabolic networks
Cited by: 5
Author(s): Pablo Rodríguez-Mier, Nathalie Poupin, Carlo De Blasio, Laurent Le Cam, Fabien Jourdan
Software Mentions: 3
Published: almost 4 years ago
10.1186/1752-0509-5-200
Individualized therapy of HHT driven by network analysis of metabolomic profiles
Cited by: 19
Author(s): Neema Jamshidi, Franklin J. Miller, Jess Mandel, Timothy Evans, Michael Kuo
Software Mentions: 3
Published: almost 13 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
10.3390/metabo11020113
The Metano Modeling Toolbox MMTB: An Intuitive, Web-Based Toolbox Introduced by Two Use Cases
Cited by: 2
Author(s): Julia Koblitz, Sabine Eva Will, S Alexander Riemer, Thomas Ulas, Meina Neumann‐Schaal, Dietmar Schomburg
Software Mentions: 3
Published: almost 4 years ago
10.1371/journal.pcbi.1006541
RAVEN 2.0: A versatile toolbox for metabolic network reconstruction and a case study on Streptomyces coelicolor
Cited by: 208
Author(s): Hao Wang, Simonas Marcišauskas, Benjamín J. Sánchez, Iván Domenzain, Daniel Hermansson, Rasmus Ågren, Jens Nielsen, Eduard J. Kerkhoven
Software Mentions: 3
Published: about 6 years ago
10.1371/journal.pcbi.1007308
Fast uncertainty quantification for dynamic flux balance analysis using non-smooth polynomial chaos expansions
Cited by: 14
Author(s): Joel A. Paulson, Marc Martin-Casas, Ali Mesbah
Software Mentions: 3
Published: about 5 years ago
10.1371/journal.pcbi.1004321
Escher: A Web Application for Building, Sharing, and Embedding Data-Rich Visualizations of Biological Pathways
Cited by: 274
Author(s): Zachary A. King, Andreas Dräger, Ali Ebrahim, Nikolaus Sonnenschein, Nathan E. Lewis, Bernhard Ø. Palsson
Software Mentions: 3
Published: about 9 years ago
10.1111/pbi.13372
PANOMICS meets germplasm
Cited by: 69
Author(s): Wolfram Weckwerth, Arindam Ghatak, Anke Bellaire, Palak Chaturvedi, Rajeev K. Varshney
Software Mentions: 3
Published: over 4 years ago
10.1186/1755-8794-5-26
Screening significantly hypermethylated genes in fetal tissues compared with maternal blood using a methylated-CpG island recovery assay-based microarray
Cited by: 7
Author(s): Aihua Yin, Xiangzhong Zhang, Jing Wu, Lili Du, Tao He, Xiaozhuang Zhang
Software Mentions: 3
Published: over 12 years ago
10.1186/1471-2172-13-58
DNA methylation profile of Aire-deficient mouse medullary thymic epithelial cells
Cited by: 7
Author(s): Guoying Wu, Keiji Hirabayashi, Shinya Sato, Nobuko Akiyama, Taishin Akiyama, Kunio Shiota, Shusuke Yagi
Software Mentions: 3
Published: about 12 years ago