pypi: Escher | Projects | Ecosyste.ms: Papers

10.1016/j.mec.2019.e00089

Impact framework: A python package for writing data analysis workflows to interpret microbial physiology
Cited by: 4
Author(s): Naveen Venayak, Kaushik Raj, Radhakrishnan Mahadevan
Software Mentions: 7
Published: almost 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

10.1371/journal.pcbi.1007099

Transcriptome-guided parsimonious flux analysis improves predictions with metabolic networks in complex environments
Cited by: 46
Author(s): Matthew L. Jenior, Thomas J. Moutinho, Bonnie V. Dougherty, Jason A. Papin
Software Mentions: 5
Published: over 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

10.1186/s12859-020-03632-0

Escher-Trace: a web application for pathway-based visualization of stable isotope tracing data
Cited by: 9
Author(s): Avi Kumar, Jack Mitchener, Zachary A. King, Christian M. Metallo
Software Mentions: 4
Published: over 4 years ago

10.1186/s12864-016-3219-8

Genome-wide gene expression and RNA half-life measurements allow predictions of regulation and metabolic behavior in Methanosarcina acetivorans
Cited by: 21
Author(s): J.R. Peterson, Sheng Shee Thor, Lars Köhler, Petra R. A. Kohler, William W. Metcalf, Zaida Luthey‐Schulten
Software Mentions: 4
Published: about 8 years ago

10.3390/metabo11040232

First Genome-Scale Metabolic Model of Dolosigranulum pigrum Confirms Multiple Auxotrophies
Cited by: 7
Author(s): Alina Renz, Lina Widerspick, Andreas Dräger
Software Mentions: 4
Published: over 3 years ago

10.7554/eLife.49305

Evolution of C4 photosynthesis predicted by constraint-based modelling
Cited by: 42
Author(s): Mary Ann Blätke, Andrea Bräutigam
Software Mentions: 4
Published: almost 5 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

10.1093/bioinformatics/btz160

Interoperable and scalable data analysis with microservices: applications in metabolomics
Cited by: 24
Author(s): Payam Emami Khoonsari, Pablo Moreno-Ger, Sven Bergmann, Joachim Burman, Marco Capuccini, Matteo Carone, Marta Cascante, Pedro de Atauri, Carles Foguet, Alejandra N. González-Beltrán, Thomas Hankemeier, Kenneth Haug, Sijin He, Stephanie Herman, David Johnson, Namrata Kale, Anders Larsson, Steffen Neumann, Kristian Peters, Luca Pireddu, Philippe Rocca-Serra, Pierrick Roger, Rico Rueedi, Christoph Ruttkies, Noureddin Sadawi, Reza M. Salek, Susanna-Assunta Sansone, Daniel Schober, Vitaly A. Selivanov, Etienne Thévenot, Michael Van Vliet, Gianluigi Zanetti, Christoph Steinbeck, Kim Kultima, Ola Spjuth
Software Mentions: 4
Published: over 5 years ago

10.15252/msb.20188462

Enzyme promiscuity shapes adaptation to novel growth substrates
Cited by: 47
Author(s): Gabriela I. Guzmán, Troy E. Sandberg, Ryan A. LaCroix, Ákos Nyerges, Henrietta Papp, Markus de Raad, Zachary A. King, Ying Hefner, Trent Northen, Richard A. Notebaart, Csaba Pál, Bernhard Palsson, Balázs Papp, Adam M. Feist
Software Mentions: 3
Published: over 5 years ago

10.3389/fmolb.2019.00002

Multi-Omics and Genome-Scale Modeling Reveal a Metabolic Shift During C. elegans Aging
Cited by: 40
Author(s): Janna Hastings, Abraham Mains, Bhupinder Virk, Nicolás Rodríguez, Sharlene Murdoch, Juliette Pearce, Sven Bergmann, Nicolas Le Novère, Olivia Casanueva
Software Mentions: 3
Published: almost 6 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

10.1126/sciadv.abh2433

Metabolic control of nitrogen fixation in rhizobium-legume symbioses
Cited by: 31
Author(s): Carolin C. M. Schulte, Khushboo Borah, Rachel M. Wheatley, Jason Terpolilli, Gerhard Saalbach, Nick Crang, Daan H. de Groot, R. G. Ratcliffe, Nicholas J. Kruger, Antonis Papachristodoulou, Philip S. Poole
Software Mentions: 3
Published: over 3 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

10.1016/j.isci.2020.101525

Enzyme-Constrained Models and Omics Analysis of Streptomyces coelicolor Reveal Metabolic Changes that Enhance Heterologous Production
Cited by: 29
Author(s): Snorre Sulheim, Tjaša Kumelj, Dino van Dissel, Ali Salehzadeh‐Yazdi, Congcong Du, Gilles P. van Wezel, Kay Nieselt, Eivind Almaas, Alexander Wentzel, Eduard J. Kerkhoven
Software Mentions: 2
Published: about 4 years ago

10.1186/s12859-019-3328-x

Improving the organization and interactivity of metabolic pathfinding with precomputed pathways
Cited by: 7
Author(s): Sarah M. Kim, Matthew I. Peña, Mark Moll, George N. Bennett, Lydia E. Kavraki
Software Mentions: 2
Published: almost 5 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

10.1093/bib/bbz067

Closing the gap between formats for storing layout information in systems biology
Cited by: 11
Author(s): David Hoksza, Piotr Gawron, Marek Ostaszewski, Jan Hasenauer, Reinhard Schneider
Software Mentions: 2
Published: over 5 years ago

10.3390/metabo11050300

IDARE2—Simultaneous Visualisation of Multiomics Data in Cytoscape
Cited by: 2
Author(s): Thomas Pfau, Mafalda Galhardo, Jake Lin, Thomas Sauter
Software Mentions: 2
Published: over 3 years ago

10.3390/metabo11020064

Pathway Tools Visualization of Organism-Scale Metabolic Networks
Cited by: 8
Author(s): Suzanne M. Paley, Richard Billington, James A. Herson, Markus Krummenacker, Peter D. Karp
Software Mentions: 2
Published: almost 4 years ago

10.1186/s12934-019-1229-3

A metabolic reconstruction of Lactobacillus reuteri JCM 1112 and analysis of its potential as a cell factory
Cited by: 18
Author(s): Thordis Kristjansdottir, Elleke Fenna Bosma, Filipe Branco dos Santos, Emre Özdemir, Markus J. Herrgård, Lucas França, Bruno Sommer Ferreira, Alex Toftgaard Nielsen, Steinn Guðmundsson
Software Mentions: 2
Published: about 5 years ago

10.3390/microorganisms8030437

Genome-Scale Metabolic Model Reconstruction and in Silico Investigations of Methane Metabolism in Methylosinus trichosporium OB3b
Cited by: 18
Author(s): Sanzhar Naizabekov, Eun Yeol Lee
Software Mentions: 2
Published: over 4 years ago

10.3390/microorganisms8071002

A Genome-Scale Metabolic Model of 2,3-Butanediol Production by Thermophilic Bacteria Geobacillus icigianus
Cited by: 9
Author(s): Mikhail Kulyashov, S. E. Peltek, Ilya R. Akberdin
Software Mentions: 2
Published: over 4 years ago

10.1371/journal.pcbi.1006692

A diurnal flux balance model of Synechocystis sp. PCC 6803 metabolism
Cited by: 23
Author(s): Debolina Sarkar, Thomas Mueller, Deng Liu, Himadri B. Pakrasi, Costas D. Maranas
Software Mentions: 2
Published: almost 6 years ago

10.3389/fbioe.2020.612832

Multi-Omics Driven Metabolic Network Reconstruction and Analysis of Lignocellulosic Carbon Utilization in Rhodosporidium toruloides
Cited by: 23
Author(s): Joonhoon Kim, Samuel T. Coradetti, Young-Mo Kim, Yuqian Gao, Junko Yaegashi, Jeremy Zucker, Nathalie Munoz Munoz, Erika Zink, Kristin Burnum-Johnson, Scott E. Baker, Blake A. Simmons, Jeffrey M. Skerker, John M. Gladden, Jon Magnuson
Software Mentions: 2
Published: almost 4 years ago

10.1186/s40694-018-0060-7

A community-driven reconstruction of the Aspergillus niger metabolic network
Cited by: 19
Author(s): Julian Brandl, María Victoria Aguilar Pontes, Paul Schäpe, Anders Noerregaard, Mikko Arvas, Arthur F. J. Ram, Vera Meyer, Adrian Tsang, Ronald P. de Vries, Mikael Rørdam Andersen
Software Mentions: 2
Published: about 6 years ago

10.1093/gigascience/giz137

Compartment and hub definitions tune metabolic networks for metabolomic interpretations
Cited by: 7
Author(s): Thomas Waller, Jordan A. Berg, Alexander Lex, Brian E. Chapman, Jared Rutter
Software Mentions: 2
Published: almost 5 years ago

10.1038/s41598-018-20574-z

Methane utilization in Methylomicrobium alcaliphilum 20ZR: a systems approach
Cited by: 70
Author(s): Ilya R. Akberdin, Merlin Thompson, Richard Hamilton, Nalini Desai, Danny Alexander, Calvin A. Henard, Michael T. Guarnieri, Marina G. Kalyuzhnaya
Software Mentions: 2
Published: almost 7 years ago

10.1128/mSystems.00529-19

Metabolic Modeling of Streptococcus mutans Reveals Complex Nutrient Requirements of an Oral Pathogen
Cited by: 19
Author(s): Kenan Jijakli, Paul A. Jensen
Software Mentions: 2
Published: about 5 years ago

10.1128/mSystems.00516-19

Metabolic Analyses of Nitrogen Fixation in the Soybean Microsymbiont Sinorhizobium fredii Using Constraint-Based Modeling
Cited by: 17
Author(s): Carolina A. Contador, Siu-Kit Lo, Siu Hung Joshua Chan, Hon‐Ming Lam
Software Mentions: 2
Published: almost 5 years ago

10.1371/journal.pcbi.1006302

COBRAme: A computational framework for genome-scale models of metabolism and gene expression
Cited by: 112
Author(s): Colton J. Lloyd, Ali Ebrahim, Laurence T. Yang, Zachary A. King, Edward Catoiu, Edward J. O’Brien, Joanne K. Liu, Jaehyung Kim
Software Mentions: 1
Published: over 6 years ago

10.1186/s12859-020-3415-z

Visualizing metabolic network dynamics through time-series metabolomic data
Cited by: 12
Author(s): Lea F. Buchweitz, James T. Yurkovich, Christoph Blessing, Veronika Kohler, Fabian Schwarzkopf, Zachary A. King, Laurence T. Yang, Freyr Jóhannsson, Ólafur E. Sigurjónsson, Óttar Rolfsson, Julian Heinrich, Andreas Dräger
Software Mentions: 1
Published: over 4 years ago

10.1155/2013/437168

A Computational Approach towards the Understanding of <i>Plasmodium falciparum</i> Multidrug Resistance Protein 1
Cited by: 6
Author(s): Saumya Patel, Linz-Buoy George, Sivakumar Prasanth Kumar, Hyacinth Highland, Yogesh T. Jasrai, Himanshu A. Pandya, Ketaki R. Desai
Software Mentions: 1
Published: over 11 years ago

10.1371/journal.ppat.1006632

Rewiring monocyte glucose metabolism via C-type lectin signaling protects against disseminated candidiasis
Cited by: 66
Author(s): Jorge Domínguez‐Andrés, Rob J. W. Arts, Rob ter Horst, Mark S. Gresnigt, Sanne P. Smeekens, Jacqueline M. Ratter, Ekta Lachmandas, Lily Boutens, Frank L. van de Veerdonk, Leo A. B. Joosten, Richard A. Notebaart, Carlos Ardavı́n, Mihai G. Netea
Software Mentions: 1
Published: about 7 years ago

10.1186/s12936-021-03780-5

Inter-study and time-dependent variability of metabolite abundance in cultured red blood cells
Cited by: 7
Author(s): Shivendra G. Tewari, Krithika Rajaram, Russell P Swift, Bobby Kwan, Jaques Reifman, Sean T. Prigge, Anders Wallqvist
Software Mentions: 1
Published: over 3 years ago

10.3390/jimaging6020005

Unveiling the Secrets of Escher’s Lithographs
Cited by: 2
Author(s): Primo Coltelli, Laura Barsanti, Paolo Gualtieri
Software Mentions: 1
Published: almost 5 years ago

10.1186/s40170-020-00227-4

Disruption of redox homeostasis for combinatorial drug efficacy in K-Ras tumors as revealed by metabolic connectivity profiling
Cited by: 9
Author(s): Daniela Gaglio, Marcella Bonanomi, Silvia Valtorta, Rohit Bharat, M. Ripamonti, Federica Conte, Giulia Fiscon, Nicole Righi, Elisabetta Napodano, Federico Papa, Isabella Raccagni, Seth J. Parker, Ingrid Cifola, Tania Camboni, Paola Paci, Anna Maria Colangelo, Marco Vanoni, Christian M. Metallo, Rosa María Moresco, Lilia Alberghina
Software Mentions: 1
Published: about 4 years ago

10.3389/fbioe.2020.00772

Development of a Genome-Scale Metabolic Model of Clostridium thermocellum and Its Applications for Integration of Multi-Omics Datasets and Computational Strain Design
Cited by: 17
Author(s): Sergio Garcia, R. Adam Thompson, Richard J. Giannone, Satyakam Dash, Costas D. Maranas, Cong T. Trinh
Software Mentions: 1
Published: over 4 years ago

10.1371/journal.pone.0192891

FindPrimaryPairs: An efficient algorithm for predicting element-transferring reactant/product pairs in metabolic networks
Cited by: 0
Author(s): Jon Lund Steffensen, Keith Dufault‐Thompson, Ying Zhang
Software Mentions: 1
Published: almost 7 years ago

10.3389/fmicb.2018.02947

A Genome-Scale Metabolic Model for Methylococcus capsulatus (Bath) Suggests Reduced Efficiency Electron Transfer to the Particulate Methane Monooxygenase
Cited by: 34
Author(s): Christian Lieven, Leander A. H. Petersen, Sten Bay Jørgensen, Krist V. Gernaey, Markus J. Herrgård, Nikolaus Sonnenschein
Software Mentions: 1
Published: almost 6 years ago

10.3389/fmicb.2019.02417

Rewiring of Metabolic Network in Mycobacterium tuberculosis During Adaptation to Different Stresses
Cited by: 27
Author(s): Arshad Rizvi, Arvind Jaya Shankar, A. Chatterjee, Tushar H. More, T. K. Bose, Anirban Dutta, Kannan Balakrishnan, Lavanya Madugulla, Srikanth Rapole, Sharmila S. Mande, Sharmistha Banerjee, Shekhar C. Mande
Software Mentions: 1
Published: about 5 years ago

10.3389/fmicb.2019.02801

Genome-Scale Metabolic Reconstruction of Acetobacter pasteurianus 386B, a Candidate Functional Starter Culture for Cocoa Bean Fermentation
Cited by: 14
Author(s): Rudy Pelicaen, Didier Gonze, Bas Teusink, Luc De Vuyst, Stefan Weckx
Software Mentions: 1
Published: almost 5 years ago

Projects: pypi: Escher

Papers Mentioning Escher 43