Ecosyste.ms: Papers

10.1186/1471-2105-11-489

Computationally efficient flux variability analysis
Cited by: 269
Author(s): Steinn Guðmundsson, Ines Thiele
Software Mentions: 1
Published: about 14 years ago

10.1186/1471-2105-10-S1-S58

Analysis on relationship between extreme pathways and correlated reaction sets
Cited by: 7
Author(s): Yanping Xi, Yi‐Ping Phoebe Chen, Ming Cao, Weirong Wang, Fei Wang
Software Mentions: 1
Published: almost 16 years ago

10.1186/s12859-019-2682-z

Metabolic and signalling network maps integration: application to cross-talk studies and omics data analysis in cancer
Cited by: 8
Author(s): Nicolas Sompairac, Jennifer Modamio, Emmanuel Barillot, Ronan M. T. Fleming, Andreï Zinovyev, Inna Kuperstein
Software Mentions: 1
Published: over 5 years ago

10.1186/s12859-019-2897-z

Identification of critical connectors in the directed reaction-centric graphs of microbial metabolic networks
Cited by: 7
Author(s): Eun-Youn Kim, Daniel Ashlock, Sung Ho Yoon
Software Mentions: 1
Published: over 5 years ago

10.1186/1471-2105-12-196

Acorn: A grid computing system for constraint based modeling and visualization of the genome scale metabolic reaction networks via a web interface
Cited by: 14
Author(s): Jacek Sroka, Łukasz Bieniasz-Krzywiec, Szymon Gwóźdź, Dariusz Leniowski, Jakub Łącki, Mateusz Markowski, Claudio Avignone–Rossa, Michael E. Bushell, Johnjoe McFadden, Andrzej M. Kierzek
Software Mentions: 1
Published: over 13 years ago

10.1186/1471-2105-13-6

MetRxn: a knowledgebase of metabolites and reactions spanning metabolic models and databases
Cited by: 114
Author(s): Akhil Kumar, Patrick F. Suthers, Costas D. Maranas
Software Mentions: 1
Published: almost 13 years ago

10.1186/1471-2105-10-S1-S62

Genome-scale analysis to the impact of gene deletion on the metabolism of E. coli: constraint-based simulation approach
Cited by: 3
Author(s): Zixiang Xu, Xiao Sun, Shu Yu
Software Mentions: 1
Published: almost 16 years ago

10.1186/1471-2105-15-140

A predictor for predicting Escherichia colitranscriptome and the effects of gene perturbations
Cited by: 5
Author(s): Maurice Ht Ling, Chueh Loo Poh
Software Mentions: 1
Published: over 10 years ago

10.1186/1472-6750-11-6

Systematic cross-validation of 454 sequencing and pyrosequencing for the exact quantification of DNA methylation patterns with single CpG resolution
Cited by: 40
Author(s): Anna Wuestefeld, Cord Albat, Britta Hasemeier, Katrin Haeussler, Stella Lamprecht, Sebastian Suerbaum, Hans Kreipe, Ulrich Lehmann
Software Mentions: 1
Published: almost 14 years ago

10.1186/1472-6750-10-2

Characterization of Proton Production and Consumption Associated with Microbial Metabolism
Cited by: 33
Author(s): K. Srinivasan, Radhakrishnan Mahadevan
Software Mentions: 1
Published: almost 15 years ago

10.1186/s12885-018-5207-7

A longitudinal mixed methods study on changes in body weight, body composition, and lifestyle in breast cancer patients during chemotherapy and in a comparison group of women without cancer: study protocol
Cited by: 13
Author(s): J.Th.C.M. de Kruif, Marjolein Visser, M.M.G.A. van den Berg, M. Derks, Michiel R. de Boer, Hanneke W. M. van Laarhoven, J.H.M. de Vries, Y.C. de Vries, Ellen Kampman, R. Winkels, Marjan J. Westerman
Software Mentions: 1
Published: almost 6 years ago

10.1186/1471-2407-9-123

Quantitation of DNA methylation by melt curve analysis
Cited by: 43
Author(s): Eric Smith, Michael E. Jones, Paul A. Drew
Software Mentions: 1
Published: over 15 years ago

10.1186/1471-2407-8-163

Involvement of TSC genes and differential expression of other members of the mTOR signaling pathway in oral squamous cell carcinoma
Cited by: 88
Author(s): Sanjukta Chakraborty, SM Azeem Mohiyuddin, KS Gopinath, Arun Kumar
Software Mentions: 1
Published: over 16 years ago

10.1186/1471-2407-9-447

ECRG4 is a candidate tumor suppressor gene frequently hypermethylated in colorectal carcinoma and glioma
Cited by: 75
Author(s): Silke Götze, Valeska Feldhaus, T Traska, Marietta Wolter, Guido Reifenberger, Andrea Tannapfel, C. Kühnen, Dirk Martin, Oliver Müller, Sonja Sievers
Software Mentions: 1
Published: almost 15 years ago

10.1186/s12885-019-5616-2

High methylation levels of PCDH10 predict poor prognosis in patients with pancreatic ductal adenocarcinoma
Cited by: 17
Author(s): Maria Cristina Curia, Fabiana Fantini, Rossano Lattanzio, Francesca Tavano, Francesco Molà, Mauro Piantelli, Pasquale Battista, Pierluigi di Sebastiano, Alessandro Cama
Software Mentions: 1
Published: over 5 years ago

10.1186/1471-2407-14-308

Demethylation of the miR-146a promoter by 5-Aza-2’-deoxycytidine correlates with delayed progression of castration-resistant prostate cancer
Cited by: 41
Author(s): Xiaolu Wang, Huimin Gao, Lixin Ren, Junfei Gu, Yanping Zhang, Yong Zhang
Software Mentions: 1
Published: over 10 years ago

10.1186/1471-2156-10-73

Hypermethylation of the DLC1 CpG island does not alter gene expression in canine lymphoma
Cited by: 21
Author(s): Jeffrey N. Bryan, Mohamed Jabbes, Linda M. Berent, Gerald L. Arthur, Kristen H. Taylor, Kerry Rissetto, Carolyn J. Henry, Farah Rahmatpanah, Wendi Velando Rankin, J. Armando Villamil, Michael R. Lewis, Charles W. Caldwell
Software Mentions: 1
Published: about 15 years ago

10.1186/1471-2156-10-50

Identification of a two-marker-haplotype on Bos taurus autosome 18 associated with somatic cell score in German Holstein cattle
Cited by: 11
Author(s): Bodo Brand, C.F. Baes, M. Mayer, Norbert Reinsch, Christa Kühn
Software Mentions: 1
Published: about 15 years ago

10.1186/1471-2164-12-9

The genome sequence of E. coli W (ATCC 9637): comparative genome analysis and an improved genome-scale reconstruction of E. coli
Cited by: 144
Author(s): Colin Archer, Jihyun F. Kim, Haeyoung Jeong, Jin Hwan Park, Claudia E. Vickers, Sang Yup Lee, Lars K. Nielsen
Software Mentions: 1
Published: almost 14 years ago

10.1186/1471-2164-9-72

Human glycolipid transfer protein (GLTP) genes: organization, transcriptional status and evolution
Cited by: 20
Author(s): Xianqiong Zou, Taeowan Chung, Xin Lin, Margarita Malakhova, Helen M. Pike, Rhoderick E. Brown
Software Mentions: 1
Published: almost 17 years ago

10.1186/1471-2164-8-131

Diverse histone modifications on histone 3 lysine 9 and their relation to DNA methylation in specifying gene silencing
Cited by: 42
Author(s): Jiejun Wu, Shu‐Huei Wang, Dustin Potter, Joseph C. Liu, Laura T. Smith, Yue Wu, Tim H.M. Huang, Christoph Plass
Software Mentions: 1
Published: over 17 years ago

10.1186/1471-2164-12-S4-S5

AlgaGEM – a genome-scale metabolic reconstruction of algae based on the Chlamydomonas reinhardtii genome
Cited by: 98
Author(s): Cristiana Gomes de Oliveira Dal’Molin, Lake‐Ee Quek, Robin W. Palfreyman, Lars K. Nielsen
Software Mentions: 1
Published: almost 14 years ago

10.1186/s12864-018-4905-5

Development and validation of an updated computational model of Streptomyces coelicolor primary and secondary metabolism
Cited by: 20
Author(s): Adam Amara, Eriko Takano, Rainer Breitling
Software Mentions: 1
Published: over 6 years ago

10.1186/1471-2164-12-582

Human native lipoprotein-induced de novo DNA methylation is associated with repression of inflammatory genes in THP-1 macrophages
Cited by: 36
Author(s): Rubén Rangel-Salazar, Marie Wickström-Lindholm, Carlos A. Aguilar-Salinas, Yolanda Alvarado‐Caudillo, Kristina B. V. Døssing, Manel Esteller, Emmanuel Labourier, Gertrud Lund, Finn C. Nielsen, Dalia Rodríguez‐Ríos, Martha Olivia Solís-Martínez, Katarzyna Wróbel, Kazimierz Wróbel, Silvio Zaina
Software Mentions: 1
Published: almost 13 years ago

10.1186/1755-8794-1-57

Discovery of DNA methylation markers in cervical cancer using relaxation ranking
Cited by: 32
Author(s): Maté Ongenaert, G. Bea A. Wisman, Haukeline H. Volders, Alice J. Koning, Ate G.J. van der Zee, Wim Van Criekinge, Ed Schuuring
Software Mentions: 1
Published: almost 16 years ago

10.1186/1471-2288-10-100

New directions in childhood obesity research: how a comprehensive biorepository will allow better prediction of outcomes
Cited by: 19
Author(s): Matthew A. Sabin, Susan Clemens, Richard Saffery, Zoë McCallum, Michele Campbell, Wieland Kieß, Nancy A. Crimmins, Jessica G. Woo, Gary M. Leong, George A. Werther, Obioha C Ukoumunne, Melissa Wake
Software Mentions: 1
Published: about 14 years ago

10.1186/1471-2199-15-24

Expression of GBGT1 is epigenetically regulated by DNA methylation in ovarian cancer cells
Cited by: 12
Author(s): Francis Jacob, Megan P. Hitchins, André Fedier, Kevin Brennan, Sheri Nixdorf, Neville F. Hacker, Robyn L. Ward, Viola Heinzelmann‐Schwarz
Software Mentions: 1
Published: almost 11 years ago

10.1186/1471-2202-14-136

Parkinson’s disease: dopaminergic nerve cell model is consistent with experimental finding of increased extracellular transport of α-synuclein
Cited by: 14
Author(s): Finja Büchel, Sandra Saliger, Andreas Dräger, Stephanie Hoffmann, Clemens Wrzodek, Andreas Zell, Philipp J. Kahle
Software Mentions: 1
Published: about 11 years ago

10.1186/1753-6561-7-S6-O5

First CpG island microarray for genome-wide analyses of DNA methylation in Chinese hamster ovary cells: new insights into the epigenetic answer to butyrate treatment
Cited by: 1
Author(s): Anna Wippermann, Sandra Klausing, Oliver Rupp, Thomas Noll, Raimund Hoffrogge
Software Mentions: 1
Published: almost 11 years ago

10.1186/1753-6561-9-S9-P26

A novel low-parameter computational model to aid in-silico glycoengineering
Cited by: 0
Author(s): Philipp N. Spahn, Anders Højgaard Hansen, Henning Gram Hansen, Jens Aage Hansen, Helene Faustrup Kildegaard, Nathan E. Lewis
Software Mentions: 1
Published: almost 9 years ago

10.1186/1753-6561-8-S4-P256

System biology of bacterial cellulose production
Cited by: 1
Author(s): Samara Silva de Souza, Luismar Marques Porto
Software Mentions: 1
Published: about 10 years ago

10.1186/s12918-017-0441-1

Reconstruction of the microalga Nannochloropsis salina genome-scale metabolic model with applications to lipid production
Cited by: 38
Author(s): Nicolás Loira, Sebastián N. Mendoza, María Paz Cortés, Natalia Palacios-Rojas, Dante Travisany, Alex Di Génova, Natalia Gajardo, Nicole Ehrenfeld, Alejandro Maass
Software Mentions: 1
Published: over 7 years ago

10.1186/1752-0509-5-20

MEMOSys: Bioinformatics platform for genome-scale metabolic models
Cited by: 31
Author(s): Stephan Pabinger, Robert Rader, Rasmus Ågren, Jens Nielsen, Zlatko Trajanoski
Software Mentions: 1
Published: almost 14 years ago

10.1186/1752-0509-6-140

A proof for loop-law constraints in stoichiometric metabolic networks
Cited by: 26
Author(s): Elad Noor, Nathan E. Lewis, Ron Milo
Software Mentions: 1
Published: almost 13 years ago

10.1186/1752-0509-4-145

Further developments towards a genome-scale metabolic model of yeast
Cited by: 99
Author(s): Paul D. Dobson, Kieran Smallbone, Daniel Jameson, Evangelos Simeonidis, Karin Lanthaler, Pınar Pir, Chuan-Zhen Lü, Neil Swainston, Warwick B. Dunn, Paul Fisher, Duncan Hull, Marie Brown, Olusegun Oshota, Natalie J. Stanford, Douglas B. Kell, Ross D. King, Stephen G. Oliver, Robert Stevens, Pedro Mendes
Software Mentions: 1
Published: about 14 years ago

10.1186/1752-0509-8-S1-S10

Comparison on extreme pathways reveals nature of different biological processes
Cited by: 0
Author(s): Yanping Xi, Yue Zhao, Li Wang, Fei Wang
Software Mentions: 1
Published: almost 11 years ago

10.1186/1752-0509-3-24

A fragile metabolic network adapted for cooperation in the symbiotic bacterium Buchnera aphidicola
Cited by: 94
Author(s): Gavin H. Thomas, Jeremy Zucker, Sandy MacDonald, Anatoly Sorokin, Igor Goryanin, Angela E. Douglas
Software Mentions: 1
Published: over 15 years ago

10.1186/s12918-015-0232-5

Resource constrained flux balance analysis predicts selective pressure on the global structure of metabolic networks
Cited by: 5
Author(s): Nima Abedpour, Markus Kollmann
Software Mentions: 1
Published: almost 9 years ago

10.1186/1752-0509-6-9

Predicting outcomes of steady-state 13C isotope tracing experiments using Monte Carlo sampling
Cited by: 28
Author(s): Jan Schellenberger, Daniel C. Zielinski, Wing‐Kit Choi, Sunthosh Madireddi, Vasiliy A. Portnoy, David A. Scott, Jennifer L. Reed, Andrei L. Osterman, Bernhard Ø. Palsson
Software Mentions: 1
Published: almost 13 years ago

10.1186/1752-0509-5-102

A metabolic model of the mitochondrion and its use in modelling diseases of the tricarboxylic acid cycle
Cited by: 60
Author(s): Anthony C. Smith, Alan J. Robinson
Software Mentions: 1
Published: almost 14 years ago

10.1186/1752-0509-5-83

Exploring the metabolic network of the epidemic pathogen Burkholderia cenocepacia J2315 via genome-scale reconstruction
Cited by: 39
Author(s): Kechi Fang, Hansheng Zhao, Cheng Sun, Carolyn M.C. Lam, Suhua Chang, Kunlin Zhang, Gurudutta Panda, Miguel Godinho, Vítor A. P. Martins dos Santos, Jing Wang
Software Mentions: 1
Published: over 13 years ago

10.1186/s12918-015-0217-4

Optimization of lipid production with a genome-scale model of Yarrowia lipolytica
Cited by: 96
Author(s): Martin Kavšček, Govindprasad Bhutada, Tobias Madl, Klaus Natter
Software Mentions: 1
Published: about 9 years ago

10.1186/s12918-017-0395-3

Making life difficult for Clostridium difficile: augmenting the pathogen’s metabolic model with transcriptomic and codon usage data for better therapeutic target characterization
Cited by: 24
Author(s): Sara Saheb Kashaf, Claudio Angione, Píetro Lió
Software Mentions: 1
Published: almost 8 years ago

10.1186/s12918-016-0383-z

The use of genome-scale metabolic network reconstruction to predict fluxes and equilibrium composition of N-fixing versus C-fixing cells in a diazotrophic cyanobacterium, Trichodesmium erythraeum
Cited by: 16
Author(s): Joseph J. Gardner, Nanette R. Boyle
Software Mentions: 1
Published: almost 8 years ago

10.1186/1752-0509-2-79

A genome-scale metabolic reconstruction of Pseudomonas putida KT2440: i JN746 as a cell factory
Cited by: 220
Author(s): Juan Nogales, Bernhard Ø. Palsson, Ines Thiele
Software Mentions: 1
Published: about 16 years ago

10.1186/1752-0509-3-37

Connecting extracellular metabolomic measurements to intracellular flux states in yeast
Cited by: 399
Author(s): Monica L. Mo, Bernhard Ø. Palsson, Markus J. Herrgård
Software Mentions: 1
Published: over 15 years ago

10.1186/s12918-014-0117-z

A curated C. difficile strain 630 metabolic network: prediction of essential targets and inhibitors
Cited by: 40
Author(s): M. Larocque, Thierry Chénard, Rafaël Najmanovich
Software Mentions: 1
Published: about 10 years ago

10.1186/1752-0509-6-42

Genome-scale modeling using flux ratio constraints to enable metabolic engineering of clostridial metabolism in silico
Cited by: 66
Author(s): Michael J. McAnulty, Jiun Y Yen, Benjamin G. Freedman, Ryan S. Senger
Software Mentions: 1
Published: over 12 years ago

10.1186/1752-0509-5-147

TIGER: Toolbox for integrating genome-scale metabolic models, expression data, and transcriptional regulatory networks
Cited by: 99
Author(s): Paul A. Jensen, Kyla Lutz, Jason A. Papin
Software Mentions: 1
Published: about 13 years ago

10.1186/1752-0509-5-122

A retrosynthetic biology approach to metabolic pathway design for therapeutic production
Cited by: 97
Author(s): Pablo Carbonell, Anne-Gaëlle Planson, Davide Fichera, Jean-Loup Faulon
Software Mentions: 1
Published: over 13 years ago

10.1186/s12918-018-0673-8

SLIMEr: probing flexibility of lipid metabolism in yeast with an improved constraint-based modeling framework
Cited by: 39
Author(s): Benjamín J. Sánchez, Feiran Li, Eduard J. Kerkhoven, Jens Nielsen
Software Mentions: 1
Published: almost 6 years ago

10.1186/1752-0509-5-155

The human metabolic reconstruction Recon 1 directs hypotheses of novel human metabolic functions
Cited by: 60
Author(s): Óttar Rolfsson, Bernhard Ø. Palsson, Ines Thiele
Software Mentions: 1
Published: about 13 years ago

10.1186/1752-0509-7-74

COBRApy: COnstraints-Based Reconstruction and Analysis for Python
Cited by: 856
Author(s): Ali Ebrahim, Joshua A. Lerman, Bernhard Ø. Palsson, Daniel R. Hyduke
Software Mentions: 1
Published: over 11 years ago

10.1186/1752-0509-6-S2-S9

Systematic Comparison of C3 and C4 Plants Based on Metabolic Network Analysis
Cited by: 67
Author(s): Chuanli Wang, Longyun Guo, Yixue Li, Zhuo Wang
Software Mentions: 1
Published: almost 13 years ago

10.1186/1752-0509-6-150

Genome-level transcription data of Yersinia pestis analyzed with a New metabolic constraint-based approach
Cited by: 68
Author(s): Ali Navid, Eivind Almaas
Software Mentions: 1
Published: almost 13 years ago

10.1186/1752-0509-7-132

A multi-level multi-scale approach to study essential genes in Mycobacterium tuberculosis
Cited by: 17
Author(s): Soma Ghosh, Priyanka Baloni, Sumanta Mukherjee, Praveen Anand, Nagasuma Chandra
Software Mentions: 1
Published: almost 11 years ago

10.1186/s12918-018-0675-6

DynamicME: dynamic simulation and refinement of integrated models of metabolism and protein expression
Cited by: 40
Author(s): Laurence T. Yang, Ali Ebrahim, Colton J. Lloyd, Michael A. Saunders, Bernhard Ø. Palsson
Software Mentions: 1
Published: almost 6 years ago

10.1186/1752-0509-1-26

Investigating the metabolic capabilities of Mycobacterium tuberculosis H37Rv using the in silico strain iNJ 661 and proposing alternative drug targets
Cited by: 252
Author(s): Neema Jamshidi, Bernhard Ø. Palsson
Software Mentions: 1
Published: over 17 years ago

10.1186/1752-0509-3-38

Constraint-based analysis of metabolic capacity of Salmonella typhimurium during host-pathogen interaction
Cited by: 140
Author(s): Anu Raghunathan, Jennifer L. Reed, Sook-il Shin, Bernhard Ø. Palsson, Simon Daefler
Software Mentions: 1
Published: over 15 years ago

10.1186/s12918-014-0085-3

Ki MoSys: a web-based repository of experimental data for KInetic MOdels of biological SYStems
Cited by: 20
Author(s): Rafael S. Costa, André Veríssimo, Susana Vinga
Software Mentions: 1
Published: over 10 years ago

10.1186/1752-0509-2-67

Machine learning based analyses on metabolic networks supports high-throughput knockout screens
Cited by: 44
Author(s): Kitiporn Plaimas, Jan‐Philipp Mallm, Marcus Oswald, Fabian Svara, Victor Sourjik, Roland Eils, Rainer König
Software Mentions: 1
Published: over 16 years ago

10.1186/s12918-017-0438-9

Remodeling adipose tissue through in silico modulation of fat storage for the prevention of type 2 diabetes
Cited by: 7
Author(s): Thierry Chénard, Frédéric Guénard, Marie‐Claude Vohl, André C. Carpentier, André Tchernof, Rafaël Najmanovich
Software Mentions: 1
Published: over 7 years ago

10.1136/bmjopen-2016-014161

Cost and outcome of behavioural activation versus cognitive behavioural therapy for depression (COBRA): a qualitative process evaluation
Cited by: 13
Author(s): Katie Finning, David Richards, Lucy Moore, David Ekers, Dean McMillan, Paul Farrand, Heather O’Mahen, Ed Watkins, Kim Wright, Emily Fletcher, Shelley Rhodes, Rebecca Woodhouse, Faye Wray
Software Mentions: 1
Published: over 7 years ago

10.3897/BDJ.6.e29443

A DNA barcode-assisted annotated checklist of the spider (Arachnida, Araneae) communities associated to white oak woodlands in Spanish National Parks
Cited by: 18
Author(s): Luís C Crespo, Marc Domènech, Alba Enguídanos, Jagoba Malumbres‐Olarte, Pedro Cardoso, Jordi Moya‐Laraño, Cristina Frías-López, Nuria Macías–Hernández, Eva De Mas, Paola Mazzuca, Elisa Mora, Věra Opatová, Enric Planas, Carles Ribera, Marcos Roca-Cusachs, Dolores Ruiz, Pedro Sousa, Vanina Tonzo, Miquel A. Arnedo
Software Mentions: 1
Published: almost 6 years ago

10.3897/BDJ.9.e69924

SLAM Project - Long Term Ecological Study of the Impacts of Climate Change in the natural forest of Azores: I - the spiders from native forests of Terceira and Pico Islands (2012-2019)
Cited by: 10
Author(s): Ricardo Costa, Paulo A. V. Borges
Software Mentions: 1
Published: about 3 years ago

10.3897/BDJ.8.e47502

Standardised inventories of spiders (Arachnida, Araneae) of Macaronesia II: The native forests and dry habitats of Madeira archipelago (Madeira and Porto Santo islands)
Cited by: 11
Author(s): Jagoba Malumbres‐Olarte, Mário Boieiro, Pedro Cardoso, Rui Carvalho, Luís C Crespo, Rosalina Gabriel, Nuria Macías–Hernández, Octávio S. Paulo, Fernando Pereira, Carla Rego, Alejandra Ros‐Prieto, Isamberto Silva, Alberto Vieira, François Rigal, Paulo A. V. Borges
Software Mentions: 1
Published: almost 5 years ago

10.1093/bioinformatics/btx052

CHRR: coordinate hit-and-run with rounding for uniform sampling of constraint-based models
Cited by: 65
Author(s): Hulda S. Haraldsdóttir, Ben Cousins, Ines Thiele, Ronan M. T. Fleming, Santosh Vempala
Software Mentions: 1
Published: almost 8 years ago

10.1186/1745-6150-9-9

A framework for application of metabolic modeling in yeast to predict the effects of nsSNV in human orthologs
Cited by: 1
Author(s): Hayley Dingerdissen, Daniel Weaver, Peter D. Karp, Yang Pan, Vahan Simonyan, Raja Mazumder
Software Mentions: 1
Published: over 10 years ago

10.1186/1480-9222-14-5

A reinvestigation of somatic hypermethylation at the PTEN CpG island in cancer cell lines
Cited by: 24
Author(s): Luke B. Hesson, Deborah Packham, Emily Pontzer, Pauline Funchain, Charis Eng, Robyn L. Ward
Software Mentions: 1
Published: over 12 years ago

10.1155/2015/876047

Putative Epimutagens in Maternal Peripheral and Cord Blood Samples Identified Using Human Induced Pluripotent Stem Cells
Cited by: 5
Author(s): Yoshikazu Arai, Koji Hayakawa, Daisuke Arai, Rie Ito, Yusuke Iwasaki, Koichi Saito, Kazuhiko Akutsu, Satoshi Takatori, Rie Ishii, Rumiko Hayashi, Shun-ichiro Izumi, Norihiro Sugino, Fumio Kondo, Masakazu Horie, Hiroyuki Nakazawa, Tsunehisa Makino, Mitsuko Hirosawa, Kunio Shiota, Jun Ohgane
Software Mentions: 1
Published: almost 10 years ago

10.1155/2015/506782

An Integrated Modeling and Experimental Approach to Study the Influence of Environmental Nutrients on Biofilm Formation ofPseudomonas aeruginosa
Cited by: 6
Author(s): Zhaobin Xu, Sabina Islam, Thomas K. Wood, Zuyi Huang
Software Mentions: 1
Published: almost 10 years ago

10.1155/2016/1393089

Methylation Status of Alu and LINE-1 Interspersed Repetitive Sequences in Behcet’s Disease Patients
Cited by: 13
Author(s): Şahru Yüksel, Selma Ozbek Kucukazman, Gülten Sungur Karataş, Mehmet Akif Öztürk, Sasiprapa Prombhul, Nattiya Hirankarn
Software Mentions: 1
Published: almost 9 years ago

10.1155/2014/327538

Osteoponin Promoter Controlled by DNA Methylation: Aberrant Methylation in Cloned Porcine Genome
Cited by: 9
Author(s): Chi–Yen Shen, Yung‐An Tsou, Hsiao‐Ling Chen, Hung-Jin Huang, Shinn-Chih Wu, Weijia Cheng, Calvin Yu-Chian Chen, Chuan-Mu Chen
Software Mentions: 1
Published: almost 11 years ago

10.1155/2015/421747

LINE-1 Methylation Patterns as a Predictor of Postmolar Gestational Trophoblastic Neoplasia
Cited by: 11
Author(s): Ruangsak Lertkhachonsuk, Krissada Paiwattananupant, Patou Tantbírójn, Prakasit Rattanatanyong, Apiwat Mutirangura
Software Mentions: 1
Published: almost 10 years ago

10.1186/s13030-020-00183-x

Associations between the depressive symptoms, subjective cognitive function, and presenteeism of Japanese adult workers: a cross-sectional survey study
Cited by: 25
Author(s): Kuniyoshi Toyoshima, Takeshi Inoue, Akiyoshi Shimura, Jiro Masuya, Masahiko Ichiki, Yota Fujimura, Ichiro Kusumi
Software Mentions: 1
Published: over 4 years ago

10.1186/s13030-021-00218-x

Subjective cognitive impairment and presenteeism mediate the associations of rumination with subjective well-being and ill-being in Japanese adult workers from the community
Cited by: 1
Author(s): Kuniyoshi Toyoshima, Masahiko Ichiki, Takeshi Inoue, Akiyoshi Shimura, Jiro Masuya, Yota Fujimura, Shinji Higashi, Ichiro Kusumi
Software Mentions: 1
Published: about 3 years ago

10.1016/j.biosystems.2017.09.014

Cyclic decomposition explains a photosynthetic down regulation for Chlamydomonas reinhardtii
Cited by: 4
Author(s): Stephen P. Chapman, M. Tadeu dos Santos, Giles N. Johnson, Mauricío Vieira Kritz, Jean-Marc Schwartz
Software Mentions: 1
Published: almost 7 years ago

10.1002/bit.26905

Extension of the yeast metabolic model to include iron metabolism and its use to estimate global levels of iron‐recruiting enzyme abundance from cofactor requirements
Cited by: 14
Author(s): Duygu Dikicioglu, Stephen G. Oliver
Software Mentions: 1
Published: almost 6 years ago

10.1186/s13068-017-0708-1

Exploring eukaryotic formate metabolisms to enhance microbial growth and lipid accumulation
Cited by: 10
Author(s): Zhiguo Liu, Tolutola Oyetunde, Whitney D. Hollinshead, Anna Hermanns, Yinjie J. Tang, Wei Liao, Yan Liu
Software Mentions: 1
Published: almost 8 years ago

10.1186/s13068-017-0792-2

Development of a core Clostridium thermocellum kinetic metabolic model consistent with multiple genetic perturbations
Cited by: 29
Author(s): Satyakam Dash, Ali Khodayari, Zhou Jing-lun, Evert K. Holwerda, Daniel G. Olson, Lee R. Lynd, Costas D. Maranas
Software Mentions: 1
Published: over 7 years ago

10.1186/1754-6834-5-72

A constraint-based model of Scheffersomyces stipitis for improved ethanol production
Cited by: 27
Author(s): Ting Liu, Wei Zou, Li Liu, Jian Chen
Software Mentions: 1
Published: almost 13 years ago

10.1186/s13068-016-0607-x

Exploring complex cellular phenotypes and model-guided strain design with a novel genome-scale metabolic model of Clostridium thermocellum DSM 1313 implementing an adjustable cellulosome
Cited by: 28
Author(s): R. Adam Thompson, Sanjeev Dahal, Sergio Garcia, Intawat Nookaew, Cong T. Trinh
Software Mentions: 1
Published: about 8 years ago

10.1186/bcr1762

Correlation between CpG methylation profiles and hormone receptor status in breast cancers
Cited by: 140
Author(s): Weiwei Feng, Lanlan Shen, Sijin Wen, Daniel Rosen, Jaroslav Jelı́nek, Xin Hu, Shaoyi Huan, Miao Huang, Jinsong Liu, Ayşegül Şahin, Kelly K. Hunt, Robert C. Bast, Yu Shen, Jean–Pierre J. Issa, Yinhua Yu
Software Mentions: 1
Published: over 17 years ago

10.1186/s12935-021-01925-9

Cyproheptadine, an epigenetic modifier, exhibits anti-tumor activity by reversing the epigenetic silencing of IRF6 in urothelial carcinoma
Cited by: 1
Author(s): Yeong‐Chin Jou, Guan‐Ling Lin, Hon‐Yi Lin, Wan-Hong Huang, Yu-Ming Chuang, Ru-Inn Lin, Pie-Che Chen, Shu-Fen Wu, Cheng‐Huang Shen, Michael W.Y. Chan
Software Mentions: 1
Published: over 3 years ago

10.1002/cam4.780

Prognostic value of the ubiquitin ligase carboxyl terminus of the Hsc70‐interacting protein in postmenopausal breast cancer
Cited by: 10
Author(s): Sasagu Kurozumi, Yuri Yamaguchi, Shin Ichi Hayashi, Hiromi Hiyoshi, Tetsuji Suda, Tatsuyuki Gohno, Hiroshi Matsumoto, Hiroyuki Takei, Jun Horiguchi, Izumi Takeyoshi, Tetsunari Oyama, Masafumi Kurosumi
Software Mentions: 1
Published: over 8 years ago

10.1002/cam4.22

Strategies for discovery and validation of methylated and hydroxymethylated <scp>DNA</scp> biomarkers
Cited by: 105
Author(s): Ekaterina Olkhov‐Mitsel, Bharati Bapat
Software Mentions: 1
Published: about 12 years ago

10.1080/19420862.2021.1976705

Selective depletion of radiolabeled HER2-specific antibody for contrast improvement during PET
Cited by: 2
Author(s): Priyanka Khare, Wei Sun, Sreevidhya Ramakrishnan, Guiyang Hao, Su Tang Lo, Kien Nham, Xiankai Sun, Raimund J. Ober, E. Sally Ward, Rafal Swiercz
Software Mentions: 1
Published: almost 4 years ago

10.1007/s10334-020-00891-z

15 Years MR-encephalography
Cited by: 9
Author(s): Jürgen Hennig, Vesa Kiviniemi, Bruno Riemenschneider, Antonia Barghoorn, Burak Akın, Fei Wang, Pierre LeVan
Software Mentions: 1
Published: about 4 years ago

10.3390/md16080272

Chemical Mutagenesis and Fluorescence-Based High-Throughput Screening for Enhanced Accumulation of Carotenoids in a Model Marine Diatom Phaeodactylum tricornutum
Cited by: 30
Author(s): Zhaoxiang Yi, Yixi Su, Maonian Xu, Andreas Bergmann, Sævar Ingþórsson, Óttar Rolfsson, Kourosh Salehi‐Ashtiani, Sigurður Brynjólfsson, Weiqi Fu
Software Mentions: 1
Published: over 6 years ago

10.3390/ma12111787

Effect of the Nano-Ca(OH)2 Addition on the Portland Clinker Cooking Efficiency
Cited by: 1
Author(s): Azzurra Zucchini, Paola Comodi, Alessandro Di Michele, Riccardo Vivani, Lucia Mancini, Gabriele Lanzafame, S. Casagrande, Silvia Gentili, Francesco Vetere, Luca Bartolucci, Gianluca Polidori, F. Santinelli, Alessandro Neri
Software Mentions: 1
Published: over 5 years ago

10.1016/j.mec.2020.e00132

Modeling of nitrogen fixation and polymer production in the heterotrophic diazotroph Azotobacter vinelandii DJ
Cited by: 14
Author(s): Diego Tec-Campos, Cristal Zuñiga, Anurag Passi, John Del Toro, Juan D. Tibocha‐Bonilla, Alejandro Zepeda, Michael J. Betenbaugh, Karsten Zengler
Software Mentions: 1
Published: almost 4 years ago

10.1016/j.meteno.2017.08.001

UP Finder: A COBRA toolbox extension for identifying gene overexpression strategies for targeted overproduction
Cited by: 5
Author(s): Xi Wang, Liang Yu, Shulin Chen
Software Mentions: 1
Published: almost 7 years ago

10.3390/metabo5020211

Fermentative Production of the Diamine Putrescine: System Metabolic Engineering of Corynebacterium Glutamicum
Cited by: 62
Author(s): Anh Q. Nguyen, Jens Schneider, Gajendar Komati Reddy, Volker F. Wendisch
Software Mentions: 1
Published: over 9 years ago

10.3390/metabo2030614

What mRNA Abundances Can Tell us about Metabolism
Cited by: 35
Author(s): Andreas Hoppe
Software Mentions: 1
Published: about 12 years ago

10.3390/metabo10040159

Drought Stress Responses in Context-Specific Genome-Scale Metabolic Models of Arabidopsis thaliana
Cited by: 12
Author(s): Ratklao Siriwach, Fumio Mizutani, Kentarô Yano, Masami Yokota Hirai
Software Mentions: 1
Published: over 4 years ago

10.3390/metabo11070456

A Metabolic Model of Intestinal Secretions: The Link between Human Microbiota and Colorectal Cancer Progression
Cited by: 9
Author(s): Pejman Salahshouri, Modjtaba Emadi‐Baygi, Mahdi Jalili, Faiz M. Khan, Olaf Wolkenhauer, Ali Salehzadeh‐Yazdi
Software Mentions: 1
Published: over 3 years ago

10.3390/metabo2010242

Human Metabolic Network: Reconstruction, Simulation, and Applications in Systems Biology
Cited by: 9
Author(s): Ming Tsang Wu, Christina Chan
Software Mentions: 1
Published: over 12 years ago

10.3390/metabo5040601

Design Principles as a Guide for Constraint Based and Dynamic Modeling: Towards an Integrative Workflow
Cited by: 6
Author(s): Christiana Sehr, Andreas Kremling, Alberto Marı́n-Sanguino
Software Mentions: 1
Published: about 9 years ago

10.3390/metabo8010004

Machine Learning Methods for Analysis of Metabolic Data and Metabolic Pathway Modeling
Cited by: 109
Author(s): Miroslava Čuperlović-Culf
Software Mentions: 1
Published: almost 7 years ago

10.1186/1475-2859-12-118

Characterizing acetogenic metabolism using a genome-scale metabolic reconstruction of Clostridium ljungdahlii
Cited by: 128
Author(s): Harish Nagarajan, Merve Şahin, Juan Nogales, Haythem Latif, Derek R. Lovley, Ali Ebrahim, Karsten Zengler
Software Mentions: 1
Published: almost 11 years ago