pypi: cutadapt | Projects | Ecosyste.ms: Papers

10.3389/fimmu.2019.00330

Persistence of Candida albicans in the Oral Mucosa Induces a Curbed Inflammatory Host Response That Is Independent of Immunosuppression
Cited by: 37
Author(s): Florian Kirchner, Katharina Littringer, Simon Altmeier, Van Du T. Tran, Franziska Annett Schönherr, Christina Braunsdorf, Marco Pagni, Dominique Sanglard, Nicole Joller, Salomé LeibundGut‐Landmann
Software Mentions: 5
Published: over 5 years ago

10.7554/eLife.63274

Efficient chromatin accessibility mapping in situ by nucleosome-tethered tagmentation
Cited by: 68
Author(s): Steven Henikoff, Hatice S Kaya-Okur, Kami Ahmad
Software Mentions: 5
Published: about 4 years ago

10.3389/fgene.2018.00671

UTRme: A Scoring-Based Tool to Annotate Untranslated Regions in Trypanosomatid Genomes
Cited by: 20
Author(s): Santiago Radío, Rafael Sebastián Fort, Beatríz Garat, José Sotelo‐Silveira, Pablo Smircich
Software Mentions: 5
Published: almost 6 years ago

10.7554/eLife.03549

Zinc finger protein Zfp335 is required for the formation of the naïve T cell compartment
Cited by: 21
Author(s): Brenda Y. Han, Shuang Wu, Chuan-Sheng Foo, Robert M. Horton, Craig N. Jenne, Susan R. Watson, Belinda Whittle, Christopher C. Goodnow, Jason G. Cyster
Software Mentions: 5
Published: about 10 years ago

10.1186/s12864-019-6432-4

Pan-tissue transcriptome analysis of long noncoding RNAs in the American beaver Castor canadensis
Cited by: 2
Author(s): Amita Kashyap, Adelaide Rhodes, Brent Kronmiller, Josie Berger, Ashley Champagne, Edward W. Davis, Mitchell V. Finnegan, Matthew Geniza, David A. Hendrix, Christiane V. Löhr, Vanessa M. Petro, Thomas J. Sharpton, Jackson Wells, Clinton W. Epps, Pankaj Jaiswal, Brett M. Tyler, Stephen A. Ramsey
Software Mentions: 5
Published: almost 5 years ago

10.7554/eLife.42499

A combination of transcription factors mediates inducible interchromosomal contacts
Cited by: 15
Author(s): Seungsoo Kim, Maitreya J. Dunham, Jay Shendure
Software Mentions: 5
Published: over 5 years ago

10.1186/s40168-017-0322-2

Genomic insights into potential interdependencies in microbial hydrocarbon and nutrient cycling in hydrothermal sediments
Cited by: 147
Author(s): Nina Dombrowski, Kiley W. Seitz, Andreas Teske, Brett J. Baker
Software Mentions: 5
Published: about 7 years ago

10.1186/s40168-017-0261-y

Fecal metagenomic profiles in subgroups of patients with myalgic encephalomyelitis/chronic fatigue syndrome
Cited by: 127
Author(s): Dorottya Nagy‐Szakal, Brent L. Williams, Nischay Mishra, Xiaoyu Che, Bohyun Lee, Lucinda Bateman, Nancy G. Klimas, Anthony L. Komaroff, Susan Levine, José G. Montoya, Daniel L. Peterson, Devi Ramanan, Komal Jain, M L Eddy, Mady Hornig, W. Ian Lipkin
Software Mentions: 5
Published: over 7 years ago

10.1186/s12915-021-01084-3

Long-term persistence of crAss-like phage crAss001 is associated with phase variation in Bacteroides intestinalis
Cited by: 31
Author(s): Andrey N. Shkoporov, Е. В. Хохлова, Niamh Stephens, Cara M. Hueston, Samuel Seymour, Andrew J. Hryckowian, Dimitri Scholz, R. Paul Ross, Colin Hill
Software Mentions: 5
Published: over 3 years ago

10.1371/journal.pone.0175464

Identification of potential biomarkers in donor cows for in vitro embryo production by granulosa cell transcriptomics
Cited by: 12
Author(s): Gianluca Mazzoni, Suraya Mohamad Salleh, Kristine Freude, Helene Helboe Pedersen, Lotte Stroebech, Henrik Callesen, Poul Hyttel, Haja N. Kadarmideen
Software Mentions: 5
Published: over 7 years ago

10.7554/eLife.07295

Negative regulation of ABA signaling by WRKY33 is critical for Arabidopsis immunity towards Botrytis cinerea 2100
Cited by: 179
Author(s): Shouan Liu, Barbara Kracher, J. Ziegler, Rainer P. Birkenbihl, Imre E. Somssich
Software Mentions: 5
Published: over 9 years ago

10.1186/s40168-017-0279-1

A novel ultra high-throughput 16S rRNA gene amplicon sequencing library preparation method for the Illumina HiSeq platform
Cited by: 79
Author(s): Eric J. de Muinck, Pål Trosvik, Gregor D. Gilfillan, Johannes R. Hov, Arvind Sundaram
Software Mentions: 5
Published: over 7 years ago

10.7554/eLife.38619

Mapping the transcriptional diversity of genetically and anatomically defined cell populations in the mouse brain
Cited by: 52
Author(s): Ken Sugino, Erin Clark, Anton Schulmann, Yasuyuki Shima, Lihua Wang, David Hunt, Bryan M. Hooks, Dimitri Tränkner, Jayaram Chandrashekar, Serge Picard, Andrew Lemire, Nelson Spruston, Adam W. Hantman, Sacha B. Nelson
Software Mentions: 5
Published: over 5 years ago

10.1186/s40168-019-0668-8

Rhizosphere microbiomes diverge among Populus trichocarpa plant-host genotypes and chemotypes, but it depends on soil origin
Cited by: 91
Author(s): Allison M. Veach, Reese M. Morris, Daniel Z. Yip, Zamin K. Yang, Nancy L. Engle, Melissa Cregger, Timothy J. Tschaplinski, Christopher W. Schadt
Software Mentions: 5
Published: over 5 years ago

10.1186/s12864-017-4031-9

unitas: the universal tool for annotation of small RNAs
Cited by: 83
Author(s): Daniel Gebert, Charlotte Hewel, David Rosenkranz
Software Mentions: 5
Published: over 7 years ago

10.1002/advs.202001402

TRADES: Targeted RNA Demethylation by SunTag System
Cited by: 25
Author(s): Jing Mo, Zonggui Chen, Shanshan Qin, Shu Li, Chuangang Liu, Lu Zhang, Ruoxi Ran, Ying Kong, Fang Wang, Song-Mei Liu, Yu Zhou, Xiaolian Zhang, Xiaocheng Weng, Xiang Zhou
Software Mentions: 5
Published: over 4 years ago

10.7554/eLife.54508

Spen links RNA-mediated endogenous retrovirus silencing and X chromosome inactivation
Cited by: 24
Author(s): Ava C. Carter, Jin Xu, Meagan Y Nakamoto, Yuning Wei, Brian Zarnegar, Quanming Shi, James P. Broughton, Ryan C. Ransom, Ankit Salhotra, Surya Nagaraja, Rui Li, Diana R. Dou, Kathryn E. Yost, Seung Woo Cho, Anil Mistry, Michael T. Longaker, Paul A. Khavari, Robert T. Batey, Deborah S. Wuttke, Howard Y. Chang
Software Mentions: 5
Published: over 4 years ago

10.1186/s12915-021-01001-8

Evolution of the codling moth pheromone via an ancient gene duplication
Cited by: 9
Author(s): Jean-Marc Lassance, Bao‐Jian Ding, Christer Löfstedt
Software Mentions: 5
Published: over 3 years ago

10.1186/1471-2164-15-917

Differential expression of endogenous plant cell wall degrading enzyme genes in the stick insect (Phasmatodea) midgut
Cited by: 37
Author(s): Matan Shelomi, W. Cameron Jasper, Joel Atallah, Lynn S. Kimsey, Brian R. Johnson
Software Mentions: 5
Published: almost 11 years ago

10.3389/fcell.2021.664178

Differential Transcriptomes and Methylomes of Trophoblast Stem Cells From Naturally-Fertilized and Somatic Cell Nuclear-Transferred Embryos
Cited by: 0
Author(s): Jin Sun, Weisheng Zheng, Wenqiang Liu, Xiaochen Kou, Yanhong Zhao, Zehang Liang, Lu Wang, Zihao Zhang, Jing Xiao, Rui Gao, Shaorong Gao, Cizhong Jiang
Software Mentions: 5
Published: over 3 years ago

10.7717/peerj.7014

Soil bacterial and fungal communities of six bahiagrass cultivars
Cited by: 10
Author(s): Lukas Beule, Ko‐Hsuan Chen, Chih‐Ming Hsu, Cheryl L. Mackowiak, José C. B. Dubeux, Ann R. Blount, Hui‐Ling Liao
Software Mentions: 5
Published: over 5 years ago

10.3389/fcell.2020.580848

Adherent Intestinal Cells From Atlantic Salmon Show Phagocytic Ability and Express Macrophage-Specific Genes
Cited by: 5
Author(s): Youngjin Park, Qirui Zhang, G.F. Wiegertjes, Jorge M. O. Fernandes, Viswanath Kiron
Software Mentions: 5
Published: about 4 years ago

10.7717/peerj.11237

NGScloud2: optimized bioinformatic analysis using Amazon Web Services
Cited by: 4
Author(s): Fernando Mora‐Márquez, José Luis Vázquez-Poletti, Unai López de Heredia
Software Mentions: 5
Published: over 3 years ago

10.1371/journal.pone.0222737

Annual replication is essential in evaluating the response of the soil microbiome to the genetic modification of maize in different biogeographical regions
Cited by: 6
Author(s): Márton Szoboszlay, Astrid Näther, Ewen Mullins, Christoph C. Tebbe
Software Mentions: 5
Published: almost 5 years ago

10.7554/eLife.13926

Activation of individual L1 retrotransposon instances is restricted to cell-type dependent permissive loci
Cited by: 122
Author(s): Claude Philippe, Dulce B Vargas-Landin, Aurélien J. Doucet, Dominic van Essen, Jorge Vera-Otárola, Monika Kuciak, Antoine Corbin, Pilvi Nigumann, Gaël Cristofari
Software Mentions: 5
Published: over 8 years ago

10.1371/journal.pone.0092663

Towards Decrypting Cryptobiosis—Analyzing Anhydrobiosis in the Tardigrade Milnesium tardigradum Using Transcriptome Sequencing
Cited by: 48
Author(s): Chong Wang, Markus A. Grohme, Brahim Mali, Ralph O. Schill, Marcus Frohme
Software Mentions: 5
Published: over 10 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 4 years ago

10.3389/fcell.2021.595744

A Highly Conserved Shh Enhancer Coordinates Hypothalamic and Craniofacial Development
Cited by: 2
Author(s): Zoe Crane-Smith, Jeffrey J. Schoenebeck, Katy A. Graham, Paul S. Devenney, Lorraine Rose, Mark Ditzell, E. S. Anderson, Joseph I. Thomson, Natalia Klenin, Deborah M. Kurrasch, Laura A. Lettice, Robert E. Hill
Software Mentions: 5
Published: over 3 years ago

10.1371/journal.pone.0223691

The bacterial community in potato is recruited from soil and partly inherited across generations
Cited by: 31
Author(s): Franziska Buchholz, Livio Antonielli, Tanja Kostić, Angela Sessitsch, Birgit Mitter
Software Mentions: 5
Published: about 5 years ago

10.1172/JCI133187

Mesenchymal niche remodeling impairs hematopoiesis via stanniocalcin 1 in acute myeloid leukemia
Cited by: 45
Author(s): Alexander Waclawiczek, Ashley Hamilton, Kevin Rouault-Pierre, Ander Abarrategi, Manuel Garcia-Albornoz, Farideh Miraki-Moud, Nourdine Bah, John G. Gribben, Jude Fitzgibbon, David Taussig, Dominique Bonnet
Software Mentions: 5
Published: over 4 years ago

10.7554/eLife.61894

Epigenetic reprogramming rewires transcription during the alternation of generations in Arabidopsis
Cited by: 45
Author(s): Michael Borg, Ranjith Papareddy, Rodolphe Dombey, Elin Axelsson, Michael D. Nodine, David Twell, Frédéric Berger
Software Mentions: 5
Published: almost 4 years ago

10.7554/eLife.49673

Rbfox1 up-regulation impairs BDNF-dependent hippocampal LTP by dysregulating TrkB isoform expression levels
Cited by: 25
Author(s): Francesco Tomassoni-Ardori, Gianluca Fulgenzi, Jodi Becker, Colleen Barrick, Mary Ellen Palko, Skyler Kuhn, Vishal N. Kopardé, Maggie Cam, Sudhirkumar Yanpallewar, Shalini Oberdoerffer, Lino Tessarollo
Software Mentions: 5
Published: over 5 years ago

10.3389/fneur.2020.528056

Oral Health, Oral Microbiota, and Incidence of Stroke-Associated Pneumonia—A Prospective Observational Study
Cited by: 14
Author(s): Fabian Cieplik, Alma Maria Wiedenhofer, Verena Pietsch, Karl‐Anton Hiller, Andreas Hiergeist, Andrea Wagner, Dobri Baldaranov, Ralf A. Linker, Jonathan Jantsch, Wolfgang Buchalla, Felix Schlachetzki, André Gessner
Software Mentions: 5
Published: about 4 years ago

10.1534/g3.120.401345

Reference Genome for the Highly Transformable Setaria viridis ME034V
Cited by: 30
Author(s): Peter Thielen, Amanda L. Pendleton, Robert A. Player, Kenneth V. Bowden, Thomas J. Lawton, Jennifer H. Wisecaver
Software Mentions: 5
Published: about 4 years ago

10.3389/fmicb.2020.01075

Depth-Differentiation and Seasonality of Planktonic Microbial Assemblages in the Monterey Bay Upwelling System
Cited by: 18
Author(s): Linta Reji, Bradley B. Tolar, Francisco P. Chávez, Christopher A. Francis
Software Mentions: 5
Published: over 4 years ago

10.1084/jem.20171738

A broad atlas of somatic hypermutation allows prediction of activation-induced deaminase targets
Cited by: 75
Author(s): Ángel F. Álvarez-Prado, Pablo Pérez-Durán, Arantxa Pérez-García, Alberto Benguría, Carlos Torroja, Virginia G. de Yébenes, Almudena R. Ramiro
Software Mentions: 5
Published: almost 7 years ago

10.3389/fmicb.2019.02095

A Metabarcoding Analysis of the Mycobiome of Wheat Ears Across a Topographically Heterogeneous Field
Cited by: 13
Author(s): Gabriele Schiro, Pierluigi Colangeli, Marina Müller
Software Mentions: 5
Published: about 5 years ago

10.3389/fmicb.2016.00459

Characterization of the Gut Microbiome Using 16S or Shotgun Metagenomics
Cited by: 585
Author(s): Juan Jovel, Jordan Patterson, Weiwei Wang, Naomi Hotte, Sandra O’Keefe, Troy Mitchel, Troy Perry, Dina Kao, Andrew L. Mason, Karen Madsen, Gane Ka‐Shu Wong
Software Mentions: 5
Published: over 8 years ago

10.7150/ijbs.37399

Gut microbiome associated with APC gene mutation in patients with intestinal adenomatous polyps
Cited by: 38
Author(s): Sai Liang, Yan Mao, Ming Liao, Yali Xu, Ying‐Chun Chen, Xiaoliang Huang, Chuangyi Wei, Changtao Wu, Qiuyan Wang, Xiaoyan Pan, Weizhong Tang
Software Mentions: 5
Published: almost 5 years ago

10.1038/s41598-021-94761-w

Microbiome pattern of Lucilia sericata (Meigen) (Diptera: Calliphoridae) and feeding substrate in the presence of the foodborne pathogen Salmonella enterica
Cited by: 3
Author(s): Lavinia Iancu, Iulia Roxana Angelescu, Victoria Ioana Paun, Carlos Henríquez‐Castillo, Paris Lavín, Cristina Purcărea
Software Mentions: 5
Published: over 3 years ago

10.1038/s41598-021-93863-9

MYCN-induced nucleolar stress drives an early senescence-like transcriptional program in hTERT-immortalized RPE cells
Cited by: 6
Author(s): Sofia Zanotti, Suzanne Vanhauwaert, Christophe Van Neste, Volodimir Olexiouk, Jolien Van Laere, Marlies Verschuuren, Joni Van der Meulen, Liselot Mus, Kaat Durinck, Laurentijn Tilleman, Dieter Deforce, Filip Van Nieuwerburgh, Michael D. Hogarty, Bieke Decaesteker, Winnok H. De Vos, Frank Speleman
Software Mentions: 5
Published: over 3 years ago

10.3389/fpls.2020.01005

Similar Seed Composition Phenotypes Are Observed From CRISPR-Generated In-Frame and Knockout Alleles of a Soybean KASI Ortholog
Cited by: 8
Author(s): Kamaldeep S. Virdi, Madison Spencer, Adrian O. Stec, Yer Xiong, Ryan Merry, Gary J. Muehlbauer, Robert M. Stupar
Software Mentions: 5
Published: over 4 years ago

10.1534/genetics.120.303038

Genetic Associations in Four Decades of Multienvironment Trials Reveal Agronomic Trait Evolution in Common Bean
Cited by: 22
Author(s): Alice MacQueen, Jeffrey W. White, Rian Lee, Juan M. Osorno, Jeremy Schmutz, Phillip N. Miklas, James R. Myers, Phillip E. McClean, Thomas E. Juenger
Software Mentions: 5
Published: over 4 years ago

10.3389/fmicb.2020.587306

An Improved Sequencing-Based Bioinformatics Pipeline to Track the Distribution and Clonal Architecture of Proviral Integration Sites
Cited by: 4
Author(s): Nicolas Rosewick, Vincent Hahaut, Keith Durkin, Maria Artesi, Snehal D. Karpe, Jérôme Wayet, Philip Griebel, Natasa Arsic, Ambroise Marçais, Olivier Hermine, Arsène Burny, Michel Georges, Anne Van den Broeke
Software Mentions: 5
Published: about 4 years ago

10.3389/fnmol.2019.00236

Sex-Dependent Changes in miRNA Expression in the Bed Nucleus of the Stria Terminalis Following Stress
Cited by: 16
Author(s): Maria Mavrikaki, Lorena Pantano, David N. Potter, Maximilian Rogers-Grazado, Eleni Anastasiadou, Frank J. Slack, Sami S. Amr, Kerry J. Ressler, Nikolaos P. Daskalakis, Elena H. Chartoff
Software Mentions: 5
Published: about 5 years ago

10.1038/s41396-019-0584-8

Evidence for phylogenetically and catabolically diverse active diazotrophs in deep-sea sediment
Cited by: 36
Author(s): Bennett J. Kapili, Samuel E. Barnett, Daniel H. Buckley, Anne E. Dekas
Software Mentions: 5
Published: almost 5 years ago

10.3389/fnins.2021.620899

Integrated miRNA-Seq and mRNA-Seq Study to Identify miRNAs Associated With Alzheimer’s Disease Using Post-mortem Brain Tissue Samples
Cited by: 21
Author(s): Qingqin Li, Diana Cai
Software Mentions: 5
Published: over 3 years ago

10.1128/mSystems.01306-20

Cultivating the Bacterial Microbiota of Populus Roots
Cited by: 12
Author(s): Dana L. Carper, David J. Weston, Aditya Barde, Collin M. Timm, Tse-Yuan S. Lu, Leah H. Burdick, Sara Jawdy, Dawn M. Klingeman, Michael S. Robeson, Allison M. Veach, Melissa Cregger, Udaya C. Kalluri, Christopher W. Schadt, Mircea Podar, Mitchel J. Doktycz, Dale A. Pelletier
Software Mentions: 5
Published: over 3 years ago

10.1128/mSystems.00471-20

Press Disturbance Alters Community Structure and Assembly Mechanisms of Bacterial Taxa and Functional Genes in Mesocosm-Scale Bioreactors
Cited by: 14
Author(s): Ezequiel Santillan, Florentin Constancias, Stefan Wuertz
Software Mentions: 4
Published: about 4 years ago

10.1038/s41598-021-85909-9

Elucidation of Japanese pepper (Zanthoxylum piperitum De Candolle) domestication using RAD-Seq
Cited by: 7
Author(s): Maddumage Dona Ginushika Priyadarshani Premarathne, Nami Fukutome, Kazuaki Yamasaki, Fumiyo Hayakawa, Atsushi J. Nagano, Hisataka Mizuno, Nobuo Ibaragi, Yukio Nagano
Software Mentions: 4
Published: over 3 years ago

10.3389/fpls.2018.00902

Functional Microbial Features Driving Community Assembly During Seed Germination and Emergence
Cited by: 74
Author(s): Gloria Torres-Cortés, Sophie Bonneau, Olivier Bouchez, Clémence Genthon, Martial Briand, Marie‐Agnès Jacques, Matthieu Barret
Software Mentions: 4
Published: over 6 years ago

10.1038/s41598-021-84691-y

Gene expression for secondary metabolite biosynthesis in hop (Humulus lupulus L.) leaf lupulin glands exposed to heat and low-water stress
Cited by: 12
Author(s): Renée L. Eriksen, Lillian K. Padgitt-Cobb, M. Shaun Townsend, Jimmy C. Henning
Software Mentions: 4
Published: over 3 years ago

10.3389/fpls.2020.01003

The MADS-Box Gene MdDAM1 Controls Growth Cessation and Bud Dormancy in Apple
Cited by: 33
Author(s): Mirko Moser, Elisa Asquini, Giulia Valentina Miolli, Kathleen Weigl, Magda‐Viola Hanke, Henryk Flachowsky, Azeddine Si‐Ammour
Software Mentions: 4
Published: over 4 years ago

10.3390/jof7030194

The Banana Root Endophytome: Differences between Mother Plants and Suckers and Evaluation of Selected Bacteria to Control Fusarium oxysporum f.sp. cubense
Cited by: 23
Author(s): Carmen Gómez-Lama Cabanás, Antonio José Fernández-González, Martina Cardoni, Antonio Valverde-Corredor, Javier López-Cepero Borrego, Manuel Fernández‐López, Jesús Mercado‐Blanco
Software Mentions: 4
Published: over 3 years ago

10.1038/s41598-020-77907-0

Integrated analyses of the microbiological, immunological and ontological transitions in the calf ileum during early life
Cited by: 6
Author(s): Tamsin Lyons, Hanne Jahns, Joseph Brady, Eóin O’Hara, Sinéad M. Waters, David A. Kenny, Evelyn Doyle, Kieran G. Meade
Software Mentions: 4
Published: almost 4 years ago

10.1155/2018/1243858

Characterization of Transcription Termination-Associated RNAs: New Insights into their Biogenesis, Tailing, and Expression in Primary Tumors
Cited by: 4
Author(s): Ilaria Laudadio, Sara Formichetti, Silvia Gioiosa, Filippos Klironomos, Nikolaus Rajewsky, Giuseppe Macino, Claudia Carissimi, Valerio Fulci
Software Mentions: 4
Published: almost 7 years ago

10.1038/s41598-020-77028-8

PRMT1 inhibition induces differentiation of colon cancer cells
Cited by: 19
Author(s): A.N. Plotnikov, Noga Kozer, Galit Cohen, Sílvia Carvalho, Shirly Duberstein, Ofir Almog, Leonardo J. Solmesky, Khriesto A. Shurrush, Ilana Babaev, Benjamin Schwessinger, Shlomit Gilad, Meital Kupervaser, Yishai Levin, Michael Gershovits, Danny Ben-Avraham, Haim Barr
Software Mentions: 4
Published: about 4 years ago

10.1038/s41598-020-75999-2

Loss of PHF6 leads to aberrant development of human neuron-like cells
Cited by: 2
Author(s): Anna Fliedner, Anne Gregor, Fulvia Ferrazzi, Arif B. Ekici, Heinrich Sticht, Christiane Zweier
Software Mentions: 4
Published: about 4 years ago

10.1186/s12711-016-0257-2

Fine mapping of a QTL on bovine chromosome 6 using imputed full sequence data suggests a key role for the group-specific component (GC) gene in clinical mastitis and milk production
Cited by: 31
Author(s): Harald Olsen, Tim Martin Knutsen, Anna Lewandowska-Sabat, Harald Grove, Torfinn Nome, Mathias Tiedemann Svendsen, Mariann Árnyasi, Marte Sodeland, Kristil Kindem Sundsaasen, Sandra Rinne Dahl, B. Heringstad, Hanne Hellerud Hansen, I. Olsaker, Matthew Kent, Sigbjørn Lien
Software Mentions: 4
Published: about 8 years ago

10.1534/g3.119.400413

The Genome Sequence of the Eastern Woodchuck (Marmota monax) – A Preclinical Animal Model for Chronic Hepatitis B
Cited by: 13
Author(s): Tyler Alioto, Fernando Cruz, Jèssica Gómez-Garrido, Miriam Triyatni, Marta Gut, Leonor Frías, Anna Esteve‐Codina, Stephan Menne, Anna Kiialainen, Nadine Kumpesa, Fabian Birzele, Roland Schmucki, Ivo Gut, Olivia Spleiss
Software Mentions: 4
Published: almost 5 years ago

10.3390/genes12091337

The Tomato ddm1b Mutant Shows Decreased Sensitivity to Heat Stress Accompanied by Transcriptional Alterations
Cited by: 4
Author(s): Prashant Kumar Singh, Golan Miller, Adi Faigenboim, Michal Lieberman‐Lazarovich
Software Mentions: 4
Published: about 3 years ago

10.3389/fmicb.2021.666936

Description of Microbial Communities of Phosphate Mine Wastes in Morocco, a Semi-Arid Climate, Using High-Throughput Sequencing and Functional Prediction
Cited by: 5
Author(s): Najoua Mghazli, Laila Sbabou, Rachid Hakkou, Ahmed Ouhammou, Mariam El Adnani, Odile Bruneel
Software Mentions: 4
Published: over 3 years ago

10.7150/ijbs.60674

Ailanthus Altissima-derived Ailanthone enhances Gastric Cancer Cell Apoptosis by Inducing the Repression of Base Excision Repair by Downregulating p23 Expression
Cited by: 7
Author(s): Chunming Wang, Hua-Fu Li, Xiaokun Wang, Wu-Guo Li, Shan Qiao, Xing Xiao, Tong Hao, Wei Chen, Yawei Zhang, Haiyong Zhang, Wei Wu, Zhenran Hu, Guochao Zhao, Mingyu Huo, Yulong He, Changhua Zhang
Software Mentions: 4
Published: almost 4 years ago

10.3389/fmicb.2016.02067

Fine Spatial Scale Variation of Soil Microbial Communities under European Beech and Norway Spruce
Cited by: 72
Author(s): Heiko Nacke, Kezia Goldmann, Ingo Schöning, Birgit Pfeiffer, Kristin Kaiser, Genis Castillo-Villamizar, Marion Schrumpf, François Buscot, Rolf Daniel, Tesfaye Wubet
Software Mentions: 4
Published: almost 8 years ago

10.3389/fmicb.2016.00603

Single-Cell (Meta-)Genomics of a Dimorphic Candidatus Thiomargarita nelsonii Reveals Genomic Plasticity
Cited by: 22
Author(s): Beverly E. Flood, Palmer Fliss, Daniel S. Jones, Gregory J. Dick, Sunit Jain, Anne‐Kristin Kaster, Matthias Winkel, Marc Mußmann, Jake V. Bailey
Software Mentions: 4
Published: over 8 years ago

10.3389/fmicb.2020.01012

The Gene Catalog and Comparative Analysis of Gut Microbiome of Big Cats Provide New Insights on Panthera Species
Cited by: 7
Author(s): Parul Mittal, Rituja Saxena, Atul Gupta, Shruti Mahajan, Vineet K. Sharma
Software Mentions: 4
Published: over 4 years ago

10.3389/fonc.2020.556497

Landscape of N6-Methyladenosine Modification Patterns in Human Ameloblastoma
Cited by: 19
Author(s): Xing Niu, Jun Xu, Jinwen Liu, Lijie Chen, Xue Qin, Ming Zhong
Software Mentions: 4
Published: about 4 years ago

10.1038/s41598-021-90863-7

Artificial neural network analysis of microbial diversity in the central and southern Adriatic Sea
Cited by: 12
Author(s): Danijela Šantić, Kasia Piwosz, Frano Matić, Ana Vrdoljak Tomaš, Jasna Arapov, Jason Dean, Mladen Šolić, Michal Koblížek, Grozdan Kušpilić, Stefanija Šestanović
Software Mentions: 4
Published: over 3 years ago

10.3389/fonc.2019.00079

Time to Treatment Prediction in Chronic Lymphocytic Leukemia Based on New Transcriptional Patterns
Cited by: 8
Author(s): Adrián Mosquera Orgueira, Beatriz Antelo Rodríguez, Natalia Alonso Vence, Ángeles Bendaña López, José Ángel Díaz Arias, Nicolas Varela, Marta Sonia González Pérez, Manuel Pérez‐Encinas, José Luis Bello López
Software Mentions: 4
Published: almost 6 years ago

10.3389/fonc.2021.653902

Fucoidan Inhibits the Progression of Hepatocellular Carcinoma via Causing lncRNA LINC00261 Overexpression
Cited by: 10
Author(s): Danhui Ma, Jiayi Wei, Sinuo Chen, Heming Wang, Ning Lv, Shihua Luo, Chieh-Lun Liu, Guangqi Song, Qunyan Yao
Software Mentions: 4
Published: over 3 years ago

10.1128/mSystems.00607-19

Carbon Assimilation Strategies in Ultrabasic Groundwater: Clues from the Integrated Study of a Serpentinization-Influenced Aquifer
Cited by: 16
Author(s): Lauren M. Seyler, William J. Brazelton, Craig McLean, Lindsay I. Putman, Alex Hyer, M. D. Kubo, Tori M. Hoehler, D. Cardace, M. O. Schrenk
Software Mentions: 4
Published: over 4 years ago

10.3389/fphar.2020.00604

Distinct Responses of Gut Microbiota to Jian-Pi-Yi-Shen Decoction Are Associated With Improved Clinical Outcomes in 5/6 Nephrectomized Rats
Cited by: 14
Author(s): Lin Zheng, Shuo Chen, Fochang Wang, Shiying Huang, Xinhui Liu, Xiaotao Yang, Haokui Zhou, Guoping Zhao, Mingjing Luo, Shunmin Li, Jianping Chen
Software Mentions: 4
Published: over 4 years ago

10.1128/mSphere.00451-20

Assessing the Variation within the Oral Microbiome of Healthy Adults
Cited by: 43
Author(s): Jacob T. Nearing, Vanessa DeClercq, Johan Van Limbergen, Morgan G. I. Langille
Software Mentions: 4
Published: about 4 years ago

10.3389/fphys.2020.588313

High Throughput Sequencing of MicroRNA in Rainbow Trout Plasma, Mucus, and Surrounding Water Following Acute Stress
Cited by: 21
Author(s): Heather Ikert, Michael Lynch, Andrew C. Doxey, John P. Giesy, Mark R. Servos, Barbara A. Katzenback, Paul M. Craig
Software Mentions: 4
Published: almost 4 years ago

10.1128/mSphere.00354-20

Light and Primary Production Shape Bacterial Activity and Community Composition of Aerobic Anoxygenic Phototrophic Bacteria in a Microcosm Experiment
Cited by: 14
Author(s): Kasia Piwosz, Ana Vrdoljak, Thijs Frenken, Juan Manuel González‐Olalla, Danijela Šantić, R. Michael L. McKay, Kristian Spilling, Louis Guttman, Petr Znachor, Izabela Mujakić, Lívia Kolesár Fecskeová, Luca Zoccarato, Martina Hanusová, Andrea Pessina, Tom Reich, Hans‐Peter Grossart, Michal Koblížek
Software Mentions: 4
Published: about 4 years ago

10.1128/mSphere.00160-20

An Extensive Meta-Metagenomic Search Identifies SARS-CoV-2-Homologous Sequences in Pangolin Lung Viromes
Cited by: 43
Author(s): Lamia Wahba, Nikhil Jain, Andrew Fire, Massa J. Shoura, Karen L. Artiles, Matthew J. McCoy, Dae‐Eun Jeong
Software Mentions: 4
Published: over 4 years ago

10.3389/fpls.2021.643137

Nepenthes × ventrata Transcriptome Profiling Reveals a Similarity Between the Evolutionary Origins of Carnivorous Traps and Floral Organs
Cited by: 4
Author(s): А. В. Щенникова, Alexey V. Beletsky, M. A. Filyushin, М. А. Слугина, Eugeny V. Gruzdev, Andrey V. Mardanov, Е. З. Кочиева, Н. В. Равин
Software Mentions: 4
Published: over 3 years ago

10.3389/fpls.2019.00235

Cold-Dependent Expression and Alternative Splicing of Arabidopsis Long Non-coding RNAs
Cited by: 49
Author(s): Cristiane P. G. Calixto, Nikoleta A. Τzioutziou, Allan B. James, Csaba Hornyik, Wenbin Guo, Runxuan Zhang, Hugh G. Nimmo, John W. Brown
Software Mentions: 4
Published: over 5 years ago

10.3389/fpls.2021.653183

Transcriptome Analysis of Tetraploid and Octoploid Common Reed (Phragmites australis)
Cited by: 5
Author(s): Cui Wang, Tong Wang, Meiqi Yin, Franziska Eller, Lele Liu, Hans Brix, Weihua Guo
Software Mentions: 4
Published: over 3 years ago

10.1128/mBio.02504-18

The Major RNA-Binding Protein ProQ Impacts Virulence Gene Expression in Salmonella enterica Serovar Typhimurium
Cited by: 73
Author(s): Alexander J. Westermann, Elisa Venturini, Mikael E. Sellin, Konrad U. Förstner, Wolf‐Dietrich Hardt, Jörg Vogel
Software Mentions: 4
Published: over 5 years ago

10.1038/s41398-017-0050-1

Gene expression associated with PTSD in World Trade Center responders: An RNA sequencing study
Cited by: 56
Author(s): Pei‐Fen Kuan, Monika A. Waszczuk, Roman Kotov, Sean Clouston, Xiaohua Yang, Prashant Singh, Sean T. Glenn, Eduardo Cortes Gomez, Jianmin Wang, Evelyn J. Bromet, Benjamin J. Luft
Software Mentions: 4
Published: almost 7 years ago

10.1016/j.stemcr.2020.05.007

Modeling and Rescue of RP2 Retinitis Pigmentosa Using iPSC-Derived Retinal Organoids
Cited by: 100
Author(s): Amelia Lane, Katarina Jovanović, Ciara Shortall, Daniele Ottaviani, Anna Brugulat Panes, Nele Schwarz, Rosellina Guarascio, Matthew J. Hayes, Arpad Palfi, Naomi Chadderton, G. Jane Farrar, Alison J. Hardcastle, Michael E. Cheetham
Software Mentions: 4
Published: over 4 years ago

10.1002/mbo3.964

Microbial composition of enigmatic bird parasites: Wolbachia and Spiroplasma are the most important bacterial associates of quill mites (Acariformes: Syringophilidae)
Cited by: 7
Author(s): Eliza Głowska, Zuzanna Karolina Filutowska, Mirosława Dabert, Michael Gerth
Software Mentions: 4
Published: over 4 years ago

10.1186/s12915-019-0677-x

Impact of genome architecture on the functional activation and repression of Hox regulatory landscapes
Cited by: 19
Author(s): Eddie Rodríguez-Carballo, Lucille Lopez-Delisle, Nayuta Yakushiji-Kaminatsui, Asier Ullate-Agote, Denis Duboule
Software Mentions: 4
Published: over 5 years ago

10.3389/fbioe.2015.00028

G-CNV: A GPU-Based Tool for Preparing Data to Detect CNVs with Read-Depth Methods
Cited by: 8
Author(s): Andrea Manconi, Elias Manca, Marco Moscatelli, Matteo Gnocchi, Alessandro Orro, Giuliano Armano, Luciano Milanesi
Software Mentions: 4
Published: over 9 years ago

10.3389/fbioe.2020.00155

Multiple Small RNAs Interact to Co-regulate Ethanol Tolerance in Zymomonas mobilis
Cited by: 9
Author(s): Richou Han, Katie Haning, Juan C. Gonzalez-Rivera, Yongqiang Yang, Runxia Li, Seung Hee Cho, Ju Huang, Bobi A. Simonsen, Shihui Yang, Lydia M. Contreras
Software Mentions: 4
Published: over 4 years ago

10.1186/s12864-019-5667-4

Postovulatory maternal transcriptome in Atlantic salmon and its relation to developmental potential of embryos
Cited by: 8
Author(s): Teshome Tilahun Bizuayehu, Maren Mommens, Arvind Sundaram, Anusha K. S. Dhanasiri, Igor Babiak
Software Mentions: 4
Published: over 5 years ago

10.1186/s12864-018-5016-z

Nascent RNA sequencing analysis provides insights into enhancer-mediated gene regulation
Cited by: 49
Author(s): Jing Wang, Yue Zhao, Xiaofan Zhou, Scott W. Hiebert, Qi Liu, Yu Shyr
Software Mentions: 4
Published: about 6 years ago

10.1111/1751-7915.13496

Preventive antibiotic treatment of calves: emergence of dysbiosis causing propagation of obese state‐associated and mobile multidrug resistance‐carrying bacteria
Cited by: 15
Author(s): Dorota A. Dobrzanska, Matthew T F Lamaudière, Jess Rollason, Lauren Acton, Michael Duncan, Sharon Compton, John Simms, Gareth D. Weedall, Igor Y. Morozov
Software Mentions: 4
Published: about 5 years ago

10.12688/f1000research.10571.2

Comprehensive comparison of Pacific Biosciences and Oxford Nanopore Technologies and their applications to transcriptome analysis
Cited by: 332
Author(s): Jason L. Weirather, Mariateresa de Cesare, Yunhao Wang, Paolo Piazza, Vittorio Sebastiano, Xiu‐Jie Wang, David Buck, Kin Fai Au
Software Mentions: 4
Published: over 7 years ago

10.1111/eva.12979

Estimating the contribution of Greenland Halibut (Reinhardtius hippoglossoides) stocks to nurseries by means of genotyping‐by‐sequencing: Sex and time matter
Cited by: 16
Author(s): Emilie Carrier, Anne‐Laure Ferchaud, Éric Normandeau, Pascal Sirois, Louis Bernatchez
Software Mentions: 4
Published: over 4 years ago

10.1038/s41598-020-65638-1

Genomic analyses of early responses to radiation in glioblastoma reveal new alterations at transcription, splicing, and translation levels
Cited by: 11
Author(s): Saket Choudhary, Suzanne Perea Burns, Hoda Mirsafian, Wenzheng Li, Dat T. Vo, Mu Qiao, Xiufen Lei, Andrew D. Smith, Luiz O. F. Penalva
Software Mentions: 4
Published: over 4 years ago

10.26508/lsa.201800080

RNase E cleavage shapes the transcriptome ofRhodobacter sphaeroidesand strongly impacts phototrophic growth
Cited by: 20
Author(s): Konrad U. Förstner, Carina M. Reuscher, Kerstin Haberzettl, Lennart Weber, Gabriele Klug
Software Mentions: 4
Published: over 6 years ago

10.26508/lsa.201900303

Rate of brain aging and APOE ε4 are synergistic risk factors for Alzheimer’s disease
Cited by: 10
Author(s): Christin Glorioso, Andreas R. Pfenning, Sam S Lee, David A. Bennett, Etienne Sibille, M Kellis, Leonard Guarente
Software Mentions: 4
Published: over 5 years ago

10.3390/antiox10020323

Antioxidant Effect of a Probiotic Product on a Model of Oxidative Stress Induced by High-Intensity and Duration Physical Exercise
Cited by: 17
Author(s): Maravillas Sánchez-Macarro, Vicente Ávila-Gandía, Silvia Pérez-Piñero, Fernando Cánovas, Ana María García-Muñoz, María Salud Abellán-Ruiz, Desirée Victoria-Montesinos, Antonio J. Luque-Rubia, Eric Climent, Salvador Genovés, Daniel Ramón, Empar Chenoll, Francisco Javier López-Román
Software Mentions: 4
Published: over 3 years ago

10.1038/s41598-019-53892-x

Performance assessment of total RNA sequencing of human biofluids and extracellular vesicles
Cited by: 46
Author(s): Celine Everaert, Hetty Helsmoortel, Anneleen Decock, Eva Hulstaert, Ruben Van Paemel, Kimberly Verniers, Justine Nuytens, Jasper Anckaert, Nele Nijs, Joeri Tulkens, Bert Dhondt, An Hendrix, Pieter Mestdagh, Jo Vandesompele
Software Mentions: 4
Published: almost 5 years ago

10.1186/s12864-016-2973-y

Transcriptome analysis of seed dormancy after rinsing and chilling in ornamental peaches (Prunus persica (L.) Batsch)
Cited by: 15
Author(s): Kanjana Worarad, Tomohiro Suzuki, Kazuo Ishii, Toshinori Kozaki, Masayuki Iigo, Kenji Yamane
Software Mentions: 4
Published: over 8 years ago

10.1371/journal.pone.0143496

Human Breast Milk miRNA, Maternal Probiotic Supplementation and Atopic Dermatitis in Offspring
Cited by: 56
Author(s): Melanie Rae Simpson, Gaute Brede, Jostein Johansen, Roar Johnsen, Ola Storrø, Pål Sætrom, Torbjørn Øien
Software Mentions: 4
Published: almost 9 years ago

10.26508/lsa.202000961

A role for condensin in mediating transcriptional adaptation to environmental stimuli
Cited by: 4
Author(s): Lucy Lancaster, Harshil Patel, Gavin Kelly, Frank Uhlmann
Software Mentions: 4
Published: over 3 years ago

10.1038/s41598-019-42865-9

Differences in resource use lead to coexistence of seed-transmitted microbial populations
Cited by: 15
Author(s): Gloria Torres-Cortés, Benjamin J. Garcia, Stéphane Compant, Samir Rezki, Piet Jones, Anne Préveaux, Martial Briand, Alain Roulet, Olivier Bouchez, Daniel Jacobson, Matthieu Barret
Software Mentions: 4
Published: over 5 years ago

Projects: pypi: cutadapt

Papers Mentioning cutadapt 1,562