cran: SAM | Projects | Ecosyste.ms: Papers

10.1371/journal.pone.0132452

Exploring Dance Movement Data Using Sequence Alignment Methods
Cited by: 11
Author(s): Seyed Hossein Chavoshi, Bernard De Baets, Tijs Neutens, Guy De Tré, Nico Van de Weghe
Software Mentions: 1
Published: about 11 years ago

10.1371/journal.pone.0068831

Distinct Pools of Non-Glycolytic Substrates Differentiate Brain Regions and Prime Region-Specific Responses of Mitochondria
Cited by: 20
Author(s): Mi Kyung Lee, Zhiyin Xun, Virginia M. Platt, Helen Budworth, Christie A. Canaria, Cynthia T. McMurray
Software Mentions: 1
Published: about 13 years ago

10.1371/journal.pone.0200288

The advantages of using drones over space-borne imagery in the mapping of mangrove forests
Cited by: 80
Author(s): Monika Ruwaimana, Behara Satyanarayana, Viviana Otero, Aidy M. Muslim, A Muhammad Syafiq, Salihu Ibrahim, Dries Raymaekers, Nico Koedam, Farid Dahdouh‐Guebas
Software Mentions: 1
Published: about 8 years ago

10.1371/journal.pone.0234992

Nonlinear adaptive NeuroFuzzy feedback linearization based MPPT control schemes for photovoltaic system in microgrid
Cited by: 14
Author(s): Muhammad Awais, Laiq Khan, Saghir Ahmad, Sidra Mumtaz, Rabiah Badar
Software Mentions: 1
Published: over 6 years ago

10.1371/journal.pone.0007592

Regulation of GABAA and Glutamate Receptor Expression, Synaptic Facilitation and Long-Term Potentiation in the Hippocampus of Prion Mutant Mice
Cited by: 61
Author(s): Alejandra Rangel, Noelia Madroñal, Agnès Gruart i. Massó, Rosalina Gavı́n, Franc Llorens, Lauro Sumoy, Juan María Torres, José M. Delgado‐García, José Antonio del Rı́o
Software Mentions: 1
Published: almost 17 years ago

10.1371/journal.pone.0068545

Discovery and Characterization of BlsE, a Radical S-Adenosyl-L-methionine Decarboxylase Involved in the Blasticidin S Biosynthetic Pathway
Cited by: 17
Author(s): Jun Feng, Jun Wu, Nan Dai, Shuangjun Lin, H. Howard Xu, Zixin Deng, Xinyi He
Software Mentions: 1
Published: about 13 years ago

10.1371/journal.pone.0002397

Virus Adaptation by Manipulation of Host's Gene Expression
Cited by: 83
Author(s): Ana Patrícia, Pablo Carbonell, Miguel A. Pérez‐Amador, Santiago F. Elena
Software Mentions: 1
Published: over 18 years ago

10.1371/journal.pone.0062752

Inhibition of DEPDC1A, a Bad Prognostic Marker in Multiple Myeloma, Delays Growth and Induces Mature Plasma Cell Markers in Malignant Plasma Cells
Cited by: 23
Author(s): Alboukadel Kassambara, Matthieu Schoenhals, Jérôme Moreaux, Jean-Luc Veyrune, Thierry Rème, Hartmut Goldschmidt, Dirk Hose, Bernard Klein
Software Mentions: 1
Published: over 13 years ago

10.1371/journal.pone.0126409

DIDA: Distributed Indexing Dispatched Alignment
Cited by: 14
Author(s): Hamid Mohamadi, Benjamin P. Vandervalk, Anthony Raymond, Shaun D. Jackman, Justin Chu, Clay P. Breshears, İnanç Birol
Software Mentions: 1
Published: over 11 years ago

10.1371/journal.pone.0051131

Systematic Analysis of the Gene Expression in the Livers of Nonalcoholic Steatohepatitis: Implications on Potential Biomarkers and Molecular Pathological Mechanism
Cited by: 17
Author(s): Yida Zhang, Susan S. Baker, Robert D. Baker, Rong Zhu, Lixin Zhu
Software Mentions: 1
Published: almost 14 years ago

10.1371/journal.pone.0107204

A Prolyl-Hydroxylase Inhibitor, Ethyl-3,4-Dihydroxybenzoate, Induces Cell Autophagy and Apoptosis in Esophageal Squamous Cell Carcinoma Cells via Up-Regulation of BNIP3 and N-myc Downstream-Regulated Gene-1
Cited by: 28
Author(s): Bo Han, Wei Li, Yulin Sun, Lanping Zhou, Yang Xu, Xiaohang Zhao
Software Mentions: 1
Published: about 12 years ago

10.1371/journal.pone.0192039

The use of geographic information system and 1860s cadastral data to model agricultural suitability before heavy mechanization. A case study from Malta
Cited by: 9
Author(s): Gianmarco Alberti, Reuben Grima, Nicholas C. Vella
Software Mentions: 1
Published: over 8 years ago

10.1371/journal.pone.0073074

Network and Data Integration for Biomarker Signature Discovery via Network Smoothed T-Statistics
Cited by: 59
Author(s): Yupeng Cun, Holger Fröhlich
Software Mentions: 1
Published: about 13 years ago

10.1371/journal.pone.0038465

γ-H2AX Kinetics as a Novel Approach to High Content Screening for Small Molecule Radiosensitizers
Cited by: 20
Author(s): Shihua Fu, Ying Yang, Das Tirtha, Yun Yen, Bing Zhou, Ming Zhou, Michael Ohlmeyer, Eric C. Ko, Ross L. Cagan, Barry S. Rosenstein, Shu hsia Chen, Johnny Kao
Software Mentions: 1
Published: over 14 years ago

10.1371/journal.pone.0011742

Comparative Membranome Expression Analysis in Primary Tumors and Derived Cell Lines
Cited by: 18
Author(s): Paolo Uva, Armin Lahm, Andrea Sbardellati, Anita Grigoriadis, Andrew Tutt, Emanuele de Rinaldis
Software Mentions: 1
Published: about 16 years ago

10.1371/journal.pone.0153903

The Influence of the Global Gene Expression Shift on Downstream Analyses
Cited by: 2
Author(s): Qifeng Xu, Xuegong Zhang
Software Mentions: 1
Published: over 10 years ago

10.1371/journal.pone.0124519

Traces of Unconscious Mental Processes in Introspective Reports and Physiological Responses
Cited by: 14
Author(s): Leonid Ivonin, He Chang, Marta Díaz, Andreu Catalá, Wei Chen, Matthias Rauterberg
Software Mentions: 1
Published: over 11 years ago

10.1371/journal.pone.0198714

Highly multiplexed genome engineering using CRISPR/Cas9 gRNA arrays
Cited by: 43
Author(s): Morito Kurata, Natalie K. Wolf, Walker S. Lahr, Madison T. Weg, Mitchell G. Kluesner, Samantha Lee, Kai Hui, Masano Shiraiwa, Beau R. Webber, Branden S. Moriarity
Software Mentions: 1
Published: about 8 years ago

10.1371/journal.pone.0022317

Cysteine-Rich Secretory Protein-3 (CRISP3) Is Strongly Up-Regulated in Prostate Carcinomas with the TMPRSS2-ERG Fusion Gene
Cited by: 38
Author(s): Franclim R. Ribeiro, Paula Paulo, Vera L. Costa, João D. Barros-Silva, João Ramalho-Carvalho, Carmen Jerónimo, Rui Henrique, Guro Elisabeth Lind, Rolf Inge Skotheim, Ragnhild Lothe, Manuel R. Teixeira
Software Mentions: 1
Published: about 15 years ago

10.1371/journal.pone.0044172

Sperm Cells Induce Distinct Cytokine Response in Peripheral Mononuclear Cells from Infertile Women with Serum Anti-Sperm Antibodies
Cited by: 6
Author(s): Miloslav Kverka, Z Ulčová-Gallová, Jiřina Bártová, J Cibulka, K Bibková, Z Mičanová, Helena Tlaskalová‐Hogenová
Software Mentions: 1
Published: about 14 years ago

10.1371/journal.pone.0030044

Host Genes Related to Paneth Cells and Xenobiotic Metabolism Are Associated with Shifts in Human Ileum-Associated Microbial Composition
Cited by: 28
Author(s): Tianyi Zhang, Robert A. DeSimone, Xiangmin Jiao, F. James Rohlf, Wei Zhu, Qing Gong, Steven R. Hunt, Themistocles Dassopoulos, Rodney D. Newberry, Erica Sodergren, George M. Weinstock, Charles E. Robertson, Daniel N. Frank, Ellen Li
Software Mentions: 1
Published: over 14 years ago

10.1371/journal.pone.0131927

Olfactomedin 4 Serves as a Marker for Disease Severity in Pediatric Respiratory Syncytial Virus (RSV) Infection
Cited by: 49
Author(s): H. Kim Brand, Inge M. L. Ahout, Dick de Ridder, Angela van Diepen, Y. Li, M. Zaalberg, Arno C. Andeweg, Nel Roeleveld, Ronald de Groot, Adilia Warris, Peter W. M. Hermans, Gerben Ferwerda, Frank J. T. Staal
Software Mentions: 1
Published: over 11 years ago

10.1371/journal.pone.0211760

Linking species functional traits of terrestrial vertebrates and environmental filters: A case study in temperate mountain systems
Cited by: 10
Author(s): Paula García-Llamas, Thiago F. Rangel, Leonor Calvo
Software Mentions: 1
Published: over 7 years ago

10.1371/journal.pone.0134757

Downstream Warming and Headwater Acidity May Diminish Coldwater Habitat in Southern Appalachian Mountain Streams
Cited by: 35
Author(s): Todd C. McDonnell, Matthew R. Sloat, Timothy J. Sullivan, C. Andrew Dolloff, Paul F. Hessburg, Nicholas A. Povak, W. A. Jackson, Christopher Sams
Software Mentions: 1
Published: about 11 years ago

10.1371/journal.pone.0009396

High Resolution Niche Models of Malaria Vectors in Northern Tanzania: A New Capacity to Predict Malaria Risk?
Cited by: 71
Author(s): Manisha A. Kulkarni, Rachelle E. Desrochers, Jeremy T. Kerr
Software Mentions: 1
Published: over 16 years ago

10.1371/journal.pone.0174297

miRNAs in the vitreous humor of patients affected by idiopathic epiretinal membrane and macular hole
Cited by: 24
Author(s): Andrea Russo, Marco Ragusa, Cristina Barbagallo, Antonio Longo, Teresio Avitabile, Maurizio G. Uva, Vincenza Bonfiglio, Mario Damiano Toro, Rosario Caltabiano, Cesare Mariotti, Francesco Boscia, Mario R. Romano, Cinzia Santa Di Pietro, Davide Barbagallo, Michele Purrello, Michele Reibaldi
Software Mentions: 1
Published: over 9 years ago

10.1371/journal.pone.0155993

Discovery and Validation of Prognostic Biomarker Models to Guide Triage among Adult Dengue Patients at Early Infection
Cited by: 12
Author(s): Junxiong Pang, Anna Lindblom, Thomas Tolfvenstam, Tun-Linn Thein, Ahmad Nazri Mohamed Naim, Ling Ling, Angelia Chow, Mark Chen, Eng Eong Ooi, Yee Sin Leo, Martin L. Hibberd
Software Mentions: 1
Published: over 10 years ago

10.1371/journal.pone.0016143

The Functional Consequences of Mutualistic Network Architecture
Cited by: 64
Author(s): José M. Gómez, Francisco Perfectti, Pedro Jordano
Software Mentions: 1
Published: over 15 years ago

10.1371/journal.pone.0007458

Genome-Wide Transcriptome Analyses of Silicon Metabolism in Phaeodactylum tricornutum Reveal the Multilevel Regulation of Silicic Acid Transporters
Cited by: 97
Author(s): Guillaume Sapriel, Michelle Quinet, Marc Heijde, Laurent Jourdren, Véronique Tanty, Guangzuo Luo, Stéphane Le Crom, Pascal J. Lopez
Software Mentions: 1
Published: almost 17 years ago

10.1371/journal.pone.0067728

Effect of Licochalcone A on Growth and Properties of Streptococcus suis
Cited by: 17
Author(s): Huaijie Hao, Wenjia Hui, Peng Liu, Qingyu Lv, Xiao-Tao Zeng, Hua Jiang, Yanzi Wang, Xin Zheng, Yinan Zheng, Jianchun Li, X. Y. Zhou, Yongqiang Jiang
Software Mentions: 1
Published: about 13 years ago

10.1371/journal.pone.0245407

One step forward, two steps back: Transcriptional advancements and fermentation phenomena in Actinobacillus succinogenes 130Z
Cited by: 3
Author(s): Dianna Long, Cheryl M. Immethun, Lisbeth Vallecilla-Yepez, Mark R. Wilkins, Rajib Saha
Software Mentions: 1
Published: over 5 years ago

10.1371/journal.pone.0134911

Comparison of the Transcriptional Profiles of Melanocytes from Dark and Light Skinned Individuals under Basal Conditions and Following Ultraviolet-B Irradiation
Cited by: 14
Author(s): Saioa López, Isabel Smith Zubiaga, Alicia García de Galdeano, María Dolores Boyano, Oscar Garcı́a, Jesús Gardeazábal, Conrado Martinez‐Cadenas, Neskuts Izagirre, Concepción de la Rúa, Santos Alonso
Software Mentions: 1
Published: about 11 years ago

10.1371/journal.pone.0017288

Fast Identification and Removal of Sequence Contamination from Genomic and Metagenomic Datasets
Cited by: 607
Author(s): Robert Schmieder, Robert A. Edwards
Software Mentions: 1
Published: over 15 years ago

10.1371/journal.pone.0102281

Gene Expression Profiling in Leiomyosarcomas and Undifferentiated Pleomorphic Sarcomas: SRC as a New Diagnostic Marker
Cited by: 28
Author(s): Rolando A R Villacis, Sara Martoreli Silveira, Mateus Camargo Barros-Filho, Fábio Albuquerque Marchi, Maria Aparecida Custódio Domingues, Cristovam Scapulatempo‐Neto, Samuel Aguiar, Ademar Lopes, Isabela Werneck da Cunha, Sílvia Regina Rogatto
Software Mentions: 1
Published: about 12 years ago

10.1371/journal.pone.0062924

Low Dose Decitabine Treatment Induces CD80 Expression in Cancer Cells and Stimulates Tumor Specific Cytotoxic T Lymphocyte Responses
Cited by: 83
Author(s): Lixin Wang, Zhen-Yang Mei, Jihao Zhou, Yushi Yao, Yonghui Li, Yihan Xu, Jingxin Li, Xiao‐Ning Gao, Min‐Hang Zhou, Mengmeng Jiang, Li Gao, Yi Ding, Xue-Chun Lu, Jianxin Shi, Xiumei Luo, Jia Wang, Lili Wang, Chunfeng Qu, Xue‐Feng Bai, Li Yu
Software Mentions: 1
Published: over 13 years ago

10.1371/journal.pone.0101786

Geographical, Temporal and Environmental Determinants of Bryophyte Species Richness in the Macaronesian Islands
Cited by: 40
Author(s): Silvia C. Aranda, Rosalina Gabriel, Paulo A. V. Borges, Ana M. C. Santos, Eduardo Brito de Azevedo, Jairo Patiño, Joaquín Hortal, Jorge M. Lobo
Software Mentions: 1
Published: over 12 years ago

10.1371/journal.pone.0148716

Arousal—But Not Valence—Reduces False Memories at Retrieval
Cited by: 37
Author(s): Chiara Mirandola, Enrico Toffalini
Software Mentions: 1
Published: over 10 years ago

10.1371/journal.pone.0061991

Acidosis Activation of the Proton-Sensing GPR4 Receptor Stimulates Vascular Endothelial Cell Inflammatory Responses Revealed by Transcriptome Analysis
Cited by: 117
Author(s): Lixue Dong, Zhigang Li, Nancy R. Leffler, Adam S. Asch, Jen‐Tsan Chi, Li V. Yang
Software Mentions: 1
Published: over 13 years ago

10.1371/journal.pone.0129560

Ground-Vegetation Clutter Affects Phyllostomid Bat Assemblage Structure in Lowland Amazonian Forest
Cited by: 30
Author(s): Rodrigo Marciente, Paulo Estefano Dineli Bobrowiec, William E. Magnusson
Software Mentions: 1
Published: over 11 years ago

10.1371/journal.pone.0002213

Replicative Senescence of Mesenchymal Stem Cells: A Continuous and Organized Process
Cited by: 932
Author(s): Wolfgang Wagner, Patrick Horn, Mirco Castoldi, Anke Diehlmann, Simone Bork, Rainer Saffrich, Vladimír Beneš, Jonathon Blake, Stefan M. Pfister, Volker Eckstein, Anthony D. Ho
Software Mentions: 1
Published: over 18 years ago

10.1371/journal.pone.0013858

Changes in Hepatic Gene Expression upon Oral Administration of Taurine-Conjugated Ursodeoxycholic Acid in ob/ob Mice
Cited by: 47
Author(s): Jae-Seong Yang, Jin Taek Kim, Jouhyun Jeon, Ho Sun Park, Gyeong Hoon Kang, Kyong Soo Park, Hong Kyu Lee, Sanguk Kim, Young Min Cho
Software Mentions: 1
Published: almost 16 years ago

10.1371/journal.pone.0101159

Optimal Screening of Children with Acute Malnutrition Requires a Change in Current WHO Guidelines as MUAC and WHZ Identify Different Patient Groups
Cited by: 77
Author(s): Arnaud Laillou, Prak Sophonneary, Richard de Groot, Sophie Whitney, Joel Conkle, Lindsey M. Horton, Sam Oeurn Un, Marjoleine A. Dijkhuizen, Frank T. Wieringa
Software Mentions: 1
Published: over 12 years ago

10.1371/journal.pone.0002444

Computational Systems Analysis of Dopamine Metabolism
Cited by: 64
Author(s): Zhengjian Qi, Gary W. Miller, Eberhard O. Voit
Software Mentions: 1
Published: over 18 years ago

10.1371/journal.pone.0220629

SNV discovery and functional candidate gene identification for milk composition based on whole genome resequencing of Holstein bulls with extremely high and low breeding values
Cited by: 7
Author(s): Lin Shan, Hongyan Zhang, Yali Hou, Lin Liu, Wenhui Li, Jianping Jiang, Bo Han, Shengli Zhang, Dongxiao Sun
Software Mentions: 1
Published: about 7 years ago

10.1371/journal.pone.0008856

Evidence for Gender-Specific Transcriptional Profiles of Nigral Dopamine Neurons in Parkinson Disease
Cited by: 114
Author(s): Filip Šimunović, Ming Yi, Yulei Wang, Robert M. Stephens, Kai‐Christian Sonntag
Software Mentions: 1
Published: over 16 years ago

10.1371/journal.pone.0153006

A Novel Prioritization Method in Identifying Recurrent Venous Thromboembolism-Related Genes
Cited by: 4
Author(s): Jing Jiang, Wan Li, Binhua Liang, Ruiqiang Xie, Binbin Chen, Hao Huang, Yiran Li, Yuehan He, Jun-Jie Liu, Weiming He, Lina Chen
Software Mentions: 1
Published: over 10 years ago

10.1371/journal.pone.0007809

Epigenetic Signatures Associated with Different Levels of Differentiation Potential in Human Stem Cells
Cited by: 99
Author(s): Pablo Aranda, Xabier Agirre, Esteban Ballestar, Enrique J. Andreu, José Román‐Gómez, Inés Prieto, José I. Martín‐Subero, Juan C. Cigudosa, Reiner Siebert, Manel Esteller, Felipe Prósper
Software Mentions: 1
Published: almost 17 years ago

10.1371/journal.pone.0060742

Land Use Explains the Distribution of Threatened New World Amphibians Better than Climate
Cited by: 28
Author(s): Fernanda Thiesen Brum, Larissa Oliveira Gonçalves, Laura Cappelatti, Marcos B. Carlucci, Vanderlei J. Debastiani, Elisa Viana Salengue, Guilherme Dubal dos Santos Seger, Camila Both, Jorge Bernardo-Silva, Rafael Loyola, Leandro da Silva Duarte
Software Mentions: 1
Published: over 13 years ago

10.1371/journal.pone.0104164

Molecular Pathogenesis of Post-Transplant Acute Kidney Injury: Assessment of Whole-Genome mRNA and MiRNA Profiles
Cited by: 60
Author(s): Julia Wilflingseder, Judith Sunzenauer, É. Toronyi, Andreas Heinzel, Alexander Kainz, Bernd Mayer, Paul Perco, Gábor Telkes, Róbert Langer, Rainer Oberbauer
Software Mentions: 1
Published: about 12 years ago

10.1371/journal.pone.0060202

Tissue-Specific Transcriptomic Profiling of Sorghum propinquum using a Rice Genome Array
Cited by: 6
Author(s): Ting Zhang, Xiuqin Zhao, Liying Huang, Xiaoyue Liu, Yuan Zong, Linghua Zhu, Daichang Yang, Binying Fu
Software Mentions: 1
Published: over 13 years ago

10.1371/journal.pone.0225426

Channel-spatial attention network for fewshot classification
Cited by: 11
Author(s): Yan Zhang, Min Fang, Nian Wang
Software Mentions: 1
Published: almost 7 years ago

10.1371/journal.pone.0252376

Shifting networks and mixing metals: Changing metal trade routes to Scandinavia correlate with Neolithic and Bronze Age transformations
Cited by: 16
Author(s): H. Nørgaard, Ernst Pernicka, Helle Vandkilde
Software Mentions: 1
Published: over 5 years ago

10.1371/journal.pone.0238887

The DROOPING LEAF (DR) gene encoding GDSL esterase is involved in silica deposition in rice (Oryza sativa L.)
Cited by: 6
Author(s): Yoye Yu, Mi-Ok Woo, Rihua Piao, Hee‐Jong Koh
Software Mentions: 1
Published: about 6 years ago

10.1371/journal.pone.0070352

Role of CTLA4 in the Proliferation and Survival of Chronic Lymphocytic Leukemia
Cited by: 37
Author(s): Amit Mittal, Nagendra K. Chaturvedi, Rae A. Rohlfsen, P. C. Sen Gupta, Avadhut D. Joshi, Ganapati V. Hegde, R. Gregory Bociek, Shantaram S. Joshi
Software Mentions: 1
Published: about 13 years ago

10.1371/journal.pone.0012028

Determining Frequent Patterns of Copy Number Alterations in Cancer
Cited by: 10
Author(s): Franck Rapaport, Christina C. Leslie
Software Mentions: 1
Published: about 16 years ago

10.1371/journal.pone.0117001

Tolerance Associated Gene Expression following Allogeneic Hematopoietic Cell Transplantation
Cited by: 9
Author(s): Joseph Pidala, Gregory Bloom, Steven Eschrich, Minnie M. Sarwal, Steve Enkemann, Brian C. Betts, Francisca Beato, Sean Yoder, Claudio Anasetti
Software Mentions: 1
Published: over 11 years ago

10.1371/journal.pone.0017035

Variability and Diversity of Nasopharyngeal Microbiota in Children: A Metagenomic Analysis
Cited by: 372
Author(s): Debby Bogaert, Bart J. F. Keijser, Susan M. Huse, John W. A. Rossen, Reinier H. Veenhoven, Elske van Gils, Jacob P. Bruin, R.C. Montijn, Marc J. M. Bonten, Elisabeth A. M. Sanders
Software Mentions: 1
Published: over 15 years ago

10.1371/journal.pone.0096305

Lipid Profiling and Transcriptomic Analysis Reveals a Functional Interplay between Estradiol and Growth Hormone in Liver
Cited by: 11
Author(s): Leandro Fernández-Pérez, Ruymán Santana-Farré, Mercedes de Mirecki-Garrido, Irma García, Borja Guerra, Carlos Mateo-Díaz, Diego Iglesias-Gato, J. C. Díaz-Chico, Amilcar Flores‐Morales, Mario Dı́az
Software Mentions: 1
Published: over 12 years ago

10.1371/journal.pone.0002937

Improved Elucidation of Biological Processes Linked to Diabetic Nephropathy by Single Probe-Based Microarray Data Analysis
Cited by: 72
Author(s): Clemens D. Cohen, Maja T. Lindenmeyer, Felix Eichinger, Alexander Hahn, Martin Seifert, Anton G. Moll, Holger Schmid, Éva Kiss, Elisabeth F. Gröne, Hermann–Josef Gröne, Matthias Kretzler, Thomás Werner, Peter J. Nelson
Software Mentions: 1
Published: about 18 years ago

10.1371/journal.pone.0111872

Metabolomic Profiling in Cattle Experimentally Infected with Mycobacterium avium subsp. paratuberculosis
Cited by: 44
Author(s): Jeroen De Buck, Rustem Shaykhutdinov, Herman W. Barkema, Hans J. Vogel
Software Mentions: 1
Published: almost 12 years ago

10.1371/journal.pone.0089262

A Core Invasiveness Gene Signature Reflects Epithelial-to-Mesenchymal Transition but Not Metastatic Potential in Breast Cancer Cell Lines and Tissue Samples
Cited by: 11
Author(s): Melike Marsan, Gert Van den Eynden, Ridha Limame, Patrick Neven, Jan Hauspy, Peter van Dam, Ignace Vergote, Luc Dirix, Peter Vermeulen, Steven J. Van Laere
Software Mentions: 1
Published: over 12 years ago

10.1371/journal.pone.0071059

Meta-Analysis of Genetic Programs between Idiopathic Pulmonary Fibrosis and Sarcoidosis
Cited by: 18
Author(s): Liubing Dong, Caijuan Huan, Ting Xie, Jiurong Liang, Jun Wang, Huaping Dai, Chen Wang, Dianhua Jiang
Software Mentions: 1
Published: about 13 years ago

10.1371/journal.pone.0065097

Distinct Transcriptional Networks in Quiescent Myoblasts: A Role for Wnt Signaling in Reversible vs. Irreversible Arrest
Cited by: 37
Author(s): Sindhu Subramaniam, Prethish Sreenivas, Sirisha Cheedipudi, Vatrapu Rami Reddy, L.S. Shashidhara, Ravi Kumar Chilukoti, Madhavi B. Mylavarapu, Jyotsna Dhawan
Software Mentions: 1
Published: over 13 years ago

10.1371/journal.pone.0179920

Unique intrahepatic transcriptomics profiles discriminate the clinical phases of a chronic HBV infection
Cited by: 17
Author(s): Jun Hou, Willem Pieter Brouwer, Kim Kreefft, Lúcio Gama, Sarah L. Price, Harry L.A. Janssen, Pim J. French, Thomas Vanwolleghem, André Boonstra
Software Mentions: 1
Published: over 9 years ago

10.1371/journal.pone.0245477

Relapse and post-discharge body composition of children treated for acute malnutrition using a simplified, combined protocol: A nested cohort from the ComPAS RCT
Cited by: 16
Author(s): Natasha Lelijveld, Eunice Musyoki, Susan Were Adongo, Amy Mayberry, Jonathan C. K. Wells, Charles Opondo, Marko Kerac, Jeanette Bailey
Software Mentions: 1
Published: over 5 years ago

10.1371/journal.pone.0097681

Integration of mRNA Expression Profile, Copy Number Alterations, and microRNA Expression Levels in Breast Cancer to Improve Grade Definition
Cited by: 53
Author(s): Claudia Cava, Gloria Bertoli, M. Ripamonti, Giancarlo Mauri, Italo Zoppis, Pasquale Anthony Della Rosa, M.C. Gilardi, Isabella Castiglioni
Software Mentions: 1
Published: over 12 years ago

10.1371/journal.pone.0007826

MicroRNA Patterns Associated with Clinical Prognostic Parameters and CNS Relapse Prediction in Pediatric Acute Leukemia
Cited by: 178
Author(s): Hua Zhang, Xue-Qun Luo, Peng Zhang, Libin Huang, Yusheng Zheng, Jun Wu, Hui Zhou, Liang‐Hu Qu, Ling Xu, Yue‐Qin Chen
Software Mentions: 1
Published: almost 17 years ago

10.1371/journal.pone.0003390

Requirement of RIZ1 for Cancer Prevention by Methyl-Balanced Diet
Cited by: 25
Author(s): Wei Zhou, Sergio Alonso, Daisaku Takai, Shelly C. Lu, Fumiichiro Yamamoto, Manuel Perucho, Shi Huang
Software Mentions: 1
Published: almost 18 years ago

10.1371/journal.pone.0015378

DNA Copy Number Changes in Human Malignant Fibrous Histiocytomas by Array Comparative Genomic Hybridisation
Cited by: 12
Author(s): Stine H. Kresse, Hege O. Ohnstad, Bodil Bjerkehagen, Ola Myklebost, Leonardo A. Meza‐Zepeda
Software Mentions: 1
Published: almost 16 years ago

10.1371/journal.pone.0140310

Landscape of Targeted Anti-Cancer Drug Synergies in Melanoma Identifies a Novel BRAF-VEGFR/PDGFR Combination Treatment
Cited by: 34
Author(s): Adam Friedman, Arnaud Amzallag, Iulian Pruteanu-Malinici, Subash Baniya, Zachary A. Cooper, Adriano Piris, Leeza Hargreaves, Vivien Igras, Dennie T. Frederick, Donald P. Lawrence, Daniel A. Haber, Keith T. Flaherty, Jennifer A. Wargo, Sridhar Ramaswamy, Cyril H. Benes, David E. Fisher
Software Mentions: 1
Published: almost 11 years ago

10.1371/journal.pone.0144310

Genomic Epidemiology of an Endoscope-Associated Outbreak of Klebsiella pneumoniae Carbapenemase (KPC)-Producing K. pneumoniae
Cited by: 64
Author(s): Jane W. Marsh, Mary G. Krauland, Jemma Nelson, Jessica L. Schlackman, Anthony M. Brooks, A. William Pasculle, Kathleen A. Shutt, Yohei Doi, Ashley Querry, Carlene A. Muto, Lee H. Harrison
Software Mentions: 1
Published: almost 11 years ago

10.1371/journal.pone.0095272

Parallel mRNA and MicroRNA Profiling of HEV71-Infected Human Neuroblastoma Cells Reveal the Up-Regulation of miR-1246 in Association with DLG3 Repression
Cited by: 34
Author(s): Lijuan Xu, Tao Jiang, Wei Zhao, Jianfeng Han, Juan Liu, Yong-Qiang Deng, Shun-Ya Zhu, Yuexiang Li, Qing-Gong Nian, Yu Zhang, Xiaoyan Wu, E-De Qin, Cheng‐Feng Qin
Software Mentions: 1
Published: over 12 years ago

10.1371/journal.pone.0007226

Skin Electroporation: Effects on Transgene Expression, DNA Persistence and Local Tissue Environment
Cited by: 124
Author(s): Anna-Karin Roos, Fredrik Eriksson, James A. Timmons, Josefine Gerhardt, Ulrika Nyman, Lindvi Gudmundsdotter, Andreas Bråve, Britta Wahrén, Pavel Pisa
Software Mentions: 1
Published: about 17 years ago

10.1371/journal.pone.0013420

Transcriptome, Methylome and Genomic Variations Analysis of Ectopic Thyroid Glands
Cited by: 43
Author(s): Rasha Abu-Khudir, Jean Paquette, Anne Lefort, Frédérick Libert, Jean‐Pierre Chanoine, Gilbert Vassart, Johnny Deladoëy
Software Mentions: 1
Published: almost 16 years ago

10.1371/journal.pone.0082469

Is Content Really King? An Objective Analysis of the Public's Response to Medical Videos on YouTube
Cited by: 204
Author(s): Tejas Desai, Afreen Shariff, Dhingra Vibhu, Deeba Minhas, Megan Eure, Марк Давидович Кац
Software Mentions: 1
Published: almost 13 years ago

10.1371/journal.pone.0211453

Improving interoceptive ability through the practice of power posing: A pilot study
Cited by: 21
Author(s): Felicitas Weineck, Matthias Messner, Gernot Hauke, Olga Pollatos
Software Mentions: 1
Published: over 7 years ago

10.1371/journal.pone.0036499

Transcriptional Homeostasis of a Mangrove Species, Ceriops tagal, in Saline Environments, as Revealed by Microarray Analysis
Cited by: 21
Author(s): Liang Shan, Fang Lü, Renchao Zhou, Tian Tang, Shulin Deng, SuiSui Dong, Yelin Huang, Cairong Zhong, Suhua Shi
Software Mentions: 1
Published: over 14 years ago

10.1371/journal.pone.0026952

Immune Response and Mitochondrial Metabolism Are Commonly Deregulated in DMD and Aging Skeletal Muscle
Cited by: 33
Author(s): Daniel Báron, Armelle Magot, Gérard Ramstein, Marja Steenman, Guy Fayet, Catherine Chevalier, Philippe Jourdon, Rémi Houlgatte, Frédérique Savagner, Yann Péreón
Software Mentions: 1
Published: almost 15 years ago

10.3390/cancers11071003

Identification of Withaferin A as a Potential Candidate for Anti-Cancer Therapy in Non-Small Cell Lung Cancer
Cited by: 37
Author(s): Jade H.M. Hsu, Peter Mu Hsin Chang, Tai Shan Cheng, Yi Chun Kuo, Alexander T.H. Wu, Thu-Ha Tran, Yusan Yang, Jing Ming Chen, Yu Chen Tsai, Yu‐Xia Chu, Tse-Hung Huang, Chi Ying F. Huang, Jin Mei Lai
Software Mentions: 1
Published: about 7 years ago

10.3390/cancers3032858

Prediction of Metastasis and Recurrence in Colorectal Cancer Based on Gene Expression Analysis: Ready for the Clinic?
Cited by: 21
Author(s): M. Shibayama, Matthias Maak, Ulrich Nitsche, Kengo Gotoh, Robert D. Rosenberg, Klaus‐Peter Janssen
Software Mentions: 1
Published: over 15 years ago

10.3390/cancers12010118

Ubiquitin Carboxyl-Terminal Hydrolase L1 (UCHL1) Promotes Uterine Serous Cancer Cell Proliferation and Cell Cycle Progression
Cited by: 22
Author(s): Suet-Ying Kwan, Chi Lam Au‐Yeung, Tsz-Lun Yeung, Ángela Rynne-Vidal, Kwong-Kwok Wong, John I. Risinger, Hui Kuan Lin, Rosemarie Schmandt, Melinda S. Yates, Samuel C. Mok, Karen H. Lu
Software Mentions: 1
Published: almost 7 years ago

10.3390/cancers12010126

Whole Genome Sequencing of Spontaneously Occurring Rat Natural Killer Large Granular Lymphocyte Leukemia Identifies JAK1 Somatic Activating Mutation
Cited by: 1
Author(s): T. Tiffany Wang, Jun Yang, Shubha Dighe, Matthew W. Schmachtenberg, Nathan T. Leigh, Emily Farber, Suna Önengüt-Gümüşcü, David J. Feith, Aakrosh Ratan, Thomas L. Olson
Software Mentions: 1
Published: almost 7 years ago

10.3390/cancers12020364

Patient-Derived Scaffolds of Colorectal Cancer Metastases as an Organotypic 3D Model of the Liver Metastatic Microenvironment
Cited by: 38
Author(s): Edoardo D’Angelo, Dipa Natarajan, Francesca Sensi, Omolola Ajayi, Matteo Fassan, Enzo Mammano, Pierluigi Pilati, Piero G. Pavan, Silvia Bresolin, Melissa Preziosi, Rosa Miquel, Yoh Zen, Shilpa Chokshi, Krishna Menon, Nigel Heaton, Gaya Spolverato, Martina Piccoli, Roger Williams, Luca Urbani, Marco Agostini
Software Mentions: 1
Published: over 6 years ago

10.3390/cancers12113180

NGS for (Hemato-) Oncology in Belgium: Evaluation of Laboratory Performance and Feasibility of a National External Quality Assessment Program
Cited by: 3
Author(s): Thomas Delcourt, Kevin Vanneste, Mohamed Rida Soumali, Wim Coucke, Vanessa Ghislain, Aline Hébrant, Els Van Valckenborgh, Sigrid C. J. De Keersmaecker, Nancy Roosens, P. Van de Walle, Marc Van den Bulcke, Aline Antoniou
Software Mentions: 1
Published: almost 6 years ago

10.3390/cancers12030742

The Role of PTEN Loss in Immune Escape, Melanoma Prognosis and Therapy Response
Cited by: 31
Author(s): Rita Cabrita, Shamik Mitra, Adriana Sanna, Henrik Ekedahl, Kristina Lövgren, Håkan Olsson, Christian Ingvar, Karolin Isaksson, Martin Lauss, Ana Carneiro, Göran Jönsson
Software Mentions: 1
Published: over 6 years ago

10.3390/cancers13081837

Identification of a Candidate Gene Set Signature for the Risk of Progression in IgM MGUS to Smoldering/Symptomatic Waldenström Macroglobulinemia (WM) by a Comparative Transcriptome Analysis of B Cells and Plasma Cells
Cited by: 7
Author(s): Alessandra Trojani, Barbara Di Camillo, Luca Emanuele Bossi, Livia Leuzzi, Antonino Greco, Alessandra Tedeschi, Anna Maria Frustaci, Marina Deodato, Giulia Zamprogna, Alessandro Beghini, Roberto Cairoli
Software Mentions: 1
Published: over 5 years ago

10.3390/cancers10050130

The EBV-Encoded Oncoprotein, LMP1, Induces an Epithelial-to-Mesenchymal Transition (EMT) via Its CTAR1 Domain through Integrin-Mediated ERK-MAPK Signalling
Cited by: 30
Author(s): Mhairi A. Morris, Louise Laverick, Wenbin Wei, Alexandra M Davis, Samantha O'Neill, Liam Wood, J. Wright, Christopher W. Dawson, Young Lw
Software Mentions: 1
Published: over 8 years ago

10.3390/cancers12061464

The miR-26b-5p/KPNA2 Axis Is an Important Regulator of Burkitt Lymphoma Cell Growth
Cited by: 17
Author(s): Fubiao Niu, Marta Kazimierska, Ilja M. Nolte, Miente Martijn Terpstra, Debora de Jong, Jasper Koerts, Tineke van der Sluis, Bea Rutgers, Ryan M. O’Connell, Klaas Kok, Anke van den Berg, Agnieszka Dzikiewicz‐Krawczyk, Joost Kluiver
Software Mentions: 1
Published: over 6 years ago

10.3390/cancers12071918

Expression of MALAT1 Promotes Trastuzumab Resistance in HER2 Overexpressing Breast Cancers
Cited by: 13
Author(s): Yanyuan Wu, Marianna Sarkissyan, Ochanya Ogah, Juri Kim, Jaydutt V. Vadgama
Software Mentions: 1
Published: about 6 years ago

10.3390/cancers10050150

Determining the Radiation Enhancement Effects of Gold Nanoparticles in Cells in a Combined Treatment with Cisplatin and Radiation at Therapeutic Megavoltage Energies
Cited by: 33
Author(s): Celina Yang, Kyle Bromma, Wonmo Sung, Jan Schuemann, Devika B. Chithrani
Software Mentions: 1
Published: over 8 years ago

10.1155/2018/2731039

A Novel Mutation in the <i>EIF2B4</i> Gene Associated with Leukoencephalopathy with Vanishing White Matter
Cited by: 3
Author(s): Dineshani Hettiaracchchi, Nilaksha Neththikumara, Sajeewani Pathirana, Anuruddha Padeniya, Vajira H. W. Dissanayake
Software Mentions: 1
Published: over 8 years ago

10.1186/1757-1626-1-352

A case of PTSD presenting with psychotic symptomatology: a case report
Cited by: 7
Author(s): Georgios Floros, I. Charatsidou, Grigorios Lavrentiadis
Software Mentions: 1
Published: almost 18 years ago

10.1016/j.cell.2018.04.015

The Cohesin Ring Uses Its Hinge to Organize DNA Using Non-topological as well as Topological Mechanisms
Cited by: 119
Author(s): Manoj Srinivasan, Johanna C. Scheinost, Naomi J Petela, Thomas G. Gligoris, Maria Wissler, Sugako Ogushi, James E. Collier, Menelaos Voulgaris, Alexander Kurze, Kok-Lung Chan, Bin Hu, Vincenzo Costanzo, Kim Nasmyth
Software Mentions: 1
Published: over 8 years ago

10.1186/2045-3701-3-44

Sorting nexin 24 genetic variation associates with coronary artery aneurysm severity in Kawasaki disease patients
Cited by: 14
Author(s): Ying Lin, Jen‐Ping Chang, Xiang Liu, Ting Hsu Lin, Shaohui Huang, Chien-Chang Liao, Cheng Wen Lin, Wen Kuei Chien, Jin Hua Chen, Jer Yuarn Wu, Chien Hsiun Chen, Li Chang, Hsinyi Tsang, Kuan Teh Jeang, Chia Yen Chen, Fuu Jen Tsai
Software Mentions: 1
Published: almost 14 years ago

10.1186/2045-3701-4-67

Genetic variants of glutamate receptor gene family in Taiwanese Kawasaki disease children with coronary artery aneurysms
Cited by: 5
Author(s): Ying Lin, Jen‐Ping Chang, Xiang Liu, Hsinyi Tsang, Ting Hsu Lin, Chien-Chang Liao, Shaohui Huang, Wen Kuei Chien, Jin Hua Chen, Jer Yuarn Wu, Chien Hsiun Chen, Li Chang, Cheng Wen Lin, Tsung Jung Ho, Fuu Jen Tsai
Software Mentions: 1
Published: almost 12 years ago

10.4161/15384101.2014.967123

The impact of the HIRA histone chaperone upon global nucleosome architecture
Cited by: 15
Author(s): Csenge Gal, Karen Moore, Konrad Paszkiewicz, Nicholas A. Kent, Simon K. Whitehall
Software Mentions: 1
Published: almost 12 years ago

10.1038/cddis.2016.464

Loss of miR-514a-3p regulation of PEG3 activates the NF-kappa B pathway in human testicular germ cell tumors
Cited by: 45
Author(s): Deniz M. Özata, Xidan Li, Linkiat Lee, Ji‐Kai Liu, Dudi Warsito, Praveensingh Hajeri, Isabell Hultman, Omid Fotouhi, Stefan L. Marklund, Lars Ährlund‐Richter, C. Christofer Juhlin, Catharina Larsson, Weng‐Onn Lui
Software Mentions: 1
Published: over 9 years ago

10.1038/cddis.2017.136

Tumor-treating fields elicit a conditional vulnerability to ionizing radiation via the downregulation of BRCA1 signaling and reduced DNA double-strand break repair capacity in non-small cell lung cancer cell lines
Cited by: 75
Author(s): Narasimha Kumar Karanam, Kannan Srinivasan, Lianghao Ding, Brock J. Sishc, Debabrata Saha, Michael D. Story
Software Mentions: 1
Published: over 9 years ago

10.1038/s41419-020-03147-9

LncRNA LINC00472 regulates cell stiffness and inhibits the migration and invasion of lung adenocarcinoma by binding to YBX1
Cited by: 49
Author(s): Xiaolei Deng, Wei Xiong, Xianjie Jiang, Shanshan Zhang, Zheng Li, Yanhong Zhou, Bo Xiang, Ming Zhou, Xiaoling Li, Guiyuan Li, Zhaoyang Zeng, Zhaojian Gong
Software Mentions: 1
Published: almost 6 years ago

10.1038/cddis.2017.406

Silencing FLI or targeting CD13/ANPEP lead to dephosphorylation of EPHA2, a mediator of BRAF inhibitor resistance, and induce growth arrest or apoptosis in melanoma cells
Cited by: 27
Author(s): Alireza Azimi, Rainer Tuominen, Fernanda Costa Svedman, Stefano Caramuta, Maria Pernemalm, Marianne Frostvik Stolt, Lena Kanter, Pedram Kharaziha, Janne Lehtiö, Carolina Johansson, Veronica Höiom, Johan Hansson, Suzanne Egyházi Brage
Software Mentions: 1
Published: about 9 years ago

Projects: cran: SAM

Science Score: 85/100

Bonuses:

Penalties:

Papers Mentioning SAM 4,566