pypi: cutadapt | Projects | Ecosyste.ms: Papers

10.7554/eLife.47809

Free circular introns with an unusual branchpoint in neuronal projections
Cited by: 11
Author(s): Harleen Saini, Alicia A. Bicknell, Sean R. Eddy, Melissa J. Moore
Software Mentions: 7
Published: about 6 years ago

10.7554/eLife.49874

Discovery proteomics in aging human skeletal muscle finds change in spliceosome, immunity, proteostasis and mitochondria
Cited by: 114
Author(s): Ceereena Ubaida‐Mohien, Alexey E. Lyashkov, Marta González-Freire, Ravi Tharakan, Michelle Shardell, Ruin Moaddel, Richard D. Semba, Chee W. Chia, Myriam Gorospe, Ranjan Sen, Luigi Ferrucci
Software Mentions: 7
Published: about 6 years ago

10.7554/eLife.31867

Stochastic tuning of gene expression enables cellular adaptation in the absence of pre-existing regulatory circuitry
Cited by: 16
Author(s): Peter L. Freddolino, Jiping Yang, Amir Momen-Roknabadi, Saeed Tavazoie
Software Mentions: 7
Published: over 7 years ago

10.1186/s13072-021-00415-6

Identification of tissue-specific and common methylation quantitative trait loci in healthy individuals using MAGAR
Cited by: 1
Author(s): Michael Scherer, Gilles Gasparoni, Souad Rahmouni, Tatiana I. Shashkova, Marion Arnoux, Édouard Louis, Arina Nostaeva, Diana Avalos, Emmanouil T. Dermitzakis, Yurii S. Aulchenko, Thomas Lengauer, Paul Lyons, Michel Georges, Jörn Walter
Software Mentions: 7
Published: about 4 years ago

10.1371/journal.pgen.1009587

The pluripotent stem cell-specific transcript ESRG is dispensable for human pluripotency
Cited by: 17
Author(s): Kazutoshi Takahashi, Michiko Nakamura, Chikako Okubo, Zane Kliesmete, Mari Ohnuki, Megumi Narita, Akira Watanabe, Mai Ueda, Yasuhiro Takashima, Ines Hellmann, Shinya Yamanaka
Software Mentions: 7
Published: over 4 years ago

10.1186/s40478-020-01020-6

Innate immune response in neuronopathic forms of Gaucher disease confers resistance against viral-induced encephalitis
Cited by: 7
Author(s): Sharon Melamed, Roy Avraham, Deborah E. Rothbard, Noam Erez, Tomer Israely, Ziv Klausner, Anthony H. Futerman, Nir Paran, Einat B. Vitner
Software Mentions: 7
Published: over 5 years ago

10.7554/eLife.58019

Isolation and transcriptomic analysis of Anopheles gambiae oenocytes enables the delineation of hydrocarbon biosynthesis
Cited by: 17
Author(s): Linda Grigoraki, Xavier Grau‐Bové, Henrietta Carrington Yates, Gareth Lycett, Hilary Ranson
Software Mentions: 7
Published: over 5 years ago

10.1038/s41597-021-00809-x

A multi-center cross-platform single-cell RNA sequencing reference dataset
Cited by: 14
Author(s): Xin Chen, Zujun Yang, Wanqiu Chen, Yongmei Zhao, Andrew Farmer, Bao Tran, Vyacheslav Furtak, Malcolm Moos, Wenming Xiao, Charles Wang
Software Mentions: 7
Published: almost 5 years ago

10.1038/s41598-017-16353-x

The microbiomes of blowflies and houseflies as bacterial transmission reservoirs
Cited by: 85
Author(s): Ana Carolina M. Junqueira, Aakrosh Ratan, Enzo Acerbi, Daniela I. Drautz–Moses, Balakrishnan N. V. Premkrishnan, Paul Igor Costea, Bodo Linz, Rikky W. Purbojati, Daniel F. Paulo, Nicolas E. Gaultier, Poorani Subramanian, Nur A. Hasan, Rita R. Colwell, Peer Bork, Ana Maria Lima de Azeredo-Espin, Donald A. Bryant, Stephan C. Schuster
Software Mentions: 7
Published: about 8 years ago

10.1038/s41598-017-18435-2

Ecological plasticity in the gastrointestinal microbiomes of Ethiopian Chlorocebus monkeys
Cited by: 32
Author(s): Pål Trosvik, Eli Knispel Rueness, Eric J. de Muinck, Amera Moges, Addisu Mekonnen
Software Mentions: 7
Published: almost 8 years ago

10.1038/s41419-021-04067-y

Single cell transcriptomics reveal trans-differentiation of pancreatic beta cells following inactivation of the TFIID subunit Taf4
Cited by: 6
Author(s): Thomas Kleiber, Guillaume Davidson, Gabrielle Mengus, Igor Martianov, Irwin Davidson
Software Mentions: 7
Published: over 4 years ago

10.1186/s40168-020-00869-y

Topography of the respiratory tract bacterial microbiota in cattle
Cited by: 36
Author(s): Christopher McMullen, Trevor W. Alexander, Renaud Léguillette, Matthew L. Workentine, Edouard Timsit
Software Mentions: 7
Published: over 5 years ago

10.1016/j.cmet.2018.04.013

The Polycomb-Dependent Epigenome Controls β Cell Dysfunction, Dedifferentiation, and Diabetes
Cited by: 104
Author(s): Tess Tsai-Hsiu Lu, Steffen Heyne, Erez Dror, Eduard Casas, Laura Leonhardt, Thorina Boenke, Ching‐Yao Yang, Sagar, Laura Arrigoni, Kevin Dalgaard, Raffaele Teperino, Lennart Enders, Madhan Selvaraj, Marius Ruf, Sunil Jayaramaiah Raja, Huafeng Xie, Ulrike Boenisch, Stuart H. Orkin, Francis C. Lynn, Brad G. Hoffman, Dominic Grün, Tanya Vavouri, Adelheid Lempradl, J. Andrew Pospisilik
Software Mentions: 7
Published: over 7 years ago

10.1534/g3.120.401325

Adapting Genotyping-by-Sequencing and Variant Calling for Heterogeneous Stock Rats
Cited by: 17
Author(s): Alexander F. Gileta, Jianjun Gao, Apurva S. Chitre, Hannah Bimschleger, Celine L. St. Pierre, Shyam Gopalakrishnan, Abraham A. Palmer
Software Mentions: 7
Published: over 5 years ago

10.1038/s41598-021-93509-w

Mapping the landscape of chromatin dynamics during naïve CD4+ T-cell activation
Cited by: 9
Author(s): Muhammad Munir Iqbal, Michael Serralha, Parwinder Kaur, David Martino
Software Mentions: 7
Published: over 4 years ago

10.1016/j.devcel.2017.07.002

The Helicase Aquarius/EMB-4 Is Required to Overcome Intronic Barriers to Allow Nuclear RNAi Pathways to Heritably Silence Transcription
Cited by: 59
Author(s): Alper Akay, Tomás Di Domenico, Kin Man Suen, Amena Nabih, Guillermo E. Parada, Mark Larance, Ragini Medhi, Ahmet C. Berkyurek, Xinlian Zhang, Christopher J. Wedeles, Konrad L. M. Rudolph, Jan Engelhardt, Martin Hemberg, Ping Ma, Angus I. Lamond, Julie M. Claycomb, Eric A. Miska
Software Mentions: 7
Published: over 8 years ago

10.3389/fonc.2019.00523

Comprehensive Gene Expression Analysis in NMIBC Using RNA-seq Reveals New Therapy Strategies
Cited by: 11
Author(s): Xiaoliang Chen, Fuquan Jiang, Jia Chen, Ming Liu, Yong-Hao Nan, Licheng Qu, Qingkuo Kong, Fangfang Hou, Wenshan Luo, Wanli Na, Xin Jin, Jiufeng Tan
Software Mentions: 7
Published: over 6 years ago

10.15252/embj.2020105565

The RNA polymerase II subunit RPB‐9 recruits the integrator complex to terminate Caenorhabditis elegans piRNA transcription
Cited by: 13
Author(s): Ahmet C. Berkyurek, Giulia Furlan, Lisa Lampersberger, Toni Beltran, Eva-Maria Weick, Emily Nischwitz, Isabela Cunha Navarro, Fabian Braukmann, Alper Akay, Jonathan Price, Falk Butter, Peter Sarkies, Eric A. Miska
Software Mentions: 7
Published: almost 5 years ago

10.1128/mSystems.00063-20

Genomic Analysis of Bovine Staphylococcus aureus Isolates from Milk To Elucidate Diversity and Determine the Distributions of Antimicrobial and Virulence Genes and Their Association with Mastitis
Cited by: 31
Author(s): Sohail Naushad, Diego Nobrega, Syed Ali Raza Naqvi, Herman W. Barkema, Jeroen De Buck
Software Mentions: 7
Published: over 5 years ago

10.18632/aging.203208

miRNAs generated from Meg3-Mirg locus are downregulated during aging
Cited by: 1
Author(s): Ana-Mihaela Lupan, Evelyn Gabriela Rusu, Mihai Bogdan Preda, Catalina Iolanda Marinescu, Cristina Ivan, Alexandrina Burlacu
Software Mentions: 7
Published: over 4 years ago

10.3389/fpls.2019.01246

Temporal Dynamics of the Sap Microbiome of Grapevine Under High Pierce’s Disease Pressure
Cited by: 43
Author(s): Elizabeth Deyett, Philippe E. Rolshausen
Software Mentions: 7
Published: about 6 years ago

10.1128/mSystems.00086-17

Linking Spatial Structure and Community-Level Biotic Interactions through Cooccurrence and Time Series Modeling of the Human Intestinal Microbiota
Cited by: 8
Author(s): Eric J. de Muinck, Knut E.A. Lundin, Pål Trosvik
Software Mentions: 7
Published: about 8 years ago

10.7554/eLife.49658

Nanopore direct RNA sequencing maps the complexity of Arabidopsis mRNA processing and m6A modification
Cited by: 278
Author(s): Matthew T Parker, Katarzyna Knop, Anna V. Sherwood, Nicholas J. Schurch, Katarzyna Mackinnon, Peter D Gould, Anthony Hall, Geoffrey J. Barton, Gordon G. Simpson
Software Mentions: 7
Published: almost 6 years ago

10.1371/journal.pone.0187735

Transcriptome profile of lung dendritic cells after in vitro porcine reproductive and respiratory syndrome virus (PRRSV) infection
Cited by: 16
Author(s): Maren Pröll, Christiane Neuhoff, K. Schellander, Muhammad Jasim Uddin, Mehmet Ulaş Çınar, Sudeep Sahadevan, Xuecheng Qu, M. S. Islam, Mikhaël Poirier, Marcel A. Müller, Christian Drosten, Dawit Tesfaye, Ernst Tholen, Christine Große‐Brinkhaus
Software Mentions: 7
Published: about 8 years ago

10.1038/s42003-021-02581-5

Selective feeding in Southern Ocean key grazers—diet composition of krill and salps
Cited by: 17
Author(s): Nora‐Charlotte Pauli, Katja Metfies, Evgeny A. Pakhomov, Stefan Neuhaus, Martín Graeve, Philipp Wenta, Clara M. Flintrop, Thomas H. Badewien, Morten Hvitfeldt Iversen, Bettina Meyer
Software Mentions: 7
Published: about 4 years ago

10.1111/mec.15743

The strength and form of natural selection on transcript abundance in the wild
Cited by: 9
Author(s): Freed Ahmad, Paul V. Debes, Ilkka Nousiainen, Siim Kahar, Lilian Pukk, Riho Gross, Mikhail Ozerov, Anti Vasemägi
Software Mentions: 6
Published: about 5 years ago

10.3389/fmicb.2020.571983

Large Enrichment of Anthropogenic Organic Matter Degrading Bacteria in the Sea-Surface Microlayer at Coastal Livingston Island (Antarctica)
Cited by: 12
Author(s): Alícia Martinez-Varela, Gemma Casas, Benjamı́n Piña, Jordi Dachs, Maria Vila‐Costa
Software Mentions: 6
Published: about 5 years ago

10.3389/fimmu.2018.00056

The Immune and Non-Immune Pathways That Drive Chronic Gastrointestinal Helminth Burdens in the Wild
Cited by: 20
Author(s): Simon A. Babayan, Wei Liu, Graham Hamilton, Elizabeth Kilbride, Evelyn C. Rynkiewicz, Melanie Clerc, Amy B. Pedersen
Software Mentions: 6
Published: almost 8 years ago

10.1186/s12864-019-5797-8

Concurrent and long-term associations between the endometrial microbiota and endometrial transcriptome in postpartum dairy cows
Cited by: 13
Author(s): S.G. Moore, Aaron C. Ericsson, Susanta K. Behura, W. R. Lamberson, Timothy J. Evans, Matthew S. McCabe, S.E. Poock, M.C. Lucy
Software Mentions: 6
Published: over 6 years ago

10.1111/1755-0998.13022

A DNA barcode library for 5,200 German flies and midges (Insecta: Diptera) and its implications for metabarcoding‐based biomonitoring
Cited by: 64
Author(s): Jérôme Morinière, Michael Balke, Dieter Doczkal, Matthias F. Geiger, Laura A. Hardulak, Gerhard Haszprunar, Axel Hausmann, Lars Hendrich, Ledis Regalado, Björn Rulik, Stefan Schmidt, Johann‐Wolfgang Wägele, Paul D. N. Hebert
Software Mentions: 6
Published: over 6 years ago

10.3389/fimmu.2021.651254

High Dose IFN-β Activates GAF to Enhance Expression of ISGF3 Target Genes in MLE12 Epithelial Cells
Cited by: 5
Author(s): Kensei Kishimoto, Catera L. Wilder, Justin Buchanan, Minh Anh Nguyen, Chidera Okeke, Alexander Hoffmann, Quen J. Cheng
Software Mentions: 6
Published: over 4 years ago

10.1186/s40168-021-01136-4

Longitudinal study on the effects of growth-promoting and therapeutic antibiotics on the dynamics of chicken cloacal and litter microbiomes and resistomes
Cited by: 24
Author(s): Chhedi Lal Gupta, Shlomo E. Blum, Karuppasamy Kattusamy, Tali Daniel, S. Druyan, Roni Shapira, O. Krifucks, Yan Zhu, Xinyuan Zhou, Jian‐Qiang Su, Eddie Cytryn
Software Mentions: 6
Published: over 4 years ago

10.1371/journal.pone.0252365

Fusarium graminearum DICER-like-dependent sRNAs are required for the suppression of host immune genes and full virulence
Cited by: 19
Author(s): B. Werner, Aline Koch, Ena Šečić, Jonas Engelhardt, Lukas Jelonek, Jens Steinbrenner, Karl‐Heinz Kogel
Software Mentions: 6
Published: over 4 years ago

10.1371/journal.pone.0150705

Changes in the miRNA-mRNA Regulatory Network Precede Motor Symptoms in a Mouse Model of Multiple System Atrophy: Clinical Implications
Cited by: 26
Author(s): Simon Schafferer, Rimpi Khurana, Violetta Refolo, Serena Venezia, Edith Sturm, Paolo Piatti, Clara Hechenberger, Hubert Hackl, Roman Kessler, Michaela Willi, Ronald Gstir, Anne Krogsdam, Alexandra Lusser, Werner Poewe, Gregor K. Wenning, Alexander Hüttenhofer, Nadia Stefanova
Software Mentions: 6
Published: over 9 years ago

10.1371/journal.pone.0106084

Patterns of MiRNA Expression in Arctic Charr Development
Cited by: 24
Author(s): Kalina H. Kapralova, Sigríður Rut Franzdóttir, Hákon Jónsson, Sigurður S. Snorrason, Zophonı́as O. Jónsson
Software Mentions: 6
Published: over 11 years ago

10.1002/evl3.148

Field cricket genome reveals the footprint of recent, abrupt adaptation in the wild
Cited by: 28
Author(s): Sónia Pascoal, Judith Risse, Xiao Zhang, Mark Blaxter, Timothée Cézard, Richard Challis, Karim Gharbi, John Hunt, Sujai Kumar, Emma Langan, Xuan Li, Jack G. Rayner, Michael G. Ritchie, L. Basten Snoek, Urmi Trivedi, Nathan W. Bailey
Software Mentions: 6
Published: almost 6 years ago

10.3389/fimmu.2020.00435

Egyptian Rousette IFN-ω Subtypes Elicit Distinct Antiviral Effects and Transcriptional Responses in Conspecific Cells
Cited by: 10
Author(s): Stephanie S Pavlovich, Tamarand L. Darling, Adam J. Hume, Robert A. Davey, Feng Feng, Elke Mühlberger, Thomas B. Kepler
Software Mentions: 6
Published: over 5 years ago

10.1186/s12864-020-6714-x

DolphinNext: a distributed data processing platform for high throughput genomics
Cited by: 61
Author(s): Onur Yukselen, Osman Turkyilmaz, Ahmet Öztürk, Manuel Garber, Alper Küçükural
Software Mentions: 6
Published: over 5 years ago

10.3389/fimmu.2020.00978

Pseudozyma Priming Influences Expression of Genes Involved in Metabolic Pathways and Immunity in Zebrafish Larvae
Cited by: 8
Author(s): Prabhugouda Siriyappagouder, Jorge Galindo-Villegas, Anusha K. S. Dhanasiri, Qirui Zhang, Victoriano Mulero, Viswanath Kiron, Jorge Manuel de Oliveira Fernandes
Software Mentions: 6
Published: over 5 years ago

10.3389/fcimb.2021.609160

Exogenous Coronavirus Interacts With Endogenous Retrotransposon in Human Cells
Cited by: 27
Author(s): Ying Yin, Xiaozhao Liu, Ximiao He, Li-Quan Zhou
Software Mentions: 6
Published: almost 5 years ago

10.3389/fendo.2021.626359

Metformin Strongly Affects Gut Microbiome Composition in High-Fat Diet-Induced Type 2 Diabetes Mouse Model of Both Sexes
Cited by: 25
Author(s): Laila Silamiķele, Ivars Silamiķelis, Monta Ustinova, Zane Kalniņa, Ilze Elbere, Ramona Petrovska, Ineta Kalniņa, Jānis Kloviņš
Software Mentions: 6
Published: over 4 years ago

10.1523/JNEUROSCI.1675-19.2019

Midkine-a Is Required for Cell Cycle Progression of Müller Glia during Neuronal Regeneration in the Vertebrate Retina
Cited by: 28
Author(s): Mikiko Nagashima, Travis S. D’Cruz, Antoinette Eyram Danku, Doneen Hesse, Christopher J. Sifuentes, Pamela A. Raymond, Peter F. Hitchcock
Software Mentions: 6
Published: almost 6 years ago

10.1186/s12859-019-2961-8

FastqCleaner: an interactive Bioconductor application for quality-control, filtering and trimming of FASTQ files
Cited by: 11
Author(s): Leandro Gabriel Roser, Fernán Agüero, Daniel O. Sánchez
Software Mentions: 6
Published: over 6 years ago

10.1371/journal.pgen.1008822

An Africa-wide genomic evolution of insecticide resistance in the malaria vector Anopheles funestus involves selective sweeps, copy number variations, gene conversion and transposons
Cited by: 37
Author(s): Gareth D. Weedall, Jacob M. Riveron, Jack Hearn, Helen Irving, Colince Kamdem, Caroline Fouet, Bradley J. White, Charles S. Wondji
Software Mentions: 6
Published: over 5 years ago

10.1371/journal.pgen.1009691

Induction of a chromatin boundary in vivo upon insertion of a TAD border
Cited by: 11
Author(s): Andréa Willemin, Lucille Lopez-Delisle, Christopher Chase Bolt, Marie-Laure Gadolini, Denis Duboule, Eddie Rodríguez-Carballo
Software Mentions: 6
Published: over 4 years ago

10.3390/ijms19020357

Genotyping by Sequencing Highlights a Polygenic Resistance to Ralstonia pseudosolanacearum in Eggplant (Solanum melongena L.)
Cited by: 28
Author(s): Sylvia Salgon, Morgane Raynal, Sylvain Lebon, Jean Michel Baptiste, M. C. Daunay, Jacques Dintinger, Cyril Jourda
Software Mentions: 6
Published: almost 8 years ago

10.3390/ijms20061321

Cellular Gene Expression during Hepatitis C Virus Replication as Revealed by Ribosome Profiling
Cited by: 14
Author(s): Gesche K. Gerresheim, Jochen Bathke, Audrey M. Michel, Dmitry E. Andreev, Lyudmila Shalamova, Oliver Roßbach, Pan Hu, Dieter Glebe, Markus Fricke, Manja Marz, Alexander Goesmann, Stephen J Kiniry, Pavel V. Baranov, Ivan N. Shatsky, Michael Niepmann
Software Mentions: 6
Published: over 6 years ago

10.7554/eLife.63270

Dissecting phenotypic transitions in metastatic disease via photoconversion-based isolation
Cited by: 4
Author(s): Yogev Sela, Jinyang Li, Paola Kuri, Allyson J. Merrell, Ning Li, Chris Lengner, Pantelis Rompolas, Ben Z. Stanger
Software Mentions: 6
Published: almost 5 years ago

10.1371/journal.pgen.1008546

Chromatin accessibility established by Pou5f3, Sox19b and Nanog primes genes for activity during zebrafish genome activation
Cited by: 53
Author(s): Máté Pálfy, G Schulze, Eivind Valen, Nadine L. Vastenhouw
Software Mentions: 6
Published: almost 6 years ago

10.7554/eLife.09800

Cell type-specific transcriptomics of hypothalamic energy-sensing neuron responses to weight-loss
Cited by: 177
Author(s): Fredrick E. Henry, Ken Sugino, Adam Tozer, Tiago Branco, Scott M. Sternson
Software Mentions: 6
Published: over 10 years ago

10.1007/s00248-020-01656-w

Linking Bacterial Communities Associated with the Environment and the Ecosystem Engineer Orchestia gammarellus at Contrasting Salt Marsh Elevations
Cited by: 2
Author(s): Edisa García Hernández, Matty P. Berg, A. Raoul Van Oosten, Christian Smit, Joana Falcão Salles
Software Mentions: 6
Published: almost 5 years ago

10.3389/fnbeh.2020.581296

A Probiotic Mixture Induces Anxiolytic- and Antidepressive-Like Effects in Fischer and Maternally Deprived Long Evans Rats
Cited by: 6
Author(s): Valérie Daugé, Catherine Philippe, Mahendra Mariadassou, Olivier Rué, Jean‐Charles Martin, Marie Rossignol, Nathalie Dourmap, Ljubica Svilar, Franck Tourniaire, Magali Monnoye, Déborah Jardet, Marie Bangratz, Sophie Holowacz, Sylvie Rabot, Laurent Naudon
Software Mentions: 6
Published: about 5 years ago

10.3389/fcell.2021.690167

Sex-Specific Development in Haplodiploid Honeybee Is Controlled by the Female-Embryo-Specific Activation of Thousands of Intronic LncRNAs
Cited by: 0
Author(s): Miao Wang, Dong Chen, Huoqing Zheng, Luping Zhao, Xiao‐Feng Xue, Fengyun Yu, Yu Zhang, Chao Cheng, Qingsheng Niu, Shuai Wang, Yi Zhang, Liming Wu
Software Mentions: 6
Published: over 4 years ago

10.7554/eLife.24133

Repeated losses of PRDM9-directed recombination despite the conservation of PRDM9 across vertebrates
Cited by: 103
Author(s): Zachary Baker, Molly Schumer, Yuki Haba, Lisa Bashkirova, C. D. Holland, Gil G. Rosenthal, Molly Przeworski
Software Mentions: 6
Published: over 8 years ago

10.1186/s12974-021-02230-y

The role of interferon regulatory factor 8 for retinal tissue homeostasis and development of choroidal neovascularisation
Cited by: 9
Author(s): Peipei Zhang, Anja Schlecht, Julian Wolf, Stefaniya Boneva, Yannik Laich, Jana Koch, Franziska Ludwig, Myriam Boeck, Adrian Thien, Carmen Härdtner, Katrin Kierdorf, Hansjürgen Agostini, Günther Schlunck, Marco Prinz, Ingo Hilgendorf, Peter Wieghofer, Clemens Lange
Software Mentions: 6
Published: about 4 years ago

10.1186/s13072-021-00391-x

Mechanism and functional role of the interaction between CP190 and the architectural protein Pita in Drosophila melanogaster
Cited by: 15
Author(s): Marat Sabirov, Olga Kyrchanova, Galina V. Pokholkova, Artem Bonchuk, Natalia Klimenko, Elena Belova, И. Ф. Жимулев, Oksana Maksimenko, Pavel Georgiev
Software Mentions: 6
Published: over 4 years ago

10.7554/eLife.55249

Generation of inner ear hair cells by direct lineage conversion of primary somatic cells
Cited by: 49
Author(s): Louise Menendez, Talon Trecek, Suhasni Gopalakrishnan, Litao Tao, Alexander L. Markowitz, Haoze V Yu, Xizi Wang, Juan Llamas, Chi‐Chou Huang, James Lee, Radha Kalluri, Justin K. Ichida, Neil Segil
Software Mentions: 6
Published: over 5 years ago

10.1371/journal.pgen.1009574

Runx1 shapes the chromatin landscape via a cascade of direct and indirect targets
Cited by: 13
Author(s): Matthew R. Hass, Daniel Brissette, Sreeja Parameswaran, Mario Pujato, Omer Donmez, Leah C. Kottyan, Matthew T. Weirauch, Raphael Kopan
Software Mentions: 6
Published: over 4 years ago

10.3390/jof7080607

The Diplodia Tip Blight Pathogen Sphaeropsis sapinea Is the Most Common Fungus in Scots Pines’ Mycobiome, Irrespective of Health Status—A Case Study from Germany
Cited by: 12
Author(s): Kathrin Blumenstein, Johanna Bußkamp, Gitta Jutta Langer, Ewald Langer, Eeva Terhonen
Software Mentions: 6
Published: over 4 years ago

10.1371/journal.pgen.1007276

Argonaute2 and LaminB modulate gene expression by controlling chromatin topology
Cited by: 19
Author(s): Ezequiel Názer, Ryan Dale, Madoka Chinen, Behram Radmanesh, Elissa P. Lei
Software Mentions: 6
Published: over 7 years ago

10.1038/s41396-018-0264-0

Strong succession in arbuscular mycorrhizal fungal communities
Cited by: 78
Author(s): Cheng Gao, Liliam Montoya, Limei Xu, Mary Madera, Joy Hollingsworth, Elizabeth Purdom, Robert B. Hutmacher, Jeff Dahlberg, Devin Coleman‐Derr, Peggy G. Lemaux, John W. Taylor
Software Mentions: 6
Published: over 7 years ago

10.1128/mSystems.00446-21

Transmission of Seed and Soil Microbiota to Seedling
Cited by: 27
Author(s): Aude Rochefort, Marie Simonin, Coralie Marais, Anne‐Yvonne Guillerm‐Erckelboudt, Matthieu Barret, Alain Sarniguet
Software Mentions: 6
Published: over 4 years ago

10.1080/20013078.2020.1785746

Influence of species and processing parameters on recovery and content of brain tissue‐derived extracellular vesicles
Cited by: 62
Author(s): Yiyao Huang, Lesley Cheng, Andrey Turchinovich, Vasiliki Mahairaki, Juan C. Troncoso, Olga Pletniková, Norman J. Haughey, Laura J. Vella, Andrew F. Hill, Lei Zheng, Kenneth W. Witwer
Software Mentions: 6
Published: over 5 years ago

10.15252/embj.2020104569

Translation is required for miRNA‐dependent decay of endogenous transcripts
Cited by: 15
Author(s): Adriano Biasini, Baroj Abdulkarim, Stefano de Pretis, Jennifer Y. Tan, Rajika Arora, Harry Wischnewski, René Dreos, Mattia Pelizzola, Constance Ciaudo, Ana C. Marques
Software Mentions: 6
Published: almost 5 years ago

10.15252/embj.2019101695

Phospho‐RNA‐seq: a modified small RNA‐seq method that reveals circulating mRNA and lncRNA fragments as potential biomarkers in human plasma
Cited by: 61
Author(s): María D. Giraldez, Ryan M Spengler, Alton Etheridge, Annika Jane Goicochea, Missy Tuck, Sung Won Choi, David J. Galas, Muneesh Tewari
Software Mentions: 6
Published: over 6 years ago

10.1002/jev2.12022

Microglial derived extracellular vesicles activate autophagy and mediate multi‐target signaling to maintain cellular homeostasis
Cited by: 22
Author(s): Bram Van den Broek, Isabel Pintelon, Ibrahim Hamad, Sofie Kessels, Mansour Haidar, Niels Hellings, Jerome J. A. Hendriks, Markus Kleinewietfeld, Bert Brône, Vincent Timmerman, Jean‐Pierre Timmermans, Veerle Somers, Luc Michiels, Joy Irobi
Software Mentions: 6
Published: about 5 years ago

10.7554/eLife.58931

Recurrent evolution of high virulence in isolated populations of a DNA virus
Cited by: 11
Author(s): Tom Hill, Robert L. Unckless
Software Mentions: 6
Published: about 5 years ago

10.1038/s41598-021-92007-3

Validity and safety of ID-JPL934 in lower gastrointestinal symptom improvement
Cited by: 4
Author(s): Cheol Min Shin, Yoon Jin Choi, Dong Hoon Lee, Jin Seok Moon, Tae Yoon Kim, Yoon Keun Kim, Won Hee Lee, Hyuk Yoon, Young Soo Park, Nayoung Kim
Software Mentions: 6
Published: over 4 years ago

10.1038/s42003-021-02012-5

High and specific diversity of protists in the deep-sea basins dominated by diplonemids, kinetoplastids, ciliates and foraminiferans
Cited by: 22
Author(s): Alexandra Schoenle, Manon Hohlfeld, Karoline Hermanns, Frédéric Mahé, Colomban de Vargas, Frank Nitsche, Hartmut Arndt
Software Mentions: 6
Published: over 4 years ago

10.1038/s42003-020-01439-6

Predicting clinical resistance prevalence using sewage metagenomic data
Cited by: 28
Author(s): Antti Karkman, Fanny Berglund, Carl-Fredrik Flach, Erik Kristiansson, D. G. Joakim Larsson
Software Mentions: 6
Published: about 5 years ago

10.1038/s41598-020-75998-3

Transcriptomic profiling of feline teeth highlights the role of matrix metalloproteinase 9 (MMP9) in tooth resorption
Cited by: 8
Author(s): S. Lee, Stephen J. Bush, Susan Thorne, Nicola Mawson, Colin Farquharson, Guraa Bergkvist
Software Mentions: 6
Published: about 5 years ago

10.1186/s12863-021-00983-2

Insights into 6S RNA in lactic acid bacteria (LAB)
Cited by: 1
Author(s): Pablo G. Cataldo, Paul Klemm, Marietta Thüring, Lucila Saavedra, Elvira María Hébert, Roland K. Hartmann, Marcus Lechner
Software Mentions: 6
Published: over 4 years ago

10.1038/s41598-020-80568-8

Annual phytoplankton dynamics in coastal waters from Fildes Bay, Western Antarctic Peninsula
Cited by: 15
Author(s): Nicole Trefault, Rodrigo De la Iglesia, Mario Moreno-Pino, Adriana Lopes dos Santos, Catherine Gérikas Ribeiro, Génesis Parada-Pozo, Antonia Cristi, Dominique Marie, Daniel Vaulot
Software Mentions: 6
Published: almost 5 years ago

10.1038/s41598-021-93468-2

Integrative biology defines novel biomarkers of resistance to strongylid infection in horses
Cited by: 5
Author(s): Guillaume Sallé, Cécile Canlet, Jacques Cortet, Christine Koch, Joshua Malsa, Fabrice Reigner, Mickaël Riou, Noémie Perrot, Alexandra Blanchard, Núria Mach
Software Mentions: 6
Published: over 4 years ago

10.1038/s41598-020-65089-8

Immunorthodontics: in vivo gene expression of orthodontic tooth movement
Cited by: 28
Author(s): Yehuda Klein, Omer Fleissig, David Polak, Yechezkel Barenholz, Ofer Mandelboim, Stella Chaushu
Software Mentions: 6
Published: over 5 years ago

10.1098/rstb.2019.0255

Dormancy dynamics and dispersal contribute to soil microbiome resilience
Cited by: 34
Author(s): Jackson W Sorensen, Ashley Shade
Software Mentions: 6
Published: over 5 years ago

10.1038/s41598-020-70535-8

Bacterial microbiota diversity and composition in red and white wines correlate with plant-derived DNA contributions and botrytis infection
Cited by: 16
Author(s): Alena M. Bubeck, Lena C. Preiss, Anna Jung, Elisabeth Dörner, Daniel Podlesny, Marija Kulis, Cynthia Maddox, Cesar Arze, Christian Zörb, Nikolaus Merkt, W. Florian Fricke
Software Mentions: 6
Published: over 5 years ago

10.1038/s41598-021-92405-7

Microplastics accumulate fungal pathogens in terrestrial ecosystems
Cited by: 73
Author(s): Gerasimos Gkoutselis, Stephan Rohrbach, Janno Harjes, Martin Obst, Andreas Brachmann, Marcus A. Horn, Gerhard Rambold
Software Mentions: 6
Published: over 4 years ago

10.12688/wellcomeopenres.16791.1

Ultraplex: A rapid, flexible, all-in-one fastq demultiplexer
Cited by: 9
Author(s): Oscar G. Wilkins, Charlotte Capitanchik, Nicholas M. Luscombe, Jernej Ule
Software Mentions: 6
Published: over 4 years ago

10.1038/s41597-019-0172-9

Bacterial succession along a sediment porewater gradient at Lake Neusiedl in Austria
Cited by: 20
Author(s): Avril Jean Elisabeth von Hoyningen-Huene, Dominik Schneider, Dario Fussmann, Andreas Reimer, Gernot Arp, Rolf Daniel
Software Mentions: 6
Published: over 6 years ago

10.1038/sdata.2017.44

Construction of a map-based reference genome sequence for barley, Hordeum vulgare L.
Cited by: 119
Author(s): Sebastian Beier, Axel Himmelbach, Christian Colmsee, Xiao Qi Zhang, Roberto A. Barrero, Qisen Zhang, Lin Li, Micha Bayer, Dan Bolser, Stefan Taudien, Marco Groth, Marius Felder, Alex Hastie, Hana Šimková, Helena Staňková, Jan Vrána, Saki Chan, María Muñoz‐Amatriaín, Rachid Ounit, Steve Wanamaker, Thomas Schmutzer, Lala Aliyeva-Schnorr, Stefano Grasso, Jaakko Tanskanen, Dharanya Sampath, Darren Heavens, Sujie Cao, Brett Chapman, Fei Dai, Yong Han, Hua Li, Xuan Li, Chongyun Lin, John K. McCooke, Cong Tan, Songbo Wang, Shuya Yin, Gaofeng Zhou, Jesse Poland, M. Bellgard, Andreas Houben, Jaroslav Doležel, Sarah Ayling, Stefano Lonardi, Peter Langridge, Gary J. Muehlbauer, Paul J. Kersey, Matthew D. Clark, Mario Cáccamo, Alan H. Schulman, Matthias Platzer, Timothy J. Close, Mats Hansson, Guoping Zhang, Ilka Braumann, Chengdao Li, Robbie Waugh, Uwe Scholz, Nils Stein, Martin Mascher
Software Mentions: 6
Published: over 8 years ago

10.1186/s12284-016-0098-1

Comparative Leaf and Root Transcriptomic Analysis of two Rice Japonica Cultivars Reveals Major Differences in the Root Early Response to Osmotic Stress
Cited by: 32
Author(s): Elena Baldoni, Paolo Bagnaresi, Franca Locatelli, Monica Mattana, Annamaria Genga
Software Mentions: 6
Published: over 9 years ago

10.1098/rsos.160350

Two species of Southeast Asian cats in the genus Catopuma with diverging histories: an island endemic forest specialist and a widespread habitat generalist
Cited by: 13
Author(s): Riddhi P. Patel, Daniel W. Förster, Andrew C. Kitchener, Mark D. Rayan, Shariff W. Mohamed, Laura Werner, Dorina Lenz, Hans Pfestorf, Stephanie Kramer‐Schadt, Viktoriia Radchuk, Jörns Fickel, Andreas Wilting
Software Mentions: 6
Published: about 9 years ago

10.1016/j.celrep.2020.108629

VELCRO-IP RNA-seq reveals ribosome expansion segment function in translation genome-wide
Cited by: 10
Author(s): Kathrin Leppek, Gun Woo Byeon, Kotaro Fujii, Maria Barna
Software Mentions: 6
Published: almost 5 years ago

10.1111/acel.13153

Epigenome signatures landscaped by histone H3K9me3 are associated with the synaptic dysfunction in Alzheimer's disease
Cited by: 44
Author(s): Min Young Lee, Jung‐Hee Lee, Seung Jae Hyeon, Hyesun Cho, Yu Jin Hwang, Jong Yeon Shin, Ann C. McKee, Neil W. Kowall, Jong‐Il Kim, Thor D. Stein, Daehee Hwang, Hoon Ryu
Software Mentions: 6
Published: over 5 years ago

10.1093/g3journal/jkab189

Long-read transcriptome and other genomic resources for the angiosperm Silene noctiflora
Cited by: 7
Author(s): Alissa M. Williams, Michael W. Itgen, Amanda K. Broz, Olivia G. Carter, Daniel B Sloan
Software Mentions: 6
Published: over 4 years ago

10.1007/s00784-020-03613-w

Limited antimicrobial efficacy of oral care antiseptics in microcosm biofilms and phenotypic adaptation of bacteria upon repeated exposure
Cited by: 22
Author(s): Sophia R. Schwarz, Stefanie Hirsch, Andreas Hiergeist, Christian Kirschneck, Denise Muehler, Karl‐Anton Hiller, Tim Maisch, Ali Al‐Ahmad, André Gessner, Wolfgang Buchalla, Fabian Cieplik
Software Mentions: 6
Published: about 5 years ago

10.1098/rsos.191480

Mid and hindgut transcriptome profiling analysis of Atlantic salmon ( Salmon salar ) under unpredictable chronic stress
Cited by: 2
Author(s): Signe Dille Løvmo, Angelico Madaro, Paul Whatmore, Tora Bardal, Mari‐Ann Östensen, Simen Rød Sandve, Rolf Erik Olsen
Software Mentions: 6
Published: almost 6 years ago

10.1038/s41598-018-31192-0

Disruption of mesoderm formation during cardiac differentiation due to developmental exposure to 13-cis-retinoic acid
Cited by: 18
Author(s): Qing Liu, Kevin Van Bortle, Yue Zhang, Ming Zhao, Joe Z. Zhang, Benjamin Geller, Joshua J. Gruber, Chao Jiang, Joseph C. Wu, M Snyder
Software Mentions: 6
Published: over 7 years ago

10.3389/fonc.2019.00221

Non-coding and Coding Transcriptional Profiles Are Significantly Altered in Pediatric Retinoblastoma Tumors
Cited by: 25
Author(s): Swetha Rajasekaran, Lakshmi Dhevi N. Selvan, Kathleen Dotts, Ranjith Kumar, Pukhraj Rishi, Vikas Khetan, Madhoolika Bisht, Karthikeyan Sivaraman, Subrmanian Krishnakumar, Debashis Sahoo, Moray J. Campbell, Sailaja Elchuri, Wayne Miles
Software Mentions: 6
Published: over 6 years ago

10.3389/fphys.2019.01370

A Dynamic Transcriptional Analysis Reveals IL-6 Axis as a Prominent Mediator of Surgical Acute Response in Non-ischemic Mouse Heart
Cited by: 1
Author(s): Sally Badawi, Alexandre Paccalet, Zeina Harhous, Bruno Pillot, Lionel Augeul, Fabien Van Coppenolle, Joël Lachuer, Mazen Kurdi, Claire Crola Da Silva, Michel Ovize, Gabriel Bidaux
Software Mentions: 6
Published: about 6 years ago

10.3389/fpls.2018.01212

A Bioinformatics Pipeline for the Analysis and Target Prediction of RNA Effectors in Bidirectional Communication During Plant–Microbe Interactions
Cited by: 12
Author(s): Silvia Zanini, Ena Šečić, Lukas Jelonek, Karl-Heinz Kögel
Software Mentions: 6
Published: over 7 years ago

10.3390/biomedicines9091120

Neural Precursor Cells Expanded Inside the 3D Micro-Scaffold Nichoid Present Different Non-Coding RNAs Profiles and Transcript Isoforms Expression: Possible Epigenetic Modulation by 3D Growth
Cited by: 3
Author(s): Letizia Messa, Bianca Barzaghini, Federica Rey, Cecilia Pandini, Gian Vincenzo Zuccotti, Cristina Cereda, Stephana Carelli, Manuela Teresa Raimondi
Software Mentions: 6
Published: over 4 years ago

10.3389/fmicb.2021.614634

Terrestrial Inputs Shape Coastal Bacterial and Archaeal Communities in a High Arctic Fjord (Isfjorden, Svalbard)
Cited by: 14
Author(s): Lisa-Marie Delpech, Tobias R. Vonnahme, Maeve McGovern, Rolf Gradinger, Kim Præbel, Amanda Poste
Software Mentions: 6
Published: almost 5 years ago

10.15252/msb.202110253

Model‐guided development of an evolutionarily stable yeast chassis
Cited by: 5
Author(s): Filipa Pereira, Helena Lopes, Paulo Maia, Britta Meyer, Justyna Nocon, Paula Jouhten, D. Konstantinidis, Eleni Kafkia, Miguel Rocha, Peter Kötter, Isabel Rocha, Kiran R. Patil
Software Mentions: 6
Published: over 4 years ago

10.3389/fmicb.2018.02364

Accounting for Bacterial Overlap Between Raw Water Communities and Contaminating Sources Improves the Accuracy of Signature-Based Microbial Source Tracking
Cited by: 16
Author(s): Moa Hägglund, Stina Bäckman, Anna Macellaro, Petter Lindgren, Emmy Borgmästars, Karin Jacobsson, Rikard Dryselius, Per Stenberg, Andreas Sjödin, Mats Forsman, Jon Ahlinder
Software Mentions: 6
Published: about 7 years ago

10.1186/s13148-020-00944-z

Epigenome-wide association study of Alzheimer’s disease replicates 22 differentially methylated positions and 30 differentially methylated regions
Cited by: 38
Author(s): Qingqin Li, Yu Sun, Tania Wang
Software Mentions: 6
Published: about 5 years ago

10.1002/1878-0261.12786

Allele‐specific proximal promoter hypomethylation of the telomerase reverse transcriptase gene (TERT) associates with TERT expression in multiple cancers
Cited by: 20
Author(s): Teisha J. Rowland, Andrew J. Bonham, Thomas R. Cech
Software Mentions: 6
Published: about 5 years ago

10.3389/fmicb.2017.00744

Alterations in the Rumen Liquid-, Particle- and Epithelium-Associated Microbiota of Dairy Cows during the Transition from a Silage- and Concentrate-Based Ration to Pasture in Spring
Cited by: 36
Author(s): Melanie Schären, Kerstin Kiri, Susanne Riede, Mark C. Gardener, Ulrich Meyer, Jürgen Hummel, Tim Urich, Gerhard Breves, Sven Dänicke
Software Mentions: 6
Published: over 8 years ago

10.1186/s13100-019-0156-5

Subtype classification and functional annotation of L1Md retrotransposon promoters
Cited by: 15
Author(s): Meng Zhou, Andrew D. Smith
Software Mentions: 6
Published: over 6 years ago

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Papers Mentioning cutadapt 1,562