cran: SAM | Projects | Ecosyste.ms: Papers

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

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: over 5 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: about 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: almost 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: about 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: over 13 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: almost 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: over 16 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: about 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: over 18 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: almost 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: about 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: about 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: over 12 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: almost 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.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

Projects: cran: SAM

Science Score: 85/100

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Papers Mentioning SAM 4,566