cran: gplots | Projects | Ecosyste.ms: Papers

10.1016/j.dnarep.2021.103158

Damage-Net: A program for DNA repair meta-analysis identifies a network of novel repair genes that facilitate cancer evolution
Cited by: 1
Author(s): Aldo S. Bader, Martin Bushell
Software Mentions: 10
Published: about 3 years ago

10.7554/eLife.18683

Differences and similarities between human and chimpanzee neural progenitors during cerebral cortex development
Cited by: 185
Author(s): Felipe Mora‐Bermúdez, Farhath Badsha, Sabina Kanton, J. Gray Camp, Benjamin Vernot, Kathrin Köhler, Birger Voigt, Keisuke Okita, Tomislav Maričić, Zhisong He, Robert Lachmann, Svante Pääbo, Barbara Treutlein, Wieland B. Huttner
Software Mentions: 10
Published: about 8 years ago

10.1371/journal.pone.0191601

Highly multiplexed single-cell quantitative PCR
Cited by: 12
Author(s): Michael VanInsberghe, Hans Zahn, Alexander D. White, Oleh I. Petriv, Carl L. Hansen
Software Mentions: 10
Published: almost 7 years ago

10.1186/s12864-021-07995-3

Neurogenomic divergence during speciation by reinforcement of mating behaviors in chorus frogs (Pseudacris)
Cited by: 4
Author(s): Oscar E. Ospina, Alan R. Lemmon, Mysia Dye, Christopher Zdyrski, Sean Holland, Daniel Stribling, Michelle L Kortyna, Emily Moriarty Lemmon
Software Mentions: 9
Published: about 3 years ago

10.1186/s12864-019-5692-3

Expanding the biodiversity of Oenococcus oeni through comparative genomics of apple cider and kombucha strains
Cited by: 14
Author(s): Marc Lorentzen, Hugo Campbell-Sills, Tue Sparholt Jørgensen, Tue Kjærgaard Nielsen, Monika Coton, Emmanuel Coton, Lars Hansen, Patrick Lucas
Software Mentions: 9
Published: over 5 years ago

10.1038/s41598-019-55984-0

Patterns of diverse gene functions in genomic neighborhoods predict gene function and phenotype
Cited by: 16
Author(s): Matej Mihelčić, Tomislav Šmuc, Fran Supek
Software Mentions: 9
Published: almost 5 years ago

10.7717/peerj.3795

Multivariate ordination identifies vegetation types associated with spider conservation in brassica crops
Cited by: 4
Author(s): Hafiz Sohaib Ahmed Saqib, Minsheng You, Geoff M. Gurr
Software Mentions: 9
Published: about 7 years ago

10.1038/s41421-021-00274-1

Integrating longitudinal clinical laboratory tests with targeted proteomic and transcriptomic analyses reveal the landscape of host responses in COVID-19
Cited by: 21
Author(s): Yun Tan, Wei Zhang, Zhaoqin Zhu, Na Qiao, Yun Ling, Mingquan Guo, Tong Yin, Hai Fang, Xiaoguang Xu, Gang Lu, Peipei Zhang, Shuangshuang Yang, Ziyu Fu, Dongguo Liang, Yinyin Xie, Ruihong Zhang, Lu Jiang, Shuting Yu, Jing Lu, Fang-Ying Jiang, Jian Chen, Chenlu Xiao, Shengyue Wang, Shuo Chen, Xiu‐Wu Bian, Hongzhou Lu, Feng Liu, Sai‐Juan Chen
Software Mentions: 9
Published: over 3 years ago

10.1186/s12859-021-04020-y

MeltingPlot, a user-friendly online tool for epidemiological investigation using High Resolution Melting data
Cited by: 4
Author(s): Matteo Perini, Gherard Batisti Biffignandi, Domenico Di Carlo, Ajay Ratan Pasala, Aurora Piazza, Simona Panelli, Gian Vincenzo Zuccotti, Francesco Comandatore
Software Mentions: 9
Published: almost 4 years ago

10.1016/j.molcel.2018.08.004

Methylation of Structured RNA by the m6A Writer METTL16 Is Essential for Mouse Embryonic Development
Cited by: 226
Author(s): Mateusz Mendel, Kuan-Ming Chen, David Homolka, Pascal Gos, Radha Raman Pandey, A.A. McCarthy, Ramesh S. Pillai
Software Mentions: 9
Published: about 6 years ago

10.1186/s40168-018-0535-z

High-resolution ISR amplicon sequencing reveals personalized oral microbiome
Cited by: 30
Author(s): Chiranjit Mukherjee, Clifford J. Beall, Ann L. Griffen, Eugene J. Leys
Software Mentions: 9
Published: about 6 years ago

10.1186/s13073-020-00731-8

Integrative -omics and HLA-ligandomics analysis to identify novel drug targets for ccRCC immunotherapy
Cited by: 28
Author(s): Anna Reustle, Moreno Di Marco, Carolin Meyerhoff, Annika Nelde, Juliane S. Walz, Stefan Winter, Siahei Kandabarau, Florian Büttner, Mathias Haag, Linus Backert, Daniel J. Kowalewski, Steffen Rausch, Jörg Hennenlotter, Viktoria Stühler, Marcus Scharpf, Falko Fend, Arnulf Stenzl, Hans‐Georg Rammensee, Jens Bedke, Stefan Stevanović, Matthias Schwab, Elke Schaeffeler
Software Mentions: 9
Published: over 4 years ago

10.3389/fvets.2021.627894

Factors Affecting the Development of Bovine Respiratory Disease: A Cross-Sectional Study in Beef Steers Shipped From France to Italy
Cited by: 14
Author(s): Barbara Padalino, Francesco Cirone, Martina Zappaterra, Daniele Tullio, Gigliola Ficco, Antonio Giustino, Linda Amarachi Ndiana, Annamaria Pratelli
Software Mentions: 9
Published: over 3 years ago

10.3389/fvets.2020.603990

Modeling Thermal Suitability for Reindeer (Rangifer tarandus ssp.) Brainworm (Elaphostrongylus rangiferi) Transmission in Fennoscandia
Cited by: 2
Author(s): Hannah Rose Vineer, Torill Mørk, Diana Williams, Rebecca K. Davidson
Software Mentions: 9
Published: almost 4 years ago

10.1371/journal.pone.0149237

Optimizing Viral Discovery in Bats
Cited by: 35
Author(s): Caroline Young, Kevin J. Olival
Software Mentions: 9
Published: almost 9 years ago

10.3389/fpls.2015.01172

The Potential of the MAGIC TOM Parental Accessions to Explore the Genetic Variability in Tomato Acclimation to Repeated Cycles of Water Deficit and Recovery
Cited by: 23
Author(s): Julie Ripoll, Laurent Urban, Nadia Bertin
Software Mentions: 9
Published: almost 9 years ago

10.1186/s12983-017-0241-x

Trabecular architecture in the forelimb epiphyses of extant xenarthrans (Mammalia)
Cited by: 37
Author(s): Eli Amson, Patrick Arnold, Anneke H. van Heteren, Aurore Canoville, John A. Nyakatura
Software Mentions: 9
Published: almost 7 years ago

10.3389/fpls.2014.00078

Plasma membrane lipidâ€“protein interactions affect signaling processes in sterol-biosynthesis mutants in Arabidopsis thaliana
Cited by: 24
Author(s): Henrik Zauber, Asdrúbal Burgos, Prashanth Garapati, Waltraud X. Schulze
Software Mentions: 9
Published: over 10 years ago

10.3389/fnana.2018.00010

Cerebral Artery Diameter in Inbred Mice Varies as a Function of Strain
Cited by: 23
Author(s): Baogang Qian, Robert F. Rudy, Tianxi Cai, Rose Du
Software Mentions: 9
Published: almost 7 years ago

10.3389/fmolb.2021.683671

Dissecting Metabolism of Leaf Nodules in Ardisia crenata and Psychotria punctata
Cited by: 7
Author(s): Florian Schindler, Lena Fragner, Johannes B Herpell, Andreas Berger, Martin Brenner, Sonja Tischler, Anke Bellaire, Jürg Schönenberger, Weimin Liu, Xiaoliang Sun, Johann Schinnerl, Lothar Brecker, Wolfram Weckwerth
Software Mentions: 9
Published: over 3 years ago

10.3389/fmolb.2021.686110

Investigating the Role of Root Exudates in Recruiting Streptomyces Bacteria to the Arabidopsis thaliana Microbiome
Cited by: 14
Author(s): Sarah F. Worsley, Michael C. Macey, Samuel M. M. Prudence, Barrie Wilkinson, J. Colin Murrell, Matthew I. Hutchings
Software Mentions: 9
Published: over 3 years ago

10.1038/s41598-021-86638-9

Entomopathogenic fungi as the microbial frontline against the alien Eucalyptus pest Gonipterus platensis in Brazil
Cited by: 17
Author(s): Carolina Jordan, Pâmela Letícia dos Santos, Leiliane Oliveira, Maurício Magalhães Domingues, Bianca Cristina Costa Gêa, M. F. S. Ribeiro, Gabriel Moura Mascarin, Carlos Frederico Wilcken
Software Mentions: 9
Published: over 3 years ago

10.1371/journal.pone.0121102

ShapeR: An R Package to Study Otolith Shape Variation among Fish Populations
Cited by: 100
Author(s): Lísa Anne Libungan, Snæbjörn Pálsson
Software Mentions: 9
Published: over 9 years ago

10.1186/s12867-018-0111-x

Coincidence cloning recovery of Brucella melitensis RNA from goat tissues: advancing the in vivo analysis of pathogen gene expression in brucellosis
Cited by: 4
Author(s): Paola M. Boggiatto, Daniel Fitzsimmons, Darrell O. Bayles, David P. Alt, Catherine E. Vrentas, Steven C. Olsen
Software Mentions: 9
Published: over 6 years ago

10.1186/s12864-018-5092-0

High-throughput proteomic profiling of the fish liver following bacterial infection
Cited by: 58
Author(s): Dwight R. Causey, Moritz A N Pohl, David Stead, Samuel Martín, Christopher J. Secombes, Daniel J. Macqueen
Software Mentions: 9
Published: about 6 years ago

10.1186/s12864-018-4870-z

WHAM!: a web-based visualization suite for user-defined analysis of metagenomic shotgun sequencing data
Cited by: 11
Author(s): Joseph C. Devlin, Thomas Battaglia, Martin J. Blaser, Kelly V. Ruggles
Software Mentions: 9
Published: over 6 years ago

10.7717/peerj.4555

Small tropical islands with dense human population: differences in water quality of near-shore waters are associated with distinct bacterial communities
Cited by: 10
Author(s): Hauke Kegler, Christiane Hassenrück, Pia Kegler, Tim C Jennerjahn, Muhammad Lukman, Jamaluddin Jompa, Astrid Gärdes
Software Mentions: 9
Published: over 6 years ago

10.1371/journal.pbio.3001365

PhyloFisher: A phylogenomic package for resolving eukaryotic relationships
Cited by: 34
Author(s): Alexander K. Tice, David Žihala, Tomáš Pánek, Robert E. Jones, Eric D. Salomaki, Serafim Nenarokov, Fabien Burki, Marek Eliáš, Laura Eme, Andrew J. Roger, Antonis Rokas, Xing‐Xing Shen, Jürgen F. H. Strassert, Martin Kolísko, Matthew W. Brown
Software Mentions: 9
Published: over 3 years ago

10.3390/md18120649

Sustainable Low-Volume Analysis of Environmental Samples by Semi-Automated Prioritization of Extracts for Natural Product Research (SeaPEPR)
Cited by: 6
Author(s): Riyanti, Michael Marner, Christoph Hartwig, Maria A. Patras, Stevy Imelda Murniati Wodi, Frets Jonas Rieuwpassa, Frans Gruber Ijong, Walter Balansa, Till F. Schäberle
Software Mentions: 9
Published: almost 4 years ago

10.1186/s12859-016-1442-6

Unboxing cluster heatmaps
Cited by: 25
Author(s): Sophie Engle, Sean Whalen, Alark Joshi, Katherine S. Pollard
Software Mentions: 9
Published: almost 8 years ago

10.7554/eLife.39380

Intergenerational epigenetic inheritance of cancer susceptibility in mammals
Cited by: 38
Author(s): Bluma J. Lesch, Zuzana Tóthová, Elizabeth A. Morgan, Zhicong Liao, Roderick T. Bronson, Benjamin L. Ebert, David C. Page
Software Mentions: 9
Published: over 5 years ago

10.1038/s41598-017-04141-6

The Microbiome of Endophytic, Wood Colonizing Bacteria from Pine Trees as Affected by Pine Wilt Disease
Cited by: 53
Author(s): Diogo Neves Proença, Romeu Francisco, Susanne Kublik, Anne Schöler, Gisle Vestergaard, Michael Schloter, Paula V. Morais
Software Mentions: 9
Published: over 7 years ago

10.5334/jors.277

Using SAS Macros for Multiple Mediation Analysis in R
Cited by: 2
Author(s): Paige L. Fisher, Wentao Cao, Qingzhao Yu
Software Mentions: 9
Published: about 4 years ago

10.1111/1462-2920.14631

Effect of long‐term organic and mineral fertilization strategies on rhizosphere microbiota assemblage and performance of lettuce
Cited by: 41
Author(s): Soumitra Paul Chowdhury, Doreen Babin, Martin Sandmann, Samuel Jacquiod, Loreen Sommermann, Søren J. Sørensen, Andreas Fließbach, Paul Mäder, Joerg Geistlinger, Kornelia Smalla, Michael Rothballer, Rita Grosch
Software Mentions: 9
Published: over 5 years ago

10.1038/s41598-017-07880-8

Global mapping of miRNA-target interactions in cattle (Bos taurus)
Cited by: 19
Author(s): Troels K. H. Scheel, Michael J. Moore, Joseph M. Luna, Eiko Nishiuchi, John Fak, Robert B. Darnell, Charles M. Rice
Software Mentions: 9
Published: over 7 years ago

10.3389/fnbeh.2019.00036

Prolonged Bat Call Exposure Induces a Broad Transcriptional Response in the Male Fall Armyworm (Spodoptera frugiperda; Lepidoptera: Noctuidae) Brain
Cited by: 13
Author(s): Scott D Cinel, Steven J. Taylor
Software Mentions: 9
Published: over 5 years ago

10.7554/eLife.65228

Egr2 induction in spiny projection neurons of the ventrolateral striatum contributes to cocaine place preference in mice
Cited by: 8
Author(s): Diptendu Mukherjee, Ben J. Gonzales, Reut Ashwal-Fluss, Hagit Turm, Maya Groysman, Ami Citri
Software Mentions: 8
Published: over 3 years ago

10.3389/fgene.2021.683037

De novo Transcriptome Sequencing Coupled With Co-expression Analysis Reveal the Transcriptional Regulation of Key Genes Involved in the Formation of Active Ingredients in Peucedanum praeruptorum Dunn Under Bolting Period
Cited by: 7
Author(s): Cheng Song, Xiaoli Li, Bin Jia, Li Liu, Jinmei Ou, Bangxing Han
Software Mentions: 8
Published: over 3 years ago

10.1007/s10661-016-5710-8

Is the macrophyte diversification along the trophic gradient distinct enough for river monitoring?
Cited by: 14
Author(s): Krzysztof Szoszkiewicz, Anna Budka, Karol Pietruczuk, Dariusz Kayzer, Daniel Gebler
Software Mentions: 8
Published: almost 8 years ago

10.1038/srep42719

A pan-cancer analysis of secreted Frizzled-related proteins: re-examining their proposed tumour suppressive function
Cited by: 37
Author(s): Krista Vincent, Lynne-Marie Postovit
Software Mentions: 8
Published: almost 8 years ago

10.18632/oncotarget.14443

Investigating the utility of human melanoma cell lines as tumour models
Cited by: 48
Author(s): Krista Vincent, Lynne-Marie Postovit
Software Mentions: 8
Published: almost 8 years ago

10.18632/oncotarget.9346

<i>De novo</i> HAPLN1 expression hallmarks Wnt-induced stem cell and fibrogenic networks leading to aggressive human hepatocellular carcinomas
Cited by: 30
Author(s): Sihem Mebarki, Romain Désert, Laurent Sulpice, Marie Sicard, Mireille Desille, Frédéric Canal, Hélène Dubois-Pot Schneider, Damien Bergeat, Bruno Turlin, Pascale Bellaud, Elise Lavergne, Rémy Le Guével, Anne Corlu, Christine Perret, Cédric Coulouarn, Bruno Clément, Orlando Musso
Software Mentions: 8
Published: over 8 years ago

10.1038/s41598-017-13731-3

The Role of Chromatin Density in Cell Population Heterogeneity during Stem Cell Differentiation
Cited by: 16
Author(s): Mahdi Golkaram, Jaeshin Jang, Stefan Hellander, Kenneth S. Kosik, Linda R. Petzold
Software Mentions: 8
Published: about 7 years ago

10.1038/srep40655

Epigenetic regulation of Plasmodium falciparum clonally variant gene expression during development in Anopheles gambiae
Cited by: 66
Author(s): Elena Gómez-Díaz, Rakiswendé Serge Yerbanga, Thierry Léfèvre, Anna Cohuet, M. Jordan Rowley, Jean-Bosco Ouédraogo, Victor G. Corcés
Software Mentions: 8
Published: almost 8 years ago

10.1038/srep46658

Metabolism dysregulation induces a specific lipid signature of nonalcoholic steatohepatitis in patients
Cited by: 148
Author(s): Franck Chiappini, Audrey Coilly, Hanane Kadar, Philippe Gual, Albert Tran, Christophe Desterke, Didier Samuel, Jean‐Charles Duclos‐Vallée, David Touboul, Justine Bertrand‐Michel, Alain Brunelle, Catherine Guettier, François Le Naour
Software Mentions: 8
Published: over 7 years ago

10.1371/journal.pcbi.1008488

On the NF-Y regulome as in ENCODE (2019)
Cited by: 4
Author(s): Mirko Ronzio, Andrea Bernardini, Giulio Pavesi, Roberto Mantovani, Diletta Dolfini
Software Mentions: 8
Published: almost 4 years ago

10.1186/s13148-021-01144-z

Whole-genome methylation analysis of testicular germ cells from cryptozoospermic men points to recurrent and functionally relevant DNA methylation changes
Cited by: 9
Author(s): Sara Di Persio, Elsa Leitão, Marius Wöste, Tobias Tekath, Jann‐Frederik Cremers, Martin Dugas, Xiaolin Liao, Gerd Meyer zu Hörste, Sabine Kliesch, Sandra Laurentino, Nina Neuhaus, Bernhard Horsthemke
Software Mentions: 8
Published: over 3 years ago

10.1038/s41598-020-69160-2

Individual-based population genomics reveal different drivers of adaptation in sympatric fish
Cited by: 10
Author(s): Héctor Torrado, Carlos Carreras, Núria Raventós, Enrique Macpherson, Marta Pascual
Software Mentions: 8
Published: over 4 years ago

10.1038/s41598-020-74139-0

Statistical models for identifying frequent hitters in high throughput screening
Cited by: 4
Author(s): Samuel Goodwin, Golnaz Shahtahmassebi, Quentin S. Hanley
Software Mentions: 8
Published: about 4 years ago

10.1093/braincomms/fcab141

Amyotrophic lateral sclerosis transcriptomics reveals immunological effects of low-dose interleukin-2
Cited by: 11
Author(s): Ilaria Giovannelli, Nadhim Bayatti, A.G. Brown, Dennis Wang, Marius Mickunas, William Camu, Jean-Luc Veyrune, Christine Payan, Cecilia Garlanda, Massimo Locati, Raul Juntas-Moralès, Nicolas Pageot, Andrea Malaspina, Ulf Andréasson, Carey Suehs, Safa Saker, Christophe Masseguin, John de Vos, Henrik Zetterberg, Ammar Al‐Chalabi, P. Nigel Leigh, Timothy Tree, G. Bensimon, Paul R. Heath, Pamela J. Shaw, Janine Kirby
Software Mentions: 8
Published: almost 4 years ago

10.1186/s12920-020-0729-7

ERα-related chromothripsis enhances concordant gene transcription on chromosome 17q11.1-q24.1 in luminal breast cancer
Cited by: 6
Author(s): Chun-Lin Lin, Xueying Tan, Chun-Liang Chen, Meena Kusi, Chia-Nung Hung, Chih-Wei Chou, Ya-Ting Hsu, Chiou‐Miin Wang, Nameer B. Kirma, Ching-Hung Lin, Kate Lathrop, Richard M. Elledge, Virginia Kaklamani, Kohzoh Mitsuya, Tim H.M. Huang
Software Mentions: 8
Published: over 4 years ago

10.1038/s41598-020-59524-z

Cryptic species in the parasitic Amoebophrya species complex revealed by a polyphasic approach
Cited by: 16
Author(s): Ruibo Cai, Ehsan Kayal, Catharina Alves‐de‐Souza, Estelle Bigeard, Erwan Corre, Christian Jeanthon, Dominique Marie, Betina M. Porcel, Raffaele Siano, Jeremy Szymczak, Matthias Wolf, Laure Guillou
Software Mentions: 8
Published: almost 5 years ago

10.1038/s41598-020-76256-2

Selection of sponge-associated bacteria with high potential for the production of antibacterial compounds
Cited by: 11
Author(s): Riyanti, Walter Balansa, Yang Liu, Abha Sharma, Sanja Mihajlović, Christoph Hartwig, Benedikt Leis, Frets Jonas Rieuwpassa, Frans Gruber Ijong, Heike Wägele, Gabriele M. König, Till F. Schäberle
Software Mentions: 8
Published: about 4 years ago

10.1155/2021/8892849

Correlation Analysis between GDM and Gut Microbial Composition in Late Pregnancy
Cited by: 17
Author(s): Genxia Li, Pan Yin, Shuhui Chu, Wen Gao, Shihong Cui, Shuhua Guo, Yajuan Xu, Enwu Yuan, Texuan Zhu, Jie You, Junya Zhang, Manman Yang
Software Mentions: 8
Published: almost 4 years ago

10.3390/cancers13133374

Major Oncogenic Drivers and Their Clinicopathological Correlations in Sporadic Childhood Papillary Thyroid Carcinoma in Belarus
Cited by: 5
Author(s): Tatiana Rogounovitch, Svetlana Mankovskaya, Mikhail Fridman, Tatiana A. Leonova, Victor Alexandrovich Kondratovitch, N. E. Konoplya, Shunichi Yamashita, Norisato Mitsutake, Vladimir Saenko
Software Mentions: 8
Published: over 3 years ago

10.3390/cancers13071734

Role for the Histone Demethylase KDM4B in Rhabdomyosarcoma via CDK6 and CCNA2: Compensation by KDM4A and Apoptotic Response of Targeting Both KDM4B and KDM4A
Cited by: 5
Author(s): Zoë S. Walters, Ewa Aładowicz, Bárbara Villarejo-Balcells, Gary Nugent, Joanna Selfe, Paul D. Eve, Julian Blagg, Olivia W. Rossanese, Janet Shipley
Software Mentions: 8
Published: over 3 years ago

10.3390/cancers11101606

A Toolbox for Functional Analysis and the Systematic Identification of Diagnostic and Prognostic Gene Expression Signatures Combining Meta-Analysis and Machine Learning
Cited by: 12
Author(s): Johannes A Vey, Lorenz A. Kapsner, Maximilian Fuchs, Philipp Unberath, Giulia Veronesi, Meik Kunz
Software Mentions: 8
Published: about 5 years ago

10.1371/journal.pbio.2002054

Genomic dissection of conserved transcriptional regulation in intestinal epithelial cells
Cited by: 76
Author(s): Colin R. Lickwar, J. Gray Camp, Matthew Weiser, Jordan L. Cocchiaro, David M. Kingsley, Terrence S. Furey, Shehzad Z. Sheikh, John F. Rawls
Software Mentions: 8
Published: about 7 years ago

10.1371/journal.pone.0246491

Trophic structure of a nektobenthic community exploited by a multispecific bottom trawling fishery in Northeastern Brazil
Cited by: 3
Author(s): Alex Souza Lira, Flávia Lucena‐Frédou, Frédéric Ménard, Thierry Frédou, Júlio Guazzelli Gonzalez, Valdimere Ferreira, José Souto Rosa Filho, Jean-Marie Munaron, François Le Loc’h
Software Mentions: 8
Published: almost 4 years ago

10.1038/s42003-021-01658-5

Colonization and genetic diversification processes of Leishmania infantum in the Americas
Cited by: 30
Author(s): Philipp Schwabl, Mariana Côrtes Boité, Giovanni Bussotti, Arne Jacobs, Björn Andersson, Otacílio C. Moreira, Anita Leocádio Freitas-Mesquita, José Roberto Meyer‐Fernandes, Erich Loza Telleria, Yara M. Traub-Csekö, Slavica Vaselek, Tereza Leštinová, Petr Volf, Fernanda Nazaré Morgado, Renato Porrozzi, Martin S. Llewellyn, Gérald F. Späth, Elisa Cupolillo
Software Mentions: 8
Published: almost 4 years ago

10.1186/s12864-015-2319-1

Global expression differences and tissue specific expression differences in rice evolution result in two contrasting types of differentially expressed genes
Cited by: 3
Author(s): Youko Horiuchi, Yoshiaki Harushima, Hironori Fujisawa, Takako Mochizuki, Masahiro Fujita, Hajime Ohyanagi, Nori Kurata
Software Mentions: 8
Published: almost 9 years ago

10.1016/j.immuni.2019.02.006

Anti-commensal IgG Drives Intestinal Inflammation and Type 17 Immunity in Ulcerative Colitis
Cited by: 121
Author(s): Tomas Castro‐Dopico, Thomas W. Dennison, John R. Ferdinand, Rebeccah J. Mathews, Aaron Fleming, Dean Clift, Benjamin J Stewart, Chenzhi Jing, Konstantina Strongili, Larisa I. Labzin, Edward J M Monk, Kourosh Saeb‐Parsy, Clare E. Bryant, Simon Clare, Miles Parkes, Menna R. Clatworthy
Software Mentions: 8
Published: over 5 years ago

10.1038/s41598-019-50642-x

Transcriptome Sequencing of Peripheral Blood Mononuclear Cells from Elite Controller-Long Term Non Progressors
Cited by: 11
Author(s): Francisco Díez-Fuertes, Humberto Erick De La Torre Tarazona, Esther Calonge, María Pernas, María del Mar Alonso-Socas, Laura Capa, Javier García-Pérez, Anavaj Sakuntabhai, José Alcamı́
Software Mentions: 8
Published: about 5 years ago

10.1186/s40168-019-0716-4

The association between pneumococcal vaccination, ethnicity, and the nasopharyngeal microbiota of children in Fiji
Cited by: 11
Author(s): Laura K. Boelsen, Eileen M. Dunne, Moana Mika, Stefanie Eggers, Cattram Nguyen, Felisita Tupou Ratu, Fiona M. Russell, E. Kim Mulholland, Markus Hilty, Catherine Satzke
Software Mentions: 8
Published: over 5 years ago

10.7717/peerj.1360

Getting the most out of RNA-seq data analysis
Cited by: 22
Author(s): Tsung Fei Khang, Ching Yee Lau
Software Mentions: 8
Published: about 9 years ago

10.1186/s40168-019-0630-9

Environmental filtering drives distinct continental atlases of soil archaea between dryland and wetland agricultural ecosystems
Cited by: 103
Author(s): Shuo Jiao, Ye Xu, Jie Zhang, Yahai Lu
Software Mentions: 8
Published: almost 6 years ago

10.1186/s13059-021-02260-y

LINE retrotransposons characterize mammalian tissue-specific and evolutionarily dynamic regulatory regions
Cited by: 31
Author(s): Maša Roller, Ericca L. Stamper, Diego Villar, Osagie Izuogu, Fergal J. Martin, Aisling M. Redmond, Raghavendra Ramachanderan, Louise Harewood, Duncan T. Odom, Paul Flicek
Software Mentions: 8
Published: almost 4 years ago

10.1186/gb-2013-14-12-r137

Integrative DNA methylation and gene expression analysis in high-grade soft tissue sarcomas
Cited by: 76
Author(s): Marcus Renner, Thomas Wolf, Hannah Meyer, Wolfgang Hartmann, Roland Penzel, Alexis Ulrich, Burkhard Lehner, Volker Hovestadt, Esteban Czwan, Gerlinde Egerer, Thomas Schmitt, Ingo Alldinger, Eva Kristin Renker, Volker Ehemann, Roland Eils, Eva Wardelmann, Reinhard Büttner, Peter Lichter, Benedikt Brors, Peter Schirmacher, Gunhild Mechtersheimer
Software Mentions: 8
Published: almost 12 years ago

10.1371/journal.pone.0183264

The transcriptional profiling of human in vivo-generated plasma cells identifies selective imbalances in monoclonal gammopathies
Cited by: 12
Author(s): Luis M. Valor, Beatriz Rodrı́guez-Bayona, Ana Ramos-Amaya, José A. Brieva, Antonio Campos‐Caro
Software Mentions: 8
Published: over 7 years ago

10.1371/journal.pone.0200925

PNPase knockout results in mtDNA loss and an altered metabolic gene expression program
Cited by: 12
Author(s): Eriko Shimada, Fasih M. Ahsan, Mahta Nili, Dian Huang, Sean Atamdede, Tara TeSlaa, Dana Case, Xiang Yu, Brian D. Gregory, Benjamin J. Perrin, Carla M. Koehler, Michael A. Teitell
Software Mentions: 8
Published: over 6 years ago

10.1128/AEM.02755-17

Microbial Diversity and Putative Opportunistic Pathogens in Dishwasher Biofilm Communities
Cited by: 45
Author(s): Prem K. Raghupathi, Jerneja Zupančič, Asker Brejnrod, Samuel Jacquiod, Kurt Houf, Mette Burmølle, Nina Gunde‐Cimerman, Søren J. Sørensen
Software Mentions: 8
Published: over 6 years ago

10.1186/s12885-021-08012-2

Identification of a five-immune gene model as an independent prognostic factor in hepatocellular carcinoma
Cited by: 5
Author(s): Haitao Chen, Yueying Li, Shu–Yuan Xiao, Jingyi Guo
Software Mentions: 8
Published: over 3 years ago

10.1371/journal.pone.0224879

Long non-coding RNAs and latent HIV – A search for novel targets for latency reversal
Cited by: 17
Author(s): Wim Trypsteen, Cory H. White, Amey Mukim, Celsa A. Spina, Ward De Spiegelaere, Steve Lefever, Vicente Planelles, Alberto Bosque, Christopher H. Woelk, Linos Vandekerckhove, Nadejda Beliakova-Bethell
Software Mentions: 8
Published: about 5 years ago

10.7717/peerj.8667

Element concentrations in pelagic<i>Sargassum</i>along the Mexican Caribbean coast in 2018-2019
Cited by: 78
Author(s): Rosa E. Rodríguez-Martínez, Priyadarsi D. Roy, Nuria Torrescano-Valle, Nancy Cabañillas-Terán, Silvia Carrillo‐Domínguez, Ligia Collado‐Vides, Marta García-Sánchez, Brigitta I. van Tussenbroek
Software Mentions: 8
Published: over 4 years ago

10.1371/journal.pone.0127163

Genetic Deletion of the Transcriptional Repressor NFIL3 Enhances Axon Growth In Vitro but Not Axonal Repair In Vivo
Cited by: 2
Author(s): L.R. van der Kallen, Ruben Eggers, Erich Ehlert, Joost Verhaagen, August B. Smit, Ronald E. van Kesteren
Software Mentions: 8
Published: over 9 years ago

10.1186/s12864-020-6653-6

Novel approach in whole genome mining and transcriptome analysis reveal conserved RiPPs in Trichoderma spp
Cited by: 14
Author(s): Gabriel A. Vignolle, Robert L. Mach, Astrid R. Mach-Aigner, Christian Derntl
Software Mentions: 8
Published: over 4 years ago

10.1016/j.gpb.2019.09.007

Antidiabetic Effects of Gegen Qinlian Decoction via the Gut Microbiota Are Attributable to Its Key Ingredient Berberine
Cited by: 59
Author(s): Xizhan Xu, Zezheng Gao, Fuchao Yang, Yingying Yang, Liang Chen, Han Chieh Lin, Na Zhao, Jiayue Xu, Xinmiao Wang, Yue Ma, Lian Shu, Xueyou Hu, Na Lyu, Yuanlong Pan, Baoli Zhu, Linhua Zhao, Xiaolin Tong, Jun Wang
Software Mentions: 8
Published: almost 4 years ago

10.3389/fpls.2018.01625

Integrative Analysis of Three RNA Sequencing Methods Identifies Mutually Exclusive Exons of MADS-Box Isoforms During Early Bud Development in Picea abies
Cited by: 9
Author(s): Shirin Akhter, Warren W. Kretzschmar, Veronika Nordal, Nicolas Delhomme, Nathaniel R. Street, Ove Nilsson, Olof Emanuelsson, Jens F. Sundström
Software Mentions: 8
Published: about 6 years ago

10.1007/s11306-017-1284-x

Metabolomic analysis of tomato seed germination
Cited by: 31
Author(s): Rashid H. Kazmi, Leo A.J. Willems, Ronny V.L. Joosen, Naveed Ahmad Khan, Wilco Ligterink, Henk W. M. Hilhorst
Software Mentions: 8
Published: about 7 years ago

10.7554/eLife.47859

Persistent epigenetic memory impedes rescue of the telomeric phenotype in human ICF iPSCs following DNMT3B correction
Cited by: 15
Author(s): Shir Toubiana, Miriam Gagliardi, Mariarosaria Papa, Roberta Manco, Maty Tzukerman, Maria R. Matarazzo, Sara Selig
Software Mentions: 8
Published: about 5 years ago

10.3389/fpls.2021.693285

SNP Alleles Associated With Low Bolting Tendency in Sugar Beet
Cited by: 5
Author(s): Samathmika Ravi, G. Campagna, Maria Cristina Della Lucia, Chiara Broccanello, Giovanni Bertoldo, Claudia Chiodi, Laura Maretto, Matteo Moro, Azam Sadat Eslami, Subhashini Srinivasan, Andrea Squartini, Giuseppe Concheri, Piergiorgio Stevanato
Software Mentions: 8
Published: over 3 years ago

10.1371/journal.pone.0051609

Comparative Transcriptome Profiling of the Early Response to Magnaporthe oryzae in Durable Resistant vs Susceptible Rice (Oryza sativa L.) Genotypes
Cited by: 129
Author(s): Paolo Bagnaresi, Chiara Biselli, Luigi Orrù, Simona Urso, Laura Crispino, Pamela Abbruscato, Pietro Piffanelli, Elisabetta Lupotto, Luigi Cattivelli, Giampiero Valè
Software Mentions: 8
Published: almost 12 years ago

10.1186/s40168-017-0235-0

Mentholation affects the cigarette microbiota by selecting for bacteria resistant to harsh environmental conditions and selecting against potential bacterial pathogens
Cited by: 30
Author(s): Jessica Chopyk, Suhana Chattopadhyay, Prachi Kulkarni, Emma Claye, Kelsey R. Babik, Molly C. Reid, Eoghan M. Smyth, Lauren E. Hittle, Joseph N. Paulson, Raul Cruz‐Cano, Mihai Pop, Stephanie Buehler, Pamela I. Clark, Amy R. Sapkota, Emmanuel F. Mongodin
Software Mentions: 8
Published: almost 8 years ago

10.1186/s12859-016-1235-y

BTR: training asynchronous Boolean models using single-cell expression data
Cited by: 62
Author(s): Chee Lim, Huange Wang, Steven Woodhouse, Nir Piterman, Lorenz Wernisch, Jasmin Fisher, Berthold Göttgens
Software Mentions: 8
Published: about 8 years ago

10.3389/fmicb.2020.01376

Mobilization of Antibiotic Resistance: Are Current Approaches for Colocalizing Resistomes and Mobilomes Useful?
Cited by: 28
Author(s): Ilya B. Slizovskiy, Kingshuk Mukherjee, Christopher Dean, Christina Boucher, Noelle Noyes
Software Mentions: 8
Published: over 4 years ago

10.3389/fmicb.2021.627437

A Taxon-Wise Insight Into Rock Weathering and Nitrogen Fixation Functional Profiles of Proglacial Systems
Cited by: 4
Author(s): Gilda Varliero, Alexandre M. Anesio, Gary Barker
Software Mentions: 8
Published: about 3 years ago

10.1128/mSphere.00126-19

Spatial and Temporal Analysis of the Stomach and Small-Intestinal Microbiota in Fasted Healthy Humans
Cited by: 47
Author(s): Anna M. Seekatz, Matthew K. Schnizlein, Mark J. Koenigsknecht, Jason Baker, William L. Hasler, Barry E. Bleske, Vincent B. Young, Duxin Sun
Software Mentions: 8
Published: over 5 years ago

10.2196/15431

Ensemble Learning Models Based on Noninvasive Features for Type 2 Diabetes Screening: Model Development and Validation
Cited by: 9
Author(s): Tianzhou Yang, Li Zhang, Liwei Yi, Huawei Feng, Shimeng Li, Haoyu Chen, Jü Zhu, Zhao Jian, Yingyue Zeng, Huan Liu
Software Mentions: 8
Published: over 4 years ago

10.1186/s40168-018-0434-3

Microbiome and ecotypic adaption of Holcus lanatus (L.) to extremes of its soil pH range, investigated through transcriptome sequencing
Cited by: 20
Author(s): Ellen L. Young, Manus Carey, Andrew A. Meharg, Caroline Meharg
Software Mentions: 8
Published: over 6 years ago

10.7554/eLife.64513

Chondrocytes in the resting zone of the growth plate are maintained in a Wnt-inhibitory environment
Cited by: 25
Author(s): Shawn A Hallett, Yuki Matsushita, Wanida Ono, Naoko Sakagami, Koji Mizuhashi, Nicha Tokavanich, Mizuki Nagata, Annabelle Zhou, Takao Hanabusa, Henry M. Kronenberg, Noriaki Ono
Software Mentions: 8
Published: over 3 years ago

10.1038/s41598-021-94853-7

Unique chemical parameters and microbial activity lead to increased archaeological preservation at the Roman frontier site of Vindolanda, UK
Cited by: 3
Author(s): Caroline Orr, Rhys Williams, Hrafnhildur Halldórsdóttir, Andrew Birley, Elizabeth M. Greene, Andrew Nelson, T. Komang Ralebitso-Senior, Gillian Taylor
Software Mentions: 8
Published: over 3 years ago

10.3390/plants10030550

Phenolic Compounds and Biological Activity of Selected Mentha Species
Cited by: 51
Author(s): Sanja Ćavar Zeljković, Jana Šišková, Karolína Komzáková, Nuria De Diego, K. Kaffková, Petr Tarkowski
Software Mentions: 8
Published: over 3 years ago

10.1128/mSphere.00176-18

High Rate of Infection by Only Oncogenic Human Papillomavirus in Amerindians
Cited by: 10
Author(s): Daniela Vargas-Robles, Magda Magris, Natalia Morales, Maurits N.C. de Koning, Iveth Rodríguez, Tahidid Nieves, Filipa Godoy-Vitorino, Gloria Inés Sánchez, Luis David Alcaraz, Larry J. Forney, María-Eglée Pérez, Luis García-Briceño, Leen–Jan van Doorn, Maria Gloria Domínguez-Bello
Software Mentions: 8
Published: over 6 years ago

10.3390/molecules24162977

VOC Profiles of Saliva in Assessment of Halitosis and Submandibular Abscesses Using HS-SPME-GC/MS Technique
Cited by: 32
Author(s): Fernanda Monedeiro, Maciej Milanowski, Ileana-Andreea Raţiu, Hubert Zmysłowski, Tomasz Ligor, Bogusław Buszewski
Software Mentions: 7
Published: over 5 years ago

10.1186/s13148-019-0658-5

Gene domain-specific DNA methylation episignatures highlight distinct molecular entities of ADNP syndrome
Cited by: 65
Author(s): Eric G. Bend, Erfan Aref‐Eshghi, David B. Everman, R. Curtis Rogers, Sara Cathey, Eloise J. Prijoles, Michael J. Lyons, Heather L. Davis, Katie Clarkson, Karen W. Gripp, Dong Liu, Elizabeth Bhoj, Elaine H. Zackai, Paul R. Mark, Hákon Hákonarson, Laurie A. Demmer, Michael A. Levy, Jennifer Kerkhof, Alan Stuart, David I. Rodenhiser, Michael J. Friez, Roger E. Stevenson, Charles E. Schwartz, Bekim Sadiković
Software Mentions: 7
Published: over 5 years ago

10.1186/s12864-018-5145-4

Dissection of the molecular bases of genotype x environment interactions: a study of phenotypic plasticity of Saccharomyces cerevisiae in grape juices
Cited by: 21
Author(s): Emilien Peltier, Vikas Sharma, Maria Martí Raga, Miguel Roncoroni, Margaux Bernard, Vladimir Jiranek, Yves Gibon, Philippe Marullo
Software Mentions: 7
Published: about 6 years ago

10.3390/cells10092215

Autophagy-Associated IL-15 Production Is Involved in the Pathogenesis of Leprosy Type 1 Reaction
Cited by: 0
Author(s): Bruno Jorge de Andrade Silva, Tamiris Lameira Bittencourt, Thyago Leal-Calvo, Mayara Abud Mendes, Rhana Berto da Silva Prata, Mayara Garcia de Mattos Barbosa, Priscila Ribeiro Andrade, Suzana Côrte-Real, Gilberto Marcelo Sperandio da Silva, Milton Ozório Moraes, Euzenir Nunes Sarno, Roberta Olmo Pinheiro
Software Mentions: 7
Published: about 3 years ago

10.1186/s13148-021-01145-y

Childhood-onset dystonia-causing KMT2B variants result in a distinctive genomic hypermethylation profile
Cited by: 17
Author(s): Andrea Ciolfi, Aidin Foroutan, Alessandro Capuano, Lucia Pedace, Lorena Travaglini, Simone Pizzi, Marco Andreani, Evelina Miele, Federica Invernizzi, Chiara Reale, Celeste Panteghini, Maria Iascone, Marcello Niceta, Ralitza H. Gavrilova, Laura Schultz‐Rogers, Emanuele Agolini, Maria Francesca Bedeschi, Paolo Prontera, Matteo Garibaldi, Serena Galosi, Vincenzo Leuzzi, Paola Soliveri, Rory J. Olson, Giovanna Zorzi, Barbara Garavaglia, Marco Tartaglia, Bekim Sadiković
Software Mentions: 7
Published: over 3 years ago

10.1038/s42003-020-01416-z

Genome-wide association studies and heritability analysis reveal the involvement of host genetics in the Japanese gut microbiota
Cited by: 37
Author(s): Sachiko Ishida, Koichi Kato, Masami Tanaka, Toshitaka Odamaki, Rieko Kubo, Eri Mitsuyama, Jin‐zhong Xiao, Rui Yamaguchi, Satoshi Uematsu, Seiya Imoto, Satoru Miyano
Software Mentions: 7
Published: about 4 years ago

10.1038/s41598-019-44491-x

The LL-100 panel: 100 cell lines for blood cancer studies
Cited by: 67
Author(s): Hilmar Quentmeier, Claudia Pommerenke, Wilhelm G. Dirks, Sonja Eberth, Max Koeppel, Roderick A.F. MacLeod, Stefan Nagel, Klaus G. Steube, Cord C. Uphoff, Hans G. Drexler
Software Mentions: 7
Published: over 5 years ago

Projects: cran: gplots

Papers Mentioning gplots 2,122