cran: SAM | Projects | Ecosyste.ms: Papers

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: about 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: almost 15 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: about 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: about 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: almost 14 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: over 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: about 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: almost 9 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: almost 11 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: over 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: about 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: almost 14 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.0184702

Multi-layered mutation in hedgehog-related genes in Gorlin syndrome may affect the phenotype
Cited by: 24
Author(s): Shin Onodera, Akiko Saito, Daigo Hasegawa, Nana Morita, Kiichi Watanabe, Takeshi Nomura, Takahiko Shibahara, Shinsuke Ohba, Akira Yamaguchi
Software Mentions: 1
Published: about 9 years ago

10.1371/journal.pone.0149086

A Model-Based Joint Identification of Differentially Expressed Genes and Phenotype-Associated Genes
Cited by: 2
Author(s): Samuel Sunghwan Cho, Yongkang Kim, Joon Yoon, Minseok Seo, Su‐Kyung Shin, Eun‐Young Kwon, Sang Hoon Kim, Yun Jung Bae, Seungyeoun Lee, Mi‐Kyung Sung, Myung‐Sook Choi, Taesung Park
Software Mentions: 1
Published: over 10 years ago

10.1371/journal.pone.0084570

Fluorescence-Based Classification of Caribbean Coral Reef Organisms and Substrates
Cited by: 22
Author(s): David G. Zawada, Charles H. Mazel
Software Mentions: 1
Published: over 12 years ago

10.1371/journal.pone.0129056

The Influence of Emotion on Keyboard Typing: An Experimental Study Using Auditory Stimuli
Cited by: 23
Author(s): Po Ming Lee, Wei Hsuan Tsui, Tzu‐Chien Hsiao
Software Mentions: 1
Published: over 11 years ago

10.1371/journal.pone.0048814

Differential Expression of Exosomal microRNAs in Prefrontal Cortices of Schizophrenia and Bipolar Disorder Patients
Cited by: 197
Author(s): Meredith G. Banigan, Patricia F. Kao, James Kozubek, Ashley R. Winslow, Juan Medina, Joan Costa, Andrea Schmitt, Anja Schneider, Howard Cabral, Ozge Cagsal‐Getkin, Charles R. Vanderburg, Ivana Delalle
Software Mentions: 1
Published: over 13 years ago

10.1371/journal.pone.0013494

Study on Differences in the Pathology, T Cell Subsets and Gene Expression in Susceptible and Non-Susceptible Hosts Infected with Schistosoma japonicum
Cited by: 36
Author(s): Weibin Jiang, Yang Hong, Jinbiao Peng, Zhiqiang Fu, Xiao Feng, Jinming Liu, Yiting Shi, Jiaojiao Lin
Software Mentions: 1
Published: almost 16 years ago

10.1371/journal.pone.0204114

A multiple hypothesis approach to explain species richness patterns in neotropical stream-dweller fish communities
Cited by: 10
Author(s): Thiago Bernardi Vieira, Carla Simone Pavanelli, Lílian Casatti, Welber Senteio Smith, Evanilde Benedito, Rosana Mazzoni, Jorge Iván Sánchez-Botero, Danielle Sequeira Garcez, Sergio Maia Queiroz Lima, Paulo Santos Pompeu, Carlos Sérgio Agostinho, Luciano Fogaça de Assis Montag, Jansen Zuanon, Pedro de Podestà Uchôa de Aquino, Maurício Cetra, Francisco Leonardo Tejerina‐Garro, Luiz Fernando Duboc, Ruanny Casarim Corrêa, María Angélica Pérez‐Mayorga, Gabriel Lourenço Brejão, Nadayca Thayane Bonani Mateussi, Miriam A. Castro, Rafael P. Leitão, Fernando Pereira de Mendonça, Leandra Rose Palheta da Silva, Renata G. Frederico, Paulo de Marco Júnior
Software Mentions: 1
Published: almost 8 years ago

10.1371/journal.pone.0019137

Upregulation of MiR-155 in Nasopharyngeal Carcinoma is Partly Driven by LMP1 and LMP2A and Downregulates a Negative Prognostic Marker JMJD1A
Cited by: 91
Author(s): Zhiheng Du, Li‐Fu Hu, Hai Yun Wang, Yan Li, Yi Xin Zeng, Jian Yong Shao, Ingemar Ernberg
Software Mentions: 1
Published: over 15 years ago

10.1371/journal.pone.0006139

Modulation of Gene Expression in Actinobacillus pleuropneumoniae Exposed to Bronchoalveolar Fluid
Cited by: 23
Author(s): Abdul G. Lone, Vincent Deslandes, John H. E. Nash, Mario Jacques, Janet I. MacInnes
Software Mentions: 1
Published: about 17 years ago

10.1371/journal.pone.0003329

Evolution of the Aging Brain Transcriptome and Synaptic Regulation
Cited by: 274
Author(s): Patrick Loerch, Tao Lu, Kelly A. Dakin, James M. Vann, Adrian M. Isaacs, Chengiz Geula, Jianbin Wang, Y. Albert Pan, Dana Gabuzda, Cheng Li, Tomas A. Prolla, Bruce A. Yankner
Software Mentions: 1
Published: almost 18 years ago

10.1371/journal.pone.0113772

Transcriptomic Analysis of Grape (Vitis vinifera L.) Leaves after Exposure to Ultraviolet C Irradiation
Cited by: 23
Author(s): Hongwei Xi, Lifeng Ma, Guotian Liu, Nian Wang, Junfang Wang, Lina Wang, Zhanwu Dai, Shaohua Li, Lijun Wang
Software Mentions: 1
Published: almost 12 years ago

10.1371/journal.pone.0023294

Generalized Fragment Picking in Rosetta: Design, Protocols and Applications
Cited by: 176
Author(s): Dominik Gront, Daniel W. Kulp, Robert Vernon, Charlie E. M. Strauss, David Baker
Software Mentions: 1
Published: about 15 years ago

10.1371/journal.pone.0103047

Construction and Analysis of the Protein-Protein Interaction Networks Based on Gene Expression Profiles of Parkinson's Disease
Cited by: 57
Author(s): Hindol Rakshit, Nitin Rathi, Dilip Roy
Software Mentions: 1
Published: about 12 years ago

10.1371/journal.pone.0111146

Molecular Integrative Clustering of Asian Gastric Cell Lines Revealed Two Distinct Chemosensitivity Clusters
Cited by: 2
Author(s): Meng Ling Choong, Shan Tan, Tuan Zea Tan, Sravanthy Manesh, Anna Ngo, Jacklyn Wei Yan Yong, Henry Yang, May Ann Lee
Software Mentions: 1
Published: almost 12 years ago

10.1371/journal.pone.0026502

An Integrated Analysis of miRNA and mRNA Expressions in Non-Small Cell Lung Cancers
Cited by: 70
Author(s): Lijiao Ma, Ying Huang, Wenxiu Zhu, Shuling Zhou, Ji Zhou, Fang Zeng, Xiaoguang Liu, Yongkui Zhang, Jun Yu
Software Mentions: 1
Published: almost 15 years ago

10.1371/journal.pone.0176154

Abundance profiling of specific gene groups using precomputed gut metagenomes yields novel biological hypotheses
Cited by: 26
Author(s): Konstantin Yarygin, Alexander V. Tyakht, Andrey K. Larin, Elena S. Kostryukova, Sergei Kolchenko, Vilgelm Bitner, Dmitry Alexeev
Software Mentions: 1
Published: over 9 years ago

10.1371/journal.pone.0104026

Geographical and Temporal Body Size Variation in a Reptile: Roles of Sex, Ecology, Phylogeny and Ecology Structured in Phylogeny
Cited by: 25
Author(s): Pedro Aragón, Patrick S. Fitze
Software Mentions: 1
Published: about 12 years ago

10.1371/journal.pone.0025519

Multi-Tasking Role of the Mechanosensing Protein Ankrd2 in the Signaling Network of Striated Muscle
Cited by: 31
Author(s): Anna Belgrano, Ljiljana Rakićević, Lorenza Mittempergher, Stefano Campanaro, Valentina Martinelli, Vincent Mouly, Giorgio Valle, Snežana Kojić, Georgine Faulkner
Software Mentions: 1
Published: almost 15 years ago

10.1371/journal.pone.0025364

Network Based Consensus Gene Signatures for Biomarker Discovery in Breast Cancer
Cited by: 19
Author(s): Holger Fröhlich
Software Mentions: 1
Published: almost 15 years ago

10.1371/journal.pone.0029063

Transcriptional Response of Zebrafish Embryos Exposed to Neurotoxic Compounds Reveals a Muscle Activity Dependent hspb11 Expression
Cited by: 28
Author(s): Nils Klüver, Lixin Yang, Wibke Busch, Katja Scheffler, Patrick Renner, Uwe Strähle, Stefan Scholz
Software Mentions: 1
Published: over 14 years ago

10.1371/journal.pone.0124801

Towards Unraveling the Human Tooth Transcriptome: The Dentome
Cited by: 21
Author(s): Shijia Hu, Joel S. Parker, J. Timothy Wright
Software Mentions: 1
Published: over 11 years ago

10.1371/journal.pone.0168617

The C-Terminal SynMuv/DdDUF926 Domain Regulates the Function of the N-Terminal Domain of DdNKAP
Cited by: 3
Author(s): Bhagyashri D. Burgute, Vivek S. Peche, Rolf Müller, Jan Matthias, Berthold Gaßen, Ludwig M. Eichinger, Gernot Glöckner, Angelika A. Noegel
Software Mentions: 1
Published: over 9 years ago

10.1371/journal.pone.0001664

A Specific and Rapid Neural Signature for Parental Instinct
Cited by: 220
Author(s): Morten L. Kringelbach, Annukka Lehtonen, Sarah Squire, Allison G. Harvey, Michelle G. Craske, Ian Holliday, Alexander L. Green, Tipu Z. Aziz, P. Hansen, Piers L. Cornelissen, Alan Stein
Software Mentions: 1
Published: over 18 years ago

10.1371/journal.pone.0071025

Exposure of Clinical MRSA Heterogeneous Strains to β-Lactams Redirects Metabolism to Optimize Energy Production through the TCA Cycle
Cited by: 19
Author(s): Mignon Keaton, Roberto R. Rosato, Konrad Plata, Christopher R. Singh, Adriana E. Rosato
Software Mentions: 1
Published: about 13 years ago

10.1371/journal.pone.0082164

Broad-Scale Phosphoprotein Profiling of Beta Adrenergic Receptor (β-AR) Signaling Reveals Novel Phosphorylation and Dephosphorylation Events
Cited by: 11
Author(s): Andrzej Chruscinski, Harvir Singh, Steven M. Chan, Paul J. Utz
Software Mentions: 1
Published: almost 13 years ago

10.1371/journal.pone.0189695

Molecular analysis of stomach contents reveals important grass seeds in the winter diet of Baird's and Grasshopper sparrows, two declining grassland bird species
Cited by: 9
Author(s): Mieke Titulaer, Alicia Melgoza‐Castillo, Arvind O. Panjabi, Alejandro Sánchez-Flores, José Hugo Martínez-Guerrero, Alberto Macías‐Duarte, Jesús A. Fernández
Software Mentions: 1
Published: over 8 years ago

10.1371/journal.pone.0040240

Host-Selective Toxins of Pyrenophora tritici-repentis Induce Common Responses Associated with Host Susceptibility
Cited by: 36
Author(s): Iovanna Pandelova, Melania Figueroa, Larry J. Wilhelm, Viola A. Manning, Aakash N. Mankaney, Todd C. Mockler, Lynda M. Ciuffetti
Software Mentions: 1
Published: about 14 years ago

10.1371/journal.pone.0035867

Transcriptional Analysis of Arabidopsis thaliana Response to Lima Bean Volatiles
Cited by: 17
Author(s): Sufang Zhang, Jianing Wei, Le Kang
Software Mentions: 1
Published: over 14 years ago

10.1371/journal.pone.0051961

A Combined Approach for the Assessment of Cell Viability and Cell Functionality of Human Fibrochondrocytes for Use in Tissue Engineering
Cited by: 16
Author(s): Ingrid Garzón, Víctor Carriel, Ana Belén Marín-Fernández, Ana Celeste Oliveira, Juan Garrido-Gómez, Antonìo Campos, María del Carmen Sánchez-Quevedo, Miguel Alaminos
Software Mentions: 1
Published: almost 14 years ago

10.1371/journal.pone.0139165

Identification of Biomarker and Co-Regulatory Motifs in Lung Adenocarcinoma Based on Differential Interactions
Cited by: 6
Author(s): Ning Zhao, Yongjing Liu, Zhiqiang Chang, Kening Li, Rui Zhang, Yuanshuai Zhou, Fujun Qiu, Xiaole Han, Yan Xu
Software Mentions: 1
Published: almost 11 years ago

10.1371/journal.pone.0003840

Pattern Recognition in Pulmonary Tuberculosis Defined by High Content Peptide Microarray Chip Analysis Representing 61 Proteins from M. tuberculosis
Cited by: 71
Author(s): Simani Gaseitsiwe, Davide Valentini, Shahnaz Mahdavifar, Isabelle Magalhaes, Daniel F. Hoft, Johannes Zerweck, Mike Schutkowski, Jan Andersson, Marie Reilly, Markus Maeurer
Software Mentions: 1
Published: almost 18 years ago

10.1371/journal.pone.0005763

Detection of Transgenerational Spermatogenic Inheritance of Adult Male Acquired CNS Gene Expression Characteristics Using a Drosophila Systems Model
Cited by: 25
Author(s): Abhay Sharma, Priyanka Singh
Software Mentions: 1
Published: over 17 years ago

10.1371/journal.pone.0037510

Assessment Method for a Power Analysis to Identify Differentially Expressed Pathways
Cited by: 16
Author(s): Shailesh Tripathi, Frank Emmert‐Streib
Software Mentions: 1
Published: over 14 years ago

10.1371/journal.pone.0045965

MiR-145 Regulates Epithelial to Mesenchymal Transition of Breast Cancer Cells by Targeting Oct4
Cited by: 59
Author(s): Jiajia Hu, Hua Guo, Hongyan Li, Yan Liu, Jingjing Liu, Liwei Chen, Jin Zhang, Ning Zhang
Software Mentions: 1
Published: almost 14 years ago

10.1371/journal.pone.0162534

Challenges of Estimating the Annual Caseload of Severe Acute Malnutrition: The Case of Niger
Cited by: 7
Author(s): Hedwig Deconinck, Anaïs A. Pesonen, Mahaman Elh Hallarou, Jean Christophe J.C. Gérard, André Briend, Philippe Donnen, Jean Macq
Software Mentions: 1
Published: about 10 years ago

10.1371/journal.pone.0184057

The latitudinal diversity gradient in South American mammals revisited using a regional analysis approach: The importance of climate at extra-tropical latitudes and history towards the tropics
Cited by: 7
Author(s): Paula Nilda Fergnani, Adriana Ruggiero
Software Mentions: 1
Published: about 9 years ago

10.1371/journal.pone.0111640

Patient-Based Transcriptome-Wide Analysis Identify Interferon and Ubiquination Pathways as Potential Predictors of Influenza A Disease Severity
Cited by: 18
Author(s): Long Hoàng, Thomas Tolfvenstam, Eng Eong Ooi, Chiea‐Chuen Khor, Ahmand Nazri Mohamed Naim, Eliza Xin Pei Ho, Swee Hoe Ong, Heiman Wertheim, Annette Fox, Chau Nguyen, Ngoc My Nghiem, Tuan Manh Ha, Anh Thi Tran, Paul Tambayah, Raymond Tzer Pin Lin, Chariya Sangsajja, Weerawat Manosuthi, Chareon Chuchottaworn, Piamlarp Sansayunh, Tawee Chotpitayasunondh, Piyarat Suntarattiwong, Kulkanya Chokephaibulkit, Pilaipan Puthavathana, Menno D. de Jong, Jeremy Farrar, H. Rogier van Doorn, Martin L. Hibberd
Software Mentions: 1
Published: almost 12 years ago

10.1371/journal.pone.0179865

The role of Patient Health Engagement Model (PHE-model) in affecting patient activation and medication adherence: A structural equation model
Cited by: 92
Author(s): Guendalina Graffigna, Serena Barello, Andrea Bonanomi
Software Mentions: 1
Published: about 9 years ago

10.1371/journal.pone.0047635

Identification of a CO2 Responsive Regulon in Bordetella
Cited by: 23
Author(s): Sara E. Hester, Minghsun Lui, Tracy L. Nicholson, Daryl Nowacki, Eric T. Harvill
Software Mentions: 1
Published: almost 14 years ago

10.1371/journal.pone.0045683

Demographic Amplification of Climate Change Experienced by the Contiguous United States Population during the 20th Century
Cited by: 4
Author(s): Jason Samson, Dominique Berteaux, Brian J. McGill, Murray M. Humphries
Software Mentions: 1
Published: almost 14 years ago

10.1371/journal.pone.0069282

Primary Respiratory Chain Disease Causes Tissue-Specific Dysregulation of the Global Transcriptome and Nutrient-Sensing Signaling Network
Cited by: 42
Author(s): Zhe Zhang, Mai Tsukikawa, Min Peng, Erzsébet Polyák, Eiko Nakamaru‐Ogiso, Julian Ostrovsky, Shana E. McCormack, Emily Place, Colleen Clarke, Gail Reiner, Elizabeth McCormick, Eric Rappaport, Richard R. de Haas, Joseph A. Baur, Marni J. Falk
Software Mentions: 1
Published: about 13 years ago

10.1371/journal.pone.0118029

Comparison of Effects of p53 Null and Gain-of-Function Mutations on Salivary Tumors in MMTV-Hras Transgenic Mice
Cited by: 3
Author(s): Dadi Jiang, Catherine I. Dumur, H. Davis Massey, Viswanathan Ramakrishnan, Mark A. Subler, Jolene J. Windle
Software Mentions: 1
Published: over 11 years ago

10.1371/journal.pone.0010267

Transcriptional Analysis of the Pre-Erythrocytic Stages of the Rodent Malaria Parasite, Plasmodium yoelii
Cited by: 20
Author(s): Calvin T. Williams, Abdu F. Azad
Software Mentions: 1
Published: over 16 years ago

10.1371/journal.pone.0049011

Please Don't! The Automatic Extrapolation of Dangerous Intentions
Cited by: 8
Author(s): Alessia Tessari, Giovanni Ottoboni, Andrea Mazzatenta, Arcangelo Merla, Roberto Nicoletti
Software Mentions: 1
Published: almost 14 years ago

10.1371/journal.pone.0230452

Acute malnutrition recovery energy requirements based on mid-upper arm circumference: Secondary analysis of feeding program data from 5 countries, Combined Protocol for Acute Malnutrition Study (ComPAS) Stage 1
Cited by: 14
Author(s): Rachel P. Chase, Marko Kerac, Alison Grant, Mark Manary, André Briend, Charles Opondo, Jeanette Bailey
Software Mentions: 1
Published: over 6 years ago

10.1371/journal.pone.0002293

Yeast Mitochondrial Biogenesis: A Role for the PUF RNA-Binding Protein Puf3p in mRNA Localization
Cited by: 210
Author(s): Yann Saint-Georges, Mathilde Garcia, Thierry Delaveau, Laurent Jourdren, Stéphane Le Crom, Sophie Lemoine, Véronique Tanty, Frédéric Devaux, Claude Jacq
Software Mentions: 1
Published: over 18 years ago

10.1371/journal.pone.0152983

Brain Cortical Thickness Differences in Adolescent Females with Substance Use Disorders
Cited by: 15
Author(s): Peter K. Boulos, Manish Dalwani, Jody Tanabe, Susan K. Mikulich‐Gilbertson, Marie T. Banich, Thomas J. Crowley, Joseph T. Sakai
Software Mentions: 1
Published: over 10 years ago

10.1371/journal.pone.0014049

Menin Links the Stress Response to Genome Stability in Drosophila melanogaster
Cited by: 6
Author(s): Maria Papaconstantinou, Alicia N. Pepper, Ying Wu, Dahlia Kasimer, Tim Westwood, Ana Regina Nascimento Campos, Pierre-André Bédard
Software Mentions: 1
Published: almost 16 years ago

10.1371/journal.pone.0007315

Cancer Genomics Identifies Regulatory Gene Networks Associated with the Transition from Dysplasia to Advanced Lung Adenocarcinomas Induced by c-Raf-1
Cited by: 33
Author(s): Astrid Rohrbeck, Jürgen Borlak
Software Mentions: 1
Published: almost 17 years ago

10.1371/journal.pone.0009482

Increasing Alternative Promoter Repertories Is Positively Associated with Differential Expression and Disease Susceptibility
Cited by: 14
Author(s): Song Liu
Software Mentions: 1
Published: over 16 years ago

10.1371/journal.pone.0125171

MicroRNA-27a Contributes to Rhabdomyosarcoma Cell Proliferation by Suppressing RARA and RXRA
Cited by: 21
Author(s): Lucia Tombolan, Matteo Zampini, Silvia Casara, Elena Boldrin, Angelica Zin, Gianni Bisogno, Angelo Rosolen, Cristiano De Pittà, Gerolamo Lanfranchi
Software Mentions: 1
Published: over 11 years ago

10.1371/journal.pone.0178485

Global transcriptome profiling identifies KLF15 and SLC25A10 as modifiers of adipocytes insulin sensitivity in obese women
Cited by: 25
Author(s): Agné Kulyté, Anna Ehrlund, Peter Arner, Ingrid Dahlman
Software Mentions: 1
Published: over 9 years ago

10.1371/journal.pone.0035553

A Unique Combination of Male Germ Cell miRNAs Coordinates Gonocyte Differentiation
Cited by: 72
Author(s): Skye C McIver, Simone J. Stanger, Danielle M. Santarelli, Shaun D. Roman, Brett Nixon, Eileen A. McLaughlin
Software Mentions: 1
Published: over 14 years ago

10.1371/journal.pone.0038870

A Bioinformatics Filtering Strategy for Identifying Radiation Response Biomarker Candidates
Cited by: 17
Author(s): Jung Hun Oh, Harry P. Wong, Xiaowei Wang, Joseph O. Deasy
Software Mentions: 1
Published: about 14 years ago

10.1371/journal.pone.0025357

Metabolomic Profiling from Formalin-Fixed, Paraffin-Embedded Tumor Tissue Using Targeted LC/MS/MS: Application in Sarcoma
Cited by: 72
Author(s): Andrew D. Kelly, Susanne B. Breitkopf, Min Yuan, Jeffrey D. Goldsmith, Dimitrios Spentzos, John M. Asara
Software Mentions: 1
Published: almost 15 years ago

Projects: cran: SAM

Science Score: 85/100

Bonuses:

Penalties:

Papers Mentioning SAM 4,566