pypi: cutadapt | Projects | Ecosyste.ms: Papers

10.1002/edm2.191

Sex and oestrogen receptor β have modest effects on gene expression in the mouse brain posterior cortex
Cited by: 1
Author(s): Jasmine A. Fels, Gabriella Casalena, Giovanni Manfredi
Software Mentions: 7
Published: over 3 years ago

10.1002/mc.23147

Loss of myeloid‐specific lamin A/C drives lung metastasis through Gfi‐1 and C/EBPε‐mediated granulocytic differentiation
Cited by: 3
Author(s): Hiroki Ishii, Woo‐Yong Park, Jae-Young So, Skyler Kuhn, Vishal N. Kopardé, Yanli Pang, Tim F. Greten, M. Christine Hollander, Li Yang
Software Mentions: 7
Published: over 4 years ago

10.1186/s13059-018-1521-2

omniCLIP: probabilistic identification of protein-RNA interactions from CLIP-seq data
Cited by: 18
Author(s): Philipp Drewe-Boß, Hans-Hermann Wessels, Uwe Ohler
Software Mentions: 7
Published: over 5 years ago

10.1186/s13059-021-02450-8

INFIMA leverages multi-omics model organism data to identify effector genes of human GWAS variants
Cited by: 3
Author(s): Chenyang Dong, Shane P. Simonett, Sun‐Young Shin, Donnie S. Stapleton, Kathryn L. Schueler, Gary A. Churchill, Leina Lu, Huan Liu, Fulai Jin, Yan Li, Alan D. Attie, Mark P. Keller, Sündüz Keleş
Software Mentions: 7
Published: over 2 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: almost 3 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: over 4 years ago

10.7554/eLife.59610

Odd-paired is a pioneer-like factor that coordinates with Zelda to control gene expression in embryos
Cited by: 29
Author(s): Theodora Koromila, Fan Gao, Yohei Iwasaki, Peng He, Lior Pachter, J. Peter Gergen, Angelike Stathopoulos
Software Mentions: 7
Published: almost 4 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: over 2 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: over 6 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 3 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 3 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: almost 3 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: almost 3 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: almost 4 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: almost 6 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: almost 7 years ago

10.1186/s13059-020-1948-0

Regenerating zebrafish fin epigenome is characterized by stable lineage-specific DNA methylation and dynamic chromatin accessibility
Cited by: 42
Author(s): Hyung Joo Lee, Yiran Hou, Yujie Chen, Zea Z. Dailey, Aiyana Riddihough, Hyo Sik Jang, Ting Wang, Stephen L. Johnson
Software Mentions: 7
Published: about 4 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: over 3 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: over 2 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: 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: over 4 years ago

10.1186/s13059-021-02466-0

Acute depletion of CTCF rewires genome-wide chromatin accessibility
Cited by: 26
Author(s): Beisi Xu, Hong Wang, Shaela Wright, Judith Hyle, Yang Zhang, Ying Shao, Mingming Niu, Yiping Fan, Wojciech Rosikiewicz, Mohamed Nadhir Djekidel, Junmin Peng, Rui Lu, Chunliang Li
Software Mentions: 7
Published: over 2 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: almost 3 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: over 6 years ago

10.1016/j.isci.2021.102870

Single paternal dexamethasone challenge programs offspring metabolism and reveals multiple candidates in RNA-mediated inheritance
Cited by: 14
Author(s): Katharina Gapp, Guillermo E. Parada, Fridolin Groß, Alberto Corcoba, Jasmine Kaur, Evelyn Grau, Martin Hemberg, Johannes Bohacek, Eric A. Miska
Software Mentions: 7
Published: almost 3 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: over 3 years ago

10.1186/s13059-017-1367-z

MICRA: an automatic pipeline for fast characterization of microbial genomes from high-throughput sequencing data
Cited by: 9
Author(s): Ségolène Caboche, Gaël Even, Alexandre Loywick, Christophe Audebert, David Hot
Software Mentions: 6
Published: over 6 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: almost 5 years ago

10.1186/s13059-018-1415-3

Discovery of physiological and cancer-related regulators of 3′ UTR processing with KAPAC
Cited by: 49
Author(s): Andreas J. Gruber, Ralf Schmidt, Souvik Ghosh, Georges Martín, Erik van Nimwegen, Mihaela Zavolan
Software Mentions: 6
Published: about 6 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 9 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: about 5 years ago

10.3390/microorganisms8030405

Agroforestry Management Systems Drive the Composition, Diversity, and Function of Fungal and Bacterial Endophyte Communities in Theobroma Cacao Leaves
Cited by: 19
Author(s): Franziska Wemheuer, Dirk Hölscher, Bernd Wemheuer, Rolf Daniel, Stefan Vidal, Hervé Bertin Bisseleua Daghela
Software Mentions: 6
Published: about 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: almost 3 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: about 8 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: almost 3 years ago

10.26508/lsa.202000974

GATA transcription factors, SOX17 and TFAP2C, drive the human germ-cell specification program
Cited by: 30
Author(s): Yôji Kojima, Chika Yamashiro, Yusuke Murase, Yukihiro Yabuta, Ikuhiro Okamoto, Chizuru Iwatani, Hideaki Tsuchiya, Masataka Nakaya, Tomoyuki Tsukiyama, Tomonori Nakamura, Takuya Yamamoto, Mitinori Saitou
Software Mentions: 6
Published: about 3 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: about 4 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: over 4 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 5 years ago

10.3389/fvets.2021.733357

Chytridiomycosis Outbreak in a Chilean Giant Frog (Calyptocephalella gayi) Captive Breeding Program: Genomic Characterization and Pathological Findings
Cited by: 5
Author(s): Mario Alvarado‐Rybak, Paz Acuña, Alexandra Peñafiel‐Ricaurte, Thomas R. Sewell, Simon J. O’Hanlon, Matthew C. Fisher, Andrés Valenzuela‐Sánchez, Andrew A. Cunningham, Claudio Soto‐Azat
Software Mentions: 6
Published: over 2 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: about 5 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 8 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: almost 5 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: almost 4 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: almost 3 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: over 5 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 2 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: over 4 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: over 3 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: about 3 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: almost 7 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: about 3 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: over 6 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: almost 3 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: about 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: about 3 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: 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: over 3 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: almost 4 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: over 3 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: about 5 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: over 2 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: over 3 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: over 3 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: almost 3 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 5 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: over 3 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 2 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: almost 4 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: almost 3 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: about 4 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: almost 3 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: almost 3 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: over 4 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: over 3 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: almost 3 years ago

10.1073/pnas.2104315118

Global range expansion history of pepper (Capsicumspp.) revealed by over 10,000 genebank accessions
Cited by: 39
Author(s): Pasquale Tripodi, M. Timothy Rabanus‐Wallace, Lorenzo Barchi, Sandip M. Kale, Salvatore Esposito, Alberto Acquadro, Roland Schafleitner, Maarten van Zonneveld, Jaime Prohens, María José Díez, Andreas Börner, Jérémy Salinier, Bernard Caromel, Arnaud Bovy, Filiz Boyaci, Gancho Pasev, Ronny Brandt, Axel Himmelbach, Ezio Portis, Richard Finkers, Sergio Lanteri, Ilan Paran, Véronique Lefebvre, Giovanni Giuliano, Nils Stein
Software Mentions: 6
Published: almost 3 years ago

10.1371/journal.ppat.1007852

The landscape of transcription initiation across latent and lytic KSHV genomes
Cited by: 11
Author(s): Xiang Ye, Yang Zhao, John Karijolich
Software Mentions: 6
Published: almost 5 years ago

10.1371/journal.ppat.1007518

Comprehensive profiling of translation initiation in influenza virus infected cells
Cited by: 22
Author(s): Heather M. Machkovech, Jesse D. Bloom, Arvind R. Subramaniam
Software Mentions: 6
Published: over 5 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: over 3 years ago

10.1186/s13073-020-00825-3

Mode and dynamics of vanA-type vancomycin resistance dissemination in Dutch hospitals
Cited by: 15
Author(s): Sergio Arredondo-Alonso, Janetta Top, Jukka Corander, Rob J. L. Willems, Anita C. Schürch
Software Mentions: 6
Published: over 3 years ago

10.1038/s41438-020-0316-2

Draft genome of the Native American cold hardy grapevine Vitis riparia Michx. ‘Manitoba 37’
Cited by: 16
Author(s): Sagar Patel, Michael Robben, Anne Fennell, Jason P. Londo, Dilmini Alahakoon, Roberto Villegas-Diaz, Padmapriya Swaminathan
Software Mentions: 6
Published: almost 4 years ago

10.1093/gbe/evab069

Synteny-Based Genome Assembly for 16 Species of Heliconius Butterflies, and an Assessment of Structural Variation across the Genus
Cited by: 13
Author(s): Fernando Seixas, Nathaniel B. Edelman, James Mallet
Software Mentions: 6
Published: about 3 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: over 3 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: about 4 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: almost 3 years ago

10.1186/s13059-020-02160-7

Removing reference bias and improving indel calling in ancient DNA data analysis by mapping to a sequence variation graph
Cited by: 33
Author(s): Rui Martiniano, Erik Garrison, Eppie R. Jones, Andrea Manica, Richard Durbin
Software Mentions: 6
Published: over 3 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 2 years ago

10.1186/s13059-020-1947-1

Assembly of hundreds of novel bacterial genomes from the chicken caecum
Cited by: 95
Author(s): Laura Glendinning, Robert D. Stewart, Mark J. Pallen, Kellie Watson, Mick Watson
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: about 3 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: almost 3 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: over 3 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: about 7 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: over 3 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: about 5 years ago

10.3390/biomedicines9091192

Self-Organization Provides Cell Fate Commitment in MSC Sheet Condensed Areas via ROCK-Dependent Mechanism
Cited by: 3
Author(s): Peter Nimiritsky, Ekaterina Novoseletskaya, Roman Eremichev, Natalya Alexandrushkina, Maxim Karagyaur, O. V. Vetrovoy, Nataliya Basalova, А. М. Хрусталева, Alexander Tyakht, Anastasia Efimenko, В. А. Ткачук
Software Mentions: 6
Published: over 2 years ago

10.1002/1878-0261.12435

Detection of human papillomavirus in cases of head and neck squamous cell carcinoma by RNA‐seq and VirTect
Cited by: 7
Author(s): Atlas Khan, Qian Liu, Xuelian Chen, Andres Stucky, Parish P. Sedghizadeh, Daniel Adelpour, Xi Zhang, Kai Wang, Jiang Zhong
Software Mentions: 6
Published: about 5 years ago

10.1128/AEM.01285-16

Enrichment of Root Endophytic Bacteria from Populus deltoides and Single-Cell-Genomics Analysis
Cited by: 46
Author(s): Sagar M. Utturkar, W. Nathan Cude, Michael S. Robeson, Zamin K. Yang, Dawn M. Klingeman, Miriam Land, S. L. Allman, Tse-Yuan S. Lu, Steven D. Brown, Christopher W. Schadt, Mircea Podar, Mitchel J. Doktycz, Dale A. Pelletier
Software Mentions: 6
Published: over 7 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 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: over 3 years ago

Projects: pypi: cutadapt

Papers Mentioning cutadapt 1,562