pypi: cutadapt | Projects | Ecosyste.ms: Papers

10.1371/journal.pone.0126321

Leveraging the Power of High Performance Computing for Next Generation Sequencing Data Analysis: Tricks and Twists from a High Throughput Exome Workflow
Cited by: 36
Author(s): Amit Kawalia, Susanne Motameny, Stephan Wonczak, Holger Thiele, Lech Nieroda, Kamel Jabbari, Stefan Borowski, Vishal Sinha, Wilfried Gunia, Ulrich Lang, Viktor Achter, Peter Nürnberg
Software Mentions: 5
Published: over 11 years ago

10.1002/pld3.239

N6‐methyladenosine and RNA secondary structure affect transcript stability and protein abundance during systemic salt stress in Arabidopsis
Cited by: 35
Author(s): Marianne C. Kramer, Kevin A. Janssen, Kyle Palos, Andrew D. L. Nelson, Lee E. Vandivier, Benjamin A. García, Eric Lyons, Mark A. Beilstein, Brian D. Gregory
Software Mentions: 5
Published: about 6 years ago

10.1002/pld3.220

Identification of nodulation‐related genes in Medicago truncatula using genome‐wide association studies and co‐expression networks
Cited by: 4
Author(s): Jean Michel Michno, Junqi Liu, Joseph Jeffers, Robert M. Stupar, Chad L. Myers
Software Mentions: 5
Published: over 6 years ago

10.1186/s40478-017-0414-z

Serum microRNA miR-501-3p as a potential biomarker related to the progression of Alzheimer’s disease
Cited by: 118
Author(s): Norikazu Hara, Masataka Kikuchi, Akinori Miyashita, Hiroyuki Hatsuta, Yuko Saito, Kensaku Kasuga, Shigeo Murayama, Takeshi Ikeuchi, Ryozo Kuwano
Software Mentions: 5
Published: over 9 years ago

10.1371/journal.pone.0154722

Genome Sequencing and Comparative Analysis of Saccharomyces cerevisiae Strains of the Peterhof Genetic Collection
Cited by: 14
Author(s): Polina Drozdova, О. В. Тарасов, Andrew G. Matveenko, Elina A. Radchenko, Julia V. Sopova, Dmitrii E. Polev, Sergey G. Inge-Vechtomov, Pavel Dobrynin
Software Mentions: 5
Published: over 10 years ago

10.3390/microorganisms9040854

Changes in Gut Microbiota Correlates with Response to Treatment with Probiotics in Patients with Atopic Dermatitis. A Post Hoc Analysis of a Clinical Trial
Cited by: 15
Author(s): Eric Climent, Juan F. Martínez-Blanch, Laura Llobregat, Beatriz Ruzafa-Costas, Miguel A Carrión-Gutiérrez, A. Ramírez-Boscá, David Prieto‐Merino, Salvador Genovés, Francisco M. Codoñer, Daniel Ramón, Empar Chenoll, Vicente Navarro-López
Software Mentions: 5
Published: over 5 years ago

10.3390/v13081647

Monitoring SARS-CoV-2 Populations in Wastewater by Amplicon Sequencing and Using the Novel Program SAM Refiner
Cited by: 25
Author(s): Devon A. Gregory, Chris G. Wieberg, Jeff Wenzel, Chung‐Ho Lin, Marc C. Johnson
Software Mentions: 5
Published: about 5 years ago

10.3390/microorganisms9040845

Impact of Chronic Exposure to Sublethal Doses of Glyphosate on Honey Bee Immunity, Gut Microbiota and Infection by Pathogens
Cited by: 29
Author(s): Loreley Castelli, Sofía Balbuena, Belén Branchiccela, Pablo Zunino, Joanito Liberti, Philipp Engel, Karina Antúnez
Software Mentions: 5
Published: over 5 years ago

10.3390/microorganisms9040754

Active Rumen Bacterial and Protozoal Communities Revealed by RNA-Based Amplicon Sequencing on Dairy Cows Fed Different Diets at Three Physiological Stages
Cited by: 8
Author(s): Lucia Bailoni, Lisa Carraro, Marco Cardin, Barbara Cardazzo
Software Mentions: 5
Published: over 5 years ago

10.3390/microorganisms9030606

Disproportionate CH4 Sink Strength from an Endemic, Sub-Alpine Australian Soil Microbial Community
Cited by: 1
Author(s): Marshall D. McDaniel, Marcela Hernández, Marc G. Dumont, Lachlan J. Ingram, Mark A. Adams
Software Mentions: 5
Published: over 5 years ago

10.3390/microorganisms9071374

The Microbiome Associated with the Reef Builder Neogoniolithon sp. in the Eastern Mediterranean
Cited by: 2
Author(s): Shany Gefen-Treves, Alexander Bartholomäus, Fabian Horn, Adam Boleslaw Zaborowski, Dan Tchernov, Dirk Wagner, Aharon Oren, Aaron Kaplan
Software Mentions: 5
Published: about 5 years ago

10.1002/mbo3.1133

A low‐cost pipeline for soil microbiome profiling
Cited by: 5
Author(s): Anita Bollmann‐Giolai, Michael Giolai, Darren Heavens, Iain C. Macaulay, Jacob G. Malone, Matt Clark
Software Mentions: 5
Published: almost 6 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 12 years ago

10.1016/j.isci.2021.102847

High glucose macrophage exosomes enhance atherosclerosis by driving cellular proliferation & hematopoiesis
Cited by: 25
Author(s): Laura Bouchareychas, Phat Duong, Tuan Anh Phu, Eric Alsop, Bessie Meechoovet, Rebecca Reiman, M. Ng, Ryō Yamamoto, Hiromitsu Nakauchi, Warren J. Gasper, Kendall Van Keuren‐Jensen, Robert L. Raffaı̈
Software Mentions: 5
Published: about 5 years ago

10.3390/curroncol28040214

Targeted Next-Generation Sequencing of Circulating Tumor DNA Mutations among Metastatic Breast Cancer Patients
Cited by: 1
Author(s): Ming Sun, Fangqin Lin, Lu-Jia Chen, Hong Li, Wei‐De Lin, Hongwu Du, Xiaobo Yang, Ming Li
Software Mentions: 5
Published: about 5 years ago

10.3390/ijms22041989

Transcriptome Analysis of Subcutaneous Adipose Tissue from Severely Obese Patients Highlights Deregulation Profiles in Coding and Non-Coding Oncogenes
Cited by: 5
Author(s): Federica Rey, Letizia Messa, Cecilia Pandini, Rossella Launi, Bianca Barzaghini, Giancarlo Micheletto, Manuela Teresa Raimondi, Simona Bertoli, Cristina Cereda, Gian Vincenzo Zuccotti, Raffaella Cancello, Stephana Carelli
Software Mentions: 5
Published: over 5 years ago

10.3390/microorganisms8060868

Temporal Dynamics of the Gut Bacteriome and Mycobiome in the Weanling Pig
Cited by: 34
Author(s): Ann M. Arfken, Juli Foster Frey, Katie Lynn Summers
Software Mentions: 5
Published: over 6 years ago

10.7554/eLife.39800

Plasmodium-specific atypical memory B cells are short-lived activated B cells
Cited by: 42
Author(s): Damián Pérez‐Mazliah, Peter J. Gardner, Edina Schweighoffer, Sarah McLaughlin, Caroline Hosking, Irene Tumwine, Randall S. Davis, Alexandre J. Potocnik, Victor L. J. Tybulewicz, Jean Langhorne
Software Mentions: 5
Published: almost 8 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: about 7 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: almost 12 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 7 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: over 6 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: almost 6 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 10 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 9 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: about 5 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 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: about 9 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 11 years ago

10.7554/eLife.32332

Evolution and cell-type specificity of human-specific genes preferentially expressed in progenitors of fetal neocortex
Cited by: 131
Author(s): Marta Florio, Michael Heide, Anneline Pinson, Holger Brandl, Mareike Albert, Sylke Winkler, Pauline Wimberger, Wieland B. Huttner, Michael Hiller
Software Mentions: 5
Published: over 8 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 7 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: about 9 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: about 6 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: almost 6 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: almost 6 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 9 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 5 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: almost 7 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: over 12 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 7 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 6 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 5 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 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 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 7 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: almost 7 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 5 years ago

10.1371/journal.pgen.1007406

Systematic identification of factors mediating accelerated mRNA degradation in response to changes in environmental nitrogen
Cited by: 101
Author(s): Darach Miller, Nathan Brandt, David Gresham
Software Mentions: 5
Published: over 8 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 6 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: about 7 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 10 years ago

10.1186/s40303-016-0017-9

αT-catenin in restricted brain cell types and its potential connection to autism
Cited by: 20
Author(s): Stephen Sai Folmsbee, Douglas R. Wilcox, Koen Tyberghein, Pieter De Bleser, Warren G. Tourtellotte, Jolanda van Hengel, Frans van Roy, Cara J. Gottardi
Software Mentions: 4
Published: about 10 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 7 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 8 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 5 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: almost 7 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 6 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: over 8 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: about 8 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: over 5 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 7 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 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: about 10 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 11 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 5 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 6 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: over 9 years ago

10.7554/eLife.47891

Epimutations are associated with CHROMOMETHYLASE 3-induced de novo DNA methylation
Cited by: 54
Author(s): Jered M. Wendte, Yinwen Zhang, Lexiang Ji, Xiulin Shi, Rashmi R. Hazarika, Yadollah Shahryary, Frank Johannes, Robert J. Schmitz
Software Mentions: 4
Published: about 7 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: about 6 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 6 years ago

10.1371/journal.pone.0236540

Harnessing the power of eDNA metabarcoding for the detection of deep-sea fishes
Cited by: 38
Author(s): Beverly McClenaghan, Nicole A Fahner, David Côté, Julek Chawarski, Avery McCarthy, Hoda Rajabi, Gregory A. C. Singer, Mehrdad Hajibabaei
Software Mentions: 4
Published: almost 6 years ago

10.1002/ece3.1720

The transcriptomic and evolutionary signature of social interactions regulating honey bee caste development
Cited by: 34
Author(s): Svjetlana Vojvodic, Brian R. Johnson, Brock A. Harpur, Clement F. Kent, Amro Zayed, Kirk E. Anderson, Timothy A. Linksvayer
Software Mentions: 4
Published: almost 11 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: almost 6 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: about 6 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 9 years ago

10.1002/ece3.3976

Brain gene expression analyses in virgin and mated queens of fire ants reveal mating-independent and socially regulated changes
Cited by: 14
Author(s): Travis L. Calkins, Mei Er Chen, Arinder K. Arora, Chloë Hawkings, Cécilia Tamborindeguy, Patricia V. Pietrantonio
Software Mentions: 4
Published: over 8 years ago

10.1002/ece3.4559

Table for five, please: Dietary partitioning in boreal bats
Cited by: 62
Author(s): Eero J. Vesterinen, Anna I. E. Puisto, Anna Blomberg, Thomas M. Lilley
Software Mentions: 4
Published: almost 8 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 7 years ago

10.3390/ani10040577

Improvement of Cecal Commensal Microbiome Following the Insect Additive into Chicken Diet
Cited by: 30
Author(s): Agata Józefiak, Abdelbasset Benzertiha, Bartosz Kierończyk, Anna Łukomska, Izabela Wesołowska, Mateusz Rawski
Software Mentions: 4
Published: over 6 years ago

10.1186/1471-2164-14-586

The importance of tissue specificity for RNA-seq: highlighting the errors of composite structure extractions
Cited by: 46
Author(s): Brian R. Johnson, Joel Atallah, David C. Plachetzki
Software Mentions: 4
Published: over 13 years ago

10.1186/s12864-020-07072-1

B chromosomes of multiple species have intense evolutionary dynamics and accumulated genes related to important biological processes
Cited by: 18
Author(s): Syed Farhan Ahmad, Maryam Jehangir, Adauto Lima Cardoso, Ivan Rodrigo Wolf, Vladimir Pavan Margarido, Diogo Cavalcanti Cabral-de-Mello, Rachel J. O’Neill, Guilherme Targino Valente, Cesar Martins
Software Mentions: 4
Published: almost 6 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 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 5 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 5 years ago

10.1186/1471-2164-15-221

From root to fruit: RNA-Seq analysis shows that arbuscular mycorrhizal symbiosis may affect tomato fruit metabolism
Cited by: 119
Author(s): Inès Zouari, Alessandra Salvioli, Matteo Chialva, Mara Novero, Laura Miozzi, Gian Carlo Tenore, Paolo Bagnaresi, Paola Bonfante
Software Mentions: 4
Published: over 12 years ago

10.1371/journal.pone.0192947

Modulation of the peripheral blood transcriptome by the ingestion of probiotic yoghurt and acidified milk in healthy, young men
Cited by: 26
Author(s): Kathryn Burton, Grégory Pimentel, Nadine Zangger, Nathalie Vionnet, Jocelyne Drai, P. G. McTernan, François P. Pralong, Mauro Delorenzi, Guy Vergères
Software Mentions: 4
Published: over 8 years ago

10.1371/journal.pone.0204038

Shifts in ovine cardiopulmonary microRNA expression in late gestation and the perinatal period
Cited by: 3
Author(s): Ramona Krauss, Belinda Phipson, Alicia Oshlack, Nikita Prasad-Gupta, Michael Cheung, Joseph J. Smolich, Salvatore Pepe
Software Mentions: 4
Published: almost 8 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 5 years ago

10.3390/pathogens10050555

Microeukaryotic Communities on the Fruit of Gardenia thunbergia Thunb. with a Focus on Pathogenic Fungi
Cited by: 0
Author(s): Bastian Steudel, Himansu Baijnath, Thorben Schwedt, Armin O. Schmitt
Software Mentions: 4
Published: over 5 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: almost 6 years ago

10.1038/s42003-020-0813-8

Gene expression variation in the brains of harvester ant foragers is associated with collective behavior
Cited by: 16
Author(s): Daniel Friedman, Ryan A. York, Austin T. Hilliard, Deborah M. Gordon
Software Mentions: 4
Published: over 6 years ago

10.1371/journal.ppat.1009812

Mouse papillomavirus type 1 (MmuPV1) DNA is frequently integrated in benign tumors by microhomology-mediated end-joining
Cited by: 12
Author(s): Lulu Yu, Vladimır Majerčiak, Xiangyang Xue, Aayushi Uberoi, Alexei V. Lobanov, Xiongfong Chen, Maggie Cam, Stephen H. Hughes, Paul F. Lambert, Zhi-Ming Zheng
Software Mentions: 4
Published: about 5 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: almost 6 years ago

10.1242/bio.047829

Heterogeneous beta-catenin activation is sufficient to cause hepatocellular carcinoma in zebrafish
Cited by: 13
Author(s): Sharanya Maanasi Kalasekar, Srishti Kotiyal, Christopher J. Conley, Cindy Phan, Annika Young, Kimberley Evason
Software Mentions: 4
Published: over 7 years ago

10.1371/journal.pmed.1002204

The Subclonal Architecture of Metastatic Breast Cancer: Results from a Prospective Community-Based Rapid Autopsy Program “CASCADE”
Cited by: 111
Author(s): Peter Savas, Zhi L. Teo, Christophe Lefèvre, Christoffer Flensburg, Franco Caramia, Kathryn Alsop, Mariam Mansour, Prudence A. Francis, Heather Thorne, Maria João Silva, Nnennaya Kanu, Michelle Dietzen, Andrew Rowan, Maik Kschischo, Stephen B. Fox, David D.L. Bowtell, Sarah-Jane Dawson, Terence P. Speed, Charles Swanton, Sherene Loi
Software Mentions: 4
Published: over 9 years ago

10.1038/s42003-020-01214-7

Genome sequence of segmented filamentous bacteria present in the human intestine
Cited by: 20
Author(s): Hans Jonsson, Luisa W. Hugerth, John Sundh, E. Lundin, Anders F. Andersson
Software Mentions: 4
Published: about 6 years ago

10.1186/s40793-020-00364-9

Trichomes form genotype-specific microbial hotspots in the phyllosphere of tomato
Cited by: 12
Author(s): Peter Kusstatscher, Wisnu Adi Wicaksono, Alessandro Bergna, Tomislav Cernava, Nick Bergau, Alain Tissier, Bettina Hause, Gabriele Berg
Software Mentions: 4
Published: about 6 years ago

10.1371/journal.ppat.1006084

Microbial Community Composition Impacts Pathogen Iron Availability during Polymicrobial Infection
Cited by: 24
Author(s): Apollo Stacy, Nader Abraham, Peter Jorth, Marvin Whiteley
Software Mentions: 4
Published: almost 10 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 6 years ago

10.3390/v11111041

Viruses in the Invasive Hornet Vespa velutina
Cited by: 36
Author(s): Anne Dalmon, Philippe Gayral, Damien Decante, Christophe Klopp, Diane Bigot, Maxime Thomasson, Elisabeth A. Herniou, Cédric Alaux, Yves Le Conte
Software Mentions: 4
Published: almost 7 years ago

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Papers Mentioning cutadapt 1,562