Ecosyste.ms: Papers

10.1186/s12934-017-0852-0

Insights into metabolic osmoadaptation of the ectoines-producer bacterium Chromohalobacter salexigens through a high-quality genome scale metabolic model
Cited by: 20
Author(s): Francine Piubeli, Manuel Salvador, Montserrat Argandoña, Joaquı́n J. Nieto, Vicente Bernal, José M. Pastor, Manuel Cánovas, Carmen Regla Vargas
Software Mentions: 1
Published: almost 7 years ago

10.1186/s12934-015-0396-0

Simulating cyanobacterial phenotypes by integrating flux balance analysis, kinetics, and a light distribution function
Cited by: 7
Author(s): Lian He, Stephen Gang Wu, Ni Wan, Adrienne C. Reding, Yinjie J. Tang
Software Mentions: 1
Published: almost 9 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

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/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

10.1186/1475-2859-11-27

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

10.3390/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

10.3390/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/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

10.1186/1476-4598-8-124

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

10.1186/1476-4598-9-51

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/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

10.1186/1476-4598-4-42

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

10.1186/1476-4598-6-49

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

10.1186/1476-4598-11-40

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

10.1186/1476-4598-9-264

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

10.1002/1878-0261.12191

<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

10.15252/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

10.15252/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

10.15252/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

10.3390/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

10.3390/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/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/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/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

10.3390/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

10.3390/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

10.7717/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

10.7717/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

10.3390/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

10.1098/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

10.1371/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

10.1371/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

10.1371/journal.pcbi.1003848

Genome-Scale Metabolic Network Validation of Shewanella oneidensis Using Transposon Insertion Frequency Analysis
Cited by: 25
Author(s): Hong Yang, Elias W. Krumholz, Evan D. Brutinel, Nagendra P. Palani, Michael J. Sadowsky, Andrew Odlyzko, Jeffrey A. Gralnick, Igor G. L. Libourel
Software Mentions: 1
Published: about 10 years ago

10.1371/journal.pcbi.1003370

Metabolic Constraint-Based Refinement of Transcriptional Regulatory Networks
Cited by: 29
Author(s): Sriram Chandrasekaran, Nathan D. Price
Software Mentions: 1
Published: almost 11 years ago

10.1371/journal.pcbi.1003081

Flux Balance Analysis of Cyanobacterial Metabolism: The Metabolic Network of Synechocystis sp. PCC 6803
Cited by: 212
Author(s): Henning Knoop, Marianne Gründel, Yvonne Zilliges, Robert Lehmann, Sabrina Hoffmann, Wolfgang Lockau, Ralf Steuer
Software Mentions: 1
Published: over 11 years ago

10.1371/journal.pcbi.1006936

A benchmark-driven approach to reconstruct metabolic networks for studying cancer metabolism
Cited by: 24
Author(s): Oveis Jamialahmadi, Sameereh Hashemi‐Najafabadi, Ehsan Motamedian, Stefano Romeo, Fatemeh Bagheri
Software Mentions: 1
Published: over 5 years ago

10.1371/journal.pcbi.1003575

Constraint-Based Modeling of Carbon Fixation and the Energetics of Electron Transfer in Geobacter metallireducens
Cited by: 32
Author(s): Adam M. Feist, Harish Nagarajan, Amelia-Elena Rotaru, Pier-Luc Tremblay, Tian Zhang, Kelly P. Nevin, Derek R. Lovley, Karsten Zengler
Software Mentions: 1
Published: over 10 years ago

10.1371/journal.pcbi.1008528

Genome-scale metabolic modelling when changes in environmental conditions affect biomass composition
Cited by: 15
Author(s): Christian Schulz, Tjaša Kumelj, Emil Karlsen, Eivind Almaas
Software Mentions: 1
Published: over 3 years ago

10.1371/journal.pcbi.1002688

Modeling Phenotypic Metabolic Adaptations of Mycobacterium tuberculosis H37Rv under Hypoxia
Cited by: 59
Author(s): Xin Fang, Anders Wallqvist, Jaques Reifman
Software Mentions: 1
Published: about 12 years ago

10.1371/journal.pcbi.1000292

Identification of Potential Pathway Mediation Targets in Toll-like Receptor Signaling
Cited by: 54
Author(s): Liancheng Fan, Ines Thiele, Neema Jamshidi, Bernhard Ø. Palsson
Software Mentions: 1
Published: almost 16 years ago

10.1371/journal.pcbi.1005085

Efficient Reconstruction of Predictive Consensus Metabolic Network Models
Cited by: 19
Author(s): Ruben G. A. van Heck, Mathias Ganter, Vítor A. P. Martins dos Santos, Joerg Stelling
Software Mentions: 1
Published: about 8 years ago

10.1371/journal.pcbi.1000887

Characterizing the Metabolism of Dehalococcoides with a Constraint-Based Model
Cited by: 51
Author(s): Mahmudul Islam, Elizabeth A. Edwards, Radhakrishnan Mahadevan
Software Mentions: 1
Published: over 14 years ago

10.1371/journal.pcbi.1004913

Constrained Allocation Flux Balance Analysis
Cited by: 130
Author(s): Matteo Mori, Terence Hwa, Olivier Martin, Andrea De Martino, Enzo Marinari
Software Mentions: 1
Published: over 8 years ago

10.1371/journal.pcbi.1005539

SteadyCom: Predicting microbial abundances while ensuring community stability
Cited by: 131
Author(s): Siu Hung Joshua Chan, Margaret Simons, Costas D. Maranas
Software Mentions: 1
Published: over 7 years ago

10.1371/journal.pgen.1000745

Frequent Long-Range Epigenetic Silencing of Protocadherin Gene Clusters on Chromosome 5q31 in Wilms' Tumor
Cited by: 128
Author(s): Anthony R. Dallosso, Anne L. Hancock, Marianna Szemes, Kim Moorwood, Laxmi Chilukamarri, Hsin-Hao Tsai, Abby Sarkar, Jonathan Barasch, Raisa Vuononvirta, Chris Jones, Kathy Pritchard‐Jones, Brigitte Royer‐Pokora, Sean Bong Lee, Ceris Owen, Sally Malik, Feng Yue, Marcus Frank, Andrew Ward, Keith Brown, Karim Malik
Software Mentions: 1
Published: almost 15 years ago

10.1371/journal.pgen.1001212

Altered DNA Methylation in Leukocytes with Trisomy 21
Cited by: 98
Author(s): Kristi Kerkel, Nicole Schupf, Kota Hatta, Deborah Pang, Martha Salas, Alexander Kratz, Mark D. Minden, Vundavalli V. Murty, Warren B. Zigman, Richard Mayeux, Edmund C. Jenkins, Ali Torkamani, Nicholas J. Schork, Wayne Silverman, B. Anne Croy, Benjamin Tycko
Software Mentions: 1
Published: about 14 years ago

10.1371/journal.pgen.1000162

An Sp1/Sp3 Binding Polymorphism Confers Methylation Protection
Cited by: 69
Author(s): Yanis Boumber, Yutaka Kondo, Xuqi Chen, Lanlan Shen, Yi Guo, Carmen S. Tellez, Marcos R.H. Estécio, Saira Ahmed, Jean–Pierre J. Issa
Software Mentions: 1
Published: over 16 years ago

10.1371/journal.pgen.1003373

Epigenetic Upregulation of lncRNAs at 13q14.3 in Leukemia Is Linked to the In Cis Downregulation of a Gene Cluster That Targets NF-kB
Cited by: 131
Author(s): Angela Garding, Nupur Bhattacharya, Rainer Claus, Melanie Ruppel, Cordula Tschuch, Katharina Filarsky, Irina Idler, Manuela Zucknick, Maïwen Caudron-Herger, Christopher C. Oakes, Verena Fleig, Ioanna Keklikoglou, Danilo Allegra, Leticia Serra, Sudhir Thakurela, Vijay Tiwari, Dieter Weichenhan, Axel Benner, Bernhard Radlwimmer, Hanswalter Zentgraf, Stefan Wiemann, Karsten Rippe, Christoph Plass, Hartmut Döhner, Peter Lichter, Stephan Stilgenbauer, Daniel Mertens
Software Mentions: 1
Published: over 11 years ago

10.1371/journal.pgen.1000145

Antagonism between DNA and H3K27 Methylation at the Imprinted Rasgrf1 Locus
Cited by: 114
Author(s): Anders M. Lindroth, Yoon Jung Park, Chelsea McLean, Gregoriy A. Dokshin, Jenna Persson, Herry Herman, Diego Pasini, Xavier Miró, Mary E. Donohoe, Jeannie T. Lee, Kristian Helin, Paul D. Soloway
Software Mentions: 1
Published: over 16 years ago

10.1371/journal.pone.0204375

Metabolic network reconstruction and phenome analysis of the industrial microbe, Escherichia coli BL21(DE3)
Cited by: 17
Author(s): Hanseol Kim, Sinyeon Kim, Sung Ho Yoon
Software Mentions: 1
Published: about 6 years ago

10.1371/journal.pone.0009831

Dissection of Structure and Function of the N-Terminal Domain of Mouse DNMT1 Using Regional Frame-Shift Mutagenesis
Cited by: 5
Author(s): Leonardo D’Aiuto, Marco Marzulli, K. Naga Mohan, Ewa Borowczyk, Federica Saporiti, Andrew P. VanDemark, J. Richard Chaillet
Software Mentions: 1
Published: over 14 years ago

10.1371/journal.pone.0098760

Biochemical Characterization of Human Gluconokinase and the Proposed Metabolic Impact of Gluconic Acid as Determined by Constraint Based Metabolic Network Analysis
Cited by: 27
Author(s): Neha Rohatgi, T.K. Nielsen, Sara Petersen Bjørn, Ívar Axelsson, Giuseppe Paglia, Bjørn Gunnar Voldborg, Bernhard Ø. Palsson, Óttar Rolfsson
Software Mentions: 1
Published: over 10 years ago

10.1371/journal.pone.0009937

Targeting of De Novo DNA Methylation Throughout the Oct-4 Gene Regulatory Region in Differentiating Embryonic Stem Cells
Cited by: 64
Author(s): Rodoniki Athanasiadou, Dina De Sousa, Kevin Myant, Cara Merusi, Irina Stancheva, Adrian Bird
Software Mentions: 1
Published: over 14 years ago

10.1371/journal.pone.0002079

Identification of Novel Tumor Markers in Prostate, Colon and Breast Cancer by Unbiased Methylation Profiling
Cited by: 115
Author(s): Woonbok Chung, Bernard Kwabi-Addo, Michael Ittmann, Jaroslav Jelı́nek, Lanlan Shen, Yinhua Yu, Jean–Pierre J. Issa
Software Mentions: 1
Published: over 16 years ago

10.1371/journal.pone.0043658

Distinct DNA Methylation Dynamics of Spermatogenic Cell-Specific Intronless Genes Is Associated with CpG Content
Cited by: 7
Author(s): Yuzuru Kato, Masami Nozaki
Software Mentions: 1
Published: about 12 years ago

10.1371/journal.pone.0202565

A low-complexity metabolic network model for the respiratory and fermentative metabolism of Escherichia coli
Cited by: 3
Author(s): Ignace Tack, Philippe Nimmegeers, Simen Akkermans, Filip Logist, Jan Van Impe
Software Mentions: 1
Published: about 6 years ago

10.1371/journal.pone.0043006

Predictive Potential of Flux Balance Analysis of Saccharomyces cerevisiae Using as Optimization Function Combinations of Cell Compartmental Objectives
Cited by: 14
Author(s): Carlos Eduardo García Sánchez, César Augusto Vargas-García, Rodrigo Torres
Software Mentions: 1
Published: over 12 years ago

10.1371/journal.pone.0019862

Methylation Profile of Single Hepatocytes Derived from Hepatitis B Virus-Related Hepatocellular Carcinoma
Cited by: 59
Author(s): Ran Tao, Jun Li, Jiaojiao Xin, Jian Wu, Jing Guo, Liyuan Zhang, Liangliang Jiang, Wu Zhang, Zhe Yang, Lanjuan Li
Software Mentions: 1
Published: over 13 years ago

10.1371/journal.pone.0032812

Differential Differences in Methylation Status of Putative Imprinted Genes among Cloned Swine Genomes
Cited by: 26
Author(s): Chi–Yen Shen, Weijia Cheng, Shinn-Chih Wu, Hsiao Ling Chen, Tsung-Neng Tsai, Su‐Hua Yang, Chuan-Mu Chen
Software Mentions: 1
Published: over 12 years ago

10.1371/journal.pone.0007099

Lysosomal-Associated Protein Multispanning Transmembrane 5 Gene (LAPTM5) Is Associated with Spontaneous Regression of Neuroblastomas
Cited by: 42
Author(s): Jun Inoue, Akiko Misawa, Yukichi Tanaka, Shizuko Ichinose, Yuriko Sugino, Hajime Hosoi, Tohru Sugimoto, Issei Imoto, Johji Inazawa
Software Mentions: 1
Published: about 15 years ago

10.1371/journal.pone.0094103

COLD-PCR Amplification of Bisulfite-Converted DNA Allows the Enrichment and Sequencing of Rare Un-Methylated Genomic Regions
Cited by: 13
Author(s): Elena Castellanos-Rizaldos, Coren A. Milbury, Elli Karatza, Clark C. Chen, G. Mike Makrigiorgos, Anne Merewood
Software Mentions: 1
Published: over 10 years ago

10.1371/journal.pone.0176131

InMAP: A model for air pollution interventions
Cited by: 120
Author(s): Christopher W. Tessum, Jason Hill, Julian Marshall
Software Mentions: 1
Published: over 7 years ago

10.1371/journal.pone.0139590

Physiologically Shrinking the Solution Space of a Saccharomyces cerevisiae Genome-Scale Model Suggests the Role of the Metabolic Network in Shaping Gene Expression Noise
Cited by: 1
Author(s): Baofang Chi, Shiheng Tao, Yanlin Liu
Software Mentions: 1
Published: about 9 years ago

10.1371/journal.pone.0044951

Cysteine Dioxygenase 1 Is a Tumor Suppressor Gene Silenced by Promoter Methylation in Multiple Human Cancers
Cited by: 99
Author(s): Mariana Brait, Shizhang Ling, Jatin Nagpal, Xiaofei Chang, Hannah Lui Park, Juna Lee, Jun Okamura, Keishi Yamashita, David Sidransky, Myoung Sook Kim
Software Mentions: 1
Published: about 12 years ago

10.1371/journal.pone.0041977

PATHLOGIC-S: A Scalable Boolean Framework for Modelling Cellular Signalling
Cited by: 6
Author(s): Liam G. Fearnley, Lars K. Nielsen
Software Mentions: 1
Published: over 12 years ago

10.1371/journal.pone.0158004

Transcriptional Truncation of the Long Coding Imprinted Gene Usp29
Cited by: 3
Author(s): Hui He, An Ye, Joomyeong Kim
Software Mentions: 1
Published: over 8 years ago

10.1371/journal.pone.0113728

A Pragmatic Approach to Assess the Exposure of the Honey Bee (Apis mellifera) When Subjected to Pesticide Spray
Cited by: 34
Author(s): Yannick Poquet, Laurent Bodin, Marc Tchamitchian, Marion Fusellier, Barbara Giroud, Florent Lafay, Audrey Buleté, Sylvie Tchamitchian, Marianne Cousin, Michel Pélissier, Jean-Luc Brunet, Luc Belzunces
Software Mentions: 1
Published: about 10 years ago

10.1371/journal.pone.0165877

Heterogeneous Uptake of Nanoparticles in Mouse Models of Pediatric High-Risk Neuroblastoma
Cited by: 15
Author(s): Ketan B. Ghaghada, Zbigniew Starosolski, Anna Lakoma, Caterina Kaffes, Saurabh Agarwal, Khannan K. Athreya, Jason M. Shohet, Eugene Kim, Ananth Annapragada
Software Mentions: 1
Published: about 8 years ago

10.1371/journal.pone.0184435

Histone deacetylase regulates insulin signaling via two pathways in pancreatic β cells
Cited by: 20
Author(s): Yukina Kawada, Shun‐ichiro Asahara, Yumiko Sugiura, Ayaka Sato, Ayuko Furubayashi, Mitsuhiro Kawamura, Alberto Bartolomé, Emi Terashi-Suzuki, Toshihiro Takai, Ayumi Kanno, Maki Koyanagi‐Kimura, Tomokazu Matsuda, Naoko Hashimoto, Yoshiaki Kido
Software Mentions: 1
Published: about 7 years ago

10.1371/journal.pone.0212368

Implementing artificial neural networks through bionic construction
Cited by: 6
Author(s): Hongchang Hu, Xu Yang, Zhihua Xu, Ning Deng, Yingjie Shang, Lianping Guo, Mengyao Ji, Wenhao Zheng, Jinfeng Zhao, Li Min Dong
Software Mentions: 1
Published: over 5 years ago

10.1371/journal.pone.0109478

LINE-1 Hypomethylation in Blood and Tissue Samples as an Epigenetic Marker for Cancer Risk: A Systematic Review and Meta-Analysis
Cited by: 121
Author(s): Martina Barchitta, Annalisa Quattrocchi, Andrea Maugeri, Manlio Vinciguerra, Antonella Agodi
Software Mentions: 1
Published: about 10 years ago

10.1371/journal.pone.0025634

GSTP1 DNA Methylation and Expression Status Is Indicative of 5-aza-2′-Deoxycytidine Efficacy in Human Prostate Cancer Cells
Cited by: 47
Author(s): Karen Chiam, Margaret M. Centenera, Lisa M. Butler, Wayne D. Tilley, Tina Bianco‐Miotto
Software Mentions: 1
Published: about 13 years ago

10.1371/journal.pone.0050908

18F-FDG PET Imaging of Murine Atherosclerosis: Association with Gene Expression of Key Molecular Markers
Cited by: 44
Author(s): Anne Mette Fisker Hag, Sune Folke Pedersen, Christina Christoffersen, Tina Binderup, Mette Munk Jensen, Jesper Tranekjær Jørgensen, Dorthe Skovgaard, R Ripa, Andreas Kjær
Software Mentions: 1
Published: almost 12 years ago

10.1371/journal.pone.0011935

Evolutionary Systems Biology of Amino Acid Biosynthetic Cost in Yeast
Cited by: 59
Author(s): Michael D. Barton, Daniela Delneri, Stephen G. Oliver, Magnus Rattray, Casey M. Bergman
Software Mentions: 1
Published: over 14 years ago

10.1371/journal.pone.0014060

Gemcitabine Functions Epigenetically by Inhibiting Repair Mediated DNA Demethylation
Cited by: 42
Author(s): Andrea Schäfer, Lars Schomacher, Guillermo Barreto, Gabi Döderlein, Christof Niehrs
Software Mentions: 1
Published: about 14 years ago

10.1371/journal.pone.0183357

Terminal differentiation of T cells is strongly associated with CMV infection and increased in HIV-positive individuals on ART and lifestyle matched controls
Cited by: 34
Author(s): Thijs Booiman, Ferdinand W. N. M. Wit, Arginell F. Girigorie, Irma Maurer, Davide De Francesco, Caroline Sabin, Agnes M. Harskamp, Maria Prins, Claudio Franceschi, Steven G. Deeks, Alan Winston, Peter Reiss, Neeltje A. Kootstra
Software Mentions: 1
Published: over 7 years ago

10.1371/journal.pone.0115607

Delayed Contrast Enhancement Imaging of a Murine Model for Ischemia Reperfusion with Carbon Nanotube Micro-CT
Cited by: 2
Author(s): Laurel Burk, Ko Han Wang, John Matthew Wait, Eunice Kang, Monte S. Willis, Jianping Lu, Otto Zhou, Yueh Z. Lee
Software Mentions: 1
Published: almost 10 years ago

10.1371/journal.pone.0051511

MultiMetEval: Comparative and Multi-Objective Analysis of Genome-Scale Metabolic Models
Cited by: 32
Author(s): Piotr Zakrzewski, Marnix H. Medema, Albert Gevorgyan, Andrzej M. Kierzek, Rainer Breitling, Eriko Takano
Software Mentions: 1
Published: almost 12 years ago

10.1371/journal.pone.0113820

CONSTRICTOR: Constraint Modification Provides Insight into Design of Biochemical Networks
Cited by: 8
Author(s): Keesha E. Erickson, Ryan T. Gill, Anushree Chatterjee
Software Mentions: 1
Published: almost 10 years ago

10.1371/journal.pone.0239820

Structural equation modeling approach to explore the influence of childhood maltreatment in adults
Cited by: 9
Author(s): Kuniyoshi Toyoshima, Takeshi Inoue, Jiro Masuya, Yota Fujimura, Shinji Higashi, Hajime Tanabe, Ichiro Kusumi
Software Mentions: 1
Published: about 4 years ago

10.1371/journal.pone.0145821

Manipulation of Ovarian Function Significantly Influenced Trabecular and Cortical Bone Volume, Architecture and Density in Mice at Death
Cited by: 14
Author(s): Jeffrey B. Mason, Boston C. Terry, Samer Merchant, Holly M. Mason, Mahdi Nazokkarmaher
Software Mentions: 1
Published: almost 9 years ago

10.1371/journal.pone.0070386

Hypomethylation of Alu Elements in Post-Menopausal Women with Osteoporosis
Cited by: 63
Author(s): Pornrutsami Jintaridth, Rungsunn Tungtrongchitr, Sangchai Preutthipan, Apiwat Mutirangura
Software Mentions: 1
Published: over 11 years ago

10.1371/journal.pone.0087494

Genome-Scale NAD(H/+) Availability Patterns as a Differentiating Feature between Saccharomyces cerevisiae and Scheffersomyces stipitis in Relation to Fermentative Metabolism
Cited by: 6
Author(s): A Acevedo, Germán Aroca, Raúl Conejeros
Software Mentions: 1
Published: almost 11 years ago

10.1371/journal.pone.0037009

Long Interspersed Nuclear Element-1 Hypomethylation and Oxidative Stress: Correlation and Bladder Cancer Diagnostic Potential
Cited by: 67
Author(s): Maturada Patchsung, Chanchai Boonla, Passakorn Amnattrakul, Thasinas Dissayabutra, Apiwat Mutirangura, Piyaratana Tosukhowong
Software Mentions: 1
Published: over 12 years ago

10.1371/journal.pone.0025913

Spreading of Alu Methylation to the Promoter of the MLH1 Gene in Gastrointestinal Cancer
Cited by: 16
Author(s): Xiyin Wang, Jing Fan, Dong Liu, Shanlin Fu, Sigurður Ingvarsson, Huiping Chen
Software Mentions: 1
Published: about 13 years ago

10.1371/journal.pone.0034337

A Systems Biology Approach to Drug Targets in Pseudomonas aeruginosa Biofilm
Cited by: 42
Author(s): Gunnar Sigurðsson, Ronan M. T. Fleming, Almut Heinken, Ines Thiele
Software Mentions: 1
Published: over 12 years ago

10.1371/journal.pone.0116179

Trichloroethylene-Induced Gene Expression and DNA Methylation Changes in B6C3F1 Mouse Liver
Cited by: 27
Author(s): Yan Jiang, Jiahong Chen, Jian Tong, Tao Chen
Software Mentions: 1
Published: almost 10 years ago

10.1371/journal.pone.0140550

Control of Blood Pressure and Risk Attenuation: Post Trial Follow-Up of Randomized Groups
Cited by: 6
Author(s): Tazeen H. Jafar, Imtiaz Jehan, Lixia Feng, Sylvaine Barbier, Muhammad Islam, Rasool Bux, Aamir Hameed Khan, Nivedita Nadkarni, Neil Poulter, Nish Chaturvedi, Shah Ebrahim
Software Mentions: 1
Published: about 9 years ago

10.1371/journal.pone.0010726

Nucleoside Drugs Induce Cellular Differentiation by Caspase-Dependent Degradation of Stem Cell Factors
Cited by: 38
Author(s): Tanja Musch, Yuva Öz, Frank Lyko, Achim Breiling
Software Mentions: 1
Published: over 14 years ago

10.1371/journal.pone.0060105

Molecular and Clinical Studies in 138 Japanese Patients with Silver-Russell Syndrome
Cited by: 49
Author(s): Tomoko Fuke, Seiji Mizuno, Toshiro Nagai, Tomonobu Hasegawa, Reiko Horikawa, Yoko Miyoshi, Koji Muroya, Tatsuro Kondoh, Chikahiko Numakura, Seiji Sato, Kazuhiko Nakabayashi, Chiharu Tayama, Kenichiro Hata, Shinichiro Shinzaki, Kazuo Matsubara, Masayo Kagami, Kazuki Yamazawa, Tsutomu Ogata
Software Mentions: 1
Published: over 11 years ago

10.1371/journal.pone.0191791

The ‘COmorBidity in Relation to AIDS’ (COBRA) cohort: Design, methods and participant characteristics
Cited by: 12
Author(s): Davide De Francesco, Ferdinand W Wit, James H. Cole, Neeltje A. Kootstra, Alan Winston, Caroline Sabin, Jonathan Underwood, Rosan A van Zoest, Judith Schouten, Katherine W. Kooij, Maria Prins, Giovanni Guaraldi, Matthan W.A. Caan, David M. Burger, Claudio Franceschi, Claude Libert, Alexander Bürkle, Peter Reiss
Software Mentions: 1
Published: over 6 years ago

10.1371/journal.pone.0203311

Feedbacks from the metabolic network to the genetic network reveal regulatory modules in E. coli and B. subtilis
Cited by: 7
Author(s): Santhust Kumar, Saurabh Mahajan, Shaili Jain
Software Mentions: 1
Published: about 6 years ago

10.1371/journal.pone.0036947

Inferring Carbon Sources from Gene Expression Profiles Using Metabolic Flux Models
Cited by: 28
Author(s): Aaron Brandes, Desmond S. Lun, Kuhn Ip, Jeremy Zucker, Caroline Colijn, Brian Weiner, James E. Galagan
Software Mentions: 1
Published: over 12 years ago

10.1371/journal.pone.0004788

DNA Methylation of the ABO Promoter Underlies Loss of ABO Allelic Expression in a Significant Proportion of Leukemic Patients
Cited by: 52
Author(s): Tina Bianco‐Miotto, Damian J. Hussey, Tanya K. Day, Denise S. O’Keefe, Alexander Dobrovic
Software Mentions: 1
Published: over 15 years ago

10.1371/journal.pone.0042007

Extensive In Vivo Resilience of Persistent Salmonella
Cited by: 20
Author(s): Somedutta Barat, Benjamin Steeb, Alain Mazé, Dirk Bumann
Software Mentions: 1
Published: over 12 years ago

10.1371/journal.pone.0164158

Sex and Tissue Specificity of Peg3 Promoters
Cited by: 7
Author(s): Bambarendage P. U. Perera, Joomyeong Kim
Software Mentions: 1
Published: about 8 years ago

10.1371/journal.pone.0005809

Epigenetic Regulation of Adipocyte Differentiation by a Rho Guanine Nucleotide Exchange Factor, WGEF
Cited by: 25
Author(s): Takuro Horii, Sumiyo Morita, Masashi Kimura, Izuho Hatada
Software Mentions: 1
Published: over 15 years ago

10.1371/journal.pone.0114608

Predicting Growth Conditions from Internal Metabolic Fluxes in an In-Silico Model of E. coli
Cited by: 17
Author(s): Viswanadham Sridhara, Austin G. Meyer, Piyush Rai, Jeffrey E. Barrick, Pradeep Ravikumar, Daniel Segrè, Claus O. Wilke
Software Mentions: 1
Published: almost 10 years ago

10.1371/journal.pone.0010338

HOXB13, a Target of DNMT3B, Is Methylated at an Upstream CpG Island, and Functions as a Tumor Suppressor in Primary Colorectal Tumors
Cited by: 62
Author(s): Kalpana Ghoshal, Tasneem Motiwala, Rainer Claus, Pearlly S. Yan, Huban Kutay, Jharna Datta, Sarmila Majumder, Shoumei Bai, Arnab Majumder, Tim H.M. Huang, Christoph Plass, Samson T. Jacob
Software Mentions: 1
Published: over 14 years ago