bioconductor: DESeq2 | Projects | Ecosyste.ms: Papers

10.3390/v13091820

WRKY Transcription Factors in Cassava Contribute to Regulation of Tolerance and Susceptibility to Cassava Mosaic Disease through Stress Responses
Cited by: 7
Author(s): Warren Freeborough, Nikki L. Gentle, M. E. C. Rey
Software Mentions: 2
Published: about 5 years ago

10.1038/s41598-021-81790-8

Pre- and postmenopausal women have different core urinary microbiota
Cited by: 19
Author(s): Nadia Ammitzbøll, Benedikt Bau, Caspar Bundgaard‐Nielsen, Annemarie Brusen Villadsen, Ann Maria Jensen, Peter Leutscher, Karin Glavind, Søren Hagstrøm, Louise Thomsen Schmidt Arenholt, Susanne Sørensen
Software Mentions: 2
Published: almost 6 years ago

10.1038/s41598-021-81387-1

Analysis of ovarian transcriptomes reveals thousands of novel genes in the insect vector Rhodnius prolixus
Cited by: 17
Author(s): Vitor Lima Coelho, Tarcísio Fontenele de Brito, Ingrid Alexandre de Abreu Brito, Maira Arruda Cardoso, Mateus Berni, Helena Araujo, Michael Sammeth, Andrea Pane
Software Mentions: 2
Published: almost 6 years ago

10.1038/s41598-021-81226-3

A genome-wide transcriptomic analysis of embryos fathered by obese males in a murine model of diet-induced obesity
Cited by: 6
Author(s): Laura Bernhardt, Marcus Dittrich, Rabih El‐Merahbi, Antoine‐Emmanuel Saliba, Tobias Müller, Grzegorz Sumara, Jörg Vogel, Stefanie Nichols-Burns, Megan Mitchell, Thomas Haaf, Nady El Hajj
Software Mentions: 2
Published: almost 6 years ago

10.1186/s13059-015-0679-0

quantro: a data-driven approach to guide the choice of an appropriate normalization method
Cited by: 70
Author(s): Stephanie C. Hicks, Rafael A. Irizarry
Software Mentions: 2
Published: over 11 years ago

10.1371/journal.ppat.1009416

Viral genomic, metagenomic and human transcriptomic characterization and prediction of the clinical forms of COVID-19
Cited by: 23
Author(s): Christophe Rodriguez, Nicolas de Prost, Slim Fourati, Claudie Lamoureux, Guillaume Gricourt, Mélissa N’Debi, Florence Canouï‐Poitrine, Isaac Désveaux, Oriane Picard, Vanessa Démontant, Elisabeth Trawinski, R. Lepeule, Laure Surgers, William Vindrios, Jean‐Daniel Lelièvre, Nicolas Mongardon, Olivier Langeron, José L. Cohen, Armand Mekontso-Dessap, Paul‐Louis Woerther, Jean‐Michel Pawlotsky
Software Mentions: 2
Published: over 5 years ago

10.1038/s41598-020-80278-1

Neonatal intensive care unit (NICU) exposures exert a sustained influence on the progression of gut microbiota and metabolome in the first year of life
Cited by: 9
Author(s): Polly Soo Xi Yap, Chun Wie Chong, Azanna Ahmad Kamar, Ivan Kok Seng Yap, Yao Mun Choo, Nai Ming Lai, Cindy Shuan Ju Teh
Software Mentions: 2
Published: almost 6 years ago

10.3390/vaccines8040588

Contrasting Immunomodulatory Effects of Probiotic and Pathogenic Bacteria on Eastern Oyster, Crassostrea Virginica, Larvae
Cited by: 17
Author(s): Tejashree Modak, Marta Gómez-Chiarri
Software Mentions: 2
Published: about 6 years ago

10.1098/rsos.171718

Differential gene expression is not required for facultative sex allocation: a transcriptome analysis of brain tissue in the parasitoid wasp Nasonia vitripennis
Cited by: 6
Author(s): Nicola Cook, Rebecca A. Boulton, Jade Green, Urmi Trivedi, Eran Tauber, Bart Pannebakker, Michael G. Ritchie, David M. Shuker
Software Mentions: 2
Published: almost 9 years ago

10.1038/s41598-020-80859-0

Differences in the bacteriome of swab, saliva, and tissue biopsies in oral cancer
Cited by: 25
Author(s): Divya Gopinath, Rohit Kunnath Menon, Chun Wie Chong, Moinak Banerjee, Swagatika Panda, Deviprasad Mandal, Paresh Kumar Behera, Susanta Roychoudhury, Supriya Kheur, MG Botelho, Newell W. Johnson
Software Mentions: 2
Published: almost 6 years ago

10.3390/v13071303

Defense-Related Gene Expression Following an Orthotospovirus Infection Is Influenced by Host Resistance in Arachis hypogaea
Cited by: 4
Author(s): Michael A. Catto, Anita Shrestha, Mark Abney, Donald E. Champagne, A. K. Culbreath, Soraya C. M. Leal‐Bertioli, Brendan G. Hunt, Rajagopalbabu Srinivasan
Software Mentions: 2
Published: over 5 years ago

10.1080/15476286.2018.1481697

Global characterization of the Dicer-like protein DrnB roles in miRNA biogenesis in the social amoeba Dictyostelium discoideum
Cited by: 6
Author(s): Zhen Liao, Jonas Kjellin, Marc P. Hoeppner, Manfred Grabherr, Fredrik Söderbom
Software Mentions: 2
Published: over 8 years ago

10.1186/s12866-019-1399-5

Gut microbiome patterns correlate with higher postoperative complication rates after pancreatic surgery
Cited by: 34
Author(s): Felix C. F. Schmitt, Thorsten Brenner, Florian Uhle, Svenja Loesch, Thilo Hackert, Alexis Ulrich, Stefan Hofer, Alexander H. Dalpke, Markus Weigand, Sébastien Boutin
Software Mentions: 2
Published: over 7 years ago

10.1371/journal.ppat.1009565

Mitigation of endemic GI-tract pathogen-mediated inflammation through development of multimodal treatment regimen and its impact on SIV acquisition in rhesus macaques
Cited by: 9
Author(s): Rachele M. Bochart, Kathleen Busman‐Sahay, Stephen Bondoc, David W. Morrow, Alexandra M. Ortiz, Christine M. Fennessey, Miranda Fischer, Oriene Shiel, Tonya Swanson, Christine Shriver-Munsch, Hugh Crank, Kimberly Armantrout, Aaron M Barber-Axthelm, Charlotte A. Langner, Cassandra Rae Moats, Caralyn Labriola, Rhonda MacAllister, Michael K. Axthelm, Jason M. Brenchley, Brandon F. Keele, Jacob D. Estes, Scott G. Hansen, Jeremy Smedley
Software Mentions: 2
Published: over 5 years ago

10.1186/s13059-016-0980-6

MDSINE: Microbial Dynamical Systems INference Engine for microbiome time-series analyses
Cited by: 196
Author(s): Vanni Bucci, Belinda Tzen, Ning Li, Matt Simmons, Takeshi Tanoue, Elijah Bogart, Luxue Deng, Vladimir Yeliseyev, Mary L. Delaney, Qing Liu, Bernat Olle, Richard R. Stein, Kenya Honda, Lynn Bry, Georg K. Gerber
Software Mentions: 2
Published: over 10 years ago

10.1186/s13059-016-0990-4

Functional genomics analyses of RNA-binding proteins reveal the splicing regulator SNRPB as an oncogenic candidate in glioblastoma
Cited by: 78
Author(s): Bruna Corrêa, Patrícia Rosa de Araújo, Mu Qiao, Suzanne Perea Burns, Chen Chen, Richard Schlegel, Seema Agarwal, Pedro A. F. Galante, Luiz O. F. Penalva
Software Mentions: 2
Published: over 10 years ago

10.1073/pnas.2125016118

CRISPR-based targeting of DNA methylation in Arabidopsis thaliana by a bacterial CG-specific DNA methyltransferase
Cited by: 33
Author(s): Basudev Ghoshal, Colette L. Picard, Brandon Vong, Suhua Feng, Steven E. Jacobsen
Software Mentions: 2
Published: over 5 years ago

10.1186/s13059-016-1054-5

Time-resolved dual RNA-seq reveals extensive rewiring of lung epithelial and pneumococcal transcriptomes during early infection
Cited by: 94
Author(s): Rieza Aprianto, Jelle Slager, Siger Holsappel, Jan‐Willem Veening
Software Mentions: 2
Published: about 10 years ago

10.1186/s13059-016-1096-8

TET-dependent regulation of retrotransposable elements in mouse embryonic stem cells
Cited by: 78
Author(s): Lorenzo de la Rica, Özgen Deniz, Kevin Cheng, Christopher D. Todd, Cristina Cruz, Jonathan Houseley, Miguel R. Branco
Software Mentions: 2
Published: almost 10 years ago

10.1186/s13059-016-1139-1

Distinct 5-methylcytosine profiles in poly(A) RNA from mouse embryonic stem cells and brain
Cited by: 245
Author(s): Thomas Amort, Dietmar Rieder, Alexandra Wille, Daria Khokhlova-Cubberley, Christian Riml, Lukas Trixl, Xiaoteng Jia, Ronald Micura, Alexandra Lusser
Software Mentions: 2
Published: almost 10 years ago

10.1177/2045894021996190

Extracellular matrix degradation pathways and fatty acid metabolism regulate distinct pulmonary vascular cell types in pulmonary arterial hypertension
Cited by: 8
Author(s): Sharon Mumby, Frédèric Perros, Chee‐Kin Hui, Bo Xu, Weiqing Xu, Vahid Elyasigomari, Aurélie Hautefort, Grégoire Manaud, Marc Humbert, Kian Fan Chung, SJ Wort, Ian M. Adcock
Software Mentions: 2
Published: almost 6 years ago

10.1186/s13059-017-1206-2

Proximal methylation features associated with nonrandom changes in gene body methylation
Cited by: 29
Author(s): Colette L. Picard, Mary Gehring
Software Mentions: 2
Published: over 9 years ago

10.1038/s41598-019-48047-x

Functional Transcriptome Analysis in ARSACS KO Cell Model Reveals a Role of Sacsin in Autophagy
Cited by: 24
Author(s): Federica Morani, Stefano Doccini, Roberto Sirica, Marta Paterno, Francesco Pezzini, Ivana Ricca, Alessandro Simonati, Massimo Delledonne, Filippo M. Santorelli
Software Mentions: 2
Published: over 7 years ago

10.3390/v13060976

Activation of the STAT3 Signaling Pathway by the RNA-Dependent RNA Polymerase Protein of Arenavirus
Cited by: 1
Author(s): Qingxing Wang, Qilin Xin, Weijuan Shang, Weiwei Wan, Gengfu Xiao, Leike Zhang
Software Mentions: 2
Published: over 5 years ago

10.1186/s13059-018-1478-1

DNA Topoisomerase I differentially modulates R-loops across the human genome
Cited by: 103
Author(s): Stefano Giustino Manzo, Stella R. Hartono, Lionel A. Sanz, Jessica Marinello, Sara De Biasi, Andrea Cossarizza, Giovanni Capranico, Frédéric Chédin
Software Mentions: 2
Published: over 8 years ago

10.1038/s41598-019-45973-8

Chronic disturbance in the thalamus following cranial irradiation to the developing mouse brain
Cited by: 1
Author(s): Martina Boström, Yohanna Eriksson, Jolie Danial, Thomas Björk‐Eriksson, Marie Kalm
Software Mentions: 2
Published: over 7 years ago

10.1186/s13059-018-1497-y

Draft genome sequence of wild Prunus yedoensis reveals massive inter-specific hybridization between sympatric flowering cherries
Cited by: 73
Author(s): Seung-Hoon Baek, Kyung Choi, Goon-Bo Kim, Hee‐Ju Yu, Ara Cho, Hoyeol Jang, Changkyun Kim, Hyuk-Jin Kim, Kyung‐Il Chang, Joohwan Kim, Jeong‐Hwan Mun
Software Mentions: 2
Published: about 8 years ago

10.1186/s13059-018-1538-6

CRISPhieRmix: a hierarchical mixture model for CRISPR pooled screens
Cited by: 34
Author(s): Timothy Daley, Zhixiang Lin, Xueqiu Lin, Yanxia Liu, Wing Hung Wong, Lei Qi
Software Mentions: 2
Published: about 8 years ago

10.1371/journal.ppat.1009709

Transgenic expression of a T cell epitope in Strongyloides ratti reveals that helminth-specific CD4+ T cells constitute both Th2 and Treg populations
Cited by: 7
Author(s): Bonnie Douglas, Yun Wei, Xinshe Li, Annabel A. Ferguson, Li-Yin Hung, Christopher Pastore, Jonathan R. Kurtz, James B. McLachlan, Thomas J. Nolan, James B. Lok, De’Broski R. Herbert
Software Mentions: 2
Published: over 5 years ago

10.1371/journal.ppat.1009759

Altered microRNA expression in COVID-19 patients enables identification of SARS-CoV-2 infection
Cited by: 98
Author(s): Ryan J. Farr, Christina L. Rootes, Louise C. Rowntree, Thi H. O. Nguyen, Luca Hensen, Łukasz Kędzierski, Allen Cheng, Katherine Kedzierska, Gough G. Au, Glenn A. Marsh, Seshadri S. Vasan, Chwan Hong Foo, Christopher Cowled, Cameron R. Stewart
Software Mentions: 2
Published: over 5 years ago

10.1186/s13059-019-1651-1

Mitochondrial hypoxic stress induces widespread RNA editing by APOBEC3G in natural killer cells
Cited by: 49
Author(s): Shraddha Sharma, Jianmin Wang, Emad Alqassim, Scott Portwood, Eduardo Cortes Gomez, Orla Maguire, Per H. Basse, Eunice S. Wang, Brahm H. Segal, Bora E. Baysal
Software Mentions: 2
Published: over 7 years ago

10.1038/s41598-019-44727-w

Phenotypic plasticity of Escherichia coli upon exposure to physical stress induced by ZnO nanorods
Cited by: 16
Author(s): Kinga Matuła, Łukasz Richter, Marta Janczuk-Richter, Wojciech Nogala, Mikołaj Grzeszkowiak, Barbara Peplińska, Stefan Jurga, Elżbieta Wyroba, Szymon Suski, Henryk Bilski, Adrian Silesian, Hans A.R. Bluyssen, Natalia Derebecka, Joanna Wesoły, Jerzy Łoś, Marcin Łoś, Przemysław Decewicz, Łukasz Dziewit, Jan Paczesny, Robert Hołyst
Software Mentions: 2
Published: over 7 years ago

10.1073/pnas.2023050118

Molecular design of the γδT cell receptor ectodomain encodes biologically fit ligand recognition in the absence of mechanosensing
Cited by: 7
Author(s): Robert J. Mallis, Jonathan S. Duke‐Cohan, Dibyendu Das, Aoi Akitsu, Adrienne Luoma, Debasis Banik, Hannah M. Stephens, Paul W. Tetteh, Caitlin D. Castro, Sophie Krahnke, Rebecca E. Hussey, Brian Lawney, Kristine N. Brazin, Pedro A. Reche, Wonmuk Hwang, Erin J. Adams, Matthew J. Lang, Ellis L. Reinherz
Software Mentions: 2
Published: over 5 years ago

10.1371/journal.ppat.1009351

A unique GCN5 histone acetyltransferase complex controls erythrocyte invasion and virulence in the malaria parasite Plasmodium falciparum
Cited by: 19
Author(s): Jun Miao, Chengqi Wang, Amuza Byaruhanga Lucky, Xiaoying Liang, Hui Min, Swamy Rakesh Adapa, Rays H. Y. Jiang, Kami Kim, Liwang Cui
Software Mentions: 2
Published: about 5 years ago

10.1038/s41598-019-44674-6

Oral microbial dysbiosis linked to worsened periodontal condition in rheumatoid arthritis patients
Cited by: 73
Author(s): Jôice Dias Corrêa, Gabriel R. Fernandes, Débora Cerqueira Calderaro, Santuza Maria Souza de Mendonça, Janine Mayra da Silva, Mayra Laino Albiero, Fernando Q. Cunha, E. Xiao, Gilda Aparecida Ferreira, Antônio Lúcio Teixeira, Chiranjit Mukherjee, Eugene J. Leys, Dana T. Graves
Software Mentions: 2
Published: over 7 years ago

10.1186/s13059-019-1749-5

Integrative analysis of vascular endothelial cell genomic features identifies AIDA as a coronary artery disease candidate gene
Cited by: 25
Author(s): Simon Lalonde, Valérie-Anne Codina-Fauteux, Sébastian Méric de Bellefon, F. Leblanc, Mélissa Beaudoin, Simon Maguire, Rola Dali, Tony Kwan, Ken Sin Lo, Tomi Pastinen, Guillaume Lettre
Software Mentions: 2
Published: over 7 years ago

10.1038/s41598-019-44798-9

Biology and Bias in Cell Type-Specific RNAseq of Nucleus Accumbens Medium Spiny Neurons
Cited by: 23
Author(s): Hope Kronman, Felix Richter, Benoît Labonté, Ramesh Chandra, Shan Zhao, Gabriel E. Hoffman, Mary Kay Lobo, Eric E. Schadt, Eric J. Nestler
Software Mentions: 2
Published: over 7 years ago

10.1371/journal.pntd.0007383

Hindgut microbiota in laboratory-reared and wild Triatoma infestans
Cited by: 34
Author(s): Andreea Waltmann, Alexandra C Willcox, Sujata Balasubramanian, Katty Borrini Mayorí, Sandra Mendoza Guerrero, R Sánchez, Jeffrey Roach, Carlos Condori Pino, Robert H. Gilman, Caryn Bern, Jonathan J. Juliano, Michael Z. Levy, Steven R. Meshnick, Natalie M. Bowman
Software Mentions: 2
Published: over 7 years ago

10.1371/journal.pntd.0007697

Systems analysis-based assessment of post-treatment adverse events in lymphatic filariasis
Cited by: 11
Author(s): Britt Andersen, Bruce A. Rosa, Jonah Kupritz, Aboulaye Meïté, Traye Serge, Marla I. Hertz, Kurt C. Curtis, Christopher L. King, Makedonka Mitreva, Peter Fischer, Gary J. Weil
Software Mentions: 2
Published: about 7 years ago

10.1371/journal.pntd.0008125

Glutamine supplementation improves the efficacy of miltefosine treatment for visceral leishmaniasis
Cited by: 20
Author(s): Carolina Ferreira, Inês Mesquita, Amanda Pires Barbosa, Nuno S. Osório, Egídio Torrado, Charles-Joly Beauparlant, Arnaud Droit, Cristina Cunha, Agostinho Carvalho, Bhaskar Saha, Jérôme Estaquier, Ricardo Silvestre
Software Mentions: 2
Published: over 6 years ago

10.1186/s12870-016-0722-7

Shared and divergent pathways for flower abscission are triggered by gibberellic acid and carbon starvation in seedless Vitis vinifera L
Cited by: 26
Author(s): Sara Domingos, Joana Fino, Vânia Cardoso, Claudia Lara, José C. Ramalho, R. Larcher, Octávio S. Paulo, Cristina M. Oliveira, Luís F. Goulão
Software Mentions: 2
Published: almost 11 years ago

10.1371/journal.pntd.0005067

Under-Expression of Chemosensory Genes in Domiciliary Bugs of the Chagas Disease Vector Triatoma brasiliensis
Cited by: 22
Author(s): Axelle Marchant, Florence Mougel, Emmanuelle Jacquin‐Joly, Jane Costa, Carlos Eduardo Almeida, Myriam Harry
Software Mentions: 2
Published: about 10 years ago

10.1371/journal.pntd.0005789

Double impact: natural molluscicide for schistosomiasis vector control also impedes development of Schistosoma mansoni cercariae into adult parasites
Cited by: 18
Author(s): Ronaldo de Carvalho Augusto, Guillaume Tetreau, Philippe Chan, Marie‐Laure Walet‐Balieu, Clélia Christina Mello-Silva, Cláudia Portes Santos, Christoph Grunau
Software Mentions: 2
Published: over 9 years ago

10.1371/journal.pntd.0005398

A multistrain approach to studying the mechanisms underlying compatibility in the interaction between Biomphalaria glabrata and Schistosoma mansoni
Cited by: 34
Author(s): Richard Galinier, Emmanuel Roger, Yves Moné, David Timothy Duval, Anaïs Portet, Silvain Pinaud, Cristian Chaparro, Christoph Grunau, Clémence Genthon, Emeric Dubois, Anne Rognon, Nathalie Arancibia, Bernard Dejean, André Thèron, Benjamin Gourbal, Guillaume Mitta
Software Mentions: 2
Published: over 9 years ago

10.1186/s13059-019-1787-z

MPRAnalyze: statistical framework for massively parallel reporter assays
Cited by: 54
Author(s): Tal Ashuach, David Fischer, Anat Kreimer, Nadav Ahituv, Fabian J. Theis, Nir Yosef
Software Mentions: 2
Published: about 7 years ago

10.1186/s12870-021-02998-4

Combining targeted metabolite analyses and transcriptomics to reveal the specific chemical composition and associated genes in the incompatible soybean variety PI437654 infected with soybean cyst nematode HG1.2.3.5.7
Cited by: 12
Author(s): Song Xue, Qiansi Chen, Shiming Liu, Jiajun Wang, Deliang Peng, Lingan Kong
Software Mentions: 2
Published: over 5 years ago

10.1186/s12870-021-02880-3

Overexpression of a methyl-CpG-binding protein gene OsMBD707 leads to larger tiller angles and reduced photoperiod sensitivity in rice
Cited by: 10
Author(s): Mengyu Qu, Zhujian Zhang, Tingmin Liang, Peipei Niu, Mingji Wu, Wenchao Chi, Ziqiang Chen, Zaijie Chen, Shubiao Zhang, Songbiao Chen
Software Mentions: 2
Published: over 5 years ago

10.1186/s12870-021-02983-x

Comparative transcriptome profiling and co-expression network analysis uncover the key genes associated withearly-stage resistance to Aspergillus flavus in maize
Cited by: 13
Author(s): Huanhuan Liu, Haofeng Wu, Yan Wang, Huan Wang, Saihua Chen, Zhitong Yin
Software Mentions: 2
Published: over 5 years ago

10.3390/v12111219

Impact of Zika Virus Infection on Human Neural Stem Cell MicroRNA Signatures
Cited by: 13
Author(s): Denna Tabari, Catharina Scholl, Michael Steffens, Sandra Weickhardt, Fabian Elgner, Daniela Bender, Marie-Luise Herrlein, Catarina Sabino, Vesselina Semkova, Michael Peitz, Andreas Till, Oliver Brüstle, Eberhard Hildt, Julia Stingl
Software Mentions: 2
Published: about 6 years ago

10.1371/journal.pone.0216267

Identification of flowering-time genes in mast flowering plants using De Novo transcriptomic analysis
Cited by: 4
Author(s): * Samarth, Robyn Lee, Jiancheng Song, Richard C. Macknight, Paula E. Jameson
Software Mentions: 2
Published: over 7 years ago

10.1186/s12870-017-0998-2

Transcriptional analysis of defense mechanisms in upland tetraploid switchgrass to greenbugs
Cited by: 32
Author(s): Teresa Donze-Reiner, Nathan A. Palmer, Erin D. Scully, T. J. Prochaska, Kyle G. Koch, Tiffany Heng-Moss, Jeffrey D. Bradshaw, Paul Twigg, Keenan Amundsen, Scott E. Sattler, Gautam Sarath
Software Mentions: 2
Published: over 9 years ago

10.1371/journal.pone.0222435

PRC2 activates interferon-stimulated genes indirectly by repressing miRNAs in glioblastoma
Cited by: 4
Author(s): Haridha Shivram, Steven V. Le, Vishwanath R. Iyer
Software Mentions: 2
Published: about 7 years ago

10.1186/s12870-020-02341-3

Transcriptome analysis of responses in Brachypodium distachyon overexpressing the BdbZIP26 transcription factor
Cited by: 1
Author(s): Ruth C. Martin, Brent Kronmiller, James E. Dombrowski
Software Mentions: 2
Published: over 6 years ago

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

10.1371/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

10.1371/journal.pntd.0009363

No pre-zygotic isolation mechanisms between Schistosoma haematobium and Schistosoma bovis parasites: From mating interactions to differential gene expression
Cited by: 7
Author(s): Julien Kincaid-Smith, Eglantine Mathieu‐Bégné, Cristian Chaparro, Marta Reguera-Gómez, Stephen Mulero, Jean‐François Allienne, Ève Toulza, Jérôme Boissier
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

10.1371/journal.pntd.0006568

A transcriptomic survey of the impact of environmental stress on response to dengue virus in the mosquito, Aedes aegypti
Cited by: 10
Author(s): Dukjin Kang, Martin S. Barron, Diane D. Lovin, Joanne M. Cunningham, Matthew W. Eng, Dave D. Chadee, Jun Li, David W. Severson
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

10.1186/s13059-019-1915-9

RADAR: differential analysis of MeRIP-seq data with a random effect model
Cited by: 37
Author(s): Zijie Zhang, Qi Zhan, Mark A. Eckert, Allen Zhu, Agnieszka Chryplewicz, Dario F. De Jesus, Decheng Ren, Rohit Kulkarni, Ernst Lengyel, Chuan He, Mengjie Chen
Software Mentions: 2
Published: almost 7 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

10.1371/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

10.1186/s12864-018-5362-x

DEBrowser: interactive differential expression analysis and visualization tool for count data
Cited by: 167
Author(s): Alper Küçükural, Onur Yukselen, Deniz M. Özata, Melissa J. Moore, Manuel Garber
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

10.1186/s12870-020-2238-4

Full moonlight-induced circadian clock entrainment in Coffea arabica
Cited by: 15
Author(s): Jean‐Christophe Breitler, Doâa Djerrab, Sophie Léran, Lucile Toniutti, Charlie Guittin, Dany Séverac, Marine Pratlong, Alexis Dereeper, Hervé Etienne, Benoît Bertrand
Software Mentions: 2
Published: almost 7 years ago

10.1371/journal.pgen.1009023

TENET 2.0: Identification of key transcriptional regulators and enhancers in lung adenocarcinoma
Cited by: 19
Author(s): Daniel J. Mullen, Chunli Yan, Diane S. Kang, Baosen Zhou, Zea Borok, Crystal N. Marconett, Peggy J. Farnham, Ite A. Offringa, Suhn Kyong Rhie
Software Mentions: 2
Published: about 6 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/s12864-019-6173-4

Physiological and transcriptome analysis reveal molecular mechanism in Salvia miltiorrhiza leaves of near-isogenic male fertile lines and male sterile lines
Cited by: 3
Author(s): Ruihong Wang, Han Jiang, Ziyun Zhou, Hongbo Guo, Juane Dong
Software Mentions: 2
Published: about 7 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

10.1038/s41598-019-43421-1

Molecular Basis of Disease Resistance in Banana Progenitor Musa balbisiana against Xanthomonas campestris pv. musacearum
Cited by: 20
Author(s): Leena Tripathi, Jaindra Nath Tripathi, Trushar Shah, Kariuki Samwel Muiruri, Manpreet S. Katari
Software Mentions: 2
Published: over 7 years ago

10.1186/s12864-015-2162-4

Analysis of the FnrL regulon in Rhodobacter capsulatus reveals limited regulon overlap with orthologues from Rhodobacter sphaeroides and Escherichia coli
Cited by: 20
Author(s): Joseph E. Kumka, Carl E. Bauer
Software Mentions: 2
Published: about 11 years ago

10.1371/journal.pgen.1008039

Loss of atrx cooperates with p53-deficiency to promote the development of sarcomas and other malignancies
Cited by: 36
Author(s): F. Oppel, Ting Tao, Hui Shi, Kenneth N. Ross, Mark W. Zimmerman, Shuning He, Guangxiang Tong, Jon C. Aster, A. Thomas Look
Software Mentions: 2
Published: over 7 years ago

10.1186/s12870-019-1878-8

Comparative transcriptome analysis reveals important roles of nonadditive genes in maize hybrid An’nong 591 under heat stress
Cited by: 38
Author(s): Yang Zhao, Fangxiu Hu, Xingen Zhang, Qiye Wei, Jinlei Dong, Bo Chen, Beijiu Cheng, Qing Ma
Software Mentions: 2
Published: over 7 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/proteomes7020014

Extracellular Vesicle Integrins Distinguish Unique Cancers
Cited by: 43
Author(s): Stephanie N. Hurwitz, David G. Meckes
Software Mentions: 2
Published: over 7 years ago

10.1371/journal.pgen.1006658

DUX4-induced dsRNA and MYC mRNA stabilization activate apoptotic pathways in human cell models of facioscapulohumeral dystrophy
Cited by: 73
Author(s): Sean C. Shadle, Jun Zhong, Amy E. Campbell, Melissa Conerly, Sujatha Jagannathan, Chao-Jen Wong, Timothy Morello, Silvère M. van der Maarel, Stephen J. Tapscott
Software Mentions: 2
Published: over 9 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.pgen.1008213

The gene regulatory basis of genetic compensation during neural crest induction
Cited by: 31
Author(s): Christopher M. Dooley, Neha Wali, Ian Sealy, Richard White, Derek L. Stemple, John Collins, Elisabeth M Busch-Nentwich
Software Mentions: 2
Published: over 7 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

10.1186/s12864-017-4205-5

Integrative testis transcriptome analysis reveals differentially expressed miRNAs and their mRNA targets during early puberty in Atlantic salmon
Cited by: 35
Author(s): Kai Ove Skaftnesmo, Rolf B. Edvardsen, Tomasz Furmanek, Diego Crespo, Eva Andersson, Lene Kleppe, Geir Lasse Taranger, Jan Bogerd, Rüdiger Schulz, Anna Wargelius
Software Mentions: 2
Published: about 9 years ago

10.1186/s12870-018-1465-4

Phenotypic and transcriptomic characterization of a wheat tall mutant carrying an induced mutation in the C-terminal PFYRE motif of RHT-B1b
Cited by: 11
Author(s): Youngjun Mo, Stephen Pearce, Jorge Dubcovsky
Software Mentions: 2
Published: about 8 years ago

10.1371/journal.pgen.1006932

Control of RUNX-induced repression of Notch signaling by MLF and its partner DnaJ-1 during Drosophila hematopoiesis
Cited by: 18
Author(s): Marion S. Miller, Aichun Chen, Vanessa Gobert, Benoît Augé, Mathilde Beau, Odile Burlet‐Schiltz, Marc Haenlin, Lucas Waltzer
Software Mentions: 2
Published: over 9 years ago

10.1186/s12870-019-2081-7

Anatomy and RNA-Seq reveal important gene pathways regulating sex differentiation in a functionally Androdioecious tree, Tapiscia sinensis
Cited by: 7
Author(s): Guiliang Xin, Jia-Qian Liu, Jia Liu, Xiaolong Ren, Xiaomin Du, Wenzhe Liu
Software Mentions: 2
Published: almost 7 years ago

10.1038/s41598-019-42568-1

A molecular biomarker for prediction of clinical outcome in children with ASD, constipation, and intestinal inflammation
Cited by: 10
Author(s): Stephen J. Walker, Carl D. Langefeld, Kip D. Zimmerman, Marshall Z. Schwartz, Arthur Krigsman
Software Mentions: 2
Published: over 7 years ago

10.1186/s12870-019-1872-1

A stress-responsive bZIP transcription factor OsbZIP62 improves drought and oxidative tolerance in rice
Cited by: 80
Author(s): Shiqin Yang, Kai Xu, Shoujun Chen, Tianfei Li, Hui Xia, Liang Chen, Hongyan Liu, Lijun Luo
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

10.1371/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

Projects: bioconductor: DESeq2

Enhanced Analysis

Science Score: 100/100

Bonuses:

Papers Mentioning DESeq2 9,583