cran: gplots | Projects | Ecosyste.ms: Papers

10.1186/gm500

Analysis of epigenetic changes in survivors of preterm birth reveals the effect of gestational age and evidence for a long term legacy
Cited by: 105
Author(s): Mark N Cruickshank, Alicia Oshlack, Christiane Theda, Peter G Davis, David Martino, Penelope M. Sheehan, Yun Dai, Richard Saffery, Lex W. Doyle, Jeffrey M Craig
Software Mentions: 5
Published: almost 14 years ago

10.3390/microorganisms8121977

Alteration of Bacterial Communities in Anterior Nares and Skin Sites of Patients Undergoing Arthroplasty Surgery: Analysis by 16S rRNA and Staphylococcal-Specific tuf Gene Sequencing
Cited by: 8
Author(s): Søren Iversen, Thor Bech Johannesen, Anna Cäcilia Ingham, Sofie Marie Edslev, Staffan Tevell, Emeli Månsson, Åsa Nilsdotter-Augustinsson, Bo Söderquist, Marc Stegger, Paal Skytt Andersen
Software Mentions: 5
Published: almost 6 years ago

10.3390/microorganisms9020347

Global Transcriptional Response of Methylorubrum extorquens to Formaldehyde Stress Expands the Role of EfgA and Is Distinct from Antibiotic Translational Inhibition
Cited by: 3
Author(s): Jannell V. Bazurto, Siavash Riazi, Simon D’Alton, Daniel E. Deatherage, Eric L. Bruger, Jeffrey E. Barrick, Christopher J. Marx
Software Mentions: 5
Published: over 5 years ago

10.1186/1471-2164-15-749

Metagenomics reveals that detoxification systems are underrepresented in marine bacterial communities
Cited by: 22
Author(s): Johan Bengtsson‐Palme, Magnus Alm Rosenblad, Mikael Molin, Anders Blomberg
Software Mentions: 5
Published: almost 13 years ago

10.1186/s13059-017-1304-1

Abundant expression of somatic transposon-derived piRNAs throughout Tribolium castaneum embryogenesis
Cited by: 16
Author(s): Maria Ninova, Sam Griffiths-Jones, Matthew Ronshaugen
Software Mentions: 5
Published: about 9 years ago

10.1186/s12864-015-2096-x

The distribution and impact of common copy-number variation in the genome of the domesticated apple, Malus x domestica Borkh
Cited by: 19
Author(s): James Boocock, David Chagné, Tony R. Merriman, Michael A. Black
Software Mentions: 5
Published: about 11 years ago

10.3390/microorganisms9071457

Indicative Marker Microbiome Structures Deduced from the Taxonomic Inventory of 67 Full-Scale Anaerobic Digesters of 49 Agricultural Biogas Plants
Cited by: 7
Author(s): Julia Hassa, Johanna Klang, Dirk Benndorf, Marcel Pohl, Benedikt Hülsemann, Torsten Mächtig, Mathias Effenberger, Alfred Pühler, Andreas Schlüter, Susanne Theuerl
Software Mentions: 5
Published: over 5 years ago

10.1186/gb-2013-14-10-r112

Genome-wide analysis of condensin binding in Caenorhabditis elegans
Cited by: 74
Author(s): Anna-Lena Kranz, Chenyu Jiao, Lara Winterkorn, Sarah Elizabeth Albritton, Maxwell Kramer, Sevinç Ercan
Software Mentions: 5
Published: almost 14 years ago

10.1534/genetics.116.194688

Wheat Landrace Genome Diversity
Cited by: 67
Author(s): Luzie U. Wingen, Claire West, Michelle Leverington-Waite, Sarah Collier, Simon Orford, Richard Goram, Caiyun Yang, Julie King, Alexandra M. Allen, Amanda Burridge, Keith J. Edwards, Simon Griffiths
Software Mentions: 5
Published: over 9 years ago

10.3390/genes11050499

Unmasking Intra-Tumoral Heterogeneity and Clonal Evolution in NF1-MPNST
Cited by: 2
Author(s): Chang In Moon, William Tompkins, Yuxi Wang, Abigail Godec, Xiaochun Zhang, Patrik Pipkorn, Christopher A. Miller, Carina Dehner, Sonika Dahiya, Angela C. Hirbe
Software Mentions: 5
Published: over 6 years ago

10.3390/genes12020201

Ablation of SMUG1 Reduces Cell Viability and Increases UVC-Mediated Apoptosis in Hepatocarcinoma HepG2 Cells
Cited by: 1
Author(s): Mi-Jin An, Geun-Seup Shin, Hyun-Min Lee, Jung-Woong Kim
Software Mentions: 5
Published: almost 6 years ago

10.3390/genes12020264

Bisphenol A Exposure Changes the Transcriptomic and Proteomic Dynamics of Human Retinoblastoma Y79 Cells
Cited by: 7
Author(s): Chulhong Kim, Mi Jin Kim, Jin‐Hong Park, Jin-Ho Kim, Jiyoung Kim, Mi-Jin An, Geun-Seup Shin, Hyun-Min Lee, Jung-Woong Kim
Software Mentions: 5
Published: over 5 years ago

10.1186/s12864-016-2429-4

Genome-wide association mapping of partial resistance to Aphanomyces euteiches in pea
Cited by: 64
Author(s): Aurore Desgroux, Virginie Merot l'Anthoene, Martine Roux-Duparque, Jean-Philippe Rivière, Grégoire Aubert, Nadim Tayeh, Anne Moussart, P Mangin, Pierrick Vetel, Christophe Piriou, Rebecca J. McGee, Clarice J. Coyne, Judith Burstin, Alain Baranger, Maria Manzanares-Dauleux, Virginie Bourion, Marie‐Laure Pilet‐Nayel
Software Mentions: 5
Published: over 10 years ago

10.1186/s40168-021-01110-0

Prevotella copri increases fat accumulation in pigs fed with formula diets
Cited by: 70
Author(s): Congying Chen, Shouguo Fang, Hong Wei, Maozhang He, Hao Fu, Xinwei Xiong, Yunyan Zhou, Jingyuan Wu, Jun Gao, Hui Yang, Lusheng Huang
Software Mentions: 5
Published: about 5 years ago

10.1371/journal.pone.0224560

Transcriptional analysis of amino acid, metal ion, vitamin and carbohydrate uptake in butanol-producing Clostridium beijerinckii NRRL B-598
Cited by: 13
Author(s): Maryna Vasylkivska, Katerina Jureckova, Barbora Branská, Karel Sedlář, Jan Kolek, Ivo Provazník, Petra Patáková
Software Mentions: 5
Published: about 7 years ago

10.3945/ajcn.116.139980

What’s normal? Oligosaccharide concentrations and profiles in milk produced by healthy women vary geographically ,
Cited by: 268
Author(s): Michelle K. McGuire, Courtney L. Meehan, Mark A. McGuire, Janet E. Williams, James E. Foster, Daniel Sellen, Elizabeth Kamau-Mbuthia, Egidioh W. Kamundia, Samwel Mbugua, Sophie E. Moore, Andrew M. Prentice, Linda J. Kvist, Gloria E. Otoo, Sarah L Brooker, William J. Price, Bahman Shafii, Caitlyn Placek, Kimberly A. Lackey, Bianca Robertson, Susana Manzano, Lorena Ruíz, Juan M. Rodríguez, Rossina G. Pareja, Lars Bode
Software Mentions: 5
Published: over 9 years ago

10.1186/s40168-017-0304-4

Huanglongbing impairs the rhizosphere-to-rhizoplane enrichment process of the citrus root-associated microbiome
Cited by: 145
Author(s): Yunzeng Zhang, Jin Xu, Nadia Riera, Tao Jin, Jinyun Li, Nian Wang
Software Mentions: 5
Published: about 9 years ago

10.1186/s12263-021-00692-6

Transcriptomic changes in peripheral blood mononuclear cells with weight loss: systematic literature review and primary data synthesis
Cited by: 7
Author(s): Kaitlin Day, Aimee L. Dordevic, Helen Truby, Melissa C. Southey, Susan L. Coort, Chiara Murgia
Software Mentions: 5
Published: over 5 years ago

10.1371/journal.pone.0119002

Population Regulation in Magellanic Penguins: What Determines Changes in Colony Size?
Cited by: 31
Author(s): Luciana M. Pozzi, Pablo García Borboroglu, P. Dee Boersma, Miguel Pascual
Software Mentions: 5
Published: over 11 years ago

10.1111/pbi.13236

Molecular insight into cotton leaf curl geminivirus disease resistance in cultivated cotton ( Gossypium hirsutum )
Cited by: 42
Author(s): Syed Shan-e-Ali Zaidi, Rubab Zahra Naqvi, Muhammad Asif, Susan R. Strickler, Sara Shakir, Muhammad Shafiq, Ayesha Khan, Imran Amin, Bharat Mishra, M. Shahid Mukhtar, Brian E. Scheffler, Jodi A. Scheffler, Lukas A. Mueller, Shahid Mansoor
Software Mentions: 5
Published: about 7 years ago

10.1186/s12864-019-6179-y

Transcriptional variation and divergence of host-finding behaviour in Steinernema carpocapsae infective juveniles
Cited by: 5
Author(s): Neil D. Warnock, Deborah Cox, Ciaran J. McCoy, Robert Morris, Johnathan J. Dalzell
Software Mentions: 5
Published: almost 7 years ago

10.1186/1471-2164-14-853

Reprogramming of lysosomal gene expression by interleukin-4 and Stat6
Cited by: 18
Author(s): Louise M Brignull, Zsolt Czimmerer, Hafida Saidi, Bence Dániel, Izabel Vianna Villela, Nathan W. Bartlett, Sebastian L. Johnston, Lisiane B. Meira, László Nagy, Axel Nohturfft
Software Mentions: 5
Published: almost 13 years ago

10.1186/s13024-020-00405-4

Integrated analysis of the aging brain transcriptome and proteome in tauopathy
Cited by: 20
Author(s): Carl Grant Mangleburg, Timothy Wu, Hari Krishna Yalamanchili, Caiwei Guo, Yi-Cheng Hsieh, Duc Duong, Eric B. Dammer, Philip L. De Jager, Nicholas T. Seyfried, Zhandong Liu, Zhandong Liu
Software Mentions: 5
Published: about 6 years ago

10.3389/fpls.2018.00018

Genome-Wide Identification of Cyclic Nucleotide-Gated Ion Channel Gene Family in Wheat and Functional Analyses of TaCNGC14 and TaCNGC16
Cited by: 37
Author(s): Jia Guo, Md. Ashraful Islam, Haocheng Lin, Changan Ji, Yinghui Duan, Peng Liu, Qingdong Zeng, Brad Day, Zhensheng Kang, Jun Guo
Software Mentions: 5
Published: almost 9 years ago

10.1111/pbi.13085

Development of an integrated 200K <scp>SNP</scp> genotyping array and application for genetic mapping, genome assembly improvement and genome wide association studies in pear (Pyrus)
Cited by: 43
Author(s): Xiaolong Li, Jugpreet Singh, Mengfan Qin, Siwei Li, Xun Zhang, Mingyue Zhang, Awais Khan, Shaoling Zhang
Software Mentions: 5
Published: over 7 years ago

10.1186/s12864-015-2174-0

Extensive variation between tissues in allele specific expression in an outbred mammal
Cited by: 67
Author(s): Amanda J. Chamberlain, Christy J. Vander Jagt, Ben J. Hayes, Majid Khansefid, L. C. Marett, Catriona A. Millen, Thuy Thi Thu Nguyen, Michael E. Goddard
Software Mentions: 5
Published: almost 11 years ago

10.1186/s12864-018-4750-6

Signatures of host specialization and a recent transposable element burst in the dynamic one-speed genome of the fungal barley powdery mildew pathogen
Cited by: 124
Author(s): Lamprinos Frantzeskakis, Barbara Kracher, Stefan Kusch, Makoto Yoshikawa-Maekawa, Saskia Bauer, Carsten Pedersen, Pietro D. Spanu, Takaki Maekawa, Paul Schulze‐Lefert, Ralph Panstruga
Software Mentions: 5
Published: over 8 years ago

10.1371/journal.pone.0094162

Geographic Variation of Melanisation Patterns in a Hornet Species: Genetic Differences, Climatic Pressures or Aposematic Constraints?
Cited by: 39
Author(s): A. Perrard, Marcella Arca, Quentin Rome, Franck Müller, Jiang-Li Tan, Sanjaya Bista, Hari Nugroho, Raymond Baudoin, Michel Baylac, Jean François Silvain, James M. Carpenter, Claire Villemant
Software Mentions: 5
Published: over 12 years ago

10.1371/journal.pcbi.1005274

Tissue-Specificity of Gene Expression Diverges Slowly between Orthologs, and Rapidly between Paralogs
Cited by: 61
Author(s): Nadezda Kryuchkova-Mostacci, Marc Robinson‐Rechavi
Software Mentions: 5
Published: almost 10 years ago

10.3389/fpls.2019.00963

Identification of a Dominant Chlorosis Phenotype Through a Forward Screen of the Triticum turgidum cv. Kronos TILLING Population
Cited by: 17
Author(s): Sophie A Harrington, Nicolás Cobo, Miroslava Karafiátová, Jaroslav Doležel, Philippa Borrill, Cristóbal Uauy
Software Mentions: 5
Published: over 7 years ago

10.3389/fpls.2020.00545

Spatiotemporal Modulation of Flavonoid Metabolism in Blueberries
Cited by: 38
Author(s): Catrin S. Günther, Andrew P. Dare, Tony K. McGhie, Cecilia Deng, Declan J. Lafferty, Blue Plunkett, Ella Grierson, Janice L. Turner, Laura Jaakola, Nick W. Albert, Richard V. Espley
Software Mentions: 5
Published: over 6 years ago

10.3389/fpls.2016.01225

TALE-Like Effectors Are an Ancestral Feature of the Ralstonia solanacearum Species Complex and Converge in DNA Targeting Specificity
Cited by: 29
Author(s): Niklas Schandry, Orlando de Lange, Philippe Prior, Thomas Lahaye
Software Mentions: 5
Published: about 10 years ago

10.1186/s12864-017-3978-x

Succinyl-proteome profiling of Dendrobium officinale, an important traditional Chinese orchid herb, revealed involvement of succinylation in the glycolysis pathway
Cited by: 37
Author(s): Shi Feng, Kaili Jiao, Hong Guo, Min Jiang, Juan Hao, Huizhong Wang, Chenjia Shen
Software Mentions: 5
Published: about 9 years ago

10.1007/s12035-020-01983-6

Transcriptome Analysis of iPSC-Derived Neurons from Rubinstein-Taybi Patients Reveals Deficits in Neuronal Differentiation
Cited by: 15
Author(s): Luciano Calzari, Matteo Barcella, Valentina Alari, Daniele Braga, Rafael Muñoz‐Viana, Cristina Barlassina, Palma Finelli, Cristina Gervasini, Ángel Barco, Silvia Russo, Lidia Larizza
Software Mentions: 5
Published: over 6 years ago

10.1186/s12864-015-1546-9

Activation of defence pathways in Scots pine bark after feeding by pine weevil (Hylobius abietis)
Cited by: 31
Author(s): Andriy Kovalchuk, Tommaso Raffaello, Emad Jaber, Susanna Keriö, Rajendra P. Ghimire, W. Walter Lorenz, Jeffrey F. D. Dean, Jarmo K. Holopainen, Fred O. Asiegbu
Software Mentions: 5
Published: over 11 years ago

10.1371/journal.pone.0193417

Sex- and brain region-specific patterns of gene expression associated with socially-mediated puberty in a eusocial mammal
Cited by: 20
Author(s): Mariela Faykoo-Martinez, D. Ashley Monks, Iva B. Zovkic, Melissa M. Holmes
Software Mentions: 5
Published: over 8 years ago

10.3389/fphar.2018.00084

Proteomic Analysis of Combined Gemcitabine and Birinapant in Pancreatic Cancer Cells
Cited by: 15
Author(s): Xu Zhu, Xiaomeng Shen, Jun Qu, Robert M. Straubinger, William J. Jusko
Software Mentions: 5
Published: over 8 years ago

10.3389/fonc.2019.01206

Exploration of the Transcriptional Landscape of ALPPS Reveals the Pathways of Accelerated Liver Regeneration
Cited by: 11
Author(s): Pieter Borger, Marcel Schneider, Lukas Frick, Magda Langiewicz, Maksim Sorokin, Anton Buzdin, Ekaterina Kachaylo, Rolf Graf, Bostjan Humar, Pierre‐Alain Clavien
Software Mentions: 5
Published: almost 7 years ago

10.7554/eLife.20937

Enforcement of developmental lineage specificity by transcription factor Oct1
Cited by: 14
Author(s): Zuolian Shen, Jinsuk Kang, Arvind Shakya, Marcin Tabaka, Elke A. Jarboe, Aviv Regev, Dean Tantin
Software Mentions: 5
Published: over 9 years ago

10.1371/journal.pone.0188842

Markers of epithelial-to-mesenchymal transition reflect tumor biology according to patient age and Gleason score in prostate cancer
Cited by: 31
Author(s): Dorota Jędroszka, Magdalena Orzechowska, R. Hamouz, Karolina Górniak, Andrzej K. Bednarek
Software Mentions: 5
Published: almost 9 years ago

10.1186/s13075-015-0682-6

Autoantigen microarrays reveal autoantibodies associated with proliferative nephritis and active disease in pediatric systemic lupus erythematosus
Cited by: 42
Author(s): D. James Haddon, Vivian K. Diep, J. M. Price, Cindy Limb, Paul J. Utz, Imelda Balboni
Software Mentions: 5
Published: over 11 years ago

10.7554/eLife.62236

Identification of human glucocorticoid response markers using integrated multi-omic analysis from a randomized crossover trial
Cited by: 21
Author(s): Dimitrios Chantzichristos, Peder Svensson, Terence Garner, Camilla A M Glad, Brian R. Walker, Ragnhildur Bergthorsdottir, Oskar Ragnarsson, Penelope Trimpou, Roland H Stimson, Stina Willemoes Borresen, Ulla Feldt‐Rasmussen, Per‐Anders Jansson, Stanko Skrtic, Adam Stevens, Gudmundur Johannsson
Software Mentions: 5
Published: over 5 years ago

10.7717/peerj.5908

Assessing distinct patterns of cognitive aging using tissue-specific brain age prediction based on diffusion tensor imaging and brain morphometry
Cited by: 85
Author(s): Geneviève Richard, Knut-Kristian Kolskår, Anne-Marthe Sanders, Tobias Kaufmann, Anders Petersen, Nhat Trung Doan, Jennifer Monereo Sánchez, Dag Alnæs, Kristine M. Ulrichsen, Erlend S. Dørum, Ole A. Andreassen, Jan Egil Nordvik, Lars T. Westlye
Software Mentions: 5
Published: almost 8 years ago

10.7554/eLife.13546

Hyperosmotic stress memory in Arabidopsis is mediated by distinct epigenetically labile sites in the genome and is restricted in the male germline by DNA glycosylase activity
Cited by: 246
Author(s): Anjar Tri Wibowo, Claude Becker, G. Marconi, Julius Dürr, Jonathan Price, Jörg Hagmann, Ranjith Papareddy, Hadi Putra, Jorge Kageyama, Jörg Becker, Detlef Weigel, José Gutierrez-Marcos
Software Mentions: 5
Published: over 10 years ago

10.1186/s12864-019-6240-x

Didelphis albiventris: an overview of unprecedented transcriptome sequencing of the white-eared opossum
Cited by: 0
Author(s): Íria Gabriela Dias dos Santos, Tiago Antônio de Oliveira Mendes, Gerluza Aparecida Borges Silva, Amanda Maria Sena Reis, Cláudia Barros Monteiro-Vitorello, Patrícia Dayane Carvalho Schaker, Roberto Hirochi Herai, André Brait Carneiro Fabotti, Luiz Lehmann Coutinho, Érika Cristina Jorge
Software Mentions: 5
Published: almost 7 years ago

10.7554/eLife.49577

The Mars1 kinase confers photoprotection through signaling in the chloroplast unfolded protein response
Cited by: 40
Author(s): Karina Perlaza, Hannah Toutkoushian, Morgane Boone, Mable Lam, Masakazu Iwai, Martin C. Jonikas, Peter Walter, Silvia Ramundo
Software Mentions: 5
Published: about 7 years ago

10.3389/fimmu.2017.00308

Expression of Serum microRNAs is Altered During Acute Graft-versus-Host Disease
Cited by: 23
Author(s): Rachel E Crossland, Jean Norden, Mateja Kralj Juric, Kile Green, Kim Pearce, Clare Lendrem, Hildegard Greinix, AM Dickinson
Software Mentions: 5
Published: over 9 years ago

10.1038/s41374-020-0455-y

Multiclass cancer classification in fresh frozen and formalin-fixed paraffin-embedded tissue by DigiWest multiplex protein analysis
Cited by: 2
Author(s): Teresa Bockmayr, Gerrit Erdmann, Denise Treue, Philipp Jurmeister, Julia Schneider, Anja Arndt, Daniel Heim, Michael Bockmayr, Christoph Sachse, Frederick Klauschen
Software Mentions: 5
Published: about 6 years ago

10.1186/s12885-020-06799-0

Development and validation of a five-immune gene prognostic risk model in colon cancer
Cited by: 37
Author(s): Haitao Chen, Jun Luo, Jingyi Guo
Software Mentions: 5
Published: over 6 years ago

10.3389/fimmu.2020.01636

Immune and Metabolic Signatures of COVID-19 Revealed by Transcriptomics Data Reuse
Cited by: 101
Author(s): Luiz Gustavo Gardinassi, Camila Oliveira Silva Souza, Helioswilton Sales‐Campos, Simone Gonçalves Fonseca
Software Mentions: 5
Published: over 6 years ago

10.3389/fmicb.2019.01116

Dynamic Alterations in Yak Rumen Bacteria Community and Metabolome Characteristics in Response to Feed Type
Cited by: 116
Author(s): Chang Liu, Hao Wu, Shujie Liu, Shatuo Chai, Qingxiang Meng, Zhenming Zhou
Software Mentions: 5
Published: over 7 years ago

10.7717/peerj.9205

Human milk microbiota associated with early colonization of the neonatal gut in Mexican newborns
Cited by: 27
Author(s): Karina Corona-Cervantes, Igrid García-González, Loan Edel Villalobos-Flores, Fernando Hernández-Quiroz, Alberto Piña-Escobedo, Carlos Hoyo‐Vadillo, Martín Noé Rangel-Calvillo, Jaime García‐Mena
Software Mentions: 5
Published: over 6 years ago

10.1186/1471-2164-15-537

Distribution of segmental duplications in the context of higher order chromatin organisation of human chromosome 7
Cited by: 6
Author(s): Grit Ebert, Anne Steininger, Robert Weißmann, Vivien Boldt, Allan Lind-Thomsen, Jana Grune, Stefan Badelt, Melanie Heßler, Matthias Peiser, Manuel Hitzler, Lars Riff Jensen, Ines Müller, Hao Hu, Peter F. Arndt, Andreas W. Kuß, Katrin Tebel, Reinhard Ullmann
Software Mentions: 5
Published: over 12 years ago

10.1186/s12935-019-1002-z

Two predictive precision medicine tools for hepatocellular carcinoma
Cited by: 11
Author(s): Zhiqiao Zhang, Jing Li, Tingshan He, Yanling Ouyang, Yiyan Huang, Qingbo Liu, Peng Wang, Jianqiang Ding
Software Mentions: 5
Published: almost 7 years ago

10.1371/journal.pone.0227860

Fungal diversity in canopy soil of silver beech, Nothofagus menziesii (Nothofagaceae)
Cited by: 4
Author(s): Andy R. Nilsen, Suliana Teasdale, P. L. Guy, Tina C. Summerfield, David A. Orlovich
Software Mentions: 5
Published: almost 7 years ago

10.1155/2018/7691794

Differential Expression Profiling of Long Noncoding RNA and mRNA during Osteoblast Differentiation in Mouse
Cited by: 6
Author(s): Minjung Kim, Yi Yin Yu, Ji-Hoi Moon, Insong Koh, Jae Hyung Lee
Software Mentions: 5
Published: almost 9 years ago

10.1186/s13058-015-0613-0

Assessing breast cancer cell lines as tumour models by comparison of mRNA expression profiles
Cited by: 62
Author(s): Krista Vincent, Scott D. Findlay, Lynne-Marie Postovit
Software Mentions: 5
Published: about 11 years ago

10.3389/fgene.2020.00870

Evaluation of the Minimum Sampling Design for Population Genomic and Microsatellite Studies: An Analysis Based on Wild Maize
Cited by: 13
Author(s): Jonás A. Aguirre‐Liguori, Javier Alejandro Luna-Sanchez, Jaime Gasca-Pineda, Luis E. Eguiarte
Software Mentions: 5
Published: about 6 years ago

10.3389/fmicb.2017.00101

Freshwater Recirculating Aquaculture System Operations Drive Biofilter Bacterial Community Shifts around a Stable Nitrifying Consortium of Ammonia-Oxidizing Archaea and Comammox Nitrospira
Cited by: 163
Author(s): Ryan P. Bartelme, Sandra L. McLellan, Ryan J. Newton
Software Mentions: 5
Published: almost 10 years ago

10.1128/mSystems.00130-17

Colonic Butyrate-Producing Communities in Humans: an Overview Using Omics Data
Cited by: 284
Author(s): Marius Vital, André Karch, Dietmar H. Pieper
Software Mentions: 5
Published: almost 9 years ago

10.3389/fchem.2020.00243

An Innovative Sequence-to-Structure-Based Approach to Drug Resistance Interpretation and Prediction: The Use of Molecular Interaction Fields to Detect HIV-1 Protease Binding-Site Dissimilarities
Cited by: 4
Author(s): Nuno G. Alves, Ana I. Mata, João Luís, Rui M. M. Brito, Carlos J. V. Simões
Software Mentions: 5
Published: over 6 years ago

10.1186/s12885-017-3777-4

Multi-region and single-cell sequencing reveal variable genomic heterogeneity in rectal cancer
Cited by: 28
Author(s): Mingshan Liu, Yang Liu, Jiabo Di, Zhe Su, Hong Yang, Beihai Jiang, Zaozao Wang, Zhen Meng, Fan Bai, Xiangqian Su
Software Mentions: 5
Published: almost 9 years ago

10.1371/journal.pone.0212365

Mycobacteriophage CRB2 defines a new subcluster in mycobacteriophage classification
Cited by: 4
Author(s): Cristian Alejandro Suárez, Jorgelina Judith Franceschelli, Héctor Ricardo Morbidoni
Software Mentions: 5
Published: over 7 years ago

10.3389/fcimb.2020.588155

Proteome and Microbiome Mapping of Human Gingival Tissue in Health and Disease
Cited by: 14
Author(s): Kai Bao, Xiaofei Li, Lucy Poveda, Weihong Qi, Nathalie Selevsek, Pınar Gümüş, Gülnur Emingil, Jonas Grossmann, Patricia I. Diaz, George Hajishengallis, Nagihan Bostancı, Georgios N. Belibasakis
Software Mentions: 5
Published: about 6 years ago

10.1186/s12864-016-3254-5

Integrated metagenomic data analysis demonstrates that a loss of diversity in oral microbiota is associated with periodontitis
Cited by: 72
Author(s): Dongmei Ai, Ruocheng Huang, Ji Wen, Chao Li, Jianguo Zhu, Xia Li
Software Mentions: 5
Published: almost 10 years ago

10.1111/acel.13280

Modeling the human aging transcriptome across tissues, health status, and sex
Cited by: 23
Author(s): Maxim N. Shokhirev, Adiv A. Johnson
Software Mentions: 5
Published: almost 6 years ago

10.3389/fcell.2021.648331

Fibrillarin-GFP Facilitates the Identification of Meiotic Competent Oocytes
Cited by: 6
Author(s): Ting Wang, Jie Na
Software Mentions: 5
Published: over 5 years ago

10.3389/fcell.2021.655866

Proteomic Changes Associated With Sperm Fertilizing Ability in Meat-Type Roosters
Cited by: 4
Author(s): Anaïs Vitorino Carvalho, Laura Soler, Aurore Thélie, Isabelle Grasseau, Luiz Cordeiro, Daniel Tomas, Ana-Paula Teixeira-Gomes, Valérie Labas, Elisabeth Blesblois
Software Mentions: 5
Published: over 5 years ago

10.3389/fgene.2020.00055

Establishment of a Prognostic Model Using Immune-Related Genes in Patients With Hepatocellular Carcinoma
Cited by: 14
Author(s): Wenjie Wang, Han Wang, Ting-yan Hua, Wei Song, Jie Zhu, Jingjing Wang, Yongzhen Huang, Zhi-Liang Ding
Software Mentions: 5
Published: over 6 years ago

10.1371/journal.pone.0130847

Latitudinal Gradient in Otolith Shape among Local Populations of Atlantic Herring (Clupea harengus L.) in Norway
Cited by: 27
Author(s): Lísa Anne Libungan, Aril Slotte, Åse Husebø, Jane Aanestad Godiksen, Snæbjörn Pálsson
Software Mentions: 5
Published: over 11 years ago

10.1093/sleep/zsy186

Identifying and validating blood mRNA biomarkers for acute and chronic insufficient sleep in humans: a machine learning approach
Cited by: 30
Author(s): Emma Laing, Carla S. Möller-Levet, Derk‐Jan Dijk, Simon N. Archer
Software Mentions: 5
Published: about 8 years ago

10.1038/onc.2016.382

Genomic modelling of the ESR1 Y537S mutation for evaluating function and new therapeutic approaches for metastatic breast cancer
Cited by: 125
Author(s): Alison Harrod, Janet S. Fulton, Van Nguyen, Manikandan Periyasamy, L Ramos-Garcia, C-F Lai, Gergana Metodieva, Alex de Giorgio, Richard Williams, Delfran Batista dos Santos, Pablo Gómez, M-L Lin, Metodi V. Metodiev, Justin Stebbing, Leandro Castellano, Luca Magnani, R. Charles Coombes, Laki Buluwela, Simak Ali
Software Mentions: 5
Published: about 10 years ago

10.1371/journal.pone.0221862

Parameterization-induced uncertainties and impacts of crop management harmonization in a global gridded crop model ensemble
Cited by: 38
Author(s): Christian Folberth, Joshua Elliott, Christoph Müller, Juraj Balkovič, James Chryssanthacopoulos, R. C. Izaurralde, Curtis D. Jones, Nikolay Khabarov, Wenfeng Liu, Ashwan Reddy, Erwin Schmid, Rastislav Skalský, Hong Yang, Almut Arneth, Philippe Ciais, Delphine Deryng, P. Lawrence, Stefan Olin, Thomas A. M. Pugh, Alex C. Ruane, Xuhui Wang
Software Mentions: 5
Published: about 7 years ago

10.1038/s41598-021-82136-0

A high-throughput RNA-Seq approach to elucidate the transcriptional response of Piriformospora indica to high salt stress
Cited by: 13
Author(s): Nivedita, Abdul Rawoof, Nirala Ramchiary, M. Z. Abdin
Software Mentions: 5
Published: over 5 years ago

10.1038/s41598-021-84860-z

Characterisation, identification, clustering, and classification of disease
Cited by: 17
Author(s): Anthony J Webster, Kezia Gaitskell, Iain Turnbull, B J Cairns, Robert Clarke
Software Mentions: 5
Published: over 5 years ago

10.1038/s41598-021-81359-5

Aldehyde-specific responses of olfactory sensory neurons in the praying mantis
Cited by: 3
Author(s): Kota Ezaki, Takashi Yamashita, Thomas Carle, Hidehiro Watanabe, Fumio Yokohari, Yoshifumi Yamawaki
Software Mentions: 5
Published: almost 6 years ago

10.1186/s12864-017-4100-0

Comparative transcriptomics of female and male gametocytes in Plasmodium berghei and the evolution of sex in alveolates
Cited by: 61
Author(s): Lee M. Yeoh, Christopher D. Goodman, Vanessa Mollard, Geoffrey I. McFadden, Stuart A. Ralph
Software Mentions: 5
Published: about 9 years ago

10.1002/mbo3.1146

Deeper below the surface—transcriptional changes in selected genes of Clostridium beijerinckii in response to butanol shock
Cited by: 5
Author(s): Petra Patáková, Jan Kolek, Katerina Jureckova, Barbora Branská, Karel Sedlář, Maryna Vasylkivska, Ivo Provazník
Software Mentions: 5
Published: almost 6 years ago

10.3389/fbioe.2019.00229

The White-Rot Basidiomycete Dichomitus squalens Shows Highly Specific Transcriptional Response to Lignocellulose-Related Aromatic Compounds
Cited by: 21
Author(s): Joanna E. Kowalczyk, Mao Peng, Megan Pawlowski, Anna Lipzen, Vivian Ng, Vasanth Singan, Mei Wang, Igor V. Grigoriev, Miia Mäkelä
Software Mentions: 5
Published: about 7 years ago

10.1371/journal.pone.0118876

Plant Trait Variation along an Altitudinal Gradient in Mediterranean High Mountain Grasslands: Controlling the Species Turnover Effect
Cited by: 72
Author(s): David S. Pescador, Francesco de Bello, Fernando Valladares, Adrián Escudero
Software Mentions: 5
Published: over 11 years ago

10.1038/s41598-020-68891-6

Structure and co-occurrence patterns of bacterial communities associated with white faeces disease outbreaks in Pacific white-leg shrimp Penaeus vannamei aquaculture
Cited by: 27
Author(s): Yustian Rovi Alfiansah, Sonja Peters, Jens Harder, Christiane Hassenrück, Astrid Gärdes
Software Mentions: 5
Published: over 6 years ago

10.1038/s41598-020-72511-8

Burn resuscitation strategy influences the gut microbiota-liver axis in swine
Cited by: 11
Author(s): Wayne Muraoka, Jose C. Granados, Belinda I. Gómez, Susannah E. Nicholson, Kevin K. Chung, Jeffrey W. Shupp, James A. Bynum, Michael A. Dubick, David M. Burmeister
Software Mentions: 5
Published: about 6 years ago

10.1371/journal.pntd.0009504

Developmental changes and metabolic reprogramming during establishment of infection and progression of Trypanosoma brucei brucei through its insect host
Cited by: 16
Author(s): Arunasalam Naguleswaran, Paula Fernandes, Shubha Bevkal, Ruth Rehmann, Pamela Nicholson, Isabel Roditi
Software Mentions: 5
Published: about 5 years ago

10.1038/s41598-020-67690-3

Transcriptomic analysis of the mechanisms of alleviating renal interstitial fibrosis using the traditional Chinese medicine Kangxianling in a rat model
Cited by: 13
Author(s): Yufeng Jiang, Yaohan Zhu, Timing Zhen, Jie Li, Kaichen Xing, Liqun He, Sibo Zhu
Software Mentions: 5
Published: over 6 years ago

10.1038/s41598-020-66558-w

Associations among neurophysiology measures in irritable bowel syndrome (IBS) and their relevance for IBS symptoms
Cited by: 11
Author(s): Irina Midenfjord, Annikka Polster, Henrik Sjövall, Peter Friberg, Hans Törnblom, Magnus Simrén
Software Mentions: 5
Published: over 6 years ago

10.3389/fbioe.2017.00084

Meta-Analysis of Aedes aegypti Expression Datasets: Comparing Virus Infection and Blood-Fed Transcriptomes to Identify Markers of Virus Presence
Cited by: 11
Author(s): Kiyoshi F. Fukutani, José Irahe Kasprzykowski, Alexandre Rossi Paschoal, Matheus de Souza Gomes, Aldina Barral, Camila I. de Oliveira, Pablo Ivan Pereira Ramos, Artur T. L. Queiroz
Software Mentions: 5
Published: almost 9 years ago

10.1002/ece3.4160

Time‐lapse cameras reveal latitude and season influence breeding phenology durations in penguins
Cited by: 7
Author(s): Caitlin Black, Ben Collen, Daniel Lunn, Dick Filby, Stephanie Winnard, Tom Hart
Software Mentions: 5
Published: over 8 years ago

10.1038/s41598-020-66721-3

Cardiac transcriptional and metabolic changes following thoracotomy
Cited by: 0
Author(s): Markus Heckmann, Ashraf Yusuf Rangrez, Daniel Finke, Andreas Jungmann, Julia S. Kreußer, Alexandra Rosskopf, Nesrin Schmiedel, Hugo A. Katus, Norbert Frey, Oliver Müller
Software Mentions: 5
Published: over 6 years ago

10.1186/s40168-018-0612-3

Design and application of a novel two-amplicon approach for defining eukaryotic microbiota
Cited by: 16
Author(s): Ana Popović, Céline Bourdon, Pauline W. Wang, David S. Guttman, Wieger Voskuijl, Michael E. Grigg, Robert Bandsma, John Parkinson
Software Mentions: 5
Published: almost 8 years ago

10.1002/eji.201847897

Expression of IL‐7Rα and KLRG1 defines functionally distinct CD8 + T‐cell populations in humans
Cited by: 24
Author(s): Ester B. M. Remmerswaal, Pleun Hombrink, Benjamin Nota, Hanspeter Pircher, Ineke J. M. ten Berge, René A. W. van Lier, Michiel C. van Aalderen
Software Mentions: 5
Published: over 7 years ago

10.1038/s41598-020-66759-3

The seed water content as a time-independent physiological trait during germination in wild tree species such as Ceiba aesculifolia
Cited by: 6
Author(s): Ximena Gómez‐Maqueo, Diana Soriano, Noé Velázquez-Rosas, Sandra Alvarado-López, Karina Jiménez‐Durán, María Del Mar Garciadiego, Alicia Gamboa‐deBuen
Software Mentions: 5
Published: over 6 years ago

10.1186/1756-0500-5-596

MetabR: an R script for linear model analysis of quantitative metabolomic data
Cited by: 30
Author(s): Ben Ernest, Jessica Gooding, Shawn R. Campagna, Arnold M. Saxton, Brynn H. Voy
Software Mentions: 5
Published: about 14 years ago

10.1186/s12859-015-0678-x

HiCdat: a fast and easy-to-use Hi-C data analysis tool
Cited by: 45
Author(s): Marc W. Schmid, Stefan Grob, Ueli Grossniklaus
Software Mentions: 5
Published: about 11 years ago

10.1016/j.wroa.2019.100033

Organic substrate diffusibility governs microbial community composition, nutrient removal performance and kinetics of granulation of aerobic granular sludge
Cited by: 74
Author(s): Manuel Layer, Aline Sondra Adler, Eva Reynaert, Antonio Hernández, Marco Pagni, Eberhard Morgenroth, Christof Holliger, Nicolas Derlon
Software Mentions: 5
Published: over 7 years ago

10.1038/s41598-019-57108-0

Transcriptional analysis identifies potential biomarkers and molecular regulators in pneumonia and COPD exacerbation
Cited by: 15
Author(s): Wilhelm Bertrams, Kathrin Griss, Maria Han, Kerstin Seidel, Andreas Klemmer, Alexandra Sittka-Stark, Stefan Hippenstiel, Norbert Suttorp, Florian Finkernagel, Jochen Wilhelm, Timm Greulich, Claus Vogelmeier, Julio Vera, Bernd Schmeck
Software Mentions: 5
Published: almost 7 years ago

10.1371/journal.pgen.1004406

Microbial Succession in the Gut: Directional Trends of Taxonomic and Functional Change in a Birth Cohort of Spanish Infants
Cited by: 139
Author(s): Yvonne Vallès, Alejandro Artacho, Alberto Pascual‐García, María Loreto Ferrús, María José Gosalbes, Juan J. Abellán, M. Pilar Francino
Software Mentions: 5
Published: over 12 years ago

10.1371/journal.pgen.1005305

Identification of Chemical Inhibitors of β-Catenin-Driven Liver Tumorigenesis in Zebrafish
Cited by: 62
Author(s): Kimberley Evason, Macrina T. Francisco, Vladislava Juric, Sanjeev Balakrishnan, Maria del Pilar Lopez Pazmino, John D. Gordan, Sanjay Kakar, Jan M. Spitsbergen, Andrei Goga, Didier Y. R. Stainier
Software Mentions: 5
Published: over 11 years ago

10.1038/s41598-018-37679-0

Acidogenesis, solventogenesis, metabolic stress response and life cycle changes in Clostridium beijerinckii NRRL B-598 at the transcriptomic level
Cited by: 46
Author(s): Petra Patáková, Barbora Branská, Karel Sedlář, Maryna Vasylkivska, Katerina Jureckova, Jan Kolek, Pavlína Koščová, Ivo Provazník
Software Mentions: 5
Published: almost 8 years ago

10.1371/journal.pgen.1006667

Elucidation of the calcineurin-Crz1 stress response transcriptional network in the human fungal pathogen Cryptococcus neoformans
Cited by: 85
Author(s): Eve W. L. Chow, Shelly Applen Clancey, R. Blake Billmyre, Anna Floyd Averette, Joshua A. Granek, Piotr A. Mieczkowski, María E. Cárdenas, Joseph Heitman
Software Mentions: 5
Published: over 9 years ago

10.1186/s12870-021-03042-1

Transcriptome and proteome analysis of walnut (Juglans regia L.) fruit in response to infection by Colletotrichum gloeosporioides
Cited by: 12
Author(s): Hongcheng Fang, Xia Liu, Yixin Dong, Shan Feng, Rui Zhou, Changxi Wang, Xinmei Ma, Jianning Liu, Ke Yang
Software Mentions: 5
Published: over 5 years ago

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