cran: SAM | Projects | Ecosyste.ms: Papers

10.1371/journal.pcbi.1004344

Inferring the Clonal Structure of Viral Populations from Time Series Sequencing
Cited by: 0
Author(s): Donatien Fotso Chedom, Pablo R. Murcia, Chris Greenman
Software Mentions: 1
Published: almost 11 years ago

10.1371/journal.pcbi.0030003

Using Phylogeny to Improve Genome-Wide Distant Homology Recognition
Cited by: 6
Author(s): Sanne Abeln, Carlo Teubner, Charlotte M. Deane
Software Mentions: 1
Published: over 19 years ago

10.1371/journal.pgen.1007075

How well do you know your mutation? Complex effects of genetic background on expressivity, complementation, and ordering of allelic effects
Cited by: 45
Author(s): Christopher H. Chandler, Sudarshan Chari, Alycia Kowalski, Lin Choi, David C. Tack, Michael DeNieu, William Pitchers, Anne Sonnenschein, Leslie Marvin, Kristen Hummel, Christian Marier, Andrew Victory, Cody K. Porter, Anna Mammel, Julie Holms, Gayatri Sivaratnam, Ian Dworkin
Software Mentions: 1
Published: over 8 years ago

10.1371/journal.pgen.1004097

CEP-1, the Caenorhabditis elegans p53 Homolog, Mediates Opposing Longevity Outcomes in Mitochondrial Electron Transport Chain Mutants
Cited by: 57
Author(s): Aiswarya Baruah, Hung‐Hao Chang, Mathew Hall, Jie Yuan, Sarah Gordon, Erik C. Johnson, Ludmila Shtessel, Callista Yee, Siegfried Hekimi, W. Brent Derry, Siu Sylvia Lee
Software Mentions: 1
Published: over 12 years ago

10.1371/journal.pgen.1002530

A Quantitative, High-Throughput Reverse Genetic Screen Reveals Novel Connections between Pre–mRNA Splicing and 5′ and 3′ End Transcript Determinants
Cited by: 31
Author(s): Laura-Oana Albulescu, Nevin Sabet, Mohanram Gudipati, Nicholas Stepankiw, Zane J. Bergman, Tim C. Huffaker, Jeffrey A. Pleiss
Software Mentions: 1
Published: over 14 years ago

10.1371/journal.pgen.0030174

Signalling Pathways Involved in Adult Heart Formation Revealed by Gene Expression Profiling in Drosophila
Cited by: 70
Author(s): Bruno Zeitouni, Sébastien Sénatore, Dany Séverac, Cindy Aknin, Michel Sémériva, Laurent Perrin
Software Mentions: 1
Published: almost 19 years ago

10.1371/journal.pgen.1003389

Molecular Networks of Human Muscle Adaptation to Exercise and Age
Cited by: 149
Author(s): Bethan E. Phillips, John P. Williams, Thomas Gustafsson, Claude Bouchard, Tuomo Rankinen, Steen Knudsen, Kenneth Smith, James A. Timmons, Philip J. Atherton
Software Mentions: 1
Published: over 13 years ago

10.1371/journal.pgen.1000999

Amplification of a Cytochrome P450 Gene Is Associated with Resistance to Neonicotinoid Insecticides in the Aphid Myzus persicae
Cited by: 380
Author(s): Alin M. Puinean, S. P. Foster, L. Oliphant, I. Denholm, L. M. Field, Neil S. Millar, Martin S. Williamson, Chris Bass
Software Mentions: 1
Published: about 16 years ago

10.1371/journal.pgen.1003369

MTL–Independent Phenotypic Switching in Candida tropicalis and a Dual Role for Wor1 in Regulating Switching and Filamentation
Cited by: 40
Author(s): Allison M. Porman, Matthew P. Hirakawa, Stephen K. Jones, Na Wang, Richard J. Bennett
Software Mentions: 1
Published: over 13 years ago

10.1371/journal.pgen.0020203

Impact of Nonsense-Mediated mRNA Decay on the Global Expression Profile of Budding Yeast
Cited by: 119
Author(s): Qiaoning Guan, Wei Zheng, Shijie Tang, Xiaosong Liu, Robert A. Zinkel, Kam‐Wah Tsui, Brian S. Yandell, Michael R. Culbertson
Software Mentions: 1
Published: over 20 years ago

10.1371/journal.pgen.1000450

A Regulated Response to Impaired Respiration Slows Behavioral Rates and Increases Lifespan in Caenorhabditis elegans
Cited by: 144
Author(s): David Cristina, Michael Cary, Adam Lunceford, Catherine F. Clarke, Cynthia Kenyon
Software Mentions: 1
Published: over 17 years ago

10.1371/journal.pgen.1004589

A Gain-of-Function Mutation in Tnni2 Impeded Bone Development through Increasing Hif3a Expression in DA2B Mice
Cited by: 26
Author(s): Xiaoquan Zhu, Fengchao Wang, Yang Zhao, Peng Yang, Jun Chen, Hanzi Sun, Lei Liu, Wenjun Li, Pei Lin, Yafei Guo, Zhaohui Kou, Yu Zhang, Cheng Zhou, Jiang He, Xue Zhang, Jianxin Li, Han Wang, Jian Li, Guanghui Liu, Shaorong Gao, Ze Yang
Software Mentions: 1
Published: almost 12 years ago

10.1371/journal.pgen.1009119

Two cis-regulatory SNPs upstream of ABCG2 synergistically cause the blue eggshell phenotype in the duck
Cited by: 8
Author(s): Li Chen, Xiaorong Gu, Xuetao Huang, Rui Liu, Jinxiu Li, Yiqing Hu, Guoqin Li, Tao Zeng, Yong Tian, Xiaoxiang Hu, Lizhi Liu, Ning Li
Software Mentions: 1
Published: almost 6 years ago

10.1371/journal.pgen.1003186

Rbfox1 Downregulation and Altered Calpain 3 Splicing by FRG1 in a Mouse Model of Facioscapulohumeral Muscular Dystrophy (FSHD)
Cited by: 32
Author(s): Mariaelena Pistoni, Lily Shiue, Melissa Cline, Sergia Bortolanza, Maria Victoria Neguembor, Alexandros Xynos, Manuel Ares, Davide Gabellini
Software Mentions: 1
Published: over 13 years ago

10.1371/journal.pgen.1006042

Heat Shock Protein Beta-1 Modifies Anterior to Posterior Purkinje Cell Vulnerability in a Mouse Model of Niemann-Pick Type C Disease
Cited by: 18
Author(s): Chan Chung, Matthew J. Elrick, Zhaohui S. Qin, Shanker Kalyana-Sundaram, Arul M. Chinnaiyan, Vikram G. Shakkottai, Andrew P. Lieberman
Software Mentions: 1
Published: over 10 years ago

10.1371/journal.pgen.1007500

Modulation of miR-210 alters phasing of circadian locomotor activity and impairs projections of PDF clock neurons in Drosophila melanogaster
Cited by: 27
Author(s): Paola Cusumano, Alberto Biscontin, Federica Sandrelli, Gabriella Mazzotta, Claudia Tregnago, Cristiano De Pittà, Rodolfo Costa
Software Mentions: 1
Published: about 8 years ago

10.1371/journal.pgen.0010028

Differential Expression of Novel Potential Regulators in Hematopoietic Stem Cells
Cited by: 265
Author(s): Erik Forsberg, Susan Prohaska, Sol Katzman, Garrett C. Heffner, Joshua M. Stuart, Irving L. Weissman
Software Mentions: 1
Published: almost 21 years ago

10.1371/journal.pgen.1004955

Pooled Sequencing of 531 Genes in Inflammatory Bowel Disease Identifies an Associated Rare Variant in BTNL2 and Implicates Other Immune Related Genes
Cited by: 58
Author(s): Natalie J. Prescott, Benjamin Lehne, Kristina Stone, James C. Lee, Kirstin M. Taylor, Jo Knight, Efterpi Papouli, Muddassar M. Mirza, Michael A. Simpson, Sarah L. Spain, Grace H C Lu, Franca Fraternali, Suzannah Bumpstead, Emma Gray, Ariella Amar, Hannah Bye, Peter Green, Guy Carrault, Bu’Hussain Hayee, Richard Pollok, Jack Satsangi, Miles Parkes, Jeffrey C. Barrett, John C. Mansfield, Jeremy Sanderson, Cathryn M. Lewis, Michael E. Weale, Thomas Schlitt, Christopher G. Mathew
Software Mentions: 1
Published: over 11 years ago

10.1371/journal.pgen.1000310

Genetic and Computational Identification of a Conserved Bacterial Metabolic Module
Cited by: 28
Author(s): Cara C. Boutte, Balaji Srinivasan, Jason Flannick, Antal F. Novak, Andrew T. Martens, Serafim Batzoglou, Patrick H. Viollier, Sean Crosson
Software Mentions: 1
Published: over 17 years ago

10.1371/journal.pgen.1003683

Comparative Genomic and Functional Analysis of 100 Lactobacillus rhamnosus Strains and Their Comparison with Strain GG
Cited by: 173
Author(s): François P. Douillard, Angela Ribbera, Ravi Kant, Taija E. Pietilä, Hanna Järvinen, Marcel Messing, Cinzia Lucia Randazzo, Lars Paulín, Pia Laine, Jarmo Ritari, Cinzia Caggia, Tanja Lähteinen, Stan J. J. Brouns, Reetta Satokari, Ingemar von Ossowski, Justus Reunanen, Airi Palva, Willem M. de Vos
Software Mentions: 1
Published: about 13 years ago

10.1371/journal.pgen.1002902

Polysome Profiling in Liver Identifies Dynamic Regulation of Endoplasmic Reticulum Translatome by Obesity and Fasting
Cited by: 47
Author(s): Suneng Fu, Jason Fan, Joshua Aaron Blanco, Alfredo Giménez-Cassina, Nika N. Danial, Simon Watkins, Gökhan S. Hotamışlıgil
Software Mentions: 1
Published: almost 14 years ago

10.1371/journal.pgen.1007135

Histological subtypes of mouse mammary tumors reveal conserved relationships to human cancers
Cited by: 51
Author(s): Daniel P. Hollern, Matthew Swiatnicki, Eran R. Andrechek
Software Mentions: 1
Published: over 8 years ago

10.1371/journal.pgen.1002862

The Yeast Rab GTPase Ypt1 Modulates Unfolded Protein Response Dynamics by Regulating the Stability of HAC1 RNA
Cited by: 31
Author(s): Nikoleta G. Tsvetanova, Daniel P. Riordan, Patrick O. Brown
Software Mentions: 1
Published: about 14 years ago

10.1371/journal.pgen.1000942

Bulk Segregant Analysis by High-Throughput Sequencing Reveals a Novel Xylose Utilization Gene from Saccharomyces cerevisiae
Cited by: 169
Author(s): Jared W. Wenger, Katja Schwartz, Gavin Sherlock
Software Mentions: 1
Published: over 16 years ago

10.1371/journal.pgen.1003027

Cooperativity of Rb, Brca1, and p53 in Malignant Breast Cancer Evolution
Cited by: 23
Author(s): Prashant Kumar, Malini Mukherjee, Jacob P. S. Johnson, Milan Patel, Bing Huey, Donna G. Albertson, Karl Simin
Software Mentions: 1
Published: almost 14 years ago

10.1371/journal.pgen.0020119

Anatomic Demarcation by Positional Variation in Fibroblast Gene Expression Programs
Cited by: 410
Author(s): John L. Rinn, Chanda Bondre, Hayes B. Gladstone, Patrick O. Brown, Howard Y. Chang
Software Mentions: 1
Published: about 20 years ago

10.1371/journal.pgen.0030101

Laser Microdissection of Narrow Sheath Mutant Maize Uncovers Novel Gene Expression in the Shoot Apical Meristem
Cited by: 76
Author(s): Xiaolan Zhang, Shahinez Madi, Lisa A. Borsuk, Dan Nettleton, Robert J. Elshire, Brent Buckner, Diane Janick-Buckner, Jon Beck, Marja C.P. Timmermans, Patrick S. Schnable, Michael J. Scanlon
Software Mentions: 1
Published: about 19 years ago

10.1371/journal.pgen.1006666

Independent introductions and admixtures have contributed to adaptation of European maize and its American counterparts
Cited by: 73
Author(s): Jean-Tristan Brandenburg, Tristan Mary‐Huard, Guillem Rigaill, Sarah Hearne, Hélène Corti, Johann Joets, Clémentine Vitte, Alain Charcosset, Stéphane Nicolas, Maud I. Tenaillon
Software Mentions: 1
Published: over 9 years ago

10.1371/journal.pgen.1002235

The Evolutionarily Conserved Longevity Determinants HCF-1 and SIR-2.1/SIRT1 Collaborate to Regulate DAF-16/FOXO
Cited by: 105
Author(s): Gizem Rizki, Terri Iwata, J i Li, Christian G. Riedel, Colette L. Picard, Max Jan, Coleen T. Murphy, Siu Sylvia Lee
Software Mentions: 1
Published: almost 15 years ago

10.1371/journal.pgen.1003368

Long Noncoding RNA MALAT1 Controls Cell Cycle Progression by Regulating the Expression of Oncogenic Transcription Factor B-MYB
Cited by: 637
Author(s): Vidisha Tripathi, Zhen Shen, Arindam Chakraborty, Sumanprava Giri, Susan M. Freier, Xiaolin Wu, Yongqing Zhang, Myriam Gorospe, Supriya G. Prasanth, Ashish Lal, Kannanganattu V. Prasanth
Software Mentions: 1
Published: over 13 years ago

10.1371/journal.pgen.0020152

Analysis of Pleiotropic Transcriptional Profiles: A Case Study of DNA Gyrase Inhibition
Cited by: 43
Author(s): Kyeong Soo Jeong, Yang Xie, Hiroshi Hiasa, Arkady B. Khodursky
Software Mentions: 1
Published: almost 20 years ago

10.1371/journal.pgen.1002380

A High-Resolution Whole-Genome Map of Key Chromatin Modifications in the Adult Drosophila melanogaster
Cited by: 55
Author(s): Hang Yin, Sarah Sweeney, Debasish Raha, M Snyder, Haifan Lin
Software Mentions: 1
Published: over 14 years ago

10.1371/journal.pgen.1002974

SWI/SNF-Like Chromatin Remodeling Factor Fun30 Supports Point Centromere Function in S. cerevisiae
Cited by: 41
Author(s): Mickaël Durand-Dubief, William Ryan Will, Edoardo Petrini, Delphine Theodorou, Rachael Rebecca Harris, Margaret Crawford, Konrad Paszkiewicz, Felix Krueger, Rosa Maria Correra, Anna T. Vetter, Jim Miller, Nicholas A. Kent, Patrick Varga‐Weisz
Software Mentions: 1
Published: almost 14 years ago

10.1371/journal.pgen.1000680

p63 and p73 Transcriptionally Regulate Genes Involved in DNA Repair
Cited by: 130
Author(s): Yu Li Lin, Shomit Sengupta, Katherine Gurdziel, George W. Bell, Tyler Jacks, Elsa R. Flores
Software Mentions: 1
Published: almost 17 years ago

10.1371/journal.pgen.1005407

A Genetic Incompatibility Accelerates Adaptation in Yeast
Cited by: 22
Author(s): Duyen Bui, Elliot Dine, James B. Anderson, Charles F. Aquadro, Eric Alani
Software Mentions: 1
Published: about 11 years ago

10.1371/journal.pgen.1000555

Distinct Roles of Non-Canonical Poly(A) Polymerases in RNA Metabolism
Cited by: 94
Author(s): Salvatore San Paolo, Štěpánka Vaňáčová, Luca Schenk, Tanja Scherrer, Diana Blank, Walter Keller, André P. Gerber
Software Mentions: 1
Published: about 17 years ago

10.1371/journal.pgen.1005471

The Arabidopsis RCC1 Family Protein TCF1 Regulates Freezing Tolerance and Cold Acclimation through Modulating Lignin Biosynthesis
Cited by: 89
Author(s): Hongtao Ji, Youning Wang, Catherine Cloix, Kexue Li, Gareth I. Jenkins, Shuangfeng Wang, Zhonglin Shang, Yiting Shi, Shuhua Yang, Xia Li
Software Mentions: 1
Published: almost 11 years ago

10.1371/journal.pgen.1004430

Ex Uno Plures: Clonal Reinforcement Drives Evolution of a Simple Microbial Community
Cited by: 38
Author(s): Margie Kinnersley, Jared W. Wenger, Evgueny Kroll, Julian Adams, Gavin Sherlock, Frank Rosenzweig
Software Mentions: 1
Published: about 12 years ago

10.1371/journal.pgen.1000129

A Precisely Regulated Gene Expression Cassette Potently Modulates Metastasis and Survival in Multiple Solid Cancers
Cited by: 121
Author(s): Kun Yu, Kumaresan Ganesan, Lay Keng Tan, Mirtha Laban, Jeanie Wu, Xiao Dong Zhao, Hongmin Li, Carol Ho Wing Leung, Yuechun Zhu, Chia Lin Wei, Shing Chuan Hooi, Lance D. Miller, Patrick Tan
Software Mentions: 1
Published: about 18 years ago

10.1371/journal.pgen.1000626

The Fission Yeast Homeodomain Protein Yox1p Binds to MBF and Confines MBF-Dependent Cell-Cycle Transcription to G1-S via Negative Feedback
Cited by: 42
Author(s): Sofia Aligianni, Daniel H. Lackner, Steffi Klier, Gabriella Rustici, Brian T. Wilhelm, Samuel Marguerat, Sandra Codlin, Alvis Brāzma, Robertus A.M. de Bruin, Jürg Bähler
Software Mentions: 1
Published: almost 17 years ago

10.1371/journal.pgen.1000713

E Unibus Plurum: Genomic Analysis of an Experimentally Evolved Polymorphism in Escherichia coli
Cited by: 62
Author(s): Margie Kinnersley, William E. Holben, Frank Rosenzweig
Software Mentions: 1
Published: almost 17 years ago

10.1371/journal.pgen.1000476

Microdissection of Shoot Meristem Functional Domains
Cited by: 71
Author(s): Lionel Brooks, Josh Strable, Xiaolan Zhang, Kazuhiro Ohtsu, Rongyan Zhou, Ananda K. Sarkar, Sarah K. Hargreaves, Robert J. Elshire, Douglas M. Eudy, Teresa E. Pawlowska, Doreen Ware, Diane Janick-Buckner, Brent Buckner, Marja C.P. Timmermans, Patrick S. Schnable, Dan Nettleton, Michael J. Scanlon
Software Mentions: 1
Published: over 17 years ago

10.1371/journal.pmed.0030486

A Genome-Wide Screen for Promoter Methylation in Lung Cancer Identifies Novel Methylation Markers for Multiple Malignancies
Cited by: 229
Author(s): David S. Shames, Luc Girard, Boning Gao, Mitsuo Sato, Cheryl Lewis, Narayan Shivapurkar, Aixiang Jiang, Charles M. Perou, Young H. Kim, Jonathan R. Pollack, Kwun M. Fong, Chi Leung Lam, Maria Pik Wong, Yu Shyr, Rita Nanda, Olufunmilayo I. Olopade, William L. Gerald, David M. Euhus, Jerry W. Shay, Adi F. Gazdar, John D. Minna
Software Mentions: 1
Published: over 19 years ago

10.1371/journal.pmed.1000307

A Six-Gene Signature Predicts Survival of Patients with Localized Pancreatic Ductal Adenocarcinoma
Cited by: 197
Author(s): Jeran K. Stratford, David J. Bentrem, Judy M. Anderson, Cheng Fan, Keith A. Volmar, J. S. Marron, Elizabeth D. Routh, Laura S. Caskey, Jonathan C. Samuel, Channing J. Der, Leigh B. Thorne, Benjamin F. Calvo, Hee Jin Kim, Mark S. Talamonti, Christine A. Iacobuzio–Donahue, Michael A. Hollingsworth, Charles M. Perou, Jen Jen Yeh
Software Mentions: 1
Published: about 16 years ago

10.1371/journal.pmed.0030254

Inflammatory Manifestations of Experimental Lymphatic Insufficiency
Cited by: 187
Author(s): Raymond Tabibiazar, Lauren Cheung, Jennifer Han, Jeffrey Swanson, Andreas Beilhack, Andrew An, Soheil S. Dadras, Ned B. Rockson, Smita Joshi, Roger A. Wagner, Stanley G. Rockson
Software Mentions: 1
Published: about 20 years ago

10.1371/journal.pmed.1002877

Impact on child acute malnutrition of integrating a preventive nutrition package into facility-based screening for acute malnutrition during well-baby consultation: A cluster-randomized controlled trial in Burkina Faso
Cited by: 22
Author(s): Elodie Becquey, Lieven Huybregts, Amanda Zongrone, Agnès Le Port, Jef L. Leroy, Rahul Raj, Mariama Touré, Marie T. Ruel
Software Mentions: 1
Published: almost 7 years ago

10.1371/journal.pntd.0007489

Phlebotomus papatasi sand fly predicted salivary protein diversity and immune response potential based on in silico prediction in Egypt and Jordan populations
Cited by: 1
Author(s): Catherine M. Flanley, Marcelo Ramalho-Ortigão, Iliano V. Coutinho-Abreu, Rami Mukbel, Hanafi A. Hanafi, Shabaan S. El-Hossary, Emadeldin Y. Fawaz, David F. Hoel, Alexander W. Bray, Gwen Stayback, Douglas A. Shoue, Shaden Kamhawi, Scott J. Emrich, Mary Ann McDowell
Software Mentions: 1
Published: about 6 years ago

10.1371/journal.pntd.0000086

Host Gene Expression Profiling of Dengue Virus Infection in Cell Lines and Patients
Cited by: 203
Author(s): Joshua Fink, Feng Gu, Ling Ling, Thomas Tolfvenstam, Farzad O. Olfat, Keh Chuang Chin, Pauline Aw, Joshy George, Vladimir A. Kuznetsov, Mark Schreiber, Subhash G. Vasudevan, Martin L. Hibberd
Software Mentions: 1
Published: almost 19 years ago

10.1371/journal.pntd.0000648

Delineation of Diverse Macrophage Activation Programs in Response to Intracellular Parasites and Cytokines
Cited by: 91
Author(s): Shuyi Zhang, Charles C. Kim, Sajeev Batra, James H. McKerrow, P’ng Loke
Software Mentions: 1
Published: over 16 years ago

10.1371/journal.pntd.0000556

Identification of the Schistosoma mansoni TNF-Alpha Receptor Gene and the Effect of Human TNF-Alpha on the Parasite Gene Expression Profile
Cited by: 32
Author(s): Kátia C. Oliveira, Mariana Carvalho, Thiago M. Venancio, Patrícia A. Miyasato, Toshie Kawano, Ricardo DeMarco, Sérgio Verjovski-Almeida
Software Mentions: 1
Published: over 16 years ago

10.1371/journal.pntd.0004086

Synergy of Omeprazole and Praziquantel In Vitro Treatment against Schistosoma mansoni Adult Worms
Cited by: 17
Author(s): Giulliana T. Almeida, Regina Coeli Gonçalves Lage, Letícia Anderson, Thiago M. Venancio, Hidehiko Nakaya, Patrícia A. Miyasato, Henrique K. Rofatto, Adhemar Zerlotini, Eliana Nakano, Guilherme Oliveira, Sérgio Verjovski-Almeida
Software Mentions: 1
Published: almost 11 years ago

10.1371/journal.pntd.0000710

Gene Expression Patterns of Dengue Virus-Infected Children from Nicaragua Reveal a Distinct Signature of Increased Metabolism
Cited by: 58
Author(s): P’ng Loke, Samantha N. Hammond, Jacqueline M. Leung, Charles C. Kim, Sajeev Batra, Crisanta Rocha, Ángel Balmaseda, Eva Harris
Software Mentions: 1
Published: about 16 years ago

10.1371/journal.pntd.0001459

Murine Dendritic Cells Transcriptional Modulation upon Paracoccidioides brasiliensis Infection
Cited by: 21
Author(s): Aldo Henrique Tavares, Lorena S Derengowski, Karen Spadari Ferreira, Simoneide S. Silva, Cristiana Santos de Macedo, Anamélia Lorenzetti Bocca, Geraldo A. S. Passos, Sandro Rogério de Almeida, Ildinete Silva-Pereira
Software Mentions: 1
Published: over 14 years ago

10.1371/journal.pntd.0004731

Early Transcriptional Signatures of the Immune Response to a Live Attenuated Tetravalent Dengue Vaccine Candidate in Non-human Primates
Cited by: 10
Author(s): Fiona R. Strouts, Stephen J. Popper, Charalambos D. Partidos, Dan T. Stinchcomb, Jorge E. Osorio, David A. Relman
Software Mentions: 1
Published: about 10 years ago

10.1371/journal.pntd.0002406

Transcriptome Analysis of Human Peripheral Blood Mononuclear Cells Exposed to Lassa Virus and to the Attenuated Mopeia/Lassa Reassortant 29 (ML29), a Vaccine Candidate
Cited by: 27
Author(s): Juan Carlos Zapata, Ricardo Carrión, Jean L. Patterson, Oswald Crasta, Yan Zhang, Sachin Mani, Marti Jett, Bhawna Poonia, Mahmoud Djavani, David M. White, Igor S. Lukashevich, María S. Salvato
Software Mentions: 1
Published: almost 13 years ago

10.1371/journal.pntd.0000308

Schistosoma mansoni Tegument Protein Sm29 Is Able to Induce a Th1-Type of Immune Response and Protection against Parasite Infection
Cited by: 156
Author(s): Fernanda C. Cardoso, Gilson Costa Macedo, Elisandra Gava, Gregory T. Kitten, Vitor Luís Tenório Mati, Alan Lane de Melo, Marcelo Vidigal Caliari, Giulliana T. Almeida, Thiago M. Venancio, Sérgio Verjovski-Almeida, Sérgio C. Oliveira
Software Mentions: 1
Published: almost 18 years ago

10.1371/journal.pone.0070051

SNP Discovery in European Anchovy (Engraulis encrasicolus, L) by High-Throughput Transcriptome and Genome Sequencing
Cited by: 40
Author(s): Iratxe Montes, Darrell Conklin, Aitor Albaina, Simon Creer, Gary R. Carvalho, M.B. Santos, Andone Estonba
Software Mentions: 1
Published: about 13 years ago

10.1371/journal.pone.0053930

Improved Discovery of Molecular Interactions in Genome-Scale Data with Adaptive Model-Based Normalization
Cited by: 2
Author(s): Julia Salzman, Daniel M. Klass, Patrick O. Brown
Software Mentions: 1
Published: over 13 years ago

10.1371/journal.pone.0115324

Geographic Wormhole Detection in Wireless Sensor Networks
Cited by: 26
Author(s): Mehdi Sookhak, Adnan Akhundzada, Alireza Sookhak, Mohammadreza Eslaminejad, Abdullah Gani, Muhammad Khurram Khan, Xiong Li, Xiaomin Wang
Software Mentions: 1
Published: over 11 years ago

10.1371/journal.pone.0009249

Agent-Based Modeling of Endotoxin-Induced Acute Inflammatory Response in Human Blood Leukocytes
Cited by: 83
Author(s): Xu Dong, Panagiota T. Foteinou, Steven E. Calvano, Stephen F. Lowry, Ioannis P. Androulakis
Software Mentions: 1
Published: over 16 years ago

10.1371/journal.pone.0008183

Stable Patterns of Gene Expression Regulating Carbohydrate Metabolism Determined by Geographic Ancestry
Cited by: 19
Author(s): Jonathan C. Schisler, Peter C. Charles, Joel S. Parker, Eleanor Hilliard, Sabeen Mapara, Dane Meredith, Robert E. Lineberger, Samuel S. Wu, Brian D Alder, George A. Stouffer, Cam Patterson
Software Mentions: 1
Published: over 16 years ago

10.1371/journal.pone.0090157

RNA Sequencing Analysis and Atrial Natriuretic Peptide Production in Patients with Dilated and Ischemic Cardiomyopathy
Cited by: 22
Author(s): Estefanía Tarazón, Esther Roselló‐Lletí, Miguel Rivera, Ana Ortega, Maria Micaela Molina‐Navarro, Juan Carlos Triviño, Francisca Lago, José Ramón González-Juanatey, Plácido Orosa, José Montero, Antonio Salvador, Manuel Portolés
Software Mentions: 1
Published: over 12 years ago

10.1371/journal.pone.0176664

Whole exome sequencing of a consanguineous family identifies the possible modifying effect of a globally rare AK5 allelic variant in celiac disease development among Saudi patients
Cited by: 14
Author(s): Jumana Y. Al‐Aama, Noor Ahmad Shaik, Babajan Banaganapalli, Mohammed A. Salama, Omran M. Rashidi, Ahmed N. Sahly, Mohammed O. Mohsen, Harbi A. Shawoosh, Hebah Ahmad Shalabi, Mohammad Al Edreesi, Sameer E. Al-Harthi, Jun Wang, Omar I. Saadah
Software Mentions: 1
Published: over 9 years ago

10.1371/journal.pone.0039139

The Effect of Iron Limitation on the Transcriptome and Proteome of Pseudomonas fluorescens Pf-5
Cited by: 62
Author(s): Chee Kent Lim, Karl A. Hassan, Sasha G. Tetu, Joyce E. Loper, Ian T. Paulsen
Software Mentions: 1
Published: about 14 years ago

10.1371/journal.pone.0175857

Modeling the shape and composition of the human body using dual energy X-ray absorptiometry images
Cited by: 12
Author(s): John Shepherd, Bennett K. Ng, Bo Fan, Ann V. Schwartz, Peggy M. Cawthon, Steven R. Cummings, Stephen B. Kritchevsky, M. Nevitt, Adam J Santanasto, Timothy F. Cootes
Software Mentions: 1
Published: over 9 years ago

10.1371/journal.pone.0227510

Factory benefits to paying workers more: The critical role of compensation systems in apparel manufacturing
Cited by: 16
Author(s): Niklas Lollo, Dara O’Rourke
Software Mentions: 1
Published: over 6 years ago

10.1371/journal.pone.0152736

Ambiguity in Tactile Apparent Motion Perception
Cited by: 21
Author(s): Emanuela Liaci, Michael Bach, Ludger Tebartz van Elst, Sven Heinrich, Jürgen Kornmeier
Software Mentions: 1
Published: over 10 years ago

10.1371/journal.pone.0081049

Machine-Based Morphologic Analysis of Glioblastoma Using Whole-Slide Pathology Images Uncovers Clinically Relevant Molecular Correlates
Cited by: 94
Author(s): Jun Kong, Lee Cooper, Fusheng Wang, Jingjing Gao, George Teodoro, Lisa Scarpace, Tom Mikkelsen, Matthew Schniederjan, Carlos S. Moreno, Joel Saltz, Daniel J. Brat
Software Mentions: 1
Published: almost 13 years ago

10.1371/journal.pone.0072609

Clinical Relevance of Gain-Of-Function Mutations of p53 in High-Grade Serous Ovarian Carcinoma
Cited by: 56
Author(s): Hyo Jeong Kang, Sung-Min Chun, Kyu-Rae Kim, Insuk Sohn, Chang‐Keun Sung
Software Mentions: 1
Published: about 13 years ago

10.1371/journal.pone.0072178

Comprehensive Analysis of Genic Male Sterility-Related Genes in Brassica rapa Using a Newly Developed Br300K Oligomeric Chip
Cited by: 47
Author(s): Xiangshu Dong, Hui Feng, Ming Xu, Jeongyeo Lee, Yeon Ki Kim, Yong Pyo Lim, Zhongyun Piao, Young-Doo Park, Hong Mā, Yoonkang Hur
Software Mentions: 1
Published: almost 13 years ago

10.1371/journal.pone.0061080

δ-Opioid Receptor Activation Modified MicroRNA Expression in the Rat Kidney under Prolonged Hypoxia
Cited by: 15
Author(s): Xiaozhou He, Yilin Yang, Feng Zhi, Meredith Moore, Xiaoming Kang, Dongman Chao, Rong Wang, Gianfranco Balboni, Severo Salvadori, Dong H. Kim, Ying Xia
Software Mentions: 1
Published: over 13 years ago

10.1371/journal.pone.0007314

MicroRNA Profiling of BRCA1/2 Mutation-Carrying and Non-Mutation-Carrying High-Grade Serous Carcinomas of Ovary
Cited by: 84
Author(s): Cheng‐Han Lee, Subbaya Subramanian, Andrew H. Beck, Íñigo Espinosa, Janine Senz, Shirley Zhu, David G. Huntsman, Matt van de Rijn, C. Blake Gilks
Software Mentions: 1
Published: almost 17 years ago

10.1371/journal.pone.0081384

Association between GRIN3A Gene Polymorphism in Kawasaki Disease and Coronary Artery Aneurysms in Taiwanese Children
Cited by: 18
Author(s): Ying Lin, Jen‐Ping Chang, Xiang Liu, Chien Hui Hung, Ting Hsu Lin, Shaohui Huang, Kuan Teh Jeang, Chia Yen Chen, Chien-Chang Liao, Cheng Wen Lin, Chih Ho Lai, Ni Tien, Yu Ching Lan, Mao Wang Ho, Wen Kuei Chien, Jin Hua Chen, Yu Chuen Huang, Hsinyi Tsang, Jer Yuarn Wu, Chien Hsiun Chen, Li Chang, Fuu Jen Tsai
Software Mentions: 1
Published: over 12 years ago

10.1371/journal.pone.0079549

Gene Expression Analysis of Peripheral Cells for Subclassification of Pediatric Inflammatory Bowel Disease in Remission
Cited by: 12
Author(s): P.P.E. van Lierop, Sigrid Swagemakers, Charlotte I. de Bie, Sabine Middendorp, Peter van Baarlen, Janneke N. Samsom, Wilfred F. J. van IJcken, Johanna C. Escher, Peter J. van der Spek, Edward E. S. Nieuwenhuis
Software Mentions: 1
Published: almost 13 years ago

10.1371/journal.pone.0064041

An Integrated Proteomic and Metabolomic Study on the Chronic Effects of Mercury in Suaeda salsa under an Environmentally Relevant Salinity
Cited by: 45
Author(s): Xiaoli Liu, Huifeng Wu, Chenglong Ji, Lei Wei, Jianmin Zhao, Junbao Yu
Software Mentions: 1
Published: over 13 years ago

10.1371/journal.pone.0212928

Emotion analysis in children through facial emissivity of infrared thermal imaging
Cited by: 33
Author(s): Christiane Goulart, Carlos Valadão, Denis Delisle-Rodríguez, Eliete Caldeira, Teodiano Bastos
Software Mentions: 1
Published: over 7 years ago

10.1371/journal.pone.0217027

Gene shaving using a sensitivity analysis of kernel based machine learning approach, with applications to cancer data
Cited by: 3
Author(s): Md. Ashad Alam, Mohammd Shahjaman, Md. Ferdush Rahman, Fokhrul Hossain, Hong‐Wen Deng
Software Mentions: 1
Published: about 7 years ago

10.1371/journal.pone.0006381

Hyperoxic Treatment Induces Mesenchymal-to-Epithelial Transition in a Rat Adenocarcinoma Model
Cited by: 66
Author(s): Ingrid Moen, Anne Margrete Øyan, Karl H. Kalland, Karl Johan Tronstad, Lars A. Akslen, Martha Chekenya, Per Øystein Sakariassen, Rolf K. Reed, Linda Elin Birkhaug Stuhr
Software Mentions: 1
Published: about 17 years ago

10.1371/journal.pone.0157215

The Influence of the ‘Trier Social Stress Test’ on Free Throw Performance in Basketball: An Interdisciplinary Study
Cited by: 12
Author(s): Nicolas Mascret, Jorge Ibáñez-Gijón, Vincent Bréjard, Mart Buekers, Rémy Casanova, Tanguy Marqueste, Gilles Montagne, Guillaume Rao, Yannick Roux, François Cury
Software Mentions: 1
Published: about 10 years ago

10.1371/journal.pone.0032200

Effect of Size and Heterogeneity of Samples on Biomarker Discovery: Synthetic and Real Data Assessment
Cited by: 25
Author(s): Barbara Di Camillo, Tiziana Sanavia, Matteo Martini, Giuseppe Jurman, Francesco Sambo, Annalisa Barla, Margherita Squillario, Cesare Furlanello, Gianna Toffolo, Claudio Cobelli
Software Mentions: 1
Published: over 14 years ago

10.1371/journal.pone.0024408

The Naked Truth: The Face and Body Sensitive N170 Response Is Enhanced for Nude Bodies
Cited by: 53
Author(s): Jari K. Hietanen, Lauri Nummenmaa
Software Mentions: 1
Published: almost 15 years ago

10.1371/journal.pone.0179879

Diet-induced adipose tissue expansion is mitigated in mice with a targeted inactivation of mesoderm specific transcript (Mest)
Cited by: 13
Author(s): Rea P. Anunciado‐Koza, José Manuel, Randall L. Mynatt, Jingying Zhang, Leslie P. Kozak, Robert A. Koza
Software Mentions: 1
Published: about 9 years ago

10.1371/journal.pone.0040037

Identification of hsa-miR-335 as a Prognostic Signature in Gastric Cancer
Cited by: 83
Author(s): Zhiqiang Yan, Yimin Xiong, Weitian Xu, Juan Gao, Yi C, Zhigang Wang, Fang Chen, Zheng Guo
Software Mentions: 1
Published: about 14 years ago

10.1371/journal.pone.0118211

Rapid Stress System Drives Chemical Transfer of Fear from Sender to Receiver
Cited by: 24
Author(s): Jasper H. B. de Groot, Monique A. M. Smeets, Gün R. Semin
Software Mentions: 1
Published: over 11 years ago

10.1371/journal.pone.0020769

Impact of Cellular miRNAs on Circulating miRNA Biomarker Signatures
Cited by: 270
Author(s): Radha Duttagupta, Rong Jiang, Jeremy Gollub, Robert C. Getts, Keith Jones
Software Mentions: 1
Published: about 15 years ago

10.1371/journal.pone.0029161

Interferon and Biologic Signatures in Dermatomyositis Skin: Specificity and Heterogeneity across Diseases
Cited by: 135
Author(s): D. Wong, Bory Kea, Rob Pesich, Brandon W. Higgs, Wei Zhu, Patrick O. Brown, Yihong Yao, David Fiorentino
Software Mentions: 1
Published: over 14 years ago

10.1371/journal.pone.0067304

Cliffs Used as Communal Roosts by Andean Condors Protect the Birds from Weather and Predators
Cited by: 31
Author(s): Sergio A. Lambertucci, Adriana Ruggiero
Software Mentions: 1
Published: about 13 years ago

10.1371/journal.pone.0068679

Landscape Movements of Anopheles gambiae Malaria Vector Mosquitoes in Rural Gambia
Cited by: 46
Author(s): Christopher Thomas, Dónall Eoin Cross, Claus Bøgh
Software Mentions: 1
Published: about 13 years ago

10.1371/journal.pone.0028403

Homogeneous Datasets of Triple Negative Breast Cancers Enable the Identification of Novel Prognostic and Predictive Signatures
Cited by: 79
Author(s): Thomas Karn, Lajos Pusztai, Uwe Holtrich, Takayuki Inomata, Christine Y. Shiang, Marcus Schmidt, Volkmar Müller, Christine Solbach, R. Gaetje, Lars Hanker, A. Ahr, Cornelia Liedtke, Eugen Ruckhäberle, M. Kaufmann, Achim Rody
Software Mentions: 1
Published: over 14 years ago

10.1371/journal.pone.0197607

Prevalence, outcome and quality of care among children hospitalized with severe acute malnutrition in Kenyan hospitals: A multi-site observational study
Cited by: 22
Author(s): Susan Gachau, Grace Irimu, Philip Ayieko, Samuel Akech, Ambrose Agweyu, Mike English
Software Mentions: 1
Published: over 8 years ago

10.1371/journal.pone.0081874

Early Gene Expression Analysis in 9L Orthotopic Tumor-Bearing Rats Identifies Immune Modulation in Molecular Response to Synchrotron Microbeam Radiation Therapy
Cited by: 51
Author(s): Audrey Bouchet, Nathalie Sakakini, Michèle El Atifi, Céline Le Clec’h, Elke Bräuer, Anaïck Moisan, Pierre Deman, Pascal Rihet, Géraldine Le Duc, Laurent Pelletier
Software Mentions: 1
Published: over 12 years ago

10.1371/journal.pone.0158294

Targeted HIV-1 Latency Reversal Using CRISPR/Cas9-Derived Transcriptional Activator Systems
Cited by: 61
Author(s): J Białek, Gábor A. Dunay, Maike Voges, Carola Schäfer, Michael Spohn, Rolf Stucka, Joachim Hauber, Ulrike Lange
Software Mentions: 1
Published: about 10 years ago

10.1371/journal.pone.0002847

Gene Expression and Functional Studies of the Optic Nerve Head Astrocyte Transcriptome from Normal African Americans and Caucasian Americans Donors
Cited by: 20
Author(s): Haixi Miao, Lin Chen, Sean M. Riordan, Wenjun Li, S. Hernández Juárez, A. M. Crabb, Thomas J. Lukas, Pan Du, Simon Lin, Alexandria Wise, Olga A. Agapova, Ping Yang, C. Charles Gu, M. Rosario Hernandez
Software Mentions: 1
Published: about 18 years ago

10.1371/journal.pone.0069318

Cognitive and Clinical Dysfunction, Altered MEG Resting-State Networks and Thalamic Atrophy in Multiple Sclerosis
Cited by: 71
Author(s): Prejaas Tewarie, Menno M. Schoonheim, Cornelis J. Stam, M.L. van der Meer, Bob W. van Dijk, Frederik Barkhof, Chris H. Polman, Arjan Hillebrand
Software Mentions: 1
Published: about 13 years ago

10.1371/journal.pone.0063032

Growth-Promoting Role of the miR-106a∼363 Cluster in Ewing Sarcoma
Cited by: 46
Author(s): Layne Dylla, Paul Jedlicka
Software Mentions: 1
Published: over 13 years ago

10.1371/journal.pone.0055395

Opportunities for Cost-Sharing in Conservation: Variation in Volunteering Effort across Protected Areas
Cited by: 8
Author(s): Paul R. Armsworth, Lisette Cantú‐Salazar, Mark Parnell, Josephine Booth, R. E. Stoneman, Zoe G. Davies
Software Mentions: 1
Published: over 13 years ago

10.1371/journal.pone.0089665

Altered Cortical Swallowing Processing in Patients with Functional Dysphagia: A Preliminary Study
Cited by: 21
Author(s): Sonja Suntrup, Inga Teismann, Andreas Wollbrink, Tobias Warnecke, Martin Winkels, Christo Pantev, Rainer Dziewas
Software Mentions: 1
Published: over 12 years ago

10.1371/journal.pone.0029860

Weighted Change-Point Method for Detecting Differential Gene Expression in Breast Cancer Microarray Data
Cited by: 7
Author(s): Yao Wang, Guang Sun, Zhaohua Ji, Chong Xing, Yanchun Liang
Software Mentions: 1
Published: over 14 years ago

10.1371/journal.pone.0037139

An Ileal Crohn's Disease Gene Signature Based on Whole Human Genome Expression Profiles of Disease Unaffected Ileal Mucosal Biopsies
Cited by: 33
Author(s): Tianyi Zhang, Bowen Song, Wei Zhu, Xiao Xu, Qing Gong, Christopher Morando, Themistocles Dassopoulos, Rodney D. Newberry, Steven R. Hunt, Ellen Li
Software Mentions: 1
Published: over 14 years ago

10.1371/journal.pone.0107643

Molecular Subtyping of Serous Ovarian Tumors Reveals Multiple Connections to Intrinsic Breast Cancer Subtypes
Cited by: 16
Author(s): Jenny-Maria Jönsson, Ida Johansson, Mev Dominguez‐Valentin, Siker Kimbung, Mats Jönsson, Jesper Bonde, Päivi Kannisto, Anna Måsbäck, Susanne Malander, Mef Nilbert, Ingrid Hedenfalk
Software Mentions: 1
Published: almost 12 years ago

Projects: cran: SAM

Science Score: 85/100

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Penalties:

Papers Mentioning SAM 4,566