Ecosyste.ms: Papers

10.1186/s12859-014-0420-0

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

10.1186/s12918-018-0677-4

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

10.1016/j.cell.2019.10.030

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

10.1186/s13148-016-0269-3

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

10.1186/s12862-016-0733-x

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

10.3390/e22101101

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

10.1371/journal.pcbi.1005895

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

10.1186/s13223-017-0198-5

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

10.1371/journal.pone.0112524

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

10.1186/1471-2180-12-S1-S5

Metabolic stasis in an ancient symbiosis: genome-scale metabolic networks from two Blattabacterium cuenoti strains, primary endosymbionts of cockroaches
Cited by: 37
Author(s): Carmen M. González-Domenech, Eugeni Belda, Rafael Patiño-Navarrete, Andrés Moya, Juli Peretó, Amparo Latorre
Software Mentions: 2
Published: almost 13 years ago

10.1371/journal.pone.0227977

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

10.1371/journal.pone.0126966

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

10.1371/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

10.1186/s12866-019-1591-7

Dynamic metabolic modelling of overproduced protein secretion in Streptomyces lividans using adaptive DFBA
Cited by: 2
Author(s): José Ramón Valverde, Sonia Gullón, Clara A. García-Herrero, Iván Campoy, Rafael P. Mellado
Software Mentions: 2
Published: about 5 years ago

10.1371/journal.pone.0253983

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

10.1371/journal.pone.0027316

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

10.1186/s12859-017-1722-9

SBMLmod: a Python-based web application and web service for efficient data integration and model simulation
Cited by: 5
Author(s): Sascha Schäuble, Anne-Kristin Stavrum, Mathias Bockwoldt, Pål Puntervoll, Ines Heiland
Software Mentions: 2
Published: over 7 years ago

10.1371/journal.pone.0027550

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

10.1371/journal.pone.0210008

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

10.1371/journal.pone.0102319

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

10.1371/journal.pone.0021554

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

10.1186/1476-4598-9-44

A Genome-wide screen identifies frequently methylated genes in haematological and epithelial cancers
Cited by: 89
Author(s): Thomas L. Dunwell, Luke B. Hesson, Tibor A. Rauch, Lihui Wang, Richard E. Clark, Ashraf Dallol, Dean Gentle, Daniel Catchpoole, Eamonn R. Maher, Gerd P. Pfeifer, Farida Latif
Software Mentions: 2
Published: over 14 years ago

10.1371/journal.pone.0154216

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

10.1371/journal.pone.0148031

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

10.1371/journal.pcbi.1000312

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

10.1371/journal.pcbi.1004924

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

10.1371/journal.pone.0028730

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

10.1371/journal.pone.0049978

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

10.1186/s12864-016-3311-0

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

10.15252/msb.20156157

Do genome‐scale models need exact solvers or clearer standards?
Cited by: 53
Author(s): Ali Ebrahim, Eivind Almaas, Eugen Bauer, Aarash Bordbar, Anthony P. Burgard, Roger L. Chang, Andreas Dräger, Imam Famili, Adam M. Feist, Ronan M. T. Fleming, Stephen S. Fong, Vassily Hatzimanikatis, Markus J. Herrgård, Allen Holder, Michael Hucka, Daniel R. Hyduke, Neema Jamshidi, Sang Yup Lee, Nicolas Le Novère, Joshua A. Lerman, Nathan E. Lewis, Ding Ma, Radhakrishnan Mahadevan, Costas D. Maranas, Harish Nagarajan, Ali Navid, Jens Nielsen, Lars K. Nielsen, Juan Nogales, Alberto Noronha, Csaba Pál, Bernhard Ø. Palsson, Jason A. Papin, Kiran Raosaheb Patil, Nathan D. Price, Jennifer L. Reed, Michael A. Saunders, Ryan S. Senger, Nikolaus Sonnenschein, Yuekai Sun, Ines Thiele
Software Mentions: 2
Published: about 9 years ago

10.1186/1752-0509-5-36

Microarray data can predict diurnal changes of starch content in the picoalga Ostreococcus
Cited by: 37
Author(s): Oksana Sorokina, Florence Corellou, David Dauvillée, Anatoly Sorokin, Igor Goryanin, Steven Ball, François‐Yves Bouget, Andrew J. Millar
Software Mentions: 2
Published: almost 14 years ago

10.1371/journal.pone.0055137

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

10.1186/s12859-020-3440-y

SWIFTCORE: a tool for the context-specific reconstruction of genome-scale metabolic networks
Cited by: 7
Author(s): Mojtaba Tefagh, Stephen Boyd
Software Mentions: 2
Published: over 4 years ago

10.1371/journal.pcbi.1007646

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

10.1186/1471-2164-14-82

DNA methylation profile dynamics of tissue-dependent and differentially methylated regions during mouse brain development
Cited by: 15
Author(s): Keiji Hirabayashi, Kunio Shiota, Shusuke Yagi
Software Mentions: 2
Published: almost 12 years ago

10.1371/journal.pone.0013017

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

10.1371/journal.pone.0044858

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

10.3390/cancers11121976

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

10.3389/fmicb.2017.02599

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

10.1038/s41598-020-65659-w

ACBM: An Integrated Agent and Constraint Based Modeling Framework for Simulation of Microbial Communities
Cited by: 18
Author(s): Emadoddin Karimian, Ehsan Motamedian
Software Mentions: 2
Published: over 4 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

10.1186/1752-0509-3-38

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

10.1371/journal.pcbi.1003098

Consistent Estimation of Gibbs Energy Using Component Contributions
Cited by: 222
Author(s): Elad Noor, Hulda S. Haraldsdóttir, Ron Milo, Ronan M. T. Fleming
Software Mentions: 1
Published: over 11 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

10.1186/1471-2164-12-582

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

10.1098/rsta.2019.0191

Some practical constraints and solutions for optical camera communication
Cited by: 40
Author(s): Weijie Liu, Zhiwei Xu
Software Mentions: 1
Published: over 4 years ago

10.3390/ph4091236

Target Profile Prediction and Practical Evaluation of a Biginelli-Type Dihydropyrimidine Compound Library
Cited by: 10
Author(s): Petra Schneider, Katharina Stutz, Ladina Kasper, Sarah Haller, Michael Reutlinger, Felix Reisen, Tim Geppert, Gisbert Schneider
Software Mentions: 1
Published: about 13 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

10.7717/peerj.6685

Genome-scale metabolic reconstruction and metabolic versatility of an obligate methanotroph<i>Methylococcus capsulatus</i>str. Bath
Cited by: 11
Author(s): Ankit Gupta, Ahmad Ahmad, Dipesh Chothwe, Midhun K. Madhu, Shireesh Srivastava, Vineet K. Sharma
Software Mentions: 1
Published: over 5 years ago

10.7717/peerj.5492

Alu hypermethylation and high oxidative stress in patients with musculoskeletal tumors
Cited by: 4
Author(s): Thamonwan Woraruthai, Chris Charoenlap, Chindanai Hongsaprabhas, Apiwat Mutirangura, Sittisak Honsawek
Software Mentions: 1
Published: over 6 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

10.3390/v13071320

Targeting Viral Surface Proteins through Structure-Based Design
Cited by: 6
Author(s): Yogesh B. Narkhede, Karen J. Gonzalez, Eva-Maria Strauch
Software Mentions: 1
Published: over 3 years ago

10.3390/v13060973

Targeting Antigens for Universal Influenza Vaccine Development
Cited by: 12
Author(s): Quyen Thi Nguyen, Young‐Ki Choi
Software Mentions: 1
Published: over 3 years ago

10.1371/journal.pcbi.1004999

Identification of Conserved Moieties in Metabolic Networks by Graph Theoretical Analysis of Atom Transition Networks
Cited by: 25
Author(s): Hulda S. Haraldsdóttir, Ronan M. T. Fleming
Software Mentions: 1
Published: about 8 years ago

10.3390/vetsci8090198

Protective Effects of Water Extract of Fructus Ligustri Lucidi against Oxidative Stress-Related Osteoporosis In Vivo and In Vitro
Cited by: 5
Author(s): Yi Wu, Yusheng Hu, Zhi Zhao, Lei Xu, Ye Chen, Tongtong Liu, Qin Li
Software Mentions: 1
Published: about 3 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/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/s12859-014-0409-8

DFBAlab: a fast and reliable MATLAB code for dynamic flux balance analysis
Cited by: 106
Author(s): Jose A. Gomez, Kai Höffner, Paul I. Barton
Software Mentions: 1
Published: almost 10 years ago

10.3390/vaccines9070793

Next Generation of Computationally Optimized Broadly Reactive HA Vaccines Elicited Cross-Reactive Immune Responses and Provided Protection against H1N1 Virus Infection
Cited by: 17
Author(s): Ying Huang, Monique França, James D. Allen, Hua Shi, Ted M. Ross
Software Mentions: 1
Published: over 3 years ago

10.3390/vaccines8010143

Vaccination with Consensus H7 Elicits Broadly Reactive and Protective Antibodies against Eurasian and North American Lineage H7 Viruses
Cited by: 4
Author(s): Gendeal M Fadlallah, Fuying Ma, Zherui Zhang, Mengchan Hao, Juefu Hu, Mingxin Li, Haizhou Liu, Biling Liang, Yanfeng Yao, Rui Gong, Bo Zhang, Di Liu, Jianjun Chen
Software Mentions: 1
Published: over 4 years ago

10.3390/vaccines7020045

Computational Approaches and Challenges to Developing Universal Influenza Vaccines
Cited by: 10
Author(s): Xing‐Biao Qiu, Venkata R. Duvvuri, Justin Bahl
Software Mentions: 1
Published: over 5 years ago

10.3390/vaccines6030046

Avian Influenza A Virus Pandemic Preparedness and Vaccine Development
Cited by: 28
Author(s): Rory D. de Vries, Sander Herfst, Mathilde Richard
Software Mentions: 1
Published: over 6 years ago

10.15252/msb.20199235

Community standards to facilitate development and address challenges in metabolic modeling
Cited by: 28
Author(s): Maureen A. Carey, Andreas Dräger, Moritz Emanuel Beber, Jason A. Papin, James T. Yurkovich
Software Mentions: 1
Published: over 4 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

10.15252/msb.202010093

Proteome constraints reveal targets for improving microbial fitness in nutrient‐rich environments
Cited by: 35
Author(s): Chen Yu, Eunice van Pelt-KleinJan, Berdien van Olst, Sieze Douwenga, Sjef Boeren, Herwig Bachmann, Douwe Molenaar, Jens Nielsen, Bas Teusink
Software Mentions: 1
Published: over 3 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

10.1186/1471-2164-12-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

10.15252/msb.20167411

Improving the phenotype predictions of a yeast genome‐scale metabolic model by incorporating enzymatic constraints
Cited by: 333
Author(s): Benjamín J. Sánchez, Cheng Cheng Zhang, Anders Nilsson, Petri‐Jaan Lahtvee, Eduard J. Kerkhoven, Jens Nielsen
Software Mentions: 1
Published: over 7 years ago

10.1002/1878-0261.12191

<scp>DNA</scp> methylation profiling reveals a pathological signature that contributes to transcriptional defects of <scp>CD</scp> 34 ⁺ <scp>CD</scp> 15 ⁻ cells in early chronic‐phase chronic myeloid leukemia
Cited by: 22
Author(s): Stéphanie Maupetit‐Mehouas, Franck Court, Céline Bourgne, Agnès Guerci‐Bresler, Pascale Cony‐Makhoul, Hyacinthe Johnson, Gabriel Étienne, Philippe Rousselot, Denis Guyotat, Alexandre Janel, Éric Hermet, Sandrine Saugues, Juliette Berger, Philippe Arnaud, Marc Berger
Software Mentions: 1
Published: over 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/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

10.1186/1476-4598-9-264

Frequent epigenetic inactivation of RASSF2 in thyroid cancer and functional consequences
Cited by: 49
Author(s): Undraga Schagdarsurengin, Antje Richter, Juliane Hornung, Cornelia Lange, Katrin Steinmann, Reinhard Dammann
Software Mentions: 1
Published: about 14 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

10.1186/1471-2164-8-131

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

10.1186/1471-2105-13-6

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

10.1155/2017/7481619

The Influence of Oblique Angle Forced Exercise in Surgically Destabilized Stifle Joints Is Synergistic with Bone, but Antagonistic with Cartilage in an Ovine Model of Osteoarthritis
Cited by: 4
Author(s): Rachel J. Hill, Holly M. Mason, Gavin Yeip, Samer Merchant, Aaron L. Olsen, Rusty Stott, Arnaud J. Van Wettere, Eadric Bressel, Jeffrey B. Mason
Software Mentions: 1
Published: over 7 years ago

10.1186/1476-4598-11-40

The RASSF gene family members RASSF5, RASSF6 and RASSF7 show frequent DNA methylation in neuroblastoma
Cited by: 70
Author(s): Anna Djos, Tommy Martinsson, Per Kogner, Helena Carén
Software Mentions: 1
Published: over 12 years ago

10.1186/1476-4598-6-49

RASSF1A promoter methylation and expression analysis in normal and neoplastic kidney indicates a role in early tumorigenesis
Cited by: 53
Author(s): Inga Peters, Kristina Rehmet, Nadine Wilke, Markus A. Kuczyk, Jörg Hennenlotter, Tyark Eilers, S. Machtens, Udo Jonas, Jürgen Serth
Software Mentions: 1
Published: over 17 years ago

10.1186/1476-4598-4-42

Metallothionien 3 expression is frequently down-regulated in oesophageal squamous cell carcinoma by DNA methylation
Cited by: 37
Author(s): Eric Smith, Paul A. Drew, Zi-Qing Tian, Neville J. De Young, Junfeng Liu, George C. Mayne, Andrew Ruszkiewicz, David I. Watson, Glyn G. Jamieson
Software Mentions: 1
Published: almost 19 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

10.1186/1471-2164-9-72

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/s12943-015-0340-2

TP53 R72P polymorphism modulates DNA methylation in hepatocellular carcinoma
Cited by: 12
Author(s): Khadija Rebbani, Agnès Marchio, Sayeh Ezzikouri, R. Afifi, Mostafa Kandil, Olfa Bahri, Henda Triki, Abdellah Essaid El Feydi, Anne S. Dejean, Soumaya Benjelloun, Pascal Pineau
Software Mentions: 1
Published: over 9 years ago

10.1186/1476-4598-9-51

Identification of 5 novel genes methylated in breast and other epithelial cancers
Cited by: 70
Author(s): Victoria Hill, Luke B. Hesson, Temuujin Dansranjavin, Ashraf Dallol, Ivan Bièche, Sophie Vacher, Stefania Tommasi, Timothy Dobbins, Dean Gentle, David M. Euhus, Cheryl Lewis, Reinhard Dammann, Robyn L. Ward, John D. Minna, ER Maher, Gerd P. Pfeifer, Farida Latif
Software Mentions: 1
Published: over 14 years ago

10.1186/1476-4598-8-124

The protein tyrosine phosphatase receptor type R gene is an early and frequent target of silencing in human colorectal tumorigenesis
Cited by: 34
Author(s): Mirco Menigatti, Elisa Cattaneo, Jacob Sabates–Bellver, Valery Ilinsky, Philip Went, Federico Buffoli, Víctor E. Márquez, Josef Jiricny, Giancarlo Marra
Software Mentions: 1
Published: almost 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

10.1186/1471-2105-12-196

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/s13229-018-0213-9

Integrated genome-wide Alu methylation and transcriptome profiling analyses reveal novel epigenetic regulatory networks associated with autism spectrum disorder
Cited by: 30
Author(s): Thanit Saeliw, Chayanin Tangsuwansri, Surangrat Thongkorn, Weerasak Chonchaiya, Kanya Suphapeetiporn, Apiwat Mutirangura, Tewin Tencomnao, Valerie W. Hu, Tewarit Sarachana
Software Mentions: 1
Published: over 6 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

10.3390/microorganisms8040539

Genome-Scale Metabolic Network Reconstruction and In Silico Analysis of Hexanoic acid Producing Megasphaera elsdenii
Cited by: 12
Author(s): Na Rae Lee, Choong Hwan Lee, Dong-Yup Lee, Jin Byung Park
Software Mentions: 1
Published: over 4 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

10.1186/1471-2156-10-50

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

10.3390/microorganisms7120620

Time Integrated Flux Analysis: Exploiting the Concentration Measurements Directly for Cost-Effective Metabolic Network Flux Analysis
Cited by: 1
Author(s): Rui M C Portela, Anne Richelle, Patrick Dumas, Moritz von Stosch
Software Mentions: 1
Published: almost 5 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

10.1186/1475-2859-11-27

Reconstruction and analysis of a genome-scale metabolic model for Scheffersomyces stipitis
Cited by: 52
Author(s): Balaji Balagurunathan, Sudhakar Jonnalagadda, Lily Tan, Rajagopalan Srinivasan
Software Mentions: 1
Published: over 12 years ago

10.1186/s12934-015-0404-4

Assessing methanotrophy and carbon fixation for biofuel production by Methanosarcina acetivorans
Cited by: 35
Author(s): Hadi Nazem‐Bokaee, Saratram Gopalakrishnan, James G. Ferry, Thomas K. Wood, Costas D. Maranas
Software Mentions: 1
Published: almost 9 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

10.1186/1471-2156-10-73

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/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/s12934-021-01614-2

Integration of enzyme constraints in a genome-scale metabolic model of Aspergillus niger improves phenotype predictions
Cited by: 11
Author(s): Jingru Zhou, Yingping Zhuang, Jian Xia
Software Mentions: 1
Published: over 3 years ago

10.1186/1475-2859-13-61

Genome-scale metabolic network reconstruction and in silico flux analysis of the thermophilic bacterium Thermus thermophilus HB27
Cited by: 17
Author(s): Na-Rae Lee, Meiyappan Lakshmanan, Shilpi Aggarwal, Ji‐Won Song, Iftekhar A. Karimi, Dong-Yup Lee, Jin Byung Park
Software Mentions: 1
Published: almost 11 years ago