cran: SAM | Projects | Ecosyste.ms: Papers

10.1371/journal.pone.0154638

Correction: Centering the Organizing Center in the Arabidopsis thaliana Shoot Apical Meristem by a Combination of Cytokinin Signaling and Self-Organization
Cited by: 0
Author(s):
Software Mentions: 1
Published: over 10 years ago

10.1371/journal.pone.0079692

Global Transcriptome Analysis of Lactococcus garvieae Strains in Response to Temperature
Cited by: 19
Author(s): Mónica Aguado-Urda, Alicia Gibello, M. Mar Blanco, J. F. Fernández‐Garayzábal, Victoria López-Alonso, Guillermo López-Campos
Software Mentions: 1
Published: over 12 years ago

10.1371/journal.pone.0081147

Snf2 Family Gene Distribution in Higher Plant Genomes Reveals DRD1 Expansion and Diversification in the Tomato Genome
Cited by: 10
Author(s): Joachim W. Bargsten, Adam Folta, Ľudmila Mlynárová, Jan-Peter Nap
Software Mentions: 1
Published: over 12 years ago

10.1371/journal.pone.0028251

Improving Transmission Efficiency of Large Sequence Alignment/Map (SAM) Files
Cited by: 17
Author(s): Muhammad N. Sakib, Jijun Tang, W. Jim Zheng, Chin Tser Huang
Software Mentions: 1
Published: over 14 years ago

10.1371/journal.pone.0013343

A Novel Secretory Poly-Cysteine and Histidine-Tailed Metalloprotein (Ts-PCHTP) from Trichinella spiralis (Nematoda)
Cited by: 12
Author(s): Georgi Radoslavov, Rositsa Jordanova, Denitsa Teofanova, K. Georgieva, Peter Hristov, Marco Salomone‐Stagni, Eva Liebau, Ilia Bankov
Software Mentions: 1
Published: almost 16 years ago

10.1371/journal.pone.0005637

Molecular Characterization of Lung Dysplasia Induced by c-Raf-1
Cited by: 12
Author(s): Astrid Rohrbeck, Volker Müller, Jürgen Borlak
Software Mentions: 1
Published: about 17 years ago

10.1371/journal.pone.0011620

Genomic Binding Profiling of the Fission Yeast Stress-Activated MAPK Sty1 and the bZIP Transcriptional Activator Atf1 in Response to H2O2
Cited by: 57
Author(s): Majid Eshaghi, Jong Hoon Lee, Li Zhu, Suk Yean Poon, Juntao Li, Kwang-Hyun Cho, Zhaoqing Chu, R. Krishna Murthy Karuturi, Jianhua Liu
Software Mentions: 1
Published: about 16 years ago

10.1371/journal.pone.0142846

Development and Validation of a Gene-Based Model for Outcome Prediction in Germ Cell Tumors Using a Combined Genomic and Expression Profiling Approach
Cited by: 18
Author(s): James E. Korkola, Sandy Heck, Adam B. Olshen, Darren R. Feldman, Victor E. Reuter, Jane Houldsworth, George J. Bosl, R. S. K. Chaganti
Software Mentions: 1
Published: over 10 years ago

10.1371/journal.pone.0200617

Genetic mapping reveals a marker for yellow skin in watermelon (Citrullus lanatus L.)
Cited by: 29
Author(s): Junling Dou, Xingrong Lu, Aslam Ali, Shengjie Zhao, Lei Zhang, Nan He, Wenge Liu
Software Mentions: 1
Published: almost 8 years ago

10.1371/journal.pone.0013721

Systematical Detection of Significant Genes in Microarray Data by Incorporating Gene Interaction Relationship in Biological Systems
Cited by: 3
Author(s): Junwei Wang, Meiwen Jia, Liping Zhu, Yuan Zeng, Peng Li, Chang Chang, Jian Luo, Mingyao Liu, Tieliu Shi
Software Mentions: 1
Published: almost 16 years ago

10.1371/journal.pone.0066165

Deep Sequencing the MicroRNA Transcriptome in Colorectal Cancer
Cited by: 133
Author(s): Kristina Schee, Susanne Lorenz, Merete Molton Worren, Clara Cecilie Günther, Matthew T. G. Holden, Eivind Hovig, Øystein Fodstad, Leonardo A. Meza‐Zepeda, Kjersti Flatmark
Software Mentions: 1
Published: about 13 years ago

10.1371/journal.pone.0023311

Differences in the Properties and Mirna Expression Profiles between Side Populations from Hepatic Cancer Cells and Normal Liver Cells
Cited by: 23
Author(s): Weihui Liu, Kaishan Tao, Nan You, Zhengcai Liu, Hongtao Zhang, Kefeng Dou
Software Mentions: 1
Published: almost 15 years ago

10.1371/journal.pone.0167100

Sam2bam: High-Performance Framework for NGS Data Preprocessing Tools
Cited by: 3
Author(s): Takeshi Ogasawara, Yinhe Cheng, Tzy-Hwa Kathy Tzeng
Software Mentions: 1
Published: over 9 years ago

10.1371/journal.pone.0034279

Genome-Wide Gene Expression Analysis in Cancer Cells Reveals 3D Growth to Affect ECM and Processes Associated with Cell Adhesion but Not DNA Repair
Cited by: 104
Author(s): Oliver Zschenker, Thomas Streichert, Stephanie Hehlgans, Nils Cordes
Software Mentions: 1
Published: over 14 years ago

10.1371/journal.pone.0234650

An analytical study of neocartilage from microtia and otoplasty surgical remnants: A possible application for BMP7 in microtia development and regeneration
Cited by: 3
Author(s): R. Childs, Hitomi Nakao, Noritaka Isogai, Ananth S. Murthy, William J. Landis
Software Mentions: 1
Published: about 6 years ago

10.1371/journal.pone.0006288

Layered Functional Network Analysis of Gene Expression in Human Heart Failure
Cited by: 18
Author(s): Wenliang Zhu, Lei Yang, Zhenhong Du
Software Mentions: 1
Published: about 17 years ago

10.1371/journal.pone.0076709

Residues in Human Arsenic (+3 Oxidation State) Methyltransferase Forming Potential Hydrogen Bond Network around S-adenosylmethionine
Cited by: 7
Author(s): Xiangli Li, Jing Cao, Shuping Wang, Zhirong Geng, Xiaoli Song, Xin Hu, Zhilin Wang
Software Mentions: 1
Published: almost 13 years ago

10.1371/journal.pone.0001385

Sex-Related Differences in Gene Expression in Human Skeletal Muscle
Cited by: 158
Author(s): Stephen Welle, Rabi Tawil, Charles A. Thornton
Software Mentions: 1
Published: over 18 years ago

10.1371/journal.pone.0087938

Microrna 130b Suppresses Migration and Invasion of Colorectal Cancer Cells through Downregulation of Integrin β1
Cited by: 32
Author(s): Yanyang Zhao, Gang Miao, Yao Li, Tomoya Isaji, Jianguo Gu, Jian Li, Ruomei Qi
Software Mentions: 1
Published: over 12 years ago

10.1371/journal.pone.0013655

Transcriptional Profiles of Treponema denticola in Response to Environmental Conditions
Cited by: 15
Author(s): Ian Howard Mchardy, Caroline Keegan, Jee Hyun Sim, Wenyuan Shi, Renate Lux
Software Mentions: 1
Published: almost 16 years ago

10.1371/journal.pone.0041373

TH17, TH22 and TReg Cells Are Enriched in the Healthy Human Cecum
Cited by: 32
Author(s): Martin Wolff, Jacqueline M. Leung, Michael Davenport, Michael A. Poles, Ilseung Cho, P’ng Loke
Software Mentions: 1
Published: about 14 years ago

10.1371/journal.pone.0132433

Small ncRNA Expression-Profiling of Blood from Hemophilia A Patients Identifies miR-1246 as a Potential Regulator of Factor 8 Gene
Cited by: 20
Author(s): Tewarit Sarachana, Neetu Dahiya, Vijaya L. Simhadri, Gouri Shankar Pandey, Surbhi Saini, Christine Guelcher, Michael F. Guerrera, Chava Kimchi-Sarfaty, Zuben E. Sauna, Chintamani D. Atreya
Software Mentions: 1
Published: about 11 years ago

10.1371/journal.pone.0192560

Spatial analysis of ecosystem service relationships to improve targeting of payments for hydrological services
Cited by: 22
Author(s): Pierre Mokondoko, Robert H. Manson, Taylor H. Ricketts, Daniel Geissert
Software Mentions: 1
Published: over 8 years ago

10.1371/journal.pone.0099593

Decellularized Allogeneic Heart Valves Demonstrate Self-Regeneration Potential after a Long-Term Preclinical Evaluation
Cited by: 69
Author(s): Laura Iop, Antonella Bonetti, Filippo Naso, Stefania Rizzo, Stefano Cagnin, Roberto Bianco, Carlo Dal Lin, Paolo Martini, Helen Poser, Paolo Franci, Gerolamo Lanfranchi, Roberto Busetto, Michel Spina, Cristina Basso, Maurizio Marchini, Alessandro Gandaglia, Fulvia Ortolani, Gino Gerosa
Software Mentions: 1
Published: about 12 years ago

10.1371/journal.pone.0017753

Genes Expressed in Specific Areas of the Human Fetal Cerebral Cortex Display Distinct Patterns of Evolution
Cited by: 66
Author(s): Nelle Lambert, Marie-Alexandra Lambot, Angéline Bilheu, Valérie Albert, Yvon Englert, Frédérick Libert, Jean‐Christophe Noël, Christos Sotiriou, Alisha K. Holloway, Katherine S. Pollard, Vincent Detours, Pierre Vanderhaeghen
Software Mentions: 1
Published: over 15 years ago

10.1371/journal.pone.0023144

Modulation of Androgen Receptor Signaling in Hormonal Therapy-Resistant Prostate Cancer Cell Lines
Cited by: 46
Author(s): Rute B. Marques, Natasja F. Dits, Sigrun Erkens-Schulze, Wilfred F. J. van IJcken, Wytske M. van Weerden, Guido Jenster
Software Mentions: 1
Published: almost 15 years ago

10.1371/journal.pone.0050095

Aberrant Neuromagnetic Activation in the Motor Cortex in Children with Acute Migraine: A Magnetoencephalography Study
Cited by: 14
Author(s): Xinyao Guo, Jing Xiang, Yingying Wang, Hope L. O’Brien, Marielle A. Kabbouche, Paul S. Horn, Scott W. Powers, Andrew D. Hershey
Software Mentions: 1
Published: over 13 years ago

10.1371/journal.pone.0201918

Identification of induced mutations in hexaploid wheat genome using exome capture assay
Cited by: 43
Author(s): Mubasher Hussain, Muhammad Munwar Iqbal, Bradley J. Till, Mehboob-ur Rahman
Software Mentions: 1
Published: almost 8 years ago

10.1371/journal.pone.0082385

Age-Related Changes in the Functional Network Underlying Specific and General Autobiographical Memory Retrieval: A Pivotal Role for the Anterior Cingulate Cortex
Cited by: 47
Author(s): Pénélope Martinelli, Marco Sperduti, Anne-Dominique Devauchelle, Sandrine Kalenzaga, Thierry Gallarda, Stéphanie Lion, Marion Delhommeau, Adèle Anssens, Isabelle Amado, J.F. Méder, Marie‐Odile Krebs, Catherine Oppenheim, Pascale Piolino
Software Mentions: 1
Published: over 12 years ago

10.1371/journal.pone.0011485

Gene Expression Profiles Characterize Inflammation Stages in the Acute Lung Injury in Mice
Cited by: 22
Author(s): Isabelle Lesur, Julien Textoris, Béatrice Loriod, C. Courbon, Stéphane Garcia, Marc Léone, Catherine Nguyen
Software Mentions: 1
Published: about 16 years ago

10.1371/journal.pone.0202286

Hotspot mutations and ColE1 plasmids contribute to the fitness of Salmonella Heidelberg in poultry litter
Cited by: 33
Author(s): Adelumola Oladeinde, Kyle DeMeo Cook, Alex Orlek, Gregory Zock, Kyler Herrington, N. A. Cox, Jodie Plumblee Lawrence, Carolina Hall
Software Mentions: 1
Published: almost 8 years ago

10.1371/journal.pone.0017091

Phosphodiesterase 4 Inhibition Reduces Innate Immunity and Improves Isoniazid Clearance of Mycobacterium tuberculosis in the Lungs of Infected Mice
Cited by: 65
Author(s): Mi Sun Koo, Claudia Manca, Guang Yang, Paul Edmond O'Brien, Nackmoon Sung, Liana Tsenova, Selvakumar Subbian, Dorothy Fallows, George W. Muller, Sabine Ehrt, Gilla Kaplan
Software Mentions: 1
Published: over 15 years ago

10.1371/journal.pone.0003225

Discovery of Porcine microRNAs and Profiling from Skeletal Muscle Tissues during Development
Cited by: 123
Author(s): Tinghua Huang, Mengjin Zhu, Xinyun Li, Zhao Song
Software Mentions: 1
Published: almost 18 years ago

10.1371/journal.pone.0001218

Proteomic Shifts in Embryonic Stem Cells with Gene Dose Modifications Suggest the Presence of Balancer Proteins in Protein Regulatory Networks
Cited by: 25
Author(s): Lei Mao, Claus Zabel, Markus Herrmann, Tobias Nolden, Florián Mertes, Laetitia Magnol, Caroline Chabert, Daniela Hartl, Yann Hérault, Jean Maurice Delabar, Thomas Manke, Heinz Himmelbauer, Joachim Klose
Software Mentions: 1
Published: over 18 years ago

10.1371/journal.pone.0242252

Dealing with an aging China—Delaying retirement or the second-child policy?
Cited by: 11
Author(s): Yantao Ling, Zhenzhen Song, Yang Yu, Tangyang Jiang
Software Mentions: 1
Published: over 5 years ago

10.1371/journal.pone.0103896

Remodeling of the Methylation Landscape in Breast Cancer Metastasis
Cited by: 33
Author(s): Marsha Reyngold, Şevin Turcan, Dilip Giri, Kasthuri Kannan, Logan A. Walsh, Agnès Viale, Marija Drobnjak, Linda T. Vahdat, William Lee, Timothy A. Chan
Software Mentions: 1
Published: almost 12 years ago

10.1371/journal.pone.0003164

Comparative Analysis of mRNA Targets for Human PUF-Family Proteins Suggests Extensive Interaction with the miRNA Regulatory System
Cited by: 265
Author(s): Alessia Galgano, Michael Forrer, Łukasz Jaśkiewicz, Alexander Kanitz, Mihaela Zavolan, André P. Gerber
Software Mentions: 1
Published: almost 18 years ago

10.1371/journal.pone.0020103

The Use of Carcasses for the Analysis of Cetacean Population Genetic Structure: A Comparative Study in Two Dolphin Species
Cited by: 24
Author(s): Kerstin Bilgmann, Luciana M. Möller, Robert Harcourt, Catherine M. Kemper, Luciano B. Beheregaray
Software Mentions: 1
Published: about 15 years ago

10.1371/journal.pone.0201942

Introduction and validation of the Natural Disasters Picture System (NDPS)
Cited by: 3
Author(s): Gaëtan Merlhiot, Martial Mermillod, Jean‐Luc Le Pennec, Laurie Mondillon
Software Mentions: 1
Published: almost 8 years ago

10.1371/journal.pone.0123745

Transcriptional Profile of Mycobacterium tuberculosis Replicating in Type II Alveolar Epithelial Cells
Cited by: 54
Author(s): Michelle B. Ryndak, Krishna K. Singh, Zheng-Yu Peng, Suman Laal
Software Mentions: 1
Published: over 11 years ago

10.1371/journal.pone.0103994

Fluorosed Mouse Ameloblasts Have Increased SATB1 Retention and Gαq Activity
Cited by: 13
Author(s): Yan Zhang, Ji Yeon Kim, Orapin V. Horst, Yukiko Nakano, Li Zhu, Ralf J. Radlanski, Sunita P. Ho, Pamela K. Den Besten
Software Mentions: 1
Published: almost 12 years ago

10.1371/journal.pone.0059503

Identifying Resistance Mechanisms against Five Tyrosine Kinase Inhibitors Targeting the ERBB/RAS Pathway in 45 Cancer Cell Lines
Cited by: 21
Author(s): Zsófia Pénzváltó, Bálint Tegze, Attila Marcell Szász, Zsófia Sztupinszki, István Láng, Attila Szendrői, Reinhold Schäfer, Balázs Györffy
Software Mentions: 1
Published: over 13 years ago

10.1371/journal.pone.0084854

Microarray Gene Expression Analysis of Tumorigenesis and Regional Lymph Node Metastasis in Laryngeal Squamous Cell Carcinoma
Cited by: 32
Author(s): Meng Lian, Jugao Fang, Demin Han, Hongzhi Ma, Feng Li, Ru Wang, Fan Yang
Software Mentions: 1
Published: over 12 years ago

10.1371/journal.pone.0047818

SIV Genome-Wide Pyrosequencing Provides a Comprehensive and Unbiased View of Variation within and outside CD8 T Lymphocyte Epitopes
Cited by: 11
Author(s): Austin L. Hughes, Ericka A. Becker, Michael Lauck, Julie A. Karl, Andrew T. Braasch, David H. O’Connor, Shelby L. O’Connor
Software Mentions: 1
Published: almost 14 years ago

10.1371/journal.pone.0029097

Elevational Gradients in Bird Diversity in the Eastern Himalaya: An Evaluation of Distribution Patterns and Their Underlying Mechanisms
Cited by: 91
Author(s): Bhoj Kumar Acharya, Nathan J. Sanders, Lalitha Vijayan, Basundhara Chettri
Software Mentions: 1
Published: over 14 years ago

10.1371/journal.pone.0002609

Transcriptome Alteration in the Diabetic Heart by Rosiglitazone: Implications for Cardiovascular Mortality
Cited by: 36
Author(s): Kitchener D. Wilson, Zongjin Li, Roger A. Wagner, Patrick Yue, Phillip S. Tsao, Gergana G. Nestorova, Mei Huang, David L. Hirschberg, Paul G. Yock, Thomas Quertermous, Joseph C. Wu
Software Mentions: 1
Published: about 18 years ago

10.1371/journal.pone.0042931

Comparative Transcriptome Analysis of Two Olive Cultivars in Response to NaCl-Stress
Cited by: 41
Author(s): Christos Bazakos, Maria Manioudaki, Ioannis Therios, D.G. Voyiatzis, Dimitris Kafetzopoulos, Tala Awada, Panagiotis Kalaitzis
Software Mentions: 1
Published: almost 14 years ago

10.1371/journal.pone.0024230

Next Generation Sequencing Provides Rapid Access to the Genome of Puccinia striiformis f. sp. tritici, the Causal Agent of Wheat Stripe Rust
Cited by: 171
Author(s): Dario Cantu, Manjula Govindarajulu, Alexander Kozik, Meinan Wang, Xianming Chen, Kenji Kojima, Jerzy Jurka, Richard W. Michelmore, Jorge Dubcovsky
Software Mentions: 1
Published: almost 15 years ago

10.1371/journal.pone.0024923

Necdin, a Negative Growth Regulator, Is a Novel STAT3 Target Gene Down-Regulated in Human Cancer
Cited by: 18
Author(s): Rachel Haviland, Steven Eschrich, Gregory Bloom, Yihong Ma, Susan Minton, Richard Jove, W. Douglas Cress
Software Mentions: 1
Published: almost 15 years ago

10.1371/journal.pone.0094729

Drosophila Microbiota Modulates Host Metabolic Gene Expression via IMD/NF-κB Signaling
Cited by: 107
Author(s): Berra Erkoşar, Arnaud Defaye, Noémie Bozonnet, Denis Puthier, Julien Royet, François Leulier
Software Mentions: 1
Published: over 12 years ago

10.1371/journal.pone.0158467

Identification of Potentially Pathogenic Variants in the Posterior Polymorphous Corneal Dystrophy 1 Locus
Cited by: 9
Author(s): Daniel Le, Duk-Won D. Chung, Ricardo F. Frausto, Michelle Kim, Anthony J. Aldave
Software Mentions: 1
Published: about 10 years ago

10.1371/journal.pone.0022508

Evidence for the Complexity of MicroRNA-Mediated Regulation in Ovarian Cancer: A Systems Approach
Cited by: 42
Author(s): Shubin Shahab, Lilya V. Matyunina, Roman Mezencev, L. DeEtte Walker, Nathan J. Bowen, Benedict B. Benigno, John F. McDonald
Software Mentions: 1
Published: about 15 years ago

10.1371/journal.pone.0054693

Negative Affect Reduces Performance in Implicit Sequence Learning
Cited by: 25
Author(s): Jianzhong Shang, Qiuping Fu, Zoltán Dienes, Chunfu Shao, Xiaolan Fu
Software Mentions: 1
Published: over 13 years ago

10.1371/journal.pone.0046935

Non-Gaussian Distributions Affect Identification of Expression Patterns, Functional Annotation, and Prospective Classification in Human Cancer Genomes
Cited by: 23
Author(s): Nicholas F. Marko, Robert J. Weil
Software Mentions: 1
Published: over 13 years ago

10.1371/journal.pone.0076166

Analysis on Differential Gene Expression Data for Prediction of New Biological Features in Permanent Atrial Fibrillation
Cited by: 10
Author(s): Ou Feng, Nini Rao, Xudong Jiang, Mengyao Qian, Wei Feng, Long Yin, Chen Xu
Software Mentions: 1
Published: almost 13 years ago

10.1371/journal.pone.0000482

Accelerated Variant of Idiopathic Pulmonary Fibrosis: Clinical Behavior and Gene Expression Pattern
Cited by: 251
Author(s): Moisés Selman, Guillermo Carrillo, Andrea Estrada, Mayra Mejía, Carina Becerril, José Cisneros, Miguel Gaxiola, Rogelio Pérez‐Padilla, Carmen Navarro, Thomas J. Richards, James H. Dauber, Talmadge E. King, Annie Pardo, Naftali Kaminski
Software Mentions: 1
Published: about 19 years ago

10.1371/journal.pone.0032341

Historical Legacies in World Amphibian Diversity Revealed by the Turnover and Nestedness Components of Beta Diversity
Cited by: 128
Author(s): Andrés Baselga, Carola Gómez‐Rodríguez, Jorge M. Lobo
Software Mentions: 1
Published: over 14 years ago

10.1371/journal.pone.0058773

Bartonella quintana Deploys Host and Vector Temperature-Specific Transcriptomes
Cited by: 7
Author(s): Stephanie Abromaitis, Christopher S. Nelson, Domenic J. Previte, Kyong Sup Yoon, J. Marshall Clark, Joseph L. DeRisi, Jane E. Koehler
Software Mentions: 1
Published: over 13 years ago

10.1371/journal.pone.0067202

Adaptive Geometric Tessellation for 3D Reconstruction of Anisotropically Developing Cells in Multilayer Tissues from Sparse Volumetric Microscopy Images
Cited by: 12
Author(s): Anirban Chakraborty, Mariano Perales, Venugopala Gonehal Reddy, Amit K. Roy-Chowdhury
Software Mentions: 1
Published: almost 13 years ago

10.1371/journal.pone.0006274

A Systems Biology-Based Gene Expression Classifier of Glioblastoma Predicts Survival with Solid Tumors
Cited by: 21
Author(s): Jing Zhang, Bing Liu, Xingpeng Jiang, Hengyu Zhao, Ming Z. Fan, Zhongwei Fan, John Lee, Tao Jiang, Tianzi Jiang, Shalei Song
Software Mentions: 1
Published: about 17 years ago

10.1371/journal.pone.0190009

Unilateral nephrectomy diminishes ischemic acute kidney injury through enhanced perfusion and reduced pro-inflammatory and pro-fibrotic responses
Cited by: 19
Author(s): Casper Kierulf‐Lassen, Per Mose Nielsen, Haiyun Qi, Mads Damgaard, Christoffer Laustsen, Michael Pedersen, Susanne Krag, Henrik Birn, Rikke Nørregaard, Bente Jespersen
Software Mentions: 1
Published: over 8 years ago

10.1371/journal.pone.0015174

Prolonged Application of High Fluid Shear to Chondrocytes Recapitulates Gene Expression Profiles Associated with Osteoarthritis
Cited by: 41
Author(s): Fei Zhu, Pu Wang, Norman H. Lee, Mary B. Goldring, Κωνσταντίνος Κωνσταντόπουλος
Software Mentions: 1
Published: over 15 years ago

10.1371/journal.pone.0035390

A Single Nucleotide Polymorphism of the Neuropeptide B/W Receptor-1 Gene Influences the Evaluation of Facial Expressions
Cited by: 18
Author(s): Noriya Watanabe, M. Wada, Yoko Irukayama-Tomobe, Yuji Ogata, Natsuko Tsujino, Masatatsu Suzuki, Naoki Furutani, Takeshi Sakurai, Miyuki Yamamoto
Software Mentions: 1
Published: over 14 years ago

10.1371/journal.pone.0204093

The Extreme Climate Event Database (EXCEED): Development of a picture database composed of drought and flood stimuli
Cited by: 6
Author(s): Sabrina de Sousa Magalhães, Diana Kraiser Miranda, Débora Marques de Miranda, Leandro Fernandes Malloy-Diniz, Marco Aurélio Romano-Silva
Software Mentions: 1
Published: almost 8 years ago

10.1371/journal.pone.0101297

Railway Embankments as New Habitat for Pollinators in an Agricultural Landscape
Cited by: 51
Author(s): Dawid Moroń, Piotr Skórka, Magdalena Lenda, Elżbieta Rożej-Pabijan, Marta Wantuch, Joanna Kajzer‐Bonk, Waldemar Celary, Łukasz Mielczarek, Piotr Tryjanowski
Software Mentions: 1
Published: about 12 years ago

10.1371/journal.pone.0215077

Chromosomal genome assembly of the ethanol production strain CBS 11270 indicates a highly dynamic genome structure in the yeast species Brettanomyces bruxellensis
Cited by: 8
Author(s): Ievgeniia A. Tiukova, Mats E. Pettersson, Marc P. Hoeppner, Remi André Olsen, Max Käller, Jens Nielsen, Jacques Dainat, Henrik Lantz, Jonas Söderberg, Volkmar Passoth
Software Mentions: 1
Published: over 7 years ago

10.1371/journal.pone.0186328

A novel, efficient method for estimating the prevalence of acute malnutrition in resource-constrained and crisis-affected settings: A simulation study
Cited by: 1
Author(s): Séverine Frison, Marko Kerac, Francesco Checchi, Jennifer M. Nicholas
Software Mentions: 1
Published: over 8 years ago

10.1371/journal.pone.0179446

Genetic factors affecting EBV copy number in lymphoblastoid cell lines derived from the 1000 Genome Project samples
Cited by: 23
Author(s): Rajendra Mandage, Marco Telford, Juan Antonio Rodríguez, Xavier Farré, Hafid Layouni, Urko M. Marigorta, Caitlin A. Cundiff, José María Heredia-Genestar, Arcadi Navarro, Gabriel Santpere
Software Mentions: 1
Published: about 9 years ago

10.1371/journal.pone.0145064

Patterns of Vertebrate Diversity and Protection in Brazil
Cited by: 57
Author(s): Clinton N. Jenkins, Maria Alice S. Alves, Alexandre Uezu, Mariana M. Vale
Software Mentions: 1
Published: over 10 years ago

10.1371/journal.pone.0088868

Thiol/Redox Metabolomic Profiling Implicates GSH Dysregulation in Early Experimental Graft versus Host Disease (GVHD)
Cited by: 19
Author(s): Jung Hee Suh, Bindu Kanathezhath, Swapna Shenvi, Hua Guo, Alicia Y. Zhou, Anureet Tiwana, Frans A. Kuypers, Bruce N. Ames, Mark C. Walters
Software Mentions: 1
Published: over 12 years ago

10.1371/journal.pone.0004017

Global Expression Profiling in Atopic Eczema Reveals Reciprocal Expression of Inflammatory and Lipid Genes
Cited by: 77
Author(s): Annika Sääf, Maria Tengvall-Linder, Howard Y. Chang, Adam S. Adler, Carl-Fredrik Wahlgren, Annika Scheynius, Magnus Nordenskjöld, Maria Bradley
Software Mentions: 1
Published: over 17 years ago

10.1371/journal.pone.0031180

Spatial Intuition in Elementary Arithmetic: A Neurocomputational Account
Cited by: 35
Author(s): Qi Chen, Tom Verguts
Software Mentions: 1
Published: over 14 years ago

10.1371/journal.pone.0147507

Adenoviral Mediated Expression of BMP2 by Bone Marrow Stromal Cells Cultured in 3D Copolymer Scaffolds Enhances Bone Formation
Cited by: 13
Author(s): Sunita Sharma, Dipak Sapkota, Ying Xue, Yang Sun, Anna Finne‐Wistrand, Ove Bruland, Kamal Mustafa
Software Mentions: 1
Published: over 10 years ago

10.1371/journal.pone.0029965

Multidimensional Characterization and Differentiation of Neurons in the Anteroventral Cochlear Nucleus
Cited by: 32
Author(s): Marei Typlt, Bernhard Englitz, Mandy Sonntag, Susanne Dehmel, Cornelia Kopp-Scheinpflug, Rudolf Ruebsamen
Software Mentions: 1
Published: over 14 years ago

10.1371/journal.pone.0250924

The aesthetic experience of critical art: The effects of the context of an art gallery and the way of providing curatorial information
Cited by: 7
Author(s): Magdalena Szubielska, Kamil K. Imbir
Software Mentions: 1
Published: about 5 years ago

10.1371/journal.pone.0076360

Targeted Exome Sequencing Integrated with Clinicopathological Information Reveals Novel and Rare Mutations in Atypical, Suspected and Unknown Cases of Alport Syndrome or Proteinuria
Cited by: 59
Author(s): Rajshekhar Chatterjee, Mary Hoffman, Paul Cliften, Surya V. Seshan, Helen Liapis, Sanjay Jain
Software Mentions: 1
Published: almost 13 years ago

10.1371/journal.pone.0046755

Uterine NK Cells Are Critical in Shaping DC Immunogenic Functions Compatible with Pregnancy Progression
Cited by: 45
Author(s): Irene González, Gabriela Barrientos, Nancy Freitag, Teresa Otto, Victor L. Thijssen, Petra Moschansky, Petra von Kwiatkowski, Burghard F. Klapp, Elke Winterhager, Stefan Bauersachs, Sandra M. Blois
Software Mentions: 1
Published: almost 14 years ago

10.1371/journal.pone.0015884

Phosphatidylserine Increases IKBKAP Levels in Familial Dysautonomia Cells
Cited by: 39
Author(s): Hadas Keren, Maya Donyo, David Zeevi, Channa Maayan, Tal Pupko, Gil Ast
Software Mentions: 1
Published: over 15 years ago

10.1371/journal.pone.0065948

Global Transcriptomic Analysis of Human Neuroblastoma Cells in Response to Enterovirus Type 71 Infection
Cited by: 27
Author(s): Lijuan Xu, Tao Jiang, Fujun Zhang, Jianfeng Han, Juan Liu, Hui Zhao, Xiaofeng Li, Liu Ruiju, Yong-Qiang Deng, Xiaoyan Wu, Shun-Ya Zhu, E-De Qin, Cheng‐Feng Qin
Software Mentions: 1
Published: about 13 years ago

10.1371/journal.pone.0160992

Whole-Genome Sequencing Analysis of Serially Isolated Multi-Drug and Extensively Drug Resistant Mycobacterium tuberculosis from Thai Patients
Cited by: 13
Author(s): Kiatichai Faksri, Jun Tan, Areeya Disratthakit, Eryu Xia, Therdsak Prammananan, Prapat Suriyaphol, Chiea‐Chuen Khor, Yik-Ying Teo, Rick Twee‐Hee Ong, Angkana Chaiprasert
Software Mentions: 1
Published: almost 10 years ago

10.1371/journal.pone.0049865

An Attempt at a Molecular Prediction of Metastasis in Patients with Primary Cutaneous Melanoma
Cited by: 13
Author(s): Melanie Gschaider, Friederike Neumann, Bettina Peters, F. Lenz, Michael Cibena, Malgorzata Goiser, Ingrid Wolf, Joerg Wenzel, Cornelia Mauch, Wolfgang Schreiner, Stephan N. Wagner
Software Mentions: 1
Published: over 13 years ago

10.1371/journal.pone.0052973

Multi-Analyte Network Markers for Tumor Prognosis
Cited by: 21
Author(s): Jong-Kwang Kim, Long Gao, Kai Tan
Software Mentions: 1
Published: over 13 years ago

10.1371/journal.pone.0199979

Bank1 and NF-kappaB as key regulators in anti-nucleolar antibody development
Cited by: 7
Author(s): Hammoudi Alkaissi, Said Havarinasab, Jesper Bo Nielsen, Peter Söderkvist, Per Hultman
Software Mentions: 1
Published: about 8 years ago

10.1371/journal.pone.0013073

Potential Tumor Suppressor Role for the c-Myb Oncogene in Luminal Breast Cancer
Cited by: 40
Author(s): Aaron R. Thorner, Joel S. Parker, Katherine A. Hoadley, Charles M. Perou
Software Mentions: 1
Published: almost 16 years ago

10.1371/journal.pone.0001502

The Enduring Hypoxic Response of Mycobacterium tuberculosis
Cited by: 419
Author(s): Tige R. Rustad, Maria I. Harrell, Reiling Liao, David R. Sherman
Software Mentions: 1
Published: over 18 years ago

10.1371/journal.pone.0059471

Gender and Facial Dominance in Gaze Cuing: Emotional Context Matters in the Eyes That We Follow
Cited by: 43
Author(s): Garian Ohlsen, Wieske van Zoest, Mark van Vugt
Software Mentions: 1
Published: over 13 years ago

10.1371/journal.pone.0152039

Profiling Ethylene-Responsive Genes Expressed in the Latex of the Mature Virgin Rubber Trees Using cDNA Microarray
Cited by: 11
Author(s): Zhiyi Nie, Guijuan Kang, Cuifang Duan, Li Yu, Longjun Dai, Rizhong Zeng
Software Mentions: 1
Published: over 10 years ago

10.1371/journal.pone.0025988

S-MART, A Software Toolbox to Aid RNA-seq Data Analysis
Cited by: 32
Author(s): Matthias Zytnicki, Hadi Quesneville
Software Mentions: 1
Published: almost 15 years ago

10.1371/journal.pone.0185612

High-throughput m6A-seq reveals RNA m6A methylation patterns in the chloroplast and mitochondria transcriptomes of Arabidopsis thaliana
Cited by: 35
Author(s): Zegang Wang, Kai Tang, Dayong Zhang, Yizhen Wan, Yan Wen, Quan-You Lu, Lei Wang
Software Mentions: 1
Published: over 8 years ago

10.1371/journal.pone.0005775

Gene Expression Profiling of Lymphoblasts from Autistic and Nonaffected Sib Pairs: Altered Pathways in Neuronal Development and Steroid Biosynthesis
Cited by: 135
Author(s): Valerie W. Hu, Anh Thu Nguyen, Kyung Soon Kim, Mara E. Steinberg, Tewarit Sarachana, Michele A. Scully, Steven J. Soldin, Truong Luu, Norman H. Lee
Software Mentions: 1
Published: about 17 years ago

10.1371/journal.pone.0106759

Cultural Differences in the Relationship between Intrusions and Trauma Narratives Using the Trauma Film Paradigm
Cited by: 12
Author(s): Laura Jobson, Tim Dalgleish
Software Mentions: 1
Published: almost 12 years ago

10.1371/journal.pone.0008549

Gene Expression in a Drosophila Model of Mitochondrial Disease
Cited by: 66
Author(s): Daniel J. M. Fernández-Ayala, Shanjun Chen, Esko Kemppainen, Kevin O’Dell, Howard T. Jacobs
Software Mentions: 1
Published: over 16 years ago

10.1371/journal.pone.0007148

Highly Sensitive Detection of Individual HEAT and ARM Repeats with HHpred and COACH
Cited by: 30
Author(s): Fred Kippert, Dietlind L. Gerloff
Software Mentions: 1
Published: almost 17 years ago

10.1371/journal.pone.0008785

Molecular Signatures of Quiescent, Mobilized and Leukemia-Initiating Hematopoietic Stem Cells
Cited by: 111
Author(s): Erik Forsberg, Emmanuelle Passegué, Susan Prohaska, Amy J. Wagers, Martina Koeva, Joshua M. Stuart, Irving L. Weissman
Software Mentions: 1
Published: over 16 years ago

10.1371/journal.pone.0042618

The Neuromagnetic Dynamics of Time Perception
Cited by: 7
Author(s): Frederick W. Carver, Brita Elvevåg, Mario Altamura, Daniel R. Weinberger, Richard Coppola
Software Mentions: 1
Published: almost 14 years ago

10.1371/journal.pone.0008599

The First Bite— Profiling the Predatosome in the Bacterial Pathogen Bdellovibrio
Cited by: 83
Author(s): Carey Lambert, Chien‐Yi Chang, Michael J. Capeness, R. Elizabeth Sockett
Software Mentions: 1
Published: over 16 years ago

10.1371/journal.pone.0060400

Daily Step Count Predicts Acute Exacerbations in a US Cohort with COPD
Cited by: 113
Author(s): Marilyn L. Moy, Merilee Teylan, Nicole Weston, David Gagnon, Eric Garshick
Software Mentions: 1
Published: over 13 years ago

10.1371/journal.pone.0106277

Diet-Induced Obesity Modulates Epigenetic Responses to Ionizing Radiation in Mice
Cited by: 27
Author(s): Guillaume Varès, Bing Wang, Hiroko Ishii-Ohba, Mitsuru Nenoi, Tetsuo Nakajima
Software Mentions: 1
Published: almost 12 years ago

10.1371/journal.pone.0009753

Dissecting Interferon-Induced Transcriptional Programs in Human Peripheral Blood Cells
Cited by: 138
Author(s): Simon J. Waddell, Stephen J. Popper, Kathleen H. Rubins, Michael J. Griffiths, Patrick O. Brown, Michael Levin, David A. Relman
Software Mentions: 1
Published: over 16 years ago

10.1371/journal.pone.0144302

Tissue Restricted Splice Junctions Originate Not Only from Tissue-Specific Gene Loci, but Gene Loci with a Broad Pattern of Expression
Cited by: 4
Author(s): Matthew S. Hestand, Zheng Zeng, Stephen J. Coleman, Jinze Liu, James N. MacLeod
Software Mentions: 1
Published: over 10 years ago

Projects: cran: SAM

Science Score: 85/100

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Papers Mentioning SAM 4,566