pypi: cutadapt | Projects | Ecosyste.ms: Papers

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

10.1186/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

10.1186/1471-2164-15-917

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

10.1038/s41419-021-03739-z

WNT/β-catenin-suppressed FTO expression increases m6A of c-Myc mRNA to promote tumor cell glycolysis and tumorigenesis
Cited by: 61
Author(s): Xueying Yang, Fei Shao, Dong Guo, Wei Wang, Juhong Wang, Rongxuan Zhu, Yibo Gao, Jie He, Zhimin Lu
Software Mentions: 5
Published: over 5 years ago

10.1002/ece3.3404

Pellets of proof: First glimpse of the dietary composition of adult odonates as revealed by metabarcoding of feces
Cited by: 62
Author(s): Kari Kaunisto, Tomas Roslin, Ilari E. Sääksjärvi, Eero J. Vesterinen
Software Mentions: 5
Published: about 9 years ago

10.1038/s41385-020-0305-7

γδ T cells compose a developmentally regulated intrauterine population and protect against vaginal candidiasis
Cited by: 32
Author(s): Leticia Monin, Dmitry S. Ushakov, Henriette Arnesen, Nourdine Bah, Anett Jandke, Miguel Muñoz-Ruiz, Joana Carvalho, Susan Joseph, Bruna Almeida, M. J. Green, Emma Nye, Shoji Hatano, Yasunobu Yoshikai, Michael Curtis, Harald Carlsen, Ulrich Steinhoff, Preben Boysen, Adrian Hayday
Software Mentions: 5
Published: almost 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

10.3390/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: over 5 years ago

10.1186/s13072-020-00359-3

UTX/KDM6A suppresses AP-1 and a gliogenesis program during neural differentiation of human pluripotent stem cells
Cited by: 5
Author(s): Beisi Xu, Brett B. Mulvey, Muneeb Salie, Xiaoyang Yang, Yurika Matsui, Anjana Nityanandam, Yiping Fan, Jamy C. Peng
Software Mentions: 5
Published: about 6 years ago

10.1186/s12864-019-5892-x

Carriage of Shiga toxin phage profoundly affects Escherichia coli gene expression and carbon source utilization
Cited by: 25
Author(s): Petya Berger, Ivan U. Kouzel, Michael Berger, Nadja Haarmann, Ulrich Dobrindt, Gerald B. Koudelka, Alexander Mellmann
Software Mentions: 5
Published: over 7 years ago

10.3389/fcell.2021.664178

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

10.3389/fcell.2021.719192

PARP1 Inhibitor Combined With Oxaliplatin Efficiently Suppresses Oxaliplatin Resistance in Gastric Cancer-Derived Organoids via Homologous Recombination and the Base Excision Repair Pathway
Cited by: 1
Author(s): Huafu Li, Chunming Wang, Linxiang Lan, Wenhui Wu, Ian M. Evans, E Josue Ruiz, Le-Ping Yan, Zhijun Zhou, Joaquím M. Oliveira, Rui L. Reis, Zhenran Hu, Wei Chen, Axel Behrens, Yulong He, Changhua Zhang
Software Mentions: 5
Published: about 5 years ago

10.1172/JCI133187

Mesenchymal niche remodeling impairs hematopoiesis via stanniocalcin 1 in acute myeloid leukemia
Cited by: 45
Author(s): Alexander Waclawiczek, Ashley Hamilton, Kevin Rouault-Pierre, Ander Abarrategi, Manuel Garcia-Albornoz, Farideh Miraki-Moud, Nourdine Bah, John G. Gribben, Jude Fitzgibbon, David Taussig, Dominique Bonnet
Software Mentions: 5
Published: over 6 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

10.1371/journal.pone.0238557

eDNA metabarcoding as a biomonitoring tool for marine protected areas
Cited by: 67
Author(s): Zachary Gold, Joshua Sprague, David J. Kushner, Erick Zerecero Marin, Paul H. Barber
Software Mentions: 5
Published: over 5 years ago

10.1038/s41598-021-94761-w

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

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

10.1038/s41598-021-93863-9

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

10.1084/jem.20171738

A broad atlas of somatic hypermutation allows prediction of activation-induced deaminase targets
Cited by: 75
Author(s): Ángel F. Álvarez-Prado, Pablo Pérez-Durán, Arantxa Pérez-García, Alberto Benguría, Carlos Torroja, Virginia G. de Yébenes, Almudena R. Ramiro
Software Mentions: 5
Published: over 8 years ago

10.1111/eva.12647

Population genomics of the introduced and cultivated Pacific kelpUndaria pinnatifida: Marinas-not farms-drive regional connectivity and establishment in natural rocky reefs
Cited by: 43
Author(s): Jaromir Guzinski, Marion Ballenghien, Claire Daguin‐Thiébaut, Laurent Lévêque, Frédérique Viard
Software Mentions: 5
Published: over 8 years ago

10.3389/fimmu.2021.633654

The SWI/SNF-Related, Matrix Associated, Actin-Dependent Regulator of Chromatin A4 Core Complex Represses Respiratory Syncytial Virus-Induced Syncytia Formation and Subepithelial Myofibroblast Transition
Cited by: 11
Author(s): Xiaofang Xu, Dianhua Qiao, Chenyang Dong, Morgan Mann, Roberto P. Garofalo, Sündüz Keleş, Allan R. Brasier
Software Mentions: 5
Published: over 5 years ago

10.1186/s13059-021-02302-5

ACME dissociation: a versatile cell fixation-dissociation method for single-cell transcriptomics
Cited by: 31
Author(s): Helena García-Castro, Nathan J. Kenny, Marta Iglesias, Patricia Álvarez‐Campos, Vincent Mason, Anamaria Elek, Anna Schönauer, Victoria A. Sleight, Jakke Neiro, A. Aziz Aboobaker, Jon Permanyer, Manuel Irimia, Arnau Sebé-Pedrós, Jordi Solana
Software Mentions: 5
Published: over 5 years ago

10.1371/journal.pone.0169087

The Genome of the Trinidadian Guppy, Poecilia reticulata, and Variation in the Guanapo Population
Cited by: 74
Author(s): Axel Künstner, Maria Hoffmann, Bonnie A. Fraser, Verena A. Kottler, Eshita Sharma, Detlef Weigel, Christine Dreyer
Software Mentions: 5
Published: almost 10 years ago

10.1186/s13059-021-02446-4

Retrotransposons as pathogenicity factors of the plant pathogenic fungus Botrytis cinerea
Cited by: 20
Author(s): Antoine Porquier, Constance Tisserant, F. Salinas, Carla Glassl, Lucas E. Wange, Wolfgang Enard, Andreas Hauser, Matthias Hahn, Arne Weiberg
Software Mentions: 5
Published: about 5 years ago

10.1186/s13059-021-02494-w

Differential regulation of mRNA fate by the human Ccr4-Not complex is driven by coding sequence composition and mRNA localization
Cited by: 12
Author(s): Sarah L. Gillen, Chiara Giacomelli, Kelly Hodge, Sara Zanivan, Martin Bushell, Ania Wilczynska
Software Mentions: 5
Published: almost 5 years ago

10.3389/fmicb.2018.01035

Effects of Ice-Algal Aggregate Export on the Connectivity of Bacterial Communities in the Central Arctic Ocean
Cited by: 45
Author(s): Josephine Z. Rapp, Mar Fernández‐Méndez, Christina Bienhold, Antje Boetius
Software Mentions: 5
Published: over 8 years ago

10.3389/fimmu.2020.01095

Peptidylarginine Deiminase 4 Promotes the Renal Infiltration of Neutrophils and Exacerbates the TLR7 Agonist-Induced Lupus Mice
Cited by: 14
Author(s): Norio Hanata, Hirofumi Shoda, Hiroaki Hatano, Yasuo Nagafuchi, Takashi Komai, Tomohisa Okamura, Akari Suzuki, I Ketut Gunarta, Katsuji Yoshioka, Kazuhiko Yamamoto, Keishi Fujio
Software Mentions: 5
Published: over 6 years ago

10.1093/gbe/evaa187

Improved Reference Genome Uncovers Novel Sex-Linked Regions in the Guppy (Poecilia reticulata)
Cited by: 29
Author(s): Bonnie A. Fraser, James R. Whiting, Josephine R. Paris, Cameron J. Weadick, Paul J. Parsons, Deborah Charlesworth, Roberta Bergero, Felix Bemm, Maria Hoffmann, Verena A. Kottler, Chang Liu, Christine Dreyer, Detlef Weigel
Software Mentions: 5
Published: about 6 years ago

10.3389/fimmu.2019.00330

Persistence of Candida albicans in the Oral Mucosa Induces a Curbed Inflammatory Host Response That Is Independent of Immunosuppression
Cited by: 37
Author(s): Florian Kirchner, Katharina Littringer, Simon Altmeier, Van Du T. Tran, Franziska Annett Schönherr, Christina Braunsdorf, Marco Pagni, Dominique Sanglard, Nicole Joller, Salomé LeibundGut‐Landmann
Software Mentions: 5
Published: over 7 years ago

10.1128/mSystems.01306-20

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

10.1186/s13073-020-00747-0

Strain-resolved microbiome sequencing reveals mobile elements that drive bacterial competition on a clinical timescale
Cited by: 37
Author(s): Soumaya Zlitni, Alex Bishara, Eli L. Moss, Е. И. Ткаченко, Joyce B. Kang, Rebecca Culver, Tessa M. Andermann, Ziming Weng, Christina M. Wood, Christine Handy, Hanlee P. Ji, Serafim Batzoglou, Ami S. Bhatt
Software Mentions: 5
Published: over 6 years ago

10.1186/s13059-016-0902-7

Comparative transcriptomics reveals the conserved building blocks involved in parallel evolution of diverse phenotypic traits in ants
Cited by: 67
Author(s): Claire Morandin, Mandy M. Y. Tin, Sílvia Abril, Crisanto Gómez, Luigi Pontieri, Morten Schiøtt, Liselotte Sundström, Kazuki Tsuji, Jes S. Pedersen, Heikki Helanterä, Alexander S. Mikheyev
Software Mentions: 5
Published: over 10 years ago

10.3389/fgene.2018.00671

UTRme: A Scoring-Based Tool to Annotate Untranslated Regions in Trypanosomatid Genomes
Cited by: 20
Author(s): Santiago Radío, Rafael Sebastián Fort, Beatríz Garat, José Sotelo‐Silveira, Pablo Smircich
Software Mentions: 5
Published: almost 8 years ago

10.1093/gigascience/giaa008

GC bias affects genomic and metagenomic reconstructions, underrepresenting GC-poor organisms
Cited by: 77
Author(s): Patrick Browne, Tue Kjærgaard Nielsen, Witold Kot, Anni Aggerholm, M. Thomas P. Gilbert, Lara Puetz, Morten Rasmussen, Athanasios Zervas, Lars Hestbjerg Hansen
Software Mentions: 5
Published: over 6 years ago

10.1093/gigascience/giaa088

A haplotype-resolved, de novo genome assembly for the wood tiger moth (Arctia plantaginis) through trio binning
Cited by: 16
Author(s): Eugenie C Yen, Shane McCarthy, Juan A. Galarza, Tomas N Generalovic, Sarah Pelan, Petr Nguyen, Joana I. Meier, Ian A. Warren, Johanna Mappes, Richard Durbin, Chris D. Jiggins
Software Mentions: 5
Published: about 6 years ago

10.1038/s41396-019-0584-8

Evidence for phylogenetically and catabolically diverse active diazotrophs in deep-sea sediment
Cited by: 36
Author(s): Bennett J. Kapili, Samuel E. Barnett, Daniel H. Buckley, Anne E. Dekas
Software Mentions: 5
Published: over 6 years ago

10.1371/journal.ppat.1007050

Isolation of a natural DNA virus of Drosophila melanogaster, and characterisation of host resistance and immune responses
Cited by: 48
Author(s): William H. Palmer, Nathan Medd, Philippa M. Beard, Darren J. Obbard
Software Mentions: 5
Published: over 8 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

10.1371/journal.pone.0244341

Exposure to traffic-related air pollution and bacterial diversity in the lower respiratory tract of children
Cited by: 9
Author(s): Christine Niemeier‐Walsh, Patrick Ryan, Jarosław Meller, Nicholas J. Ollberding, Atin Adhikari, Tiina Reponen
Software Mentions: 5
Published: over 5 years ago

10.3389/fmicb.2018.01561

A Single Vibrionales 16S rRNA Oligotype Dominates the Intestinal Microbiome in Two Geographically Separated Atlantic cod Populations
Cited by: 16
Author(s): Even Sannes Riiser, Thomas Haverkamp, Ørnulf Borgan, Kjetill S. Jakobsen, Sissel Jentoft, Bastiaan Star
Software Mentions: 5
Published: about 8 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

10.7150/ijbs.37399

Gut microbiome associated with APC gene mutation in patients with intestinal adenomatous polyps
Cited by: 38
Author(s): Sai Liang, Yan Mao, Ming Liao, Yali Xu, Ying‐Chun Chen, Xiaoliang Huang, Chuangyi Wei, Changtao Wu, Qiuyan Wang, Xiaoyan Pan, Weizhong Tang
Software Mentions: 5
Published: over 6 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

10.1371/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/fcell.2021.595744

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

10.3389/fcell.2020.580848

Adherent Intestinal Cells From Atlantic Salmon Show Phagocytic Ability and Express Macrophage-Specific Genes
Cited by: 5
Author(s): Youngjin Park, Qirui Zhang, G.F. Wiegertjes, Jorge M. O. Fernandes, Viswanath Kiron
Software Mentions: 5
Published: almost 6 years ago

10.3389/fcell.2021.641987

Timing Does Matter: Nerve-Mediated HDAC1 Paces the Temporal Expression of Morphogenic Genes During Axolotl Limb Regeneration
Cited by: 3
Author(s): Mu-Hui Wang, Chih‐Cheng Hsu, Cheng‐Hsun Wu, Ling-Ling Chiou, Yi-Tzang Tsai, Hsuan-Shu Lee, Shau-Ping Lin
Software Mentions: 5
Published: over 5 years ago

10.3389/fmicb.2018.02094

Application of MootralTM Reduces Methane Production by Altering the Archaea Community in the Rumen Simulation Technique
Cited by: 27
Author(s): Melanie Eger, Michael Graz, Susanne Riede, Gerhard Breves
Software Mentions: 4
Published: about 8 years ago

10.1172/JCI130809

A stress-responsive enhancer induces dynamic drug resistance in acute myeloid leukemia
Cited by: 25
Author(s): Mark S. Williams, Fabio Amaral, Fabrizio Simeoni, Tim C. P. Somervaille
Software Mentions: 4
Published: over 6 years ago

10.3389/fmicb.2021.643904

Predominant Microbial Colonizers in the Root Endosphere and Rhizosphere of Turfgrass Systems: Pseudomonas veronii, Janthinobacterium lividum, and Pseudogymnoascus spp.
Cited by: 10
Author(s): Qing Xia, Thomas W. Rufty, Wei Shi
Software Mentions: 4
Published: over 5 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

10.1186/s13059-019-1918-6

Enteric infection induces Lark-mediated intron retention at the 5′ end of Drosophila genes
Cited by: 4
Author(s): Maroun Bou Sleiman, Michael Frochaux, Tommaso Andreani, Dani Osman, Roderic Guigó, Bart Deplancke
Software Mentions: 4
Published: over 6 years ago

10.1186/s13059-020-02022-2

RNA structural dynamics regulate early embryogenesis through controlling transcriptome fate and function
Cited by: 28
Author(s): Boyang Shi, Jinsong Zhang, Jian Heng, Jing Gong, Ting Zhang, Li Pan, Bao‐Fa Sun, Ying Yang, Ning Zhang, Yongliang Zhao, Hailin Wang, Feng Liu, Qiangfeng Cliff Zhang, Yun‐Gui Yang
Software Mentions: 4
Published: over 6 years ago

10.1186/s13059-020-02062-8

Removal of H2Aub1 by ubiquitin-specific proteases 12 and 13 is required for stable Polycomb-mediated gene repression in Arabidopsis
Cited by: 26
Author(s): Lejon E. M. Kralemann, S. Liu, Minerva S. Trejo-Arellano, Rafael Muñoz‐Viana, Claudia Köhler, Lars Hennig
Software Mentions: 4
Published: over 6 years ago

10.1186/s13059-021-02272-8

A comprehensive enhancer screen identifies TRAM2 as a key and novel mediator of YAP oncogenesis
Cited by: 16
Author(s): Li Li, Alejandro P. Ugalde, Colinda L.G.J. Scheele, Sebastian M. Dieter, Remco Nagel, Jin Ma, Abhijeet Pataskar, Gözde Korkmaz, Ran Elkon, Miao‐Ping Chien, You Li, Pin-Rui Su, Onno B. Bleijerveld, Maarten Altelaar, Lyubomir Momchev, Zohar Manber, Ruiqi Han, Pieter C. van Breugel, Rui Lopes, Peter ten Dijke, Jacco van Rheenen, Reuven Agami
Software Mentions: 4
Published: over 5 years ago

10.1186/s13059-021-02396-x

Chromosome-level genome assembly of a regenerable maize inbred line A188
Cited by: 28
Author(s): Guifang Lin, Cheng He, Jun Zheng, Dal Hoe Koo, Ha Le, Huakun Zheng, Tej Man Tamang, Jianqing Lin, Yan Liu, Mingxia Zhao, Yangfan Hao, Frank McFraland, Bo Wang, Qin Yang, Haibao Tang, Donald R. McCarty, Hairong Wei, Myeong Je Cho, Sunghun Park, Heidi F. Kaeppler, Shawn M. Kaeppler, Yun-Jun Liu, Nathan M. Springer, Patrick S. Schnable, Guoying Wang, Frank F. White, Sanzhen Liu
Software Mentions: 4
Published: over 5 years ago

10.1093/gbe/evw262

Salmonid chromosome evolution as revealed by a novel method for comparing RADseq linkage maps
Cited by: 38
Author(s): Ben J. G. Sutherland, Thierry Gosselin, Éric Normandeau, Manuel Lamothe, Nathalie Isabel, Céline Audet, Louis Bernatchez
Software Mentions: 4
Published: almost 10 years ago

10.1093/gbe/evy155

Pattern of DNA Methylation in Daphnia: Evolutionary Perspective
Cited by: 43
Author(s): Jouni Kvist, Camila Gonçalves Athanásio, Omid Shams Solari, James Brown, John K. Colbourne, Michael E. Pfrender, Leda Mirbahai
Software Mentions: 4
Published: about 8 years ago

10.1186/s13073-021-00826-w

Comprehensive molecular characterization of gastric cancer patients from phase II second-line ramucirumab plus paclitaxel therapy trial
Cited by: 16
Author(s): Seung Tae Kim, K. Jason, Sung Yong Oh, Kyung Kim, Jung Yong Hong, Won Ki Kang, Jeeyun Lee
Software Mentions: 4
Published: over 5 years ago

10.1093/gigascience/giaa158

ChiRA: an integrated framework for chimeric read analysis from RNA-RNA interactome and RNA structurome data
Cited by: 4
Author(s): Pavankumar Videm, Anup Kumar, Oleg Zharkov, Björn Grüning, Rolf Backofen
Software Mentions: 4
Published: over 5 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

10.1371/journal.pone.0216366

Cranial deformation and genetic diversity in three adolescent male individuals from the Great Migration Period from Osijek, eastern Croatia
Cited by: 11
Author(s): Daniel Fernandes, Kendra Sirak, Olivia Cheronet, Rachel Howcroft, Mislav Čavka, Dženi Los, Josip Burmaz, Ron Pinhasi, Mario Novak
Software Mentions: 4
Published: about 7 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

10.1128/mSphere.00160-20

An Extensive Meta-Metagenomic Search Identifies SARS-CoV-2-Homologous Sequences in Pangolin Lung Viromes
Cited by: 43
Author(s): Lamia Wahba, Nikhil Jain, Andrew Fire, Massa J. Shoura, Karen L. Artiles, Matthew J. McCoy, Dae‐Eun Jeong
Software Mentions: 4
Published: over 6 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: almost 10 years ago

10.1371/journal.pone.0232715

PIWI-interacting RNAs are differentially expressed during cardiac differentiation of human pluripotent stem cells
Cited by: 11
Author(s): Alejandro La Greca, María Agustina Scarafia, María Clara Hernández Cañás, Nelba Pérez, Sheila Castañeda, Carolina Colli, Alan Miqueas Möbbs, Natalia Lucía Santín Velazque, Gabriel Neiman, Ximena Garate, Cyntia Abán, Ariel Waisman, Lucía Moro, Gustavo Sevlever, Carlos Luzzani, Santiago Gabriel Miriuka
Software Mentions: 4
Published: over 6 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

10.1371/journal.pone.0223397

Brief communication: Long-term absence of Langerhans cells alters the gene expression profile of keratinocytes and dendritic epidermal T cells
Cited by: 10
Author(s): Qingtai Su, Aurélie Bouteau, Jacob Cardenas, Uthra Balaji, Yuanyaun Wang, Cynthia Smitherman, Jin Gu, Botond Z. Igyártó
Software Mentions: 4
Published: over 6 years ago

10.1371/journal.pone.0246367

Multi-omic modelling of inflammatory bowel disease with regularized canonical correlation analysis
Cited by: 6
Author(s): Lluís Revilla, Aida Mayorgas, A M Corraliza, Maria Carme Masamunt, Amira Metwaly, Dirk Haller, Eva Tristán, Anna Carrasco, María Esteve, Julián Panés, Elena Ricart, Juan José Lozano, Azucena Salas
Software Mentions: 4
Published: over 5 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

10.1038/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

10.1371/journal.pgen.1007376

Colorectal cancer mutational profiles correlate with defined microbial communities in the tumor microenvironment
Cited by: 59
Author(s): Michael B. Burns, Emmanuel Montassier, Juan E. Abrahante, Sambhawa Priya, David Niccum, Alexander Khoruts, Timothy K. Starr, Dan Knights, Ran Blekhman
Software Mentions: 4
Published: over 8 years ago

10.1371/journal.pone.0215986

Characterization of the transcriptome of Haloferax volcanii, grown under four different conditions, with mixed RNA-Seq
Cited by: 27
Author(s): Sebastian Laaß, Vivian Monzon, Jana Kliemt, M Hammelmann, Friedhelm Pfeiffer, Konrad U. Förstner, Jörg Soppa
Software Mentions: 4
Published: over 7 years ago

10.1016/j.stemcr.2020.05.007

Modeling and Rescue of RP2 Retinitis Pigmentosa Using iPSC-Derived Retinal Organoids
Cited by: 100
Author(s): Amelia Lane, Katarina Jovanović, Ciara Shortall, Daniele Ottaviani, Anna Brugulat Panes, Nele Schwarz, Rosellina Guarascio, Matthew J. Hayes, Arpad Palfi, Naomi Chadderton, G. Jane Farrar, Alison J. Hardcastle, Michael E. Cheetham
Software Mentions: 4
Published: about 6 years ago

10.1371/journal.pone.0187150

RNA-seq transcriptome analysis of formalin fixed, paraffin-embedded canine meningioma
Cited by: 13
Author(s): Jennifer K. Grenier, Polly Foureman, Erica A. Sloma, Andrew D. Miller
Software Mentions: 4
Published: almost 9 years ago

10.3390/cancers13184518

The Tumor Microenvironment-Dependent Transcription Factors AHR and HIF-1α Are Dispensable for Leukemogenesis in the Eµ-TCL1 Mouse Model of Chronic Lymphocytic Leukemia
Cited by: 3
Author(s): Susanne Gonder, Anne Largeot, Ernesto Gargiulo, Sandrine Pierson, Iria Fernandez Botana, Giulia Pagano, Jérôme Paggetti, Etienne Moussay
Software Mentions: 4
Published: about 5 years ago

10.1111/eva.12979

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

10.12688/f1000research.10571.2

Comprehensive comparison of Pacific Biosciences and Oxford Nanopore Technologies and their applications to transcriptome analysis
Cited by: 332
Author(s): Jason L. Weirather, Mariateresa de Cesare, Yunhao Wang, Paolo Piazza, Vittorio Sebastiano, Xiu‐Jie Wang, David Buck, Kin Fai Au
Software Mentions: 4
Published: over 9 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

10.1038/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

10.1371/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: about 8 years ago

10.3389/fbioe.2015.00028

G-CNV: A GPU-Based Tool for Preparing Data to Detect CNVs with Read-Depth Methods
Cited by: 8
Author(s): Andrea Manconi, Elias Manca, Marco Moscatelli, Matteo Gnocchi, Alessandro Orro, Giuliano Armano, Luciano Milanesi
Software Mentions: 4
Published: over 11 years ago

10.3389/fbioe.2020.00155

Multiple Small RNAs Interact to Co-regulate Ethanol Tolerance in Zymomonas mobilis
Cited by: 9
Author(s): Richou Han, Katie Haning, Juan C. Gonzalez-Rivera, Yongqiang Yang, Runxia Li, Seung Hee Cho, Ju Huang, Bobi A. Simonsen, Shihui Yang, Lydia M. Contreras
Software Mentions: 4
Published: over 6 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

10.1038/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

10.1038/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

10.1371/journal.pgen.1007905

Tissue- and sex-specific small RNAomes reveal sex differences in response to the environment
Cited by: 21
Author(s): Alexandra Bezler, Fabian Braukmann, Sean M. West, Arthur Duplan, Raffaella Conconi, Frédéric Schütz, Pierre Gönczy, Fabio Piano, Kristin C. Gunsalus, Eric A. Miska, Laurent Keller
Software Mentions: 4
Published: over 7 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

10.3389/fcimb.2020.594778

Biliary Microbial Structure of Gallstone Patients With a History of Endoscopic Sphincterotomy Surgery
Cited by: 6
Author(s): Haikang Shen, Juanjuan Zhu, Fuqiang Ye, Danyi Xu, Liang Fang, Jianfeng Yang, Huijie Lv, Qifeng Lou, Hangbin Jin, Ming Ni, Xiaofeng Zhang
Software Mentions: 4
Published: over 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

10.3389/fgene.2019.00854

New Recurrent Structural Aberrations in the Genome of Chronic Lymphocytic Leukemia Based on Exome-Sequencing Data
Cited by: 7
Author(s): Adrián Mosquera Orgueira, Beatriz Antelo Rodríguez, José Ángel Díaz Arias, Marta Sonia González Pérez, José Luis Bello López
Software Mentions: 4
Published: about 7 years ago

10.3389/fgene.2020.551065

Integration of Transcriptome Resequencing and Quantitative Proteomics Analyses of Collagenase VII-Induced Intracerebral Hemorrhage in Mice
Cited by: 11
Author(s): Fang Cao, Yu Guo, Qiang Zhang, Yinchun Fan, Qian Liu, Jiancheng Song, Hua Zhong, Shengtao Yao
Software Mentions: 4
Published: almost 6 years ago

10.3389/fgene.2020.00867

Single-Cell Transcriptome Analysis Reveals Six Subpopulations Reflecting Distinct Cellular Fates in Senescent Mouse Embryonic Fibroblasts
Cited by: 13
Author(s): Wei Chen, Xuefei Wang, Gang Wei, Yin Huang, Yufang Shi, Dan Li, Shengnu Qiu, Bin Zhou, Junhong Cao, Meng Chen, Pengfei Qin, Wenfei Jin, Ting Ni
Software Mentions: 4
Published: about 6 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

10.1371/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

10.1371/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

10.3389/fimmu.2021.644350

Analysis of Bulk RNA Sequencing Data Reveals Novel Transcription Factors Associated With Immune Infiltration Among Multiple Cancers
Cited by: 5
Author(s): Lei Liu, Qiuchen Zhao, Chao Cheng, Jingwen Yi, Hongyan Sun, Qi Wang, Weili Quan, Yaqiang Xue, Luguo Sun, Xianling Cong, Yi Zhang
Software Mentions: 4
Published: about 5 years ago

10.1371/journal.pgen.1007765

Hypomorphic mutation of the mouse Huntington’s disease gene orthologue
Cited by: 12
Author(s): Vidya Murthy, Toma Tebaldi, Toshimi Yoshida, Serkan Erdin, Teresa Calzonetti, Ravi Vijayvargia, Takshashila Tripathi, Emanuela Kerschbamer, Ihn Sik Seong, Alessandro Quattrone, Michael E. Talkowski, James F. Gusella, Katia Georgopoulos, Marcy E. MacDonald, Marta Biagioli
Software Mentions: 4
Published: over 7 years ago

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Papers Mentioning cutadapt 1,562