bioconductor: DESeq2 | Projects | Ecosyste.ms: Papers

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/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/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/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

10.3390/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/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

10.3390/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

10.3390/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/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

10.3390/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/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

10.3390/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/microorganisms8040492

Impact of a Multistrain Probiotic Formulation with High Bifidobacterial Content on the Fecal Bacterial Community and Short-Chain Fatty Acid Levels of Healthy Adults
Cited by: 5
Author(s): Giorgio Gargari, Valentina Taverniti, Ranjan Koirala, Claudio Gardana, Simone Guglielmetti
Software Mentions: 2
Published: over 6 years ago

10.3390/microorganisms9051037

The Influence of Diet and Sex on the Gut Microbiota of Lean and Obese JCR:LA-cp Rats
Cited by: 5
Author(s): Craig T. Resch, Mihir Parikh, J. Alejandro Austria, Spencer Proctor, Thomas Netticadan, Heather Blewett, Grant N. Pierce
Software Mentions: 2
Published: over 5 years ago

10.3390/microorganisms9071463

Use of Oxidative Stress Responses to Determine the Efficacy of Inactivation Treatments on Cryptosporidium Oocysts
Cited by: 3
Author(s): Tefera Tadesse, Kristoffer Relling Tysnes, Lucy J. Robertson
Software Mentions: 2
Published: over 5 years ago

10.3390/microorganisms8040563

Host-Microbiota Interactions in Ileum and Caecum of Pigs Divergent in Feed Efficiency Contribute to Nutrient Utilization
Cited by: 14
Author(s): Henry Reyer, Michael Oster, Ursula M. McCormack, Eduard Muráni, Gillian E. Gardiner, Siriluck Ponsuksili, Peadar G. Lawlor, Klaus Wimmers
Software Mentions: 2
Published: over 6 years ago

10.3390/microorganisms8060845

Anti-Inflammatory and Gut Microbiota Modulatory Effect of Lactobacillus rhamnosus Strain LDTM 7511 in a Dextran Sulfate Sodium-Induced Colitis Murine Model
Cited by: 20
Author(s): Soyoung Yeo, Hyunjoon Park, Eunsol Seo, Jihee Kim, Byoung Kook Kim, In Suk Choi, Chul Sung Huh
Software Mentions: 2
Published: over 6 years ago

10.3390/microorganisms3020175

C1-Pathways in Methyloversatilis universalis FAM5: Genome Wide Gene Expression and Mutagenesis Studies
Cited by: 9
Author(s): Nathan Good, Andrew Lamb, David A. C. Beck, N. Cecilia Martinez‐Gomez, Marina G. Kalyuzhnaya
Software Mentions: 2
Published: over 11 years ago

10.3390/microorganisms9050994

Transcriptome Analysis and Autophagy Investigation of LoVo Cells Stimulated with Exosomes Derived from T. asiatica Adult Worms
Cited by: 3
Author(s): Panhong Liang, Yanping Li, Mao Li, Tingli Liu, Shaohua Zhang, Muhammad Ehsan, Liqun Wang, Aimin Guo, Guoliang Chen, Xuenong Luo
Software Mentions: 2
Published: over 5 years ago

10.3390/microorganisms7050123

Microbial and Functional Profile of the Ceca from Laying Hens Affected by Feeding Prebiotics, Probiotics, and Synbiotics
Cited by: 19
Author(s): C. Pineda-Quiroga, Daniel Borda-Molina, Diego Chaves‐Moreno, R. Ruíz, Raquel Atxaerandio, Amélia Camarinha‐Silva, A. García-Rodríguez
Software Mentions: 2
Published: over 7 years ago

10.3390/microorganisms9020354

Time-Resolved Transcriptional Profiling of Epithelial Cells Infected by Intracellular Acinetobacter baumannii
Cited by: 5
Author(s): Núria Crua Asensio, Javier Macho Rendón, M. C. Torrent
Software Mentions: 2
Published: almost 6 years ago

10.3390/microorganisms9020286

Anti-Acid Drug Treatment Induces Changes in the Gut Microbiome Composition of Hemodialysis Patients
Cited by: 7
Author(s): Yi Ting Lin, Ting Yun Lin, Szu Chun Hung, Po-Yu Liu, Ping Wu, Yun-Shiuan Chuang, Wen Chun Hung, Ya Wen Chiu, Mei Chuan Kuo, Chun Ying Wu
Software Mentions: 2
Published: almost 6 years ago

10.3390/microorganisms8111811

Duodenal Metatranscriptomics to Define Human and Microbial Functional Alterations Associated with Severe Obesity: A Pilot Study
Cited by: 10
Author(s): Ilaria Granata, Carmela Nardelli, Valeria D’Argenio, Salvatore Tramontano, Debora Compare, Mario Rosario Guarracino, Gerardo Nardone, Vincenzo Pilone, Lucia Sacchetti
Software Mentions: 2
Published: almost 6 years ago

10.3390/microorganisms8040528

Gene Expression Profile of Mexican Lime (Citrus aurantifolia) Trees in Response to Huanglongbing Disease caused by Candidatus Liberibacter asiaticus
Cited by: 19
Author(s): Ángela Paulina Arce-Leal, Rocío Bautista, Edgar A. Rodríguez-Negrete, Miguel Ángel Manzanilla-Ramírez, José Joaquín Velázquez-Monreal, María Elena Santos-Cervantes, Jesús Méndez-Lozano, Carmen R. Beuzón, Eduardo R. Bejarano, Araceli G. Castillo, M. Gonzalo Claros, Norma Elena Leyva-López
Software Mentions: 2
Published: over 6 years ago

10.1186/s13229-015-0048-6

CRISPR/Cas9-mediated heterozygous knockout of the autism gene CHD8 and characterization of its transcriptional networks in neurodevelopment
Cited by: 120
Author(s): Ping Wang, Mingyan Lin, Erika Pedrosa, Anastasia Hrabovsky, Zheng Zhang, Wenjun Guo, Herbert M. Lachman, Deyou Zheng
Software Mentions: 2
Published: about 11 years ago

10.1186/s13229-018-0239-z

Loss of the Chr16p11.2 ASD candidate gene QPRT leads to aberrant neuronal differentiation in the SH-SY5Y neuronal cell model
Cited by: 26
Author(s): Denise Haslinger, Regina Waltes, Afsheen Yousaf, Silvia Lindlar, Ines Schneider, Chai K. Lim, Meng Miao Tsai, Boyan K. Garvalov, Amparo Acker‐Palmer, Nicolas Krezdorn, Björn Rotter, Till Acker, Gilles J. Guillemin, Simone Fulda, Christine M. Freitag, Andreas G. Chiocchetti
Software Mentions: 2
Published: about 8 years ago

10.1186/s13229-017-0124-1

CRISPR/Cas9-mediated heterozygous knockout of the autism gene CHD8 and characterization of its transcriptional networks in cerebral organoids derived from iPS cells
Cited by: 190
Author(s): Ping Wang, Ryan Mokhtari, Erika Pedrosa, Michael A. Kirschenbaum, Can Bayrak, Deyou Zheng, Herbert M. Lachman
Software Mentions: 2
Published: over 9 years ago

10.1186/s13071-021-04811-5

Global transcriptome landscape of the rabbit protozoan parasite Eimeria stiedae
Cited by: 8
Author(s): Yue Xie, Jie Xiao, Xuan Zhou, Xiaobin Gu, Ran He, Jing Xu, Bo Jing, Xuerong Peng, Guangyou Yang
Software Mentions: 2
Published: over 5 years ago

10.1186/s13071-020-04212-0

Transcriptional responses in Parascaris univalens after in vitro exposure to ivermectin, pyrantel citrate and thiabendazole
Cited by: 13
Author(s): Frida Martin, Faruk Dube, Oskar Karlsson Lindsjö, Matthías Eydal, Johan Höglund, Tomas F. Bergström, Eva Tydén
Software Mentions: 2
Published: over 6 years ago

10.1186/s13071-021-04996-9

Response to comments on our article (Yin YL et al., Parasit Vectors, 10.1186/s13071-021-04739-w) by Yuqing Wang and colleagues
Cited by: 1
Author(s): Yanling Yin, Xuefei Yang, Guanghui Zhao
Software Mentions: 2
Published: about 5 years ago

10.1186/s13071-020-04096-0

Host gill attachment causes blood-feeding by the salmon louse (Lepeophtheirus salmonis) chalimus larvae and alters parasite development and transcriptome
Cited by: 13
Author(s): Erna Irene Heggland, Michael Dondrup, Frank Nilsen, Christiane Eichner
Software Mentions: 2
Published: over 6 years ago

10.1186/s13071-019-3603-8

Transcriptional responses of Leishmania (Leishmania) amazonensis in the presence of trivalent sodium stibogluconate
Cited by: 25
Author(s): Luz Helena Patiño, Carlos Muskus, Juan David Ramírez
Software Mentions: 2
Published: over 7 years ago

10.1186/s13071-020-04486-4

Comparative transcriptomic analysis of antimony resistant and susceptible Leishmania infantum lines
Cited by: 20
Author(s): Juvana Moreira Andrade, Leilane Oliveira Gonçalves, Daniel Barbosa Liarte, Davi Alvarenga Lima, Frederico Gonçalves Guimarães, Daniela de Melo Resende, Ana Maria Murta Santi, Luana Muniz de Oliveira, João Paulo Linhares Velloso, Renato Guimarães Delfino, Pascale Pescher, Gérald F. Späth, Jerônimo C. Ruiz, Silvane Maria Fonseca Murta
Software Mentions: 2
Published: almost 6 years ago

10.3390/pathogens10010043

Transcriptomic Profiling of Equine and Viral Genes in Peripheral Blood Mononuclear Cells in Horses during Equine Herpesvirus 1 Infection
Cited by: 5
Author(s): Lila M. Zarski, P.S.D. Weber, Yao Lee, Gisela Soboll Hussey
Software Mentions: 2
Published: almost 6 years ago

10.3390/pathogens9060440

Cartography of Free-Living Amoebae in Soil in Guadeloupe (French West Indies) Using DNA Metabarcoding
Cited by: 5
Author(s): Yann Reynaud, Célia Ducat, Antoine Talarmin, Isabel Marcelino
Software Mentions: 2
Published: over 6 years ago

10.3390/pathogens10060761

Profiling of Intestinal Microbiota in Patients Infected with Respiratory Influenza A and B Viruses
Cited by: 10
Author(s): Hebah A. Al-Khatib, Shilu Mathew, Maria K. Smatti, Nahla O. Eltai, Sameer A. Pathan, Asmaa A. Al Thani, Peter Coyle, Muna Al Maslamani, Hadi M. Yassine
Software Mentions: 2
Published: over 5 years ago

10.20411/pai.v4i1.270

The Microbiome of Temporal Arteries
Cited by: 15
Author(s): Gary S. Hoffman, Ted M. Getz, Roshan Padmanabhan, Alexandra Villa‐Forte, Alison Clifford, Pauline Funchain, Madhav Sankunny, Julian D. Perry, Alexander D. Blandford, Gregory S. Kosmorsky, Lisa D. Lystad, Leonard H. Calabrese, Charis Eng
Software Mentions: 2
Published: almost 8 years ago

10.1016/j.patter.2020.100087

Cellular State Transformations Using Deep Learning for Precision Medicine Applications
Cited by: 7
Author(s): Colin Targonski, M. Reed Bender, Benjamin T. Shealy, Benafsh Husain, Bill Paseman, Melinda Smith, F. Alex Feltus
Software Mentions: 2
Published: about 6 years ago

10.1038/s41390-020-01347-9

Gene signature of children with severe respiratory syncytial virus infection
Cited by: 11
Author(s): Clyde Dapat, Satoru Kumaki, Hiromu Sakurai, Hidekazu Nishimura, Hannah Karen Mina Labayo, Michiko Okamoto, Mayuko Saito, Hitoshi Oshitani
Software Mentions: 2
Published: almost 6 years ago

10.7717/peerj.10204

Transcriptome analysis of diploid and triploid Populus tomentosa
Cited by: 3
Author(s): Bin Wen, Xiaozhen Liu, Zhiming Zhang, Hanyao Zhang
Software Mentions: 2
Published: about 6 years ago

10.7717/peerj.11052

Beyond gene ontology (GO): using biocuration approach to improve the gene nomenclature and functional annotation of rice S-domain kinase subfamily
Cited by: 13
Author(s): Sushma Naithani, Daemon Dikeman, Priyanka Garg, Noor Al-Bader, Pankaj Jaiswal
Software Mentions: 2
Published: over 5 years ago

10.7717/peerj.9767

Characterization of the transcriptional response of Candida parapsilosis to the antifungal peptide MAF-1A
Cited by: 4
Author(s): Rong Cheng, Wei Li, Klarke M. Sample, Qiang Xu, Lin Liu, Fangfang Yu, Yingjie Nie, Xiangyan Zhang, Zhenhua Luo
Software Mentions: 2
Published: about 6 years ago

10.7717/peerj.10864

Expression analysis of genes related to cold tolerance in Dendroctonus valens
Cited by: 7
Author(s): Di Zhao, Chunchun Zheng, Fengming Shi, Yecheng Xu, Shixiang Zong, Jing Tao
Software Mentions: 2
Published: over 5 years ago

10.7717/peerj.8277

Biomarker potential of repetitive-element transcriptome in lung cancer
Cited by: 10
Author(s): María Castellano Arroyo, Rocío Bautista, Rafael Larrosa, Manuel Cobo, M. Gonzalo Claros
Software Mentions: 2
Published: almost 7 years ago

10.7717/peerj.11860

Expression of cyanobacterial genes enhanced CO2 assimilation and biomass production in transgenic Arabidopsis thaliana
Cited by: 5
Author(s): Anum Zeb Abbasi, Misbah Bilal, Ghazal Khurshid, Charilaos Yiotis, Iftikhar Zeb, Jamshaid Hussain, Ayesha Baig, Mohammad Maroof Shah, Safee Ullah Chaudhary, Bruce Osborne, Raza Ahmad
Software Mentions: 2
Published: over 5 years ago

10.7717/peerj.10502

miR-21 is upregulated, promoting fibrosis and blocking G2/M in irradiated rat cardiac fibroblasts
Cited by: 7
Author(s): Huan Guo, Xinke Zhao, Hongling Su, Chengxu Ma, Kai Li, Sue Kong, Kedan Liu, Haining Li, Juan Chang, Tao Wang, Hongyun Guo, Huiping Wei, Zhaoyuan Fu, Xinfang Lv, Yingdong Li
Software Mentions: 2
Published: almost 6 years ago

10.7717/peerj.6316

Increased tooth brushing frequency is associated with reduced gingival pocket bacterial diversity in patients with intracranial aneurysms
Cited by: 12
Author(s): Mikko Pyysalo, Pashupati P. Mishra, Kati Sundström, Terho Lehtimäki, Pekka J. Karhunen, Tanja Pessi
Software Mentions: 2
Published: almost 8 years ago

10.7717/peerj.6662

Mapping-by-sequencing using NGS-based 3′-MACE-Seq reveals a new mutant allele of the essential nodulation gene Sym33 (IPD3) in pea (Pisum sativum L.)
Cited by: 10
Author(s): А. И. Жернаков, O. Y. Shtark, Olga A. Kulaeva, Jaroslava V. Fedorina, Alexey М. Afonin, Anna B. Kitaeva, V. E. Tsyganov, Fabian Afonso-Grunz, Klaus Hoffmeier, Björn Rotter, Peter Winter, И. А. Тихонович, В. А. Жуков
Software Mentions: 2
Published: over 7 years ago

10.7717/peerj.9738

Comparing transcriptome profiles of human embryo cultured in closed and standard incubators
Cited by: 4
Author(s): Jingyu Li, Jiayu Huang, Wei Han, Xiaoli Shen, Ying Gao, Gangliang Huang
Software Mentions: 2
Published: over 6 years ago

10.7717/peerj.10617

Genome-wide identification and analysis of cystatin family genes in Sorghum (Sorghum bicolor (L.) Moench)
Cited by: 3
Author(s): Jie Li, Xinhao Liu, Qingmei Wang, Jianfang Sun, Dexian He
Software Mentions: 2
Published: almost 6 years ago

10.7717/peerj.6822

Transcriptional analysis reveals the metabolic state ofBurkholderia zhejiangensisCEIB S4-3 during methyl parathion degradation
Cited by: 13
Author(s): María Luisa Castrejón-Godínez, Ma. Laura Ortiz-Hernández, Emmanuel Salazar, Sergio Encarnación, Patricia Mussali-Galante, Efraín Tovar‐Sánchez, Enrique Sánchez-Salinas, A. Rodríguez
Software Mentions: 2
Published: over 7 years ago

10.7717/peerj.9311

Mining of candidate genes involved in the biosynthesis of dextrorotatory borneol in Cinnamomum burmannii by transcriptomic analysis on three chemotypes
Cited by: 15
Author(s): Zerui Yang, Wenli An, Shanshan Liu, Yuying Huang, Chunzhu Xie, Song Huang, Xiasheng Zheng
Software Mentions: 2
Published: over 6 years ago

10.7717/peerj.9172

Transcriptome profiling of avian pathogenicEscherichia coliand the mouse microvascular endothelial cell line bEnd.3 during interaction
Cited by: 6
Author(s): Peili Wang, Xianli Meng, Jianji Li, Yanfei Chen, Dong Zhang, Haoran Zhong, Pengpeng Xia, Luying Cui, Guoqiang Zhu, Heng Wang
Software Mentions: 2
Published: over 6 years ago

10.7717/peerj.5208

Marine cyanolichens from different littoral zones are associated with distinct bacterial communities
Cited by: 21
Author(s): Nyree J. West, Delphine Parrot, Claire Fayet, Martín Grube, Sophie Tomasi, Marcelino T. Suzuki
Software Mentions: 2
Published: over 8 years ago

10.7717/peerj.5502

Conserved microbiota among young Heliconius butterfly species
Cited by: 22
Author(s): Bas van Schooten, Filipa Godoy-Vitorino, W. Owen McMillan, Riccardo Papa
Software Mentions: 2
Published: about 8 years ago

10.7717/peerj.11926

Effect of elevation, season and accelerated snowmelt on biogeochemical processes during isolated conifer needle litter decomposition
Cited by: 1
Author(s): Laura Leonard, Eoin L. Brodie, Kenneth H. Williams, Jonathan O. Sharp
Software Mentions: 2
Published: over 5 years ago

10.3390/plants8070237

Molecular Characterisation of a Supergene Conditioning Super-High Vitamin C in Kiwifruit Hybrids
Cited by: 6
Author(s): John McCallum, William A. Laing, Sean Bulley, Susan Thomson, Andrew Catanach, Martin Shaw, Mareike Knaëbel, Jibran Tahir, Simon C. Deroles, Gail M. Timmerman-Vaughan, Ross N. Crowhurst, Elena Hilario, Matthew Chisnall, Robyn Lee, Richard C. Macknight, Alan Seal
Software Mentions: 2
Published: over 7 years ago

10.3390/plants9091218

Transcriptome-Wide Analysis of Nitrogen-Regulated Genes in Tea Plant (Camellia sinensis L. O. Kuntze) and Characterization of Amino Acid Transporter CsCAT9.1
Cited by: 10
Author(s): Xinwan Zhang, Hongling Liu, Elizabeth A. H. Pilon‐Smits, Wei Huang, Pu Wang, Mingle Wang, Fei Guo, Yu Wang, Ruiyuan Li, Hua Zhao, Dejiang Ni
Software Mentions: 2
Published: about 6 years ago

10.3390/plants10071478

ROS-Scavenging Enzymes as an Antioxidant Response to High Concentration of Anthracene in the Liverwort Marchantia polymorpha L
Cited by: 6
Author(s): Nahuel Spinedi, Romina Storb, Elisabet Aranda, Facundo Romani, Maya Svriz, Santiago Varela, José Moreno, Sebastián Fracchia, Juan Manuel Cabrera, Ramón Alberto Batista-García, Inés Ponce de León, José Martín Scervino
Software Mentions: 2
Published: over 5 years ago

10.3390/plants9091178

Genome-Wide Identification, Characterization, and Regulation of RWP-RK Gene Family in the Nitrogen-Fixing Clade
Cited by: 7
Author(s): Zhihua Wu, Hong Liu, Wen Huang, Lisha Yi, Erdai Qin, Jing Wang, Rui Qin
Software Mentions: 2
Published: about 6 years ago

10.1371/journal.pbio.2006247

The microRNA-29/PGC1α regulatory axis is critical for metabolic control of cardiac function
Cited by: 36
Author(s): Xurde M. Caravia, Víctor Fanjul, Eduardo Oliver, David Roiz‐Valle, Alba Morán-Álvarez, Gabriela Desdín-Micó, Marı́a Mittelbrunn, R. Cabo, J.A. Vega, Francisco Rodríguez, Antonio Fueyo, Mónica Gómez, Manuel Lobo-González, Héctor Bueno, Gloria Velasco, José M.P. Freije, Vicente Andrés, Borja Ibáñez, Alejandro P. Ugalde, Carlos López‐Otín
Software Mentions: 2
Published: about 8 years ago

10.1371/journal.pbio.3000201

Up-regulation of FOXD1 by YAP alleviates senescence and osteoarthritis
Cited by: 91
Author(s): Ling Fu, Yuqiong Hu, Moshi Song, Zunpeng Liu, Weiqi Zhang, Fa-Xing Yu, Jun Wu, Si Wang, Juan Carlos Izpisúa Belmonte, Piu Chan, Jing Qu, Fuchou Tang, Guang Hui Liu
Software Mentions: 2
Published: over 7 years ago

10.1371/journal.pbio.3000178

Spontaneously slow-cycling subpopulations of human cells originate from activation of stress-response pathways
Cited by: 55
Author(s): Mingwei Min, Sabrina L. Spencer
Software Mentions: 2
Published: over 7 years ago

10.1371/journal.pbio.3001157

The growth factor BMP11 is required for the development and evolution of a male exaggerated weapon and its associated fighting behavior in a water strider
Cited by: 11
Author(s): William Toubiana, David Armisén, Séverine Viala, Amélie Decaras, Abderrahman Khila
Software Mentions: 2
Published: over 5 years ago

10.1371/journal.pbio.2006537

Vocal practice regulates singing activity–dependent genes underlying age-independent vocal learning in songbirds
Cited by: 28
Author(s): Shin Hayase, Hongdi Wang, Eri Ohgushi, Masahiko Kobayashi, Chihiro Mori, Haruhito Horita, Katsuhiko Mineta, Wanchun Liu, Kazuhiro Wada
Software Mentions: 2
Published: about 8 years ago

10.1371/journal.pbio.2006352

Nitrogen fixation in a landrace of maize is supported by a mucilage-associated diazotrophic microbiota
Cited by: 220
Author(s): Allen Van Deynze, Pablo Zamora, Pierre‐Marc Delaux, Cristobal Heitmann, Dhileepkumar Jayaraman, Shanmugam Rajasekar, Danielle Graham, Jun Maeda, Donald J Gibson, Kevin Daniel Schwartz, Alison M. Berry, Srijak Bhatnagar, Guillaume Jospin, Aaron E. Darling, Richard Jeannotte, Javier Rodríguez López, Bart C. Weimer, Jonathan A. Eisen, Howard Shapiro, Jean‐Michel Ané, A. B. Bennett
Software Mentions: 2
Published: over 8 years ago

10.1371/journal.pbio.2005903

Lso2 is a conserved ribosome-bound protein required for translational recovery in yeast
Cited by: 27
Author(s): Yinuo J. Wang, Pavanapuresan P. Vaidyanathan, María F. Rojas-Durán, Namrata D. Udeshi, Kristen M. Bartoli, Steven A. Carr, Wendy V. Gilbert
Software Mentions: 2
Published: about 8 years ago

10.1371/journal.pbio.2002257

Lef1-dependent hypothalamic neurogenesis inhibits anxiety
Cited by: 28
Author(s): Yuanyuan Xie, Dan Kaufmann, Matthew J. Moulton, Samin Panahi, John A. Gaynes, Harrison N. Watters, Decheng Zhou, Hai-Hui Xue, Camille Fung, Edward M. Levine, Anthea Letsou, KC Brennan, Richard I. Dorsky
Software Mentions: 2
Published: about 9 years ago

10.1371/journal.pbio.2006716

miR-181a/b-1 controls thymic selection of Treg cells and tunes their suppressive capacity
Cited by: 26
Author(s): Marcin Łyszkiewicz, Samantha J Winter, Katrin Witzlau, Lisa Föhse, Rebecca J. Brownlie, Jacek Puchałka, Nikita A. Verheyden, Heike Kunze‐Schumacher, Esther Imelmann, Jonas Blume, Solaiman Raha, Takashi Sekiya, Akihiko Yoshimura, Jochen T. Frueh, Evelyn Ullrich, Jochen Huehn, Siegfried Weiß, Maximiliano G. Gutiérrez, Immo Prinz, Rose Zamoyska, Natalia Ziętara, Andreas Krueger
Software Mentions: 2
Published: over 7 years ago

10.1371/journal.pbio.3001043

Systematic analyses of the MIR172 family members of Arabidopsis define their distinct roles in regulation of APETALA2 during floral transition
Cited by: 40
Author(s): Diarmuid S. Ó’Maoiléidigh, Annabel D. van Driel, Anamika Singh, Qing Sang, N. Le Bec, Coral Vincent, E. Bertrán, Alice Vayssières, Maida Romera-Branchat, Edouard Severing, Rafael Martinez Gallegos, George Coupland
Software Mentions: 2
Published: almost 6 years ago

10.1371/journal.pbio.3000087

Inhibition of Notch signaling rescues cardiovascular development in Kabuki Syndrome
Cited by: 19
Author(s): María de los Ángeles Serrano, Bradley L. Demarest, Tarlynn Tone-Pah-Hote, Martin Tristani‐Firouzi, H. Joseph Yost
Software Mentions: 2
Published: about 7 years ago

10.1371/journal.pbio.3001385

The induction of preterm labor in rhesus macaques is determined by the strength of immune response to intrauterine infection
Cited by: 11
Author(s): Monica Cappelletti, Pietro Presicce, Feiyang Ma, Paranthaman Senthamaraikannan, Lisa Miller, Matteo Pellegrini, Myung Shin Sim, Alan H. Jobe, Senad Divanovic, Sing Sing Way, Claire Chougnet, Suhas G. Kallapur
Software Mentions: 2
Published: about 5 years ago

10.1371/journal.pcbi.1007657

Reprogramming of macrophages employing gene regulatory and metabolic network models
Cited by: 32
Author(s): Franziska Hörhold, David Eisel, Marcus Oswald, Amol Kolte, Daniela Röll, Wolfram Osen, Stefan B. Eichmüller, Rainer König
Software Mentions: 2
Published: over 6 years ago

10.1371/journal.pcbi.1008173

Capturing cell type-specific chromatin compartment patterns by applying topic modeling to single-cell Hi-C data
Cited by: 53
Author(s): Hyeon Jin Kim, Galip Gürkan Yardımcı, Giancarlo Bonora, Vijay Ramani, Jie Liu, Ruolan Qiu, Choli Lee, Jennifer Hesson, Carol B. Ware, Jay Shendure, Zhijun Duan
Software Mentions: 2
Published: about 6 years ago

10.1371/journal.pcbi.1007278

Cooperative adaptation to therapy (CAT) confers resistance in heterogeneous non-small cell lung cancer
Cited by: 22
Author(s): Morgan Craig, Kamran Kaveh, Alec N. Woosley, Andrew S. Brown, David Goldman, Elliot O. Eton, Ravindra Mehta, Andrew Dhawan, Kazuya Arai, Mahbuba Rahman, Sidi Chen, Martin A. Nowak, Aaron Goldman
Software Mentions: 2
Published: about 7 years ago

10.1371/journal.pcbi.1009132

eVIP2: Expression-based variant impact phenotyping to predict the function of gene variants
Cited by: 7
Author(s): Alexis M. Thornton, Lishan Fang, April Lo, Maria McSharry, David Haan, Casey OʼBrien, Alice H. Berger, Marios Giannakis, Angela N. Brooks
Software Mentions: 2
Published: over 5 years ago

10.1371/journal.pcbi.1008099

A practical application of generative adversarial networks for RNA-seq analysis to predict the molecular progress of Alzheimer's disease
Cited by: 23
Author(s): Jinhee Park, Hye-Rin Kim, Jae Kwang Kim, Mookyung Cheon
Software Mentions: 2
Published: over 6 years ago

10.1371/journal.pcbi.1004780

4C-ker: A Method to Reproducibly Identify Genome-Wide Interactions Captured by 4C-Seq Experiments
Cited by: 84
Author(s): Ramya Raviram, Pedro P. Rocha, Christian L. Müller, Emily R. Miraldi, Sana Badri, Yi Fu, Emily Swanzey, Charlotte Proudhon, Valentina Snetkova, Richard Bonneau, Jane A. Skok
Software Mentions: 2
Published: over 10 years ago

10.1371/journal.pcbi.1007357

SourceSet: A graphical model approach to identify primary genes in perturbed biological pathways
Cited by: 4
Author(s): Elisa Salviato, Vera Djordjilović, Monica Chiogna, Chiara Romualdi
Software Mentions: 2
Published: about 7 years ago

10.1371/journal.pcbi.1008890

Next-generation yeast-two-hybrid analysis with Y2H-SCORES identifies novel interactors of the MLA immune receptor
Cited by: 13
Author(s): Valeria Velásquez-Zapata, James M. Elmore, Sagnik Banerjee, Karin S. Dorman, Roger P. Wise
Software Mentions: 2
Published: over 5 years ago

10.1371/journal.pcbi.1004991

Metagenome and Metatranscriptome Analyses Using Protein Family Profiles
Cited by: 18
Author(s): Cuncong Zhong, Anna Edlund, Youngik Yang, Jeffrey S. McLean, Shibu Yooseph
Software Mentions: 2
Published: over 10 years ago

10.1371/journal.pgen.1007092

Flip/flop mating-type switching in the methylotrophic yeast Ogataea polymorpha is regulated by an Efg1-Rme1-Ste12 pathway
Cited by: 12
Author(s): Sara J. Hanson, Kevin Byrne, Kenneth H. Wolfe
Software Mentions: 2
Published: almost 9 years ago

10.1371/journal.pgen.1005588

Modulation of Ambient Temperature-Dependent Flowering in Arabidopsis thaliana by Natural Variation of FLOWERING LOCUS M
Cited by: 78
Author(s): Ulrich Lutz, David Posé, Matthias Pfeifer, Heidrun Gundlach, Jörg Hagmann, Congmao Wang, Detlef Weigel, Klaus Mayer, Markus Schmid, Claus Schwechheimer
Software Mentions: 2
Published: about 11 years ago

10.1371/journal.pgen.1006737

A fungal transcription factor essential for starch degradation affects integration of carbon and nitrogen metabolism
Cited by: 41
Author(s): Yi Xiong, V. Wu, Andrea Lubbe, Lu‐Ping Qin, Shijie Deng, Megan Kennedy, Diane Bauer, Vasanth Singan, Kerrie Barry, Trent Northen, Igor V. Grigoriev, N. Louise Glass
Software Mentions: 2
Published: over 9 years ago

10.1371/journal.pgen.1005251

The Regulatory T Cell Lineage Factor Foxp3 Regulates Gene Expression through Several Distinct Mechanisms Mostly Independent of Direct DNA Binding
Cited by: 34
Author(s): Xin Xie, Michael J. T. Stubbington, Jesper K. Nissen, Kristian G. Andersen, Daniel Hebenstreit, Sarah A. Teichmann, Alexander G. Betz
Software Mentions: 2
Published: over 11 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

10.1371/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

10.1371/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

10.1371/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

10.1371/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

10.1371/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

10.1371/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

Projects: bioconductor: DESeq2

Enhanced Analysis

Science Score: 100/100

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Papers Mentioning DESeq2 9,583