cran: Recon | Projects | Ecosyste.ms: Papers

10.12688/f1000research.22139.2

scRepertoire: An R-based toolkit for single-cell immune receptor analysis
Cited by: 121
Author(s): Nicholas Borcherding, Nicholas L. Bormann, Gloria Kraus
Software Mentions: 16
Published: over 4 years ago

10.3389/fimmu.2018.00462

Analyzing Immunoglobulin Repertoires
Cited by: 77
Author(s): Neha Chaudhary, Duane R. Wesemann
Software Mentions: 8
Published: almost 7 years ago

10.1186/s13059-019-1730-3

Current status and applications of genome-scale metabolic models
Cited by: 406
Author(s): Changdai Gu, Gi Bae Kim, Won Jun Kim, Hyun Uk Kim, Sang Yup Lee
Software Mentions: 7
Published: over 5 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: over 3 years ago

10.3389/fimmu.2018.00224

Computational Strategies for Dissecting the High-Dimensional Complexity of Adaptive Immune Repertoires
Cited by: 146
Author(s): Enkelejda Miho, Alexander Yermanos, Cédric R. Weber, Christoph T. Berger, Sai T. Reddy, Victor Greiff
Software Mentions: 6
Published: almost 7 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: almost 5 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

10.3390/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

10.3390/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.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/s13100-019-0150-y

RepetDB: a unified resource for transposable element references
Cited by: 37
Author(s): Joëlle Amselem, Guillaume Cornut, Nathalie Choisne, Michaël Alaux, Françoise Alfama-Depauw, Véronique Jamilloux, Florian Maumus, Thomas Letellier, Isabelle Luyten, Cyril Pommier, Anne-Françoise Adam-Blondon, Hadi Quesneville
Software Mentions: 4
Published: almost 6 years ago

10.1186/s12864-015-1984-4

Integrated metabolic modelling reveals cell-type specific epigenetic control points of the macrophage metabolic network
Cited by: 34
Author(s): Maria Pires Pacheco, Elisabeth John, Tony Kaoma, Merja Heinäniemi, Nathalie Nicot, Laurent Vallar, Jean-Luc Bueb, Lasse Sinkkonen, Thomas Sauter
Software Mentions: 4
Published: about 9 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

10.18632/aging.103253

Systematic metabolic analysis of potential target, therapeutic drug, diagnostic method and animal model applicability in three neurodegenerative diseases
Cited by: 10
Author(s): Wen‐Xing Li, Gong‐Hua Li, Xin Tong, Pengpeng Yang, Jing‐Fei Huang, Lin Xu, Shao‐Xing Dai
Software Mentions: 4
Published: over 4 years ago

10.3390/metabo9060117

Integration of Metabolomic and Other Omics Data in Population-Based Study Designs: An Epidemiological Perspective
Cited by: 42
Author(s): Su H. Chu, Mengna Huang, Rachel S. Kelly, Elisa Benedetti, Jalal K. Siddiqui, Oana A. Zeleznik, Alexandre Pereira, David M. Herrington, Craig E. Wheelock, Jan Krumsiek, Michael J. McGeachie, Steven C. Moore, Peter Kraft, Ewy A. Mathé, Jessica Lasky‐Su
Software Mentions: 4
Published: over 5 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.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

10.3390/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

10.1371/journal.pone.0230796

Transcriptome analysis reveals gender-specific differences in overall metabolic response of male and female patients in lung adenocarcinoma
Cited by: 5
Author(s): Ya Li, Chenglu He, Wen‐Xing Li, Ruixian Zhang, Yong Duan
Software Mentions: 4
Published: over 4 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

10.1186/1471-2105-11-213

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

10.1371/journal.pgen.1006777

Hybridization and polyploidy enable genomic plasticity without sex in the most devastating plant-parasitic nematodes
Cited by: 138
Author(s): Romain Blanc-Mathieu, Laetitia Perfus‐Barbeoch, Jean‐Marc Aury, Martine Da Rocha, Jérôme Gouzy, Erika Sallet, Cristina Martín-Jimenez, Marc Bailly‐Bechet, Philippe Castagnone‐Sereno, Jean‐François Flot, Djampa Kozlowski, Julie Cazareth, Arnaud Couloux, Corinne Da Silva, Julie Guy, Yujin Kim, Corinne Rancurel, Thomas Schiex, Pierre Abad, Patrick Wincker, Etienne G. J. Danchin
Software Mentions: 4
Published: over 7 years ago

10.1371/journal.pcbi.1003837

A Systems Approach to Predict Oncometabolites via Context-Specific Genome-Scale Metabolic Networks
Cited by: 59
Author(s): Hojung Nam, Miguel A. Campodonico, Aarash Bordbar, Daniel R. Hyduke, Sangwoo Kim, Daniel C. Zielinski, Bernhard Ø. Palsson
Software Mentions: 3
Published: over 10 years ago

10.15252/msb.20209730

Causal integration of multi‐omics data with prior knowledge to generate mechanistic hypotheses
Cited by: 63
Author(s): Aurélien Dugourd, Christoph Kuppe, Marco Sciacovelli, Enio Gjerga, Attila Gábor, Kristina B. Emdal, Vítor Vieira, Dorte B. Bekker-Jensen, Jennifer Kranz, Eric Bindels, Ana S.H. Costa, Abel Sousa, Pedro Beltrão, Miguel Rocha, Jesper V. Olsen, Christian Frezza, Rafael Kramann, Julio Sáez-Rodríguez
Software Mentions: 3
Published: almost 4 years ago

10.1371/journal.pcbi.1005618

Flux balance analysis predicts Warburg-like effects of mouse hepatocyte deficient in miR-122a
Cited by: 20
Author(s): Hua Qing Wu, Mei Cheng, Jin Mei Lai, Hsuan Hui Wu, Meng Chun Chen, Wen Huan Liu, Wu‐Hsiung Wu, Peter Mu Hsin Chang, Chi Ying F. Huang, Ann-Ping Tsou, Ming‐Shi Shiao, Feng Sheng Wang
Software Mentions: 3
Published: over 7 years ago

10.3389/fphys.2015.00413

Applications of Genome-Scale Metabolic Models in Biotechnology and Systems Medicine
Cited by: 96
Author(s): Cheng Cheng Zhang, Qiang Hua
Software Mentions: 3
Published: almost 9 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

10.1038/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

10.3390/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

10.1186/s12859-021-04002-0

Accelerated global sensitivity analysis of genome-wide constraint-based metabolic models
Cited by: 3
Author(s): Marco S. Nobile, Vasco Coelho, Dario Pescini, Chiara Damiani
Software Mentions: 3
Published: over 3 years ago

10.1038/srep32584

Distinct metabolic network states manifest in the gene expression profiles of pediatric inflammatory bowel disease patients and controls
Cited by: 17
Author(s): Carolin Knecht, Christoph Fretter, Philip Rosenstiel, Michael Krawczak, Marc‐Thorsten Hütt
Software Mentions: 3
Published: over 8 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: about 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: about 13 years ago

10.1016/j.ymben.2017.11.011

Post-translational regulation of metabolism in fumarate hydratase deficient cancer cells
Cited by: 21
Author(s): Emanuel Gonçalvès, Marco Sciacovelli, Ana S.H. Costa, Maxine Tran, Timothy Isaac Johnson, Daniel Machado, Christian Frezza, Julio Sáez-Rodríguez
Software Mentions: 3
Published: almost 7 years ago

10.1186/s12864-015-1380-0

The genome of the basal agaricomycete Xanthophyllomyces dendrorhous provides insights into the organization of its acetyl-CoA derived pathways and the evolution of Agaricomycotina
Cited by: 42
Author(s): Rahul Sharma, Sören Gassel, Sabine Steiger, Xiaojuan Xia, Robert Bauer, Gerhard Sandmann, Marco Thines
Software Mentions: 2
Published: over 9 years ago

10.1186/s12859-019-2685-9

Integration of transcriptomic data in a genome-scale metabolic model to investigate the link between obesity and breast cancer
Cited by: 21
Author(s): Ilaria Granata, Enrico Troiano, Mara Sangiovanni, Mario Rosario Guarracino
Software Mentions: 2
Published: over 5 years ago

10.1186/s12859-019-2779-4

Metabopolis: scalable network layout for biological pathway diagrams in urban map style
Cited by: 9
Author(s): Hsiang‐Yun Wu, Martin Nöllenburg, Filipa L. Sousa, Ivan Viola
Software Mentions: 2
Published: over 5 years ago

10.1186/s12864-019-5979-4

Stoichiometric gene-to-reaction associations enhance model-driven analysis performance: Metabolic response to chronic exposure to Aldrin in prostate cancer
Cited by: 11
Author(s): Igor Batolomé Marín de Mas, Laura Torrents, Carmen Bedia, Lars K. Nielsen, Marta Cascante, Romà Tauler
Software Mentions: 2
Published: over 5 years ago

10.1186/1471-2210-8-12

Structure-activity models of oral clearance, cytotoxicity, and LD50: a screen for promising anticancer compounds
Cited by: 9
Author(s): John C. Boik, Robert A. Newman
Software Mentions: 2
Published: over 16 years ago

10.1186/1752-0509-5-110

iAB-RBC-283: A proteomically derived knowledge-base of erythrocyte metabolism that can be used to simulate its physiological and patho-physiological states
Cited by: 83
Author(s): Aarash Bordbar, Neema Jamshidi, Bernhard Ø. Palsson
Software Mentions: 2
Published: over 13 years ago

10.1093/bioinformatics/bty588

Scalable and exhaustive screening of metabolic functions carried out by microbial consortia
Cited by: 19
Author(s): Clémence Frioux, Enora Fremy, Camille Trottier, Anne Siegel
Software Mentions: 2
Published: over 6 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

10.1093/bib/bby024

Community-driven roadmap for integrated disease maps
Cited by: 44
Author(s): Marek Ostaszewski, Stephan Gebel, Inna Kuperstein, Alexander Mazein, Andrei Zinovyev, Uḡur Doḡrusöz, Jan Hasenauer, Ronan M. T. Fleming, Nicolas Le Novère, Piotr Gawron, Thomas Ligon, Anna Niarakis, David Nickerson, Daniel Weindl, Rudi Balling, Emmanuel Barillot, Charles Auffray, Reinhard Schneider
Software Mentions: 2
Published: over 6 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: about 9 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

10.15252/msb.20209649

Modeling tissue‐relevant <i>Caenorhabditis elegans</i> metabolism at network, pathway, reaction, and metabolite levels
Cited by: 28
Author(s): L. Şafak Yılmaz, Xuhang Li, Shivani Nanda, Bennett W. Fox, Frank C. Schroeder, Albertha J.M. Walhout
Software Mentions: 2
Published: about 4 years ago

10.1371/journal.pcbi.1006867

Increasing consensus of context-specific metabolic models by integrating data-inferred cell functions
Cited by: 58
Author(s): Anne Richelle, Austin W. T. Chiang, Chih‐Chung Kuo, Nathan E. Lewis
Software Mentions: 2
Published: over 5 years ago

10.1371/journal.pcbi.1000938

Drug Off-Target Effects Predicted Using Structural Analysis in the Context of a Metabolic Network Model
Cited by: 184
Author(s): Roger L. Chang, Li Xie, Lei Xie, Philip E. Bourne, Bernhard Ø. Palsson
Software Mentions: 2
Published: about 14 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.pgen.1005274

The Human Blood Metabolome-Transcriptome Interface
Cited by: 84
Author(s): Jörg Bartel, Jan Krumsiek, Katharina Schramm, Jerzy Adamski, Christian Gieger, Christian Herder, Maren Carstensen, Annette Peters, Wolfgang Rathmann, Michael Roden, Konstantin Strauch, Karsten Suhre, Gabi Kastenmüller, Holger Prokisch, Fabian J. Theis
Software Mentions: 2
Published: over 9 years ago

10.1186/s13072-019-0260-2

Combined analysis of dissimilar promoter accessibility and gene expression profiles identifies tissue-specific genes and actively repressed networks
Cited by: 56
Author(s): Rebekah R. Starks, Anilisa Biswas, Ashish Jain, Geetu Tuteja
Software Mentions: 2
Published: almost 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

10.3389/fgene.2019.00019

Systems Biology Approaches Toward Understanding Primary Mitochondrial Diseases
Cited by: 11
Author(s): Elaina M. Maldonado, F. Taha, Joyeeta Rahman, Shamima Rahman
Software Mentions: 2
Published: almost 6 years ago

10.3389/fmicb.2019.00966

Comparative Genomics Reveals the High Copy Number Variation of a Retro Transposon in Different Magnaporthe Isolates
Cited by: 7
Author(s): Pankaj Kumar Singh, Ajay Kumar Mahato, Priyanka Jain, Rajeev Rathour, Vinay Sharma, Tilak Raj Sharma
Software Mentions: 2
Published: over 5 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: almost 11 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

10.1016/j.jbc.2021.100603

A key role for the transporter OAT1 in systemic lipid metabolism
Cited by: 16
Author(s): Jeffry C. Granados, Anisha K. Nigam, Kevin T. Bush, Neema Jamshidi, Sanjay K. Nigám
Software Mentions: 2
Published: almost 4 years ago

10.1186/s13321-017-0223-1

Comparative evaluation of atom mapping algorithms for balanced metabolic reactions: application to Recon 3D
Cited by: 21
Author(s): Germán Andrés González, Lemmer R. P. El Assal, Alberto Noronha, Ines Thiele, Hulda S. Haraldsdóttir, Ronan M. T. Fleming
Software Mentions: 2
Published: over 7 years ago

10.1098/rsos.170360

Modelling pyruvate dehydrogenase under hypoxia and its role in cancer metabolism
Cited by: 16
Author(s): Filmon Eyassu, Claudio Angione
Software Mentions: 2
Published: about 7 years ago

10.1038/srep28415

The space of enzyme regulation in HeLa cells can be inferred from its intracellular metabolome
Cited by: 13
Author(s): Christian Diener, Felipe Muñoz-Gonzalez, Sergio Encarnación, Osbaldo Resendis‐Antonio
Software Mentions: 2
Published: over 8 years ago

10.1038/s41598-018-25089-1

The quest for identifiability in human functional connectomes
Cited by: 173
Author(s): Enrico Amico, Joaquín Goñi
Software Mentions: 2
Published: over 6 years ago

10.3390/s21082587

3D Face Point Cloud Reconstruction and Recognition Using Depth Sensor
Cited by: 9
Author(s): Cheng Wei Wang, Chao-Chung Peng
Software Mentions: 2
Published: over 3 years ago

10.1093/hmg/ddt616

A missense mutation in ITGB6 causes pitted hypomineralized amelogenesis imperfecta
Cited by: 41
Author(s): James A. Poulter, Steven J. Brookes, R.C. Shore, Claire E. L. Smith, Layal Abi Farraj, Jennifer Kirkham, Chris F. Inglehearn, Alan J. Mighell
Software Mentions: 2
Published: about 11 years ago

10.1515/jib-2018-0068

A Model Integration Pipeline for the Improvement of Human Genome-Scale Metabolic Reconstructions
Cited by: 4
Author(s): Vítor Vieira, Jorge Ferreira, Rúben Rodrigues, Filipe Alexandre Wang Liu, Miguel Rocha
Software Mentions: 2
Published: about 6 years ago

10.1371/journal.pone.0072439

Insights into the Loblolly Pine Genome: Characterization of BAC and Fosmid Sequences
Cited by: 48
Author(s): Jill L. Wegrzyn, Brian Y. Lin, Jacob J. Zieve, W. Dougherty, Pedro J. Martínez-García, Maxim Koriabine, Ann Holtz-Morris, Pieter J. deJong, Marc W. Crepeau, Charles H. Langley, Daniela Puiu, Steven L. Salzberg, David B. Neale, Kristian Stevens
Software Mentions: 1
Published: over 11 years ago

10.1371/journal.pone.0102032

The p38α MAPK Function in Osteoprecursors Is Required for Bone Formation and Bone Homeostasis in Adult Mice
Cited by: 30
Author(s): Eddie Rodríguez-Carballo, Beatriz Gámez, Lara Sedó-Cabezón, Manuela Sánchez‐Feutrie, António Zorzano, María Cristina Manzanares-Céspedes, José Luís Rosa, Francesc Ventura
Software Mentions: 1
Published: over 10 years ago

10.1093/bioinformatics/btw749

Algorithm sensitivity analysis and parameter tuning for tissue image segmentation pipelines
Cited by: 19
Author(s): George Teodoro, Tahsin Kurç, Luis F. R. Taveira, Alba Cristina Magalhães Alves de Melo, Yi Gao, Jun Kong, Joel Saltz
Software Mentions: 1
Published: almost 8 years ago

10.1002/cmdc.201700724

Caveat Usor: Assessing Differences between Major Chemistry Databases
Cited by: 10
Author(s): Christopher Southan
Software Mentions: 1
Published: almost 7 years ago

10.1016/j.csbj.2015.08.002

A constraint-based modelling approach to metabolic dysfunction in Parkinson's disease
Cited by: 5
Author(s): Longfei Mao, Averina Nicolae, Miguel A. P. Oliveira, Feng He, Siham Hachi, Ronan M. T. Fleming
Software Mentions: 1
Published: almost 10 years ago

10.1093/database/bav068

Human metabolic atlas: an online resource for human metabolism
Cited by: 61
Author(s): Natapol Pornputtapong, Intawat Nookaew, Jens Nielsen
Software Mentions: 1
Published: almost 10 years ago

10.1210/er.2017-00211

Metabolic Flexibility as an Adaptation to Energy Resources and Requirements in Health and Disease
Cited by: 319
Author(s): Reuben L. Smith, Maarten R. Soeters, Rob C I Wüst, Riekelt H. Houtkooper
Software Mentions: 1
Published: over 6 years ago

10.1186/s12859-017-1545-8

SEEG assistant: a 3DSlicer extension to support epilepsy surgery
Cited by: 67
Author(s): Massimo Narizzano, Gabriele Arnulfo, Serena Ricci, Benedetta Toselli, Martin Tisdall, Andrea Canessa, Marco Fato, Francesco Cardinale
Software Mentions: 1
Published: almost 8 years ago

10.1038/s12276-021-00616-9

Alternative regulatory mechanism for the maintenance of bone homeostasis via STAT5-mediated regulation of the differentiation of BMSCs into adipocytes
Cited by: 9
Author(s): Semun Seong, Jung Ha Kim, Kabsun Kim, In-Young Kim, Jeong‐Tae Koh, Nacksung Kim
Software Mentions: 1
Published: over 3 years ago

10.1186/1752-0509-4-140

A detailed genome-wide reconstruction of mouse metabolism based on human Recon 1
Cited by: 143
Author(s): Martin I. Sigurdsson, Neema Jamshidi, Eiríkur Steingrimsson, Ines Thiele, Bernhard Ø. Palsson
Software Mentions: 1
Published: about 14 years ago

10.1186/s12918-017-0500-7

MitoCore: a curated constraint-based model for simulating human central metabolism
Cited by: 30
Author(s): Anthony C. Smith, Filmon Eyassu, Jean‐Pierre Mazat, Alan J. Robinson
Software Mentions: 1
Published: about 7 years ago

10.1038/s41598-018-19366-2

GenomeLandscaper: Landscape analysis of genome-fingerprints maps assessing chromosome architecture
Cited by: 1
Author(s): Hannan Ai, Yuncan Ai, Fanbao Meng
Software Mentions: 1
Published: almost 7 years ago

10.3389/fcimb.2020.00052

Novel Approaches for Systems Biology of Metabolism-Oriented Pathogen-Human Interactions: A Mini-Review
Cited by: 13
Author(s): Tunahan Çakır, Gianni Panagiotou, Reaz Uddin, Saliha Durmuş
Software Mentions: 1
Published: almost 5 years ago

10.2196/14116

Continuous Measurement of Reconnaissance Marines in Training With Custom Smartphone App and Watch: Observational Cohort Study
Cited by: 8
Author(s): Leslie A. Saxon, Brooks DiPaula, Glenn R. Fox, Rebecca Ebert, Josiah Duhaime, Luciano Nocera, Luan Tran, Mona Sobhani
Software Mentions: 1
Published: over 4 years ago

10.1186/1752-0509-5-180

A multi-tissue type genome-scale metabolic network for analysis of whole-body systems physiology
Cited by: 152
Author(s): Aarash Bordbar, Adam M. Feist, Renata Usaite-Black, Joseph Woodcock, Bernhard Ø. Palsson, Iman Famili
Software Mentions: 1
Published: about 13 years ago

10.1186/s12864-016-2648-8

Exploration of the Drosophila buzzatii transposable element content suggests underestimation of repeats in Drosophila genomes
Cited by: 23
Author(s): Núria Rius, Yolanda Guillén, Alejandra Delprat, Aurélie Kapusta, Cédric Feschotte, Alfredo Ruíz
Software Mentions: 1
Published: over 8 years ago

10.1186/1471-2105-11-474

ModuleOrganizer: detecting modules in families of transposable elements
Cited by: 6
Author(s): Sébastien Tempel, Christine Rousseau, Fariza Tahi, Jacques Nicolas
Software Mentions: 1
Published: over 14 years ago

10.3389/fmolb.2017.00096

Perspectives on Systems Modeling of Human Peripheral Blood Mononuclear Cells
Cited by: 58
Author(s): Partho Sen, Esko Kemppainen, Matej Orešič
Software Mentions: 1
Published: almost 7 years ago

10.3389/fmolb.2021.682559

Gaining Insights Into Metabolic Networks Using Chemometrics and Bioinformatics: Chronic Kidney Disease as a Clinical Model
Cited by: 4
Author(s): Julien Bernard, Domitille Schvartz, Santiago Codesido, Mohamed Hanafi, Yoric Gagnebin, Belén Ponte, Fabien Jourdan
Software Mentions: 1
Published: over 3 years ago

10.1186/s12915-019-0654-4

Inferring cancer dependencies on metabolic genes from large-scale genetic screens
Cited by: 15
Author(s): Shoval Lagziel, Won Dong Lee, Tomer Shlomi
Software Mentions: 1
Published: over 5 years ago

10.3389/fncir.2013.00201

Inference of neuronal network spike dynamics and topology from calcium imaging data
Cited by: 73
Author(s): Henry Lütcke, Felipe Gerhard, Friedemann Zenke, Wulfram Gerstner, Fritjof Helmchen
Software Mentions: 1
Published: almost 12 years ago

10.3389/fonc.2019.01010

Super-Resolution 1H Magnetic Resonance Spectroscopic Imaging Utilizing Deep Learning
Cited by: 46
Author(s): Zohaib Iqbal, Dan Nguyen, Gilbert Hangel, Stanislav Motyka, Wolfgang Bogner, Steve B Jiang
Software Mentions: 1
Published: about 5 years ago

10.2196/24486

Demystifying the Dark Web Opioid Trade: Content Analysis on Anonymous Market Listings and Forum Posts
Cited by: 7
Author(s): Zhengyi Li, Xiangyu Du, Xiaojing Liao, Xiaoqian Jiang, Tiffany Champagne‐Langabeer
Software Mentions: 1
Published: almost 4 years ago

10.3389/fphys.2013.00092

Novel insights into obesity and diabetes through genome-scale metabolic modeling
Cited by: 36
Author(s): Leif Väremo, Intawat Nookaew, Jens Nielsen
Software Mentions: 1
Published: almost 12 years ago

10.1186/1471-2105-6-126

Cited by: 56
Author(s): Mythily Ganapathi, Pragya Srivastava, Sushanta Kumar Das Sutar, Kaushal Kumar, Dipayan Dasgupta, Gajinder Pal Singh, Vani Brahmachari, Samir K. Brahmachari
Software Mentions: 1
Published: almost 20 years ago

10.1093/g3journal/jkab031

Genome Assembly of the Canadian two-row Malting Barley cultivar AAC Synergy
Cited by: 5
Author(s): Wayne Xu, James R. Tucker, Wubishet A. Bekele, Frank M. You, Yong‐Bi Fu, Raju Khanal, Zhen Yao, Jaswinder Singh, Brian Boyle, Aaron D. Beattie, François Belzile, Martin Mascher, Nicholas A. Tinker, Ana Badea
Software Mentions: 1
Published: almost 4 years ago

10.1186/1471-2105-11-393

Compartmentalization of the Edinburgh Human Metabolic Network
Cited by: 85
Author(s): Tong Hao, Hongwu Ma, Xiao‐Fan Zhao, Igor Goryanin
Software Mentions: 1
Published: over 14 years ago

10.3390/ijms20061385

Current Status and Future Prospects of Clinically Exploiting Cancer-specific Metabolism—Why Is Tumor Metabolism Not More Extensively Translated into Clinical Targets and Biomarkers?
Cited by: 11
Author(s): Muthu Magesh, Anders Nordström
Software Mentions: 1
Published: almost 6 years ago

10.1093/hmg/ddx090

Amelogenesis imperfecta caused by N-terminal enamelin point mutations in mice and men is driven by endoplasmic reticulum stress
Cited by: 16
Author(s): Steven J. Brookes, Martin J. Barron, Claire E. L. Smith, James A. Poulter, Alan J. Mighell, Chris F. Inglehearn, Catriona J. Brown, Helen Rodd, Jennifer Kirkham, Michael J. Dixon
Software Mentions: 1
Published: almost 8 years ago

10.1186/1758-2946-6-2

Comparative evaluation of open source software for mapping between metabolite identifiers in metabolic network reconstructions: application to Recon 2
Cited by: 24
Author(s): Hulda S. Haraldsdóttir, Ines Thiele, Ronan M. T. Fleming
Software Mentions: 1
Published: almost 11 years ago

10.3390/jfb12010011

Electrospun Poly(butylene-adipate-co-terephthalate)/Nano-hyDroxyapatite/Graphene Nanoribbon Scaffolds Improved the In Vivo Osteogenesis of the Neoformed Bone
Cited by: 10
Author(s): Luana Marotta Reis de Vasconcellos, Gabriela de Fátima Santana-Melo, Edmundo Silva, Vanessa Fernandes Pereira, Juliani Caroline Ribeiro de Araújo, André Diniz Rosa Silva, André Sales Aguiar Furtado, Conceição de Maria Vaz Elias, Bartolomeu C. Viana, Fernanda Roberta Marciano, Anderson Oliveira Lobo
Software Mentions: 1
Published: almost 4 years ago

10.1007/s11306-013-0564-3

An analysis of a ‘community-driven’ reconstruction of the human metabolic network
Cited by: 31
Author(s): Neil Swainston, Pedro Mendes, Douglas B. Kell
Software Mentions: 1
Published: over 11 years ago

10.1007/s11306-016-1051-4

Recon 2.2: from reconstruction to model of human metabolism
Cited by: 230
Author(s): Neil Swainston, Kieran Smallbone, Hooman Hefzi, Paul D. Dobson, Judy McKinley Brewer, Michael Hanscho, Daniel C. Zielinski, Kok Siong Ang, Natalie J. Gardiner, Jahir M. Gutierrez, Sarantos Kyriakopoulos, Meiyappan Lakshmanan, Shangzhong Li, Joanne K. Liu, Verónica Martı́nez, Camila A. Orellana, Lake‐Ee Quek, Asha Thomas, Juergen Zanghellini, Nicole Borth, Dong-Yup Lee, Lars K. Nielsen, Douglas B. Kell, Nathan E. Lewis, Pedro Mendes
Software Mentions: 1
Published: over 8 years ago

10.1186/1759-8753-5-9

Visual ModuleOrganizer: a graphical interface for the detection and comparative analysis of repeat DNA modules
Cited by: 0
Author(s): Sébastien Tempel, Emmanuel Talla
Software Mentions: 1
Published: almost 11 years ago

10.3390/molecules24193615

The Power of LC-MS Based Multiomics: Exploring Adipogenic Differentiation of Human Mesenchymal Stem/Stromal Cells
Cited by: 19
Author(s): Evelyn Rampler, Dominik Egger, Harald Schoeny, Mate Rusz, Maria Pires Pacheco, Giada Marino, Cornelia Kasper, Thomas Nägele, Gunda Koellensperger
Software Mentions: 1
Published: about 5 years ago

10.3390/metabo7040058

Metabolomic Modularity Analysis (MMA) to Quantify Human Liver Perfusion Dynamics
Cited by: 6
Author(s): Gautham Sridharan, Bote G. Bruinsma, Shyam Sundhar Bale, Anandh Swaminathan, Nima Saeidi, Martin L. Yarmush, Korkut Uygun
Software Mentions: 1
Published: about 7 years ago

Projects: cran: Recon

Papers Mentioning Recon 114