bioconductor: DESeq2 | Projects | Ecosyste.ms: Papers

10.1371/journal.pone.0210118

Transcriptome changes in response to temperature in the fish pathogen Photobacterium damselae subsp. damselae: Clues to understand the emergence of disease outbreaks at increased seawater temperatures
Cited by: 30
Author(s): Xosé M. Matanza, Carlos R. Osorio
Software Mentions: 2
Published: almost 8 years ago

10.3390/microorganisms8050744

Metatranscriptomic Analysis of Oil-Exposed Seawater Bacterial Communities Archived by an Environmental Sample Processor (ESP)
Cited by: 9
Author(s): Kamila Knapik, Andrea Bagi, Adriana Królicka, Thierry Baussant
Software Mentions: 2
Published: over 6 years ago

10.3390/microorganisms9081670

Coordinated Diel Gene Expression of Cyanobacteria and Their Microbiome
Cited by: 7
Author(s): Kai Wang, Xiaozhen Mou
Software Mentions: 2
Published: over 5 years ago

10.1371/journal.pone.0247392

The porcine corneal surface bacterial microbiome: A distinctive niche within the ocular surface
Cited by: 6
Author(s): Marina L. Leis, Gabriela Morais Madruga, Matheus O. Costa
Software Mentions: 2
Published: over 5 years ago

10.1371/journal.pone.0182205

A benign helminth alters the host immune system and the gut microbiota in a rat model system
Cited by: 30
Author(s): Laura Wegener Parfrey, Milan Jirků, Radek Šíma, Marie Jalovecká, Bohumil Sak, Karina Grigore, Kateřina Jirků-Pomajbíková
Software Mentions: 2
Published: over 9 years ago

10.3390/microorganisms8121922

Plant Health and Rhizosphere Microbiome: Effects of the Bionematicide Aphanocladium album in Tomato Plants Infested by Meloidogyne javanica
Cited by: 18
Author(s): Claudia Leoni, Elisabetta Piancone, N. Sasanelli, Giovanni Bruno, Caterina Manzari, Graziano Pesole, Luigi R. Ceci, Mariateresa Volpicella
Software Mentions: 2
Published: almost 6 years ago

10.3390/nu13041305

Dietary Curdlan Enhances Bifidobacteria and Reduces Intestinal Inflammation in Mice
Cited by: 9
Author(s): Shafaque Rahman, Mark Davids, Patricia H. P. van Hamersveld, Olaf Welting, H. Rahaoui, Frank Schuren, Sybren L. Meijer, René M. van den Wijngaard, Theodorus B. M. Hakvoort, Wouter J. de Jonge, Sigrid E. M. Heinsbroek
Software Mentions: 2
Published: over 5 years ago

10.1371/journal.pone.0180123

Strand specific RNA-sequencing and membrane lipid profiling reveals growth phase-dependent cold stress response mechanisms in Listeria monocytogenes
Cited by: 28
Author(s): Patricia Hingston, Jessica Chen, Kevin Allen, Lisbeth Truelstrup Hansen, Siyun Wang
Software Mentions: 2
Published: over 9 years ago

10.3390/microorganisms8040538

The Saltpan Microbiome Is Structured by Sediment Depth and Minimally Influenced by Variable Hydration
Cited by: 8
Author(s): Eric A. Weingarten, Lauren A. Lawson, Colin R. Jackson
Software Mentions: 2
Published: over 6 years ago

10.1534/g3.118.200188

A Variable Polyglutamine Repeat Affects Subcellular Localization and Regulatory Activity of a Populus ANGUSTIFOLIA Protein
Cited by: 8
Author(s): Anthony C. Bryan, Jin Zhang, Jianjun Guo, Priya Ranjan, Vasanth Singan, Kerrie Barry, Jeremy Schmutz, Deborah Weighill, Daniel Jacobson, Sara Jawdy, Gerald A. Tuskan, Jay Chen, Wellington Muchero
Software Mentions: 2
Published: over 8 years ago

10.1371/journal.pone.0134645

Heterogeneous Effects of Direct Hypoxia Pathway Activation in Kidney Cancer
Cited by: 47
Author(s): Rafik Salama, Norma Masson, Peter Simpson, Lina K. Sciesielski, Min Sun, Ya-Min Tian, Peter J. Ratcliffe, David R. Mole
Software Mentions: 2
Published: over 11 years ago

10.1371/journal.pone.0173697

Infection with diverse immune-modulating poxviruses elicits different compositional shifts in the mouse gut microbiome
Cited by: 2
Author(s): Daniel Aguirre de Cárcer, Bruno Hernáez, Alberto Rastrojo, Antonio Alcamı́
Software Mentions: 2
Published: over 9 years ago

10.1371/journal.pone.0201174

Combined bacterial and fungal intestinal microbiota analyses: Impact of storage conditions and DNA extraction protocols
Cited by: 30
Author(s): Cécile Angebault, Amine Ghozlane, Stevenn Volant, Françoise Botterel, Christophe d’Enfert, Marie Elisabeth Bougnoux
Software Mentions: 2
Published: over 8 years ago

10.1371/journal.pone.0204322

A phylogenomic study quantifies competing mechanisms for pseudogenization in prokaryotes—The Mycobacterium leprae case
Cited by: 3
Author(s): Eliran Avni, Dennis Montoya, David Lopez, Robert L. Modlin, Matteo Pellegrini, Sagi Snir
Software Mentions: 2
Published: about 8 years ago

10.1371/journal.pone.0162838

The Involvement of Mig1 from Xanthophyllomyces dendrorhous in Catabolic Repression: An Active Mechanism Contributing to the Regulation of Carotenoid Production
Cited by: 24
Author(s): Jennifer Alcaı́no, Natalia Bravo, Pamela Córdova, Andrés E. Marcoleta, Gabriela Contreras, Salvador Barahona, Dionisia Sepúlveda, María Fernández‐Lobato, Marcelo Baeza, Víctor Cifuentes
Software Mentions: 2
Published: about 10 years ago

10.1371/journal.pone.0254645

Expression of several Phytophthora cinnamomi putative RxLRs provides evidence for virulence roles in avocado
Cited by: 6
Author(s): Melissa Joubert, Robert Backer, Juanita Engelbrecht, Noëlani van den Berg
Software Mentions: 2
Published: over 5 years ago

10.1371/journal.pone.0210428

Analysis of the common bean (Phaseolus vulgaris L.) transcriptome regarding efficiency of phosphorus use
Cited by: 15
Author(s): Daiana Alves da Silva, Siu Mui Tsai, Alisson Fernando Chiorato, Sónia C. S. Andrade, José Antônio de Fátima Esteves, Gustavo Henrique Recchia, Sérgio Augusto Morais Carbonell
Software Mentions: 2
Published: almost 8 years ago

10.1534/g3.118.200398

mTOR Complex 1 Implicated in Aphid/Buchnera Host/Symbiont Integration
Cited by: 8
Author(s): Edward James, Honglin Feng, Alex C. C. Wilson
Software Mentions: 2
Published: about 8 years ago

10.1371/journal.pone.0212355

Community ecology across bacteria, archaea and microbial eukaryotes in the sediment and seawater of coastal Puerto Nuevo, Baja California
Cited by: 42
Author(s): Sabah Ul-Hasan, Robert M. Bowers, Andrea Figueroa-Montiel, Alexei F. Licea-Navarro, J. Michael Beman, Tanja Woyke, Clarissa J. Nobile
Software Mentions: 2
Published: almost 8 years ago

10.1371/journal.pone.0241732

Assessment of two DNA extraction kits for profiling poultry respiratory microbiota from multiple sample types
Cited by: 7
Author(s): Michael Edward C Abundo, John M. Ngunjiri, Kara Taylor, Hana Ji, Amir Ghorbani, Mahesh Kc, Bonnie Weber, Timothy J. Johnson, Chang-Won Lee
Software Mentions: 2
Published: almost 6 years ago

10.1371/journal.pone.0220125

Cell-autonomous and non-cell autonomous effects of neuronal BIN1 loss in vivo
Cited by: 16
Author(s): Kathleen M. McAvoy, Hameetha Rajamohamed Sait, Graham Marsh, Michael A. Peterson, Taylor L. Reynolds, Jake Gagnon, Stefanie Geisler, Prescott T. Leach, Chris Roberts, Ellen Cahir-McFarland, Richard M. Ransohoff, Andrea Crotti
Software Mentions: 2
Published: over 7 years ago

10.1534/g3.118.200300

Toward Identifying Subnetworks from FBF Binding Landscapes in Caenorhabditis Spermatogenic or Oogenic Germlines
Cited by: 15
Author(s): Douglas F. Porter, A. Krishna Prasad, Brian H Carrick, Peggy Kroll-Connor, Marvin Wickens, Judith Kimble
Software Mentions: 2
Published: almost 8 years ago

10.1371/journal.pone.0173421

mRNA N6-methyladenosine methylation of postnatal liver development in pig
Cited by: 44
Author(s): He Shen, Hong Wang, Rui Li, Mengnan He, Tiandong Che, Long Jin, Lüe Deng, Shilin Tian, Yán Li, Hongfeng Lü, Xuewei Li, Zhi Jiang, Diyan Li, Mingzhou Li
Software Mentions: 2
Published: over 9 years ago

10.1186/s40478-020-00903-y

Altered secretory and neuroprotective function of the choroid plexus in progressive multiple sclerosis
Cited by: 29
Author(s): Sabela Rodríguez‐Lorenzo, David Francisco, Ricardo Vos, Bert van het Hof, Merel Rijnsburger, Horst Schroten, Hiroshi Ishikawa, Wissam Beaino, Rémy Bruggmann, Gijs Kooij, Helga E. de Vries
Software Mentions: 2
Published: over 6 years ago

10.3390/antibiotics10080947

Interplay between Non-Coding RNA Transcription, Stringent/Relaxed Phenotype and Antibiotic Production in Streptomyces ambofaciens
Cited by: 3
Author(s): Eva Pinatel, Matteo Calcagnile, Adelfia Talà, Fabrizio Damiano, Luisa Siculella, Clelia Peano, Giuseppe E. De Benedetto, Antonio Pennetta, Gianluca De Bellis, Pietro Alifano
Software Mentions: 2
Published: over 5 years ago

10.1136/annrheumdis-2017-212603

Stratification of knee osteoarthritis: two major patient subgroups identified by genome-wide expression analysis of articular cartilage
Cited by: 82
Author(s): Jamie Soul, Sara Dunn, Sanjay Anand, Ferdinand Serracino‐Inglott, Jean-Marc Schwartz, Raymond P. Boot-Handford, Timothy E. Hardingham
Software Mentions: 2
Published: almost 9 years ago

10.1002/acn3.51242

Elevated levels of extracellular vesicles in progranulin‐deficient mice and FTD‐ GRN Patients
Cited by: 7
Author(s): Andrew E. Arrant, Skylar E. Davis, Rachael M Vollmer, Charles Murchison, James A. Mobley, Alissa L. Nana, Salvatore Spina, Lea T. Grinberg, Anna Karydas, Bruce L. Miller, William W. Seeley, Erik D. Roberson
Software Mentions: 2
Published: almost 6 years ago

10.1371/journal.pone.0240769

Glyoxal fixation facilitates transcriptome analysis after antigen staining and cell sorting by flow cytometry
Cited by: 14
Author(s): Prasanna Channathodiyil, Jonathan Houseley
Software Mentions: 2
Published: almost 6 years ago

10.1371/journal.pone.0210371

Long live the queen, the king and the commoner? Transcript expression differences between old and young in the termite Cryptotermes secundus
Cited by: 20
Author(s): José Manuel Monroy Kuhn, Karen Meusemann, Judith Korb
Software Mentions: 2
Published: almost 8 years ago

10.3390/ani10122246

Growth, Metabolite, Antioxidative Capacity, Transcriptome, and the Metabolome Response to Dietary Choline Chloride in Pacific White Shrimp Litopenaeus vannamei
Cited by: 14
Author(s): Maoxian Huang, Hongxing Lin, Chang Xu, Qiuran Yu, Xiaodan Wang, Jianguang Qin, Liqiao Chen, Fenglu Han, Erchao Li
Software Mentions: 2
Published: almost 6 years ago

10.3390/microorganisms8101486

Fecal Microbiota Transplant in Two Ulcerative Colitis Pediatric Cases: Gut Microbiota and Clinical Course Correlations
Cited by: 16
Author(s): Andrea Quagliariello, Federica Del Chierico, Sofia Reddel, Alessandra Russo, Andrea Onetti Muda, Patrizia D’Argenio, Giulia Angelino, Erminia Romeo, Luigi Dall’Oglio, Paola De Angelis, Lorenza Putignani
Software Mentions: 2
Published: about 6 years ago

10.3390/ani11051207

RNA-Seq Reveals Function of Bta-miR-149-5p in the Regulation of Bovine Adipocyte Differentiation
Cited by: 14
Author(s): Huiling Guo, Rajwali Khan, Sayed Haidar Abbas Raza, Syed Muhammad Suhail, Hamayun Khan, Sher Bahadar Khan, Ayman Hassan Abd El-Aziz, Zan Liu
Software Mentions: 2
Published: over 5 years ago

10.1534/g3.118.200873

Identification of a Rat Mammary Tumor Risk Locus That Is Syntenic with the Commonly Amplified 8q12.1 and 8q22.1 Regions in Human Breast Cancer Patients
Cited by: 5
Author(s): Cody Plasterer, Shirng‐Wern Tsaih, Angela Lemke, Rebecca Schilling, Melinda R. Dwinell, Andrea Rau, Paul L. Auer, Hallgeir Rui, Michael J. Flister
Software Mentions: 2
Published: over 7 years ago

10.3390/microorganisms9051084

Experimental Infection of the Biomphalaria glabrata Vector Snail by Schistosoma mansoni Parasites Drives Snail Microbiota Dysbiosis
Cited by: 15
Author(s): Anaïs Portet, Ève Toulza, Ana Lokmer, Camille Huot, David Timothy Duval, Richard Galinier, Benjamin Gourbal
Software Mentions: 2
Published: over 5 years ago

10.1371/journal.pone.0241698

Single-cell analysis of transcriptome and DNA methylome in human oocyte maturation
Cited by: 25
Author(s): Bo Yu, Naresh Doni Jayavelu, Stephanie L. Battle, Jessica C. Mar, Timothy Schimmel, Jacques Cohen, R. David Hawkins
Software Mentions: 2
Published: about 6 years ago

10.1371/journal.pone.0212229

A novel polyketide synthase gene cluster in the plant pathogenic fungus Pseudocercospora fijiensis
Cited by: 7
Author(s): Roslyn D. Noar, Elizabeth Thomas, Margaret E. Daub
Software Mentions: 2
Published: almost 8 years ago

10.3390/microorganisms9020240

Shedding Light on the African Enigma: In Vitro Testing of Homo sapiens-Helicobacter pylori Coevolution
Cited by: 9
Author(s): Bruno Cavadas, Marina Concli Leite, Nicole Pedro, Ana C. Magalhães, Joana Melo, Marcelo Correia, Valdemar Máximo, Rui Camacho, Nuno A. Fonseca, Céu Figueiredo, Luı́sa Pereira
Software Mentions: 2
Published: almost 6 years ago

10.1371/journal.pone.0218352

Fall armyworm (Spodoptera frugiperda Smith) feeding elicits differential defense responses in upland and lowland switchgrass
Cited by: 15
Author(s): Nathan A. Palmer, Saumik Basu, Tiffany Heng-Moss, Jeffrey D. Bradshaw, Gautam Sarath, Joe Louis
Software Mentions: 2
Published: over 7 years ago

10.1371/journal.pone.0179531

Combining 'omics and microscopy to visualize interactions between the Asian citrus psyllid vector and the Huanglongbing pathogen Candidatus Liberibacter asiaticus in the insect gut
Cited by: 96
Author(s): Angela Kruse, Somayeh Fattah-Hosseini, Surya Saha, Richard S. Johnson, EricaRose Warwick, Kasie Sturgeon, Lukas A. Mueller, Michael J. MacCoss, Robert G. Shatters, Michelle Heck
Software Mentions: 2
Published: over 9 years ago

10.3390/microorganisms8081245

Ibuprofen Degradation and Associated Bacterial Communities in Hyporheic Zone Sediments
Cited by: 22
Author(s): Cyrus Rutere, Kirsten Knoop, Malte Posselt, Adrian Ho, Marcus A. Horn
Software Mentions: 2
Published: over 6 years ago

10.3390/microorganisms8040535

Modulation of Pectin on Mucosal Innate Immune Function in Pigs Mediated by Gut Microbiota
Cited by: 18
Author(s): Weida Wu, Li Zhang, Bing Xia, Shouwei Tang, Jingjing Xie, Hongfu Zhang
Software Mentions: 2
Published: over 6 years ago

10.1371/journal.pone.0235962

Comparative transcriptome analysis provides insights into the molecular mechanism underlying double fertilization between self-crossed Solanum melongena and that hybridized with Solanum aethiopicum
Cited by: 4
Author(s): Dandan Li, Siqi Li, Wenjia Li, Ake Liu, Yaqin Jiang, Guiyun Gan, Weiliu Li, Xuyu Liang, Yu Ning, Riyuan Chen, Yikui Wang
Software Mentions: 2
Published: over 6 years ago

10.3390/ani10020344

RNA Sequencing (RNA-Seq) Based Transcriptome Analysis in Immune Response of Holstein Cattle to Killed Vaccine against Bovine Viral Diarrhea Virus Type I
Cited by: 13
Author(s): Bryan Irvine Lopez, Kier Gumangan Santiago, Dong-Hui Lee, Seungmin Ha, Kangseok Seo
Software Mentions: 2
Published: over 6 years ago

10.3390/microorganisms8030421

Microbiota Alters Urinary Bladder Weight and Gene Expression
Cited by: 5
Author(s): Blanka Roje, Anamaria Elek, Vinko Palada, Joana Bom, Aida Iljazović, Ana Šimić, Lana Sušak, Katarina Vilović, Till Strowig, Kristian Vlahoviček, Janoš Terzić
Software Mentions: 2
Published: over 6 years ago

10.3390/ani9070427

Whole Blood Transcriptome Analysis Reveals Positive Effects of Dried Olive Pomace-Supplemented Diet on Inflammation and Cholesterol in Laying Hens
Cited by: 19
Author(s): Marco Iannaccone, Andrea Ianni, Solange Ramazzotti, Lisa Grotta, Elettra Marone, Angelo Cichelli, Giuseppe Martino
Software Mentions: 2
Published: over 7 years ago

10.3390/microorganisms8121961

Spent Coffee Grounds Alter Bacterial Communities in Latxa Dairy Ewes
Cited by: 5
Author(s): Idoia Goiri, Xabier Díaz de Otálora, R. Ruíz, Jagoba Rey, Raquel Atxaerandio, José L. Lavín, David San Martín, Mikel Orive, Bruno Iñarra, Jaime Zufía, J. Urkiza, A. García-Rodríguez
Software Mentions: 2
Published: almost 6 years ago

10.3390/microorganisms9091888

RNA-Seq Provides New Insights into the Gene Expression Changes in Azoarcus olearius BH72 under Nitrogen-Deficient and Replete Conditions beyond the Nitrogen Fixation Process
Cited by: 4
Author(s): Shanmugam Solaiyappan Mani, Barbara Reinhold‐Hurek
Software Mentions: 2
Published: about 5 years ago

10.3390/ani10030534

A Novel Therapeutic Reagent, KA-1002 for Alleviating Lysophosphatidic Acid-Mediated Inflammation Related Gene Expression in Swine Macrophages
Cited by: 0
Author(s): Hyeon-Jeong Hwang, Tamina Park, Miok Kim, Hee-Su Shin, Woo-Yeon Hwang, Yong Ki Min, Sukgil Song, Daeui Park, Chang Hoon Lee
Software Mentions: 2
Published: over 6 years ago

10.3390/microorganisms9040724

Transcriptome Analysis on the Mechanism of Ethylicin Inhibiting Pseudomonas syringae pv. actinidiae on Kiwifruit
Cited by: 14
Author(s): Tao Liu, Xiaohu Ren, Guangyun Cao, Xia Zhou, Linhong Jin
Software Mentions: 2
Published: over 5 years ago

10.1534/g3.119.400051

Expression Signatures of Cisplatin- and Trametinib-Treated Early-Stage Medaka Melanomas
Cited by: 5
Author(s): Barbara Klotz, Susanne Kneitz, Yuan Lu, William Boswell, John H. Postlethwait, Wesley C. Warren, Ronald B. Walter, Manfred Schartl
Software Mentions: 2
Published: over 7 years ago

10.1371/journal.pone.0105138

Contrasting Metabolism in Perenniating Structures of Upland and Lowland Switchgrass Plants Late in the Growing Season
Cited by: 22
Author(s): Nathan A. Palmer, Aaron J. Saathoff, Christian M. Tobias, Paul Twigg, Yuannan Xia, Kenneth P. Vogel, M. Soundararajan, Scott E. Sattler, Gautam Sarath
Software Mentions: 2
Published: about 12 years ago

10.1371/journal.pone.0234427

Characterization of microRNA profiles in the mammary gland tissue of dairy goats at the late lactation, dry period and late gestation stages
Cited by: 19
Author(s): Rong Xuan, Tianle Chao, Aili Wang, Fuhong Zhang, Ping Sun, Shuang Liu, Maosen Guo, Guizhi Wang, Zhibin Ji, Jianmin Wang, Ming Cheng
Software Mentions: 2
Published: over 6 years ago

10.1371/journal.pone.0229700

Revisiting the expression signature of pks15/1 unveils regulatory patterns controlling phenolphtiocerol and phenolglycolipid production in pathogenic mycobacteria
Cited by: 3
Author(s): Beatriz Ramos, Stephen V. Gordon, Mónica V. Cunha
Software Mentions: 2
Published: over 6 years ago

10.1534/g3.119.400330

A Non-Dicer RNase III and Four Other Novel Factors Required for RNAi-Mediated Transposon Suppression in the Human Pathogenic Yeast Cryptococcus neoformans
Cited by: 15
Author(s): Jordan E. Burke, Adam D. Longhurst, Prashanthi Natarajan, Beiduo Rao, S. John Liu, Jade Sales-Lee, Yasaman Mortensen, James J. Moresco, Jolene K. Diedrich, John R. Yates, Hiten Madhani
Software Mentions: 2
Published: over 7 years ago

10.1371/journal.pone.0176734

MicroRNAs in the miR-17 and miR-15 families are downregulated in chronic kidney disease with hypertension
Cited by: 37
Author(s): Priyanka Nandakumar, Adrienne Tin, Megan L. Grove, Jianchao Ma, Eric Boerwinkle, Josef Coresh, Aravinda Chakravarti
Software Mentions: 2
Published: over 9 years ago

10.1371/journal.pone.0222501

Geographical location influences the composition of the gut microbiota in wild house mice (Mus musculus domesticus) at a fine spatial scale
Cited by: 31
Author(s): Sarah Goertz, Alexandre B. de Menezes, Richard J. Birtles, Jonathan Fenn, Ann Lowe, Andrew D. C. MacColl, Benoit Poulin, Stuart Young, Janette E. Bradley, Christopher H. Taylor
Software Mentions: 2
Published: about 7 years ago

10.3390/microorganisms8121974

Transcriptional Profiling of Immune and Inflammatory Responses in the Context of SARS-CoV-2 Fungal Superinfection in a Human Airway Epithelial Model
Cited by: 5
Author(s): Claire Nicolas de Lamballerie, Andrés Pizzorno, Julien Fouret, Lea Szpiro, Blandine Padey, Julia Dubois, Thomas Julien, Aurélien Traversier, Victoria Dulière, Pauline Brun, Bruno Lina, Manuel Rosa‐Calatrava, Benjamin Terrier
Software Mentions: 2
Published: almost 6 years ago

10.1371/journal.pone.0177513

An integrative analysis of tissue-specific transcriptomic and metabolomic responses to short-term dietary methionine restriction in mice
Cited by: 30
Author(s): Sujoy Ghosh, Laura A. Forney, Desiree Wanders, Kirsten P. Stone, Thomas W. Gettys
Software Mentions: 2
Published: over 9 years ago

10.3390/microorganisms8121918

Deletion of the Aspergillus niger Pro-Protein Processing Protease Gene kexB Results in a pH-Dependent Morphological Transition during Submerged Cultivations and Increases Cell Wall Chitin Content
Cited by: 5
Author(s): Tim M. van Leeuwe, Mark Arentshorst, Gabriel Forn-Cuní, Nicholas Geoffrion, Adrian Tsang, Frank Delvigne, Annemarie H. Meijer, Arthur F. J. Ram, Peter J. Punt
Software Mentions: 2
Published: almost 6 years ago

10.3390/ani9100755

Effect of Feeding Cold-Pressed Sunflower Cake on Ruminal Fermentation, Lipid Metabolism and Bacterial Community in Dairy Cows
Cited by: 12
Author(s): Izaro Zubiria, A. García-Rodríguez, Raquel Atxaerandio, R. Ruíz, Hanen Benhissi, N. Mandaluniz, José L. Lavín, Leticia Abecia, Idoia Goiri
Software Mentions: 2
Published: about 7 years ago

10.1371/journal.pone.0161211

Mothers Secretor Status Affects Development of Childrens Microbiota Composition and Function: A Pilot Study
Cited by: 54
Author(s): Paula Smith‐Brown, Mark Morrison, Lutz Krause, Peter S. W. Davies
Software Mentions: 2
Published: about 10 years ago

10.1371/journal.pone.0129359

Gene Expression Signature in Adipose Tissue of Acromegaly Patients
Cited by: 19
Author(s): Irit Hochberg, Quynh Tran, Ariel L. Barkan, Alan R. Saltiel, William F. Chandler, Dave Bridges
Software Mentions: 2
Published: over 11 years ago

10.1371/journal.pone.0214275

Genetic and epigenetic profiling of the infertile male
Cited by: 38
Author(s): Stephanie Cheung, Alessandra Parrella, Zev Rosenwaks, Gianpiero D. Palermo
Software Mentions: 2
Published: over 7 years ago

10.1371/journal.pone.0252066

G protein-coupled receptors as candidates for modulation and activation of the chemical senses in decapod crustaceans
Cited by: 7
Author(s): Matthew T. Rump, Mihika T. Kozma, Shrikant Pawar, Charles D. Derby
Software Mentions: 2
Published: over 5 years ago

10.1371/journal.pone.0182694

Comparison of alternative approaches for analysing multi-level RNA-seq data
Cited by: 22
Author(s): Irina Mohorianu, Amanda Bretman, Damian T. Smith, Emily K. Fowler, Tamás Dalmay, Tracey Chapman
Software Mentions: 2
Published: over 9 years ago

10.1186/s12967-020-02528-0

Down-regulation of PADI2 prevents proliferation and epithelial-mesenchymal transition in ovarian cancer through inhibiting JAK2/STAT3 pathway in vitro and in vivo, alone or in combination with Olaparib
Cited by: 14
Author(s): Lidong Liu, Zhiwei Zhang, Guoxiang Zhang, Ting Wang, Yingchun Ma, Wei Guo
Software Mentions: 2
Published: about 6 years ago

10.1186/s40478-019-0690-x

Transcriptome signatures associated with meningioma progression
Cited by: 24
Author(s): Angela N. Viaene, Bo Zhang, Maria Martinez‐Lage, Chaomei Xiang, Umberto Tosi, Jayesh P. Thawani, Busra Gungor, Yuankun Zhu, Laura Roccograndi, Logan Zhang, Robert L. Bailey, Phillip B. Storm, Donald M. O’Rourke, Adam Resnick, M. Sean Grady, Nadia Dahmane
Software Mentions: 2
Published: over 7 years ago

10.1371/journal.pone.0246610

Adherent and suspension baby hamster kidney cells have a different cytoskeleton and surface receptor repertoire
Cited by: 2
Author(s): Veronika Dill, Florian Pfaff, Aline Zimmer, Martin Beer, Michael Eschbaumer
Software Mentions: 2
Published: over 5 years ago

10.1534/g3.119.400935

Inflammation-Induced Alternative Pre-mRNA Splicing in Mouse Alveolar Macrophages
Cited by: 16
Author(s): William J. Janssen, Thomas Danhorn, Chelsea Harris, Kara J. Mould, Frank Fang‐Yao Lee, Brenna R. Hedin, Angelo D’Alessandro, Sonia M. Leach, Scott Alper
Software Mentions: 2
Published: almost 7 years ago

10.1371/journal.pone.0246107

Network mapping of primary CD34+ cells by Ampliseq based whole transcriptome targeted resequencing identifies unexplored differentiation regulatory relationships
Cited by: 0
Author(s): Jessica L. Schwaber, Darren Korbie, Stacey Andersen, Erica Lin, Panagiotis K. Chrysanthopoulos, Matt Trau, Lars K. Nielsen
Software Mentions: 2
Published: almost 6 years ago

10.3390/ani11092667

Domestication Explains Two-Thirds of Differential-Gene-Expression Variance between Domestic and Wild Animals; The Remaining One-Third Reflects Intraspecific and Interspecific Variation
Cited by: 7
Author(s): Irina Chadaeva, П. М. Пономаренко, Rimma Kozhemyakina, В. В. Суслов, Anton Bogomolov, Н. В. Климова, С. Г. Шихевич, Л. К. Савинкова, Dmitry Oshchepkov, Nikolay А. Kolchanov, A. L. Markel, М. П. Пономаренко
Software Mentions: 2
Published: about 5 years ago

10.1371/journal.pone.0132127

HIV-1 RNAs are Not Part of the Argonaute 2 Associated RNA Interference Pathway in Macrophages
Cited by: 15
Author(s): Valentina Vongrad, Jochen Imig, Pejman Mohammadi, Shivendra Kishore, Łukasz Jaśkiewicz, Jonathan Hall, Huldrych F. Günthard, Niko Beerenwinkel, Karin J. Metzner
Software Mentions: 2
Published: over 11 years ago

10.3390/mi11030322

Selective Retrieval of Individual Cells from Microfluidic Arrays Combining Dielectrophoretic Force and Directed Hydrodynamic Flow
Cited by: 11
Author(s): Pierre-Emmanuel Marie Thiriet, Jörn Pezoldt, Gabriele Gambardella, Kevin Keim, Bart Deplancke, Carlotta Guiducci
Software Mentions: 2
Published: over 6 years ago

10.1186/s40168-021-01034-9

Constraining PERMANOVA and LDM to within-set comparisons by projection improves the efficiency of analyses of matched sets of microbiome data
Cited by: 14
Author(s): Zhengyi Zhu, Glen A. Satten, Caroline Mitchell, Yi‐Juan Hu
Software Mentions: 2
Published: over 5 years ago

10.1186/s40168-018-0448-x

Drinking alcohol is associated with variation in the human oral microbiome in a large study of American adults
Cited by: 146
Author(s): Xiaozhou Fan, Brandilyn A. Peters, Eric J. Jacobs, Susan M. Gapstur, Mark P. Purdue, Neal D. Freedman, Alexander V. Alekseyenko, Jing Wu, Liying Yang, Zhiheng Pei, Richard B. Hayes, Jiyoung Ahn
Software Mentions: 2
Published: over 8 years ago

10.1371/journal.pone.0215946

Does MHC heterozygosity influence microbiota form and function?
Cited by: 17
Author(s): M.A. Wadud Khan, W. Zac Stephens, Ahmed Dawood Mohammed, June L. Round, Jason L. Kubinak
Software Mentions: 2
Published: over 7 years ago

10.1371/journal.pone.0132387

MicroRNA Profiling of Neurons Generated Using Induced Pluripotent Stem Cells Derived from Patients with Schizophrenia and Schizoaffective Disorder, and 22q11.2 Del
Cited by: 80
Author(s): Dejian Zhao, Mingyan Lin, Jian Chen, Erika Pedrosa, Anastasia Hrabovsky, H. Matthew Fourcade, Deyou Zheng, Herbert M. Lachman
Software Mentions: 2
Published: over 11 years ago

10.1186/s40168-017-0252-z

Subgingival microbiota dysbiosis in systemic lupus erythematosus: association with periodontal status
Cited by: 112
Author(s): Jôice Dias Corrêa, Débora Cerqueira Calderaro, Gilda Aparecida Ferreira, Santuza Maria Souza de Mendonça, Gabriel R. Fernandes, E. Xiao, Antônio Lúcio Teixeira, Eugene J. Leys, Dana T. Graves, Tarcı́lia Aparecida Silva
Software Mentions: 2
Published: over 9 years ago

10.1371/journal.pone.0154129

Comparative Analysis of the miRNome of Bovine Milk Fat, Whey and Cells
Cited by: 67
Author(s): Ran Li, Pier-Luc Dudemaine, Xin Zhao, Chuzhao Lei, Eveline M. Ibeagha‐Awemu
Software Mentions: 2
Published: over 10 years ago

10.1534/g3.119.401025

Reduced Function of the Glutathione S-Transferase S1 Suppresses Behavioral Hyperexcitability inDrosophilaExpressing Mutant Voltage-Gated Sodium Channels
Cited by: 1
Author(s): Hung-Lin Chen, Junko Kasuya, Patrick Lansdon, Garrett A. Kaas, Hanxi Tang, Maggie Sodders, Toshihiro Kitamoto
Software Mentions: 2
Published: over 6 years ago

10.1186/s12967-021-03056-1

UBE2T promotes autophagy via the p53/AMPK/mTOR signaling pathway in lung adenocarcinoma
Cited by: 26
Author(s): Jinhong Zhu, Haijiao Ao, Mingdong Liu, Kui Cao, Jianqun Ma
Software Mentions: 2
Published: about 5 years ago

10.1371/journal.pone.0212645

Bald thigh syndrome in sighthounds—Revisiting the cause of a well-known disease
Cited by: 5
Author(s): Magdalena A. T. Brunner, Silvia Rüfenacht, Anina Bauer, Susanne Erpel, Natasha Buchs, Sophie Braga-Lagache, Manfred Heller, Tosso Leeb, Vidhya Jagannathan, Dominique J Wiener, Monika Maria Welle
Software Mentions: 2
Published: over 7 years ago

10.1371/journal.pone.0171435

A novel RNA sequencing data analysis method for cell line authentication
Cited by: 24
Author(s): Erik Fasterius, Cinzia Raso, Susan Kennedy, Nora Rauch, Per Lundin, Walter Kölch, Mathias Uhlén, Cristina Al‐Khalili Szigyarto
Software Mentions: 2
Published: almost 10 years ago

10.1534/g3.119.400993

Epigenetic Regulation of ABA-Induced Transcriptional Responses in Maize
Cited by: 16
Author(s): Stefania Vendramin, Ji Huang, Peter A. Crisp, Thelma F. Madzima, Karen M. McGinnis
Software Mentions: 2
Published: over 6 years ago

10.1371/journal.pone.0223980

Dysregulation of macrophage development and phenotype in diabetic human macrophages can be rescued by Hoxa3 protein transduction
Cited by: 17
Author(s): Salma Saleh Alrdahe, Hadeel Al Sadoun, Tanja Torbica, Edward A. McKenzie, Frank L. Bowling, Andrew J.M. Boulton, Kimberly A. Mace
Software Mentions: 2
Published: about 7 years ago

10.1186/s40168-020-00913-x

Gut microbiota steroid sexual dimorphism and its impact on gonadal steroids: influences of obesity and menopausal status
Cited by: 57
Author(s): Jordi Mayneris‐Perxachs, María Arnoriaga-Rodríguez, D. Luque-Córdoba, Feliciano Priego‐Capote, Vicente Pérez‐Brocal, Andrés Moya, Aurelijus Burokas, Rafaël Maldonado, José Manuel Fernández-Real
Software Mentions: 2
Published: about 6 years ago

10.1371/journal.pone.0209694

Macrophages attenuate the transcription of CYP1A1 in breast tumor cells and enhance their proliferation
Cited by: 6
Author(s): Sofia Winslow, Anica Scholz, Peter Rappl, Thilo F. Brauß, Claudia Mertens, Michaela Jung, Andreas Weigert, Bernhard Brüne, Tobias Schmid
Software Mentions: 2
Published: almost 8 years ago

10.1371/journal.pone.0118269

Transcriptome Analysis of Resistant and Susceptible Alfalfa Cultivars Infected With Root-Knot Nematode Meloidogyne incognita
Cited by: 53
Author(s): Olga A. Postnikova, Maria N. Hult, Jonathan Shao, Andrea M. Skantar, Lev G. Nemchinov
Software Mentions: 2
Published: over 11 years ago

10.1371/journal.pone.0208936

A unique subset of low-risk Wilms tumors is characterized by loss of function of TRIM28 (KAP1), a gene critical in early renal development: A Children’s Oncology Group study
Cited by: 32
Author(s): Amy E. Armstrong, Samantha Gadd, Vicki Huff, Daniela S. Gerhard, Jeffrey S. Dome, Elizabeth J. Perlman
Software Mentions: 2
Published: almost 8 years ago

10.1186/s12967-020-02231-0

Gut metabolomics profiling of non-small cell lung cancer (NSCLC) patients under immunotherapy treatment
Cited by: 106
Author(s): Andrea Botticelli, Pamela Vernocchi, Federico Marini, Andrea Quagliariello, Bruna Cerbelli, Sofia Reddel, Federica Del Chierico, Francesca Di Pietro, Raffaele Giusti, Alberta Tomassini, Ottavia Giampaoli, Alfredo Miccheli, Ilaria Grazia Zizzari, Marianna Nuti, Lorenza Putignani, Paolo Marchetti
Software Mentions: 2
Published: almost 7 years ago

10.1371/journal.pone.0232863

Repetitive transcranial magnetic stimulation activates glial cells and inhibits neurogenesis after pneumococcal meningitis
Cited by: 9
Author(s): Lukas Muri, Simone Oberhänsli, Michelle Buri, Ngoc Dung Le, Denis Grandgirard, Rémy Bruggmann, René M. Müri, Stephen L. Leib
Software Mentions: 2
Published: about 6 years ago

10.1186/s40168-018-0589-y

Specialisation events of fungal metacommunities exposed to a persistent organic pollutant are suggestive of augmented pathogenic potential
Cited by: 16
Author(s): Celso Martins, Adélia Varela, Céline C. Leclercq, Óscar Núñez, Tomáš Větrovský, Jenny Renaut, Petr Baldrián, Cristina Silva Pereira
Software Mentions: 2
Published: almost 8 years ago

10.1097/MD.0000000000012018

Gene co-expression network analysis identifies the hub genes associated with immune functions for nocturnal hemodialysis in patients with end-stage renal disease
Cited by: 11
Author(s): Hongwei Dai, Jiao Zhou, Bo Zhu
Software Mentions: 2
Published: about 8 years ago

10.1097/MD.0000000000026271

Bioinformatics analysis of the key potential ceRNA biomarkers in human thymic epithelial tumors
Cited by: 4
Author(s): Kegong Chen, Long Bai, Lin Ji, Libo Wu, Guanghua Li
Software Mentions: 2
Published: over 5 years ago

10.1371/journal.pone.0226232

Investigation of the quorum-sensing regulon of the biocontrol bacterium Pseudomonas chlororaphis strain PA23
Cited by: 11
Author(s): Nidhi Shah, April S. Gislason, Michael G. Becker, Mark F. Belmonte, W. G. Dilantha Fernando, Teresa R. de Kievit
Software Mentions: 2
Published: over 6 years ago

10.3390/ani11092553

Evaluating the Inclusion of Cold-Pressed Rapeseed Cake in the Concentrate for Dairy Cows upon Ruminal Biohydrogenation Process, Ruminal Microbial Community and Milk Production and Acceptability
Cited by: 4
Author(s): Idoia Goiri, Izaro Zubiria, José Luis Lavín, Hanen Benhissi, Raquel Atxaerandio, R. Ruíz, N. Mandaluniz, A. García-Rodríguez
Software Mentions: 2
Published: about 5 years ago

10.1155/2017/5047403

Comparison of Oropharyngeal Microbiota from Children with Asthma and Cystic Fibrosis
Cited by: 29
Author(s): Sébastien Boutin, Martin Depner, Mirjam Stahl, Simon Y. Graeber, S Dittrich, Antje Legatzki, Erika von Mutius, Marcus Mall, Alexander H. Dalpke
Software Mentions: 2
Published: almost 10 years ago

10.1371/journal.pone.0220597

Exploring the basis of 2-propenyl and 3-butenyl glucosinolate synthesis by QTL mapping and RNA-sequencing in Brassica juncea
Cited by: 8
Author(s): Aimal Nawaz Khattak, Tianya Wang, Kunjiang Yu, Renqin Yang, Wei Wan, Botao Ye, Entang Tian
Software Mentions: 2
Published: about 7 years ago

10.1371/journal.pone.0258291

Locus-specific analysis of Transposable Elements during the progression of ALS in the SOD1G93A mouse model
Cited by: 5
Author(s): Braulio Valdebenito-Maturana, Esteban Arancibia, Gonzalo Riadi, Juan Carlos Tapia, Mónica A. Carrasco
Software Mentions: 2
Published: about 5 years ago

10.1186/s40478-018-0606-1

Modulation of astrocyte reactivity improves functional deficits in mouse models of Alzheimer’s disease
Cited by: 122
Author(s): Kelly Ceyzériat, Lucile Ben Haim, Audrey Denizot, Dylan Pommier, Marco Matos, Océane Guillemaud, Marie-Ange Palomares, Laurene Abjean, Fanny Petit, Pauline Gipchtein, Marie-Claude Gaillard, Martine Guillermier, Suéva Bernier, Mylène Gaudin, Gwenaëlle Aurégan, Charlène Joséphine, Nathalie Déchamps, Julien Veran, Valentin Langlais, Karine Cambon, Alexis Bémelmans, Jan Baijer, Gilles Bonvento, Marc Dhénain, Jean‐François Deleuze, Stéphane H. R. Oliet, Emmanuel Brouillet, Philippe Hantraye, María-Angeles Carrillo-de Sauvage, Robert Olaso, Aude Panatier, Carole Escartin
Software Mentions: 2
Published: about 8 years ago

Projects: bioconductor: DESeq2

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Science Score: 100/100

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Papers Mentioning DESeq2 9,583