pypi: cutadapt | Projects | Ecosyste.ms: Papers

10.7554/eLife.59485

An ABA-GA bistable switch can account for natural variation in the variability of Arabidopsis seed germination time
Cited by: 17
Author(s): Katie Abley, Pau Formosa-Jordan, Hugo Tavares, Eric J. Chan, Mana Afsharinafar, Ottoline Leyser, James Locke
Software Mentions: 3
Published: over 3 years ago

10.1016/j.molcel.2020.11.004

The Short- and Long-Range RNA-RNA Interactome of SARS-CoV-2
Cited by: 141
Author(s): Omer Ziv, Jonathan Price, Lyudmila Shalamova, Tsveta Kamenova, Ian Goodfellow, Friedemann Weber, Eric A. Miska
Software Mentions: 3
Published: almost 4 years ago

10.1016/j.molcel.2020.03.017

Division of Labor between PCNA Loaders in DNA Replication and Sister Chromatid Cohesion Establishment
Cited by: 39
Author(s): Hon Wing Liu, Céline Bouchoux, Mélanie Panarotto, Yasutaka Kakui, Harshil Patel, Frank Uhlmann
Software Mentions: 3
Published: over 4 years ago

10.18632/aging.103691

The association of serum vitamin K2 levels with Parkinson's disease: from basic case-control study to big data mining analysis
Cited by: 11
Author(s): Yanxia Yu, Xiaodan Yu, Qin-Zhang Cheng, Lian Tang, Mingqiang Shen
Software Mentions: 3
Published: about 4 years ago

10.1186/s12915-018-0509-4

Madagascar ground gecko genome analysis characterizes asymmetric fates of duplicated genes
Cited by: 39
Author(s): Yuichiro Hara, Miki Takeuchi, Yuka Kageyama, Kaori Tatsumi, Masahiko Hibi, Hiroshi Kanazawa, Shigehiro Kuraku
Software Mentions: 3
Published: over 6 years ago

10.1111/jipb.13037

Roles of DEMETER in regulating DNA methylation in vegetative tissues and pathogen resistance
Cited by: 20
Author(s): Wenjie Zhang, Huan Huang, Xin Lin, Zhu C, Ken‐ichi Kosami, Chao‐Feng Huang, Huiming Zhang, Cheng‐Guo Duan, Jian‐Kang Zhu, Daisuke Miki
Software Mentions: 3
Published: over 3 years ago

10.1186/s12885-020-07571-0

Targeted nanopore sequencing for the identification of ABCB1 promoter translocations in cancer
Cited by: 6
Author(s): Mark S. Williams, Naseer J. Basma, Fabio Amaral, Gillian Williams, John Weightman, Wolfgang Breitwieser, Louisa Nelson, Stephen S. Taylor, Daniel H. Wiseman, Tim C. P. Somervaille
Software Mentions: 3
Published: about 4 years ago

10.1111/mmi.14237

Systematic analysis of Type I‐E <i>Escherichia coli</i> CRISPR‐Cas PAM sequences ability to promote interference and primed adaptation
Cited by: 26
Author(s): Olga Musharova, Vasily Sitnik, Marnix Vlot, Ekaterina Savitskaya, Kirill A. Datsenko, Andrey Krivoy, Ivan Fedorov, Ekaterina Semenova, Stan J. J. Brouns, Konstantin Severinov
Software Mentions: 3
Published: over 5 years ago

10.1002/1878-0261.12828

TGFBI modulates tumour hypoxia and promotes breast cancer metastasis
Cited by: 30
Author(s): Flavia Fico, Albert Santamaria-Martínez
Software Mentions: 3
Published: about 4 years ago

10.1186/s12974-019-1545-x

Differential transcriptional profiles identify microglial- and macrophage-specific gene markers expressed during virus-induced neuroinflammation
Cited by: 81
Author(s): Ana Beatriz DePaula-Silva, Carlos Gorbea, Daniel J. Doty, Jane E. Libbey, John Michael S. Sanchez, Tyler J. Hanak, Demián Cazalla, Robert S. Fujinami
Software Mentions: 3
Published: over 5 years ago

10.3390/ijms22137212

Isolation and Characterization of Barley (Hordeum vulgare) Extracellular Vesicles to Assess Their Role in RNA Spray-Based Crop Protection
Cited by: 7
Author(s): Timo Schlemmer, Patrick Barth, Weipert Lisa, Preußer Christian, Martin Hardt, Möbus Anna, Tobias Busche, Aline Koch
Software Mentions: 3
Published: over 3 years ago

10.1186/s12885-018-4567-3

Deep sequencing of human papillomavirus positive loco-regionally advanced oropharyngeal squamous cell carcinomas reveals novel mutational signature
Cited by: 13
Author(s): Christian Grónhøj Larsen, David Hebbelstrup Jensen, Tina Klitmøller Agander, Katalin Kiss, Estrid Høgdall, Lena Specht, Frederik Otzen Bagger, Finn Cilius Nielsen
Software Mentions: 3
Published: over 6 years ago

10.1016/j.ijpara.2020.06.002

Extracellular vesicles from Heligmosomoides bakeri and Trichuris muris contain distinct microRNA families and small RNAs that could underpin different functions in the host
Cited by: 15
Author(s): Ruby White, Sujai Kumar, Wang Ngai Chow, E. Graeme Robertson, Kelly S. Hayes, Richard K. Grencis, María A. Duque-Correa, Amy H. Buck
Software Mentions: 3
Published: over 4 years ago

10.18632/oncotarget.19483

Identification of hub genes involved in the development of hepatocellular carcinoma by transcriptome sequencing
Cited by: 8
Author(s): Yongchang Zheng, Junyu Long, Liangcai Wu, Haohai Zhang, Lin Li, Ying Zheng, Anqiang Wang, Jianzhen Lin, Xiaobo Yang, Xinting Sang, Ke Hu, Jie Pan, Haitao Zhao
Software Mentions: 3
Published: over 7 years ago

10.1093/ve/veaa010

Linking influenza virus evolution within and between human hosts
Cited by: 39
Author(s): Katherine S Xue, Jesse D. Bloom
Software Mentions: 3
Published: almost 5 years ago

10.1186/s42523-021-00110-7

The link between broiler flock heterogeneity and cecal microbiome composition
Cited by: 13
Author(s): Randi Lundberg, Christian Scharch, Dorthe Sandvang
Software Mentions: 3
Published: over 3 years ago

10.1038/s41598-020-68437-w

Injection of seminal fluid into the hemocoel of honey bee queens (Apis mellifera) can stimulate post-mating changes
Cited by: 9
Author(s): W. Cameron Jasper, Laura M. Brutscher, Christina M. Grozinger, Elina L. Niño
Software Mentions: 3
Published: over 4 years ago

10.1186/s12862-017-0888-0

Phylogeography of red muntjacs reveals three distinct mitochondrial lineages
Cited by: 23
Author(s): Raquel A. Martins, Jörns Fickel, Minh Đức Lê, Thanh Van Nguyen, Ha L. Nguyen, Robert J. Timmins, Han Ming Gan, Jeffrine J. Rovie-Ryan, Dorina Lenz, Daniel W. Förster, Andreas Wilting
Software Mentions: 3
Published: almost 8 years ago

10.3390/ijms22136843

Comparison of Gut Bacterial Communities of Grapholita molesta (Lepidoptera: Tortricidae) Reared on Different Host Plants
Cited by: 23
Author(s): Xiangqun Yuan, Xuan Zhang, Xueying Liu, Yanlu Dong, Zizheng Yan, Dongbiao Lv, Ping Wang, Yiping Li
Software Mentions: 3
Published: over 3 years ago

10.1002/yea.3211

Proteomic and genomic characterization of a yeast model for Ogden syndrome
Cited by: 14
Author(s): Max J. Dörfel, Fang Han, Jonathan Crain, Michael E Klingener, Jake Weiser, Gholson J. Lyon
Software Mentions: 3
Published: almost 8 years ago

10.18632/oncotarget.6922

Histone H3 lysine 4 acetylation and methylation dynamics define breast cancer subtypes
Cited by: 88
Author(s): Terri L. Messier, Jonathan A. R. Gordon, Joseph R. Boyd, Coralee E. Tye, Gillian Browne, Janet L. Stein, Jane B. Lian
Software Mentions: 3
Published: almost 9 years ago

10.1038/s41598-020-65487-y

Genome sequence and comparative analysis of reindeer (Rangifer tarandus) in northern Eurasia
Cited by: 28
Author(s): Melak Weldenegodguad, Kisun Pokharel, Ming Yao, Mervi Honkatukia, Jaana Peippo, Tiina Reilas, Knut Røed, Juha Kantanen
Software Mentions: 3
Published: over 4 years ago

10.1186/s12864-018-4651-8

Transcriptional development of phospholipid and lipoprotein metabolism in different intestinal regions of Atlantic salmon (Salmo salar) fry
Cited by: 11
Author(s): Yang Jin, Rolf Erik Olsen, Mari‐Ann Östensen, Gareth Benjamin Gillard, Sven Arild Korsvoll, Nina Santi, Arne B. Gjuvsland, Jon Olav Vik, Jacob Torgersen, Simen Rød Sandve, Yngvar Ôlsen
Software Mentions: 3
Published: over 6 years ago

10.3390/ani11051433

Faecal Microbiome Transplantation as a Solution to Chronic Enteropathies in Dogs: A Case Study of Beneficial Microbial Evolution
Cited by: 11
Author(s): Michele Berlanda, Giada Innocente, Barbara Simionati, Barbara Di Camillo, Sonia Facchin, Maria Cecilia Giron, Edoardo Savarino, Federico Sebastiani, Francesca Fiorio, Ilaria Patuzzi
Software Mentions: 3
Published: over 3 years ago

10.7717/peerj.11166

Transcriptome analysis of the liver of Eospalax fontanierii under hypoxia
Cited by: 3
Author(s): Zhiqiang Hao, Lulu Xu, Li Zhao, Jianxing He, Guanglin Li, Jingang Li
Software Mentions: 3
Published: over 3 years ago

10.7717/peerj.9085

Fast sequence-based microsatellite genotyping development workflow
Cited by: 24
Author(s): Olivier Lepais, Émilie Chancerel, Christophe Boury, Franck Salin, Aurélie Manicki, Laura Taillebois, Cyril Dutech, Abdeldjalil Aissi, Cecile F. E. Bacles, Françoise Daverat, Sophie Launey, Erwan Guichoux
Software Mentions: 3
Published: over 4 years ago

10.1038/s41598-020-63263-6

Circulating MicroRNA Profiling in Non-ST Elevated Coronary Artery Syndrome Highlights Genomic Associations with Serial Platelet Reactivity Measurements
Cited by: 14
Author(s): Kristian C. Becker, Lydia Coulter Kwee, Megan L. Neely, Elizabeth Grass, Joseph A. Jakubowski, Keith Fox, Harvey D. White, Simon Gregory, Paul A. Gurbel, Leonardo de Pinto Carvalho, Richard C. Becker, E. Magnus Ohman, Matthew T. Roe, Svati H. Shah, Mark Y. Chan
Software Mentions: 3
Published: over 4 years ago

10.7717/peerj.5443

Transcriptome analysis and identification of key genes involved in 1-deoxynojirimycin biosynthesis of mulberry (<i>Morus alba</i>L.)
Cited by: 20
Author(s): Dujun Wang, Li Zhao, Dan Wang, Jia Liu, Xin Yu, Yuan Wei, Zhen Ouyang
Software Mentions: 3
Published: about 6 years ago

10.1186/s12864-016-3168-2

Novel equine tissue miRNAs and breed-related miRNA expressed in serum
Cited by: 27
Author(s): Alicja Pacholewska, Núria Mach, Xavier Mata, Anne Vaiman, Laurent Schibler, Éric Barrey, V. Gerber
Software Mentions: 3
Published: about 8 years ago

10.1038/s41598-020-59407-3

MicroRNAs regulate innate immunity against uropathogenic and commensal-like Escherichia coli infections in the surrogate insect model Galleria mellonella
Cited by: 15
Author(s): Krishnendu Mukherjee, Daniel Amsel, Miriam Kalsy, André Billion, Ulrich Dobrindt, Andreas Vilcinskas
Software Mentions: 3
Published: almost 5 years ago

10.3390/ani11041150

Whole Blood Transcriptome Profiling Reveals Positive Effects of Olive Leaves-Supplemented Diet on Cholesterol in Goats
Cited by: 1
Author(s): Andrea Ianni, Francesca Bennato, Camillo Martino, Martina Colapietro, Giuseppe Martino
Software Mentions: 3
Published: over 3 years ago

10.1002/prp2.632

Ascorbate sensitizes human osteosarcoma cells to the cytostatic effects of cisplatin
Cited by: 8
Author(s): Naohiro Oka, Akiyoshi Komuro, Hideharu Amano, Suman Dash, Masahiko Honda, Kyoko Ota, Shunji Nishimura, Takeshi Ueda, Masao Akagi, Hitoshi Okada
Software Mentions: 3
Published: over 4 years ago

10.1038/s41598-019-52712-6

Whole blood transcriptome analysis in ewes fed with hemp seed supplemented diet
Cited by: 18
Author(s): Marco Iannaccone, Andrea Ianni, Felice Contaldi, Salvatore Esposito, Camillo Martino, Francesca Bennato, Elisabetta De Angelis, Lisa Grotta, Francesco Pomilio, Daniele Giansante, Giuseppe Martino
Software Mentions: 3
Published: about 5 years ago

10.1038/s41598-019-52444-7

A specific fungal transcription factor controls effector gene expression and orchestrates the establishment of the necrotrophic pathogen lifestyle on wheat
Cited by: 27
Author(s): Darcy A. B. Jones, Evan John, Kasia Rybak, H. Phan, Karam B. Singh, Shao-Yu Lin, Peter S. Solomon, Richard P. Oliver, Kar‐Chun Tan
Software Mentions: 3
Published: about 5 years ago

10.3390/plants8020047

Intrusive Growth of Phloem Fibers in Flax Stem: Integrated Analysis of miRNA and mRNA Expression Profiles
Cited by: 16
Author(s): Oleg Gorshkov, Tatyana Chernova, Natalia Mokshina, Natalia Gogoleva, Dmitry Suslov, А.А. Ткаченко, Т. А. Горшкова
Software Mentions: 3
Published: almost 6 years ago

10.3390/plants9091080

Transcriptome-Wide N6-Methyladenosine (m6A) Methylome Profiling of Heat Stress in Pak-choi (Brassica rapa ssp. chinensis)
Cited by: 30
Author(s): Gaofeng Liu, Jin Wang, Xilin Hou
Software Mentions: 3
Published: over 4 years ago

10.3390/plants9010060

Analysis of Small RNAs of Barley Genotypes Associated with Resistance to Barley Yellow Dwarf Virus
Cited by: 8
Author(s): Jana Jarošová, Kundan Singh, J. Chrpová, Jiban Kumar Kundu
Software Mentions: 3
Published: almost 5 years ago

10.1371/journal.pbio.3000689

Telomeric TART elements target the piRNA machinery in Drosophila
Cited by: 7
Author(s): Chris Ellison, Meenakshi S. Kagda, Weihuan Cao
Software Mentions: 3
Published: almost 4 years ago

10.1371/journal.pbio.3000739

Increased prostaglandin-D2 in male STAT3-deficient hearts shifts cardiac progenitor cells from endothelial to white adipocyte differentiation
Cited by: 3
Author(s): Elisabeth Stelling, Melanie Ricke‐Hoch, Sergej Erschow, Steve Hoffmann, Anke Bergmann, Maren Heimerl, Stefan Pietzsch, Karin Battmer, Alexandra Haase, Britta Stapel, Michaela Scherr, Jean‐Luc Balligand, Ofer Binah, Denise Hilfiker‐Kleiner
Software Mentions: 3
Published: almost 4 years ago

10.1371/journal.pbio.3001121

CD74 is a regulator of hematopoietic stem cell maintenance
Cited by: 13
Author(s): Shirly Becker-Herman, Milena Rozenberg, Carmit Hillel-Karniel, Naama Gil-Yarom, Matthias P. Kramer, Avital Barak, Lital Sever, Keren David, Lihi Radomir, Hadas Lewinsky, Michal Levi, Gilgi Friedlander, Richard Bucala, Amnon Peled, Idit Shachar
Software Mentions: 3
Published: over 3 years ago

10.1371/journal.pcbi.1007309

miRWoods: Enhanced precursor detection and stacked random forests for the sensitive detection of microRNAs
Cited by: 8
Author(s): Jimmy D. Bell, Maureen K. Larson, Michelle Anne Kutzler, Massimo Bionaz, Christiane V. Löhr, David A. Hendrix
Software Mentions: 3
Published: about 5 years ago

10.1038/s41598-019-42207-9

Parallel sequencing of porA reveals a complex pattern of Campylobacter genotypes that differs between broiler and broiler breeder chickens
Cited by: 12
Author(s): Frances M. Colles, Stephen G. Preston, Kenneth Klingenberg Barfod, Patrik G. Flammer, Maiden Mcj., Adrian L. Smith
Software Mentions: 3
Published: over 5 years ago

10.1371/journal.pgen.1008582

Roles of Candida albicans Mig1 and Mig2 in glucose repression, pathogenicity traits, and SNF1 essentiality
Cited by: 32
Author(s): Katherine Lagree, Carol A. Woolford, Manning Y. Huang, Gemma E. May, C. Joel McManus, Norma V. Solis, Scott G. Filler, Aaron P. Mitchell
Software Mentions: 3
Published: almost 5 years ago

10.1371/journal.pgen.1009761

The CovR regulatory network drives the evolution of Group B Streptococcus virulence
Cited by: 11
Author(s): Maria-Vittoria Mazzuoli, Maëlle Daunesse, Hugo Varet, Isabelle Rosinski‐Chupin, Rachel Legendre, Odile Sismeiro, Myriam Gominet, P.A. Kaminski, Philippe Glaser, Claudia Chica, Patrick Trieu-Cuot, Arnaud Firon
Software Mentions: 3
Published: about 3 years ago

10.1038/s41598-019-39608-1

Field transcriptome revealed a novel relationship between nitrate transport and flowering in Japanese beech
Cited by: 16
Author(s): Akiko Satake, Kazutaka Kawatsu, Kenjiro Teshima, Daisuke Kabeya, Qingmin Han
Software Mentions: 3
Published: over 5 years ago

10.1186/s12864-017-4141-4

Single molecule counting and assessment of random molecular tagging errors with transposable giga-scale error-correcting barcodes
Cited by: 3
Author(s): Billy T. Lau, Hanlee P. Ji
Software Mentions: 3
Published: about 7 years ago

10.1186/s12864-020-06778-6

Impacts of local population history and ecology on the evolution of a globally dispersed pathogen
Cited by: 18
Author(s): Andreína I. Castillo, Carlos Chacón-Díaz, Neysa Rodríguez-Murillo, Helvécio Della Coletta-Filho, Rodrigo P. P. Almeida
Software Mentions: 3
Published: over 4 years ago

10.1038/s41598-019-39880-1

MicroRNAs from saliva of anopheline mosquitoes mimic human endogenous miRNAs and may contribute to vector-host-pathogen interactions
Cited by: 25
Author(s): Bruno Arcà, Alessio Colantoni, Carmine Fiorillo, Francesco Severini, Vladimír Beneš, Marco Di Luca, Raffaele Calogero, Fabrizio Lombardo
Software Mentions: 3
Published: over 5 years ago

10.1186/1471-2164-15-148

Improving transcriptome construction in non-model organisms: integrating manual and automated gene definition in Emiliania huxleyi
Cited by: 30
Author(s): Ester Feldmesser, Shilo Rosenwasser, Assaf Vardi, Shifra Ben‐Dor
Software Mentions: 3
Published: almost 11 years ago

10.1038/s41598-019-38932-w

Diff isomiRs: Large-scale detection of differential isomiRs for understanding non-coding regulated stress omics in plants
Cited by: 8
Author(s): Kun Yang, Xiaopeng Wen, Suresh B. Mudunuri, G. P. S. Varma, Gaurav Sablok
Software Mentions: 3
Published: almost 6 years ago

10.1038/s41598-018-36866-3

Marine biogenics in sea spray aerosols interact with the mTOR signaling pathway
Cited by: 12
Author(s): Jana Asselman, Emmanuel Van Acker, Maarten De Rijcke, Laurentijn Tilleman, Filip Van Nieuwerburgh, Jan Mees, Karel A.C. De Schamphelaere, Colin R. Janssen
Software Mentions: 3
Published: almost 6 years ago

10.1371/journal.pntd.0009297

Expression profiling of Echinococcus multilocularis miRNAs throughout metacestode development in vitro
Cited by: 7
Author(s): Natalia Macchiaroli, Matías Preza, Moira Pérez, Laura Kamenetzky, Marcela Alejandra Cucher, Uriel Koziol, Estela Castillo, Matthew Berriman, Klaus Brehm, Mara Cecília Rosenzvit
Software Mentions: 3
Published: over 3 years ago

10.1371/journal.pntd.0007811

Comparative analysis of small RNAs released by the filarial nematode Litomosoides sigmodontis in vitro and in vivo
Cited by: 19
Author(s): Juan F. Quintana, Sujai Kumar, Alasdair Ivens, Wang Ngai Chow, Anna M. Hoy, Alison Fulton, Paul Dickinson, Coralie Martin, Matthew D. Taylor, Simon A. Babayan, Amy H. Buck
Software Mentions: 3
Published: almost 5 years ago

10.1038/s41598-018-36342-y

Gene expression profiles alteration after infection of virus, bacteria, and parasite in the Olive flounder (Paralichthys olivaceus)
Cited by: 8
Author(s): Gyu-Hwi Nam, Anshuman Mishra, Jeong‐An Gim, Hee-Eun Lee, Ara Jo, Dahye Yoon, Ahran Kim, Woo Jin Kim, Kung Ahn, Do-Hyung Kim, Suhkmann Kim, Hee‐Jae Cha, Yung Hyun Choi, Chan-Il Park, Heui‐Soo Kim
Software Mentions: 3
Published: almost 6 years ago

10.1038/s41598-018-33964-0

Amyotrophic Lateral Sclerosis associated FUS mutation shortens mitochondria and induces neurotoxicity
Cited by: 54
Author(s): Tadashi Nakaya, Manolis Maragkakis
Software Mentions: 3
Published: about 6 years ago

10.1186/s12864-018-5167-y

Transcriptomic analysis reveals specific metabolic pathways of enterohemorrhagic Escherichia coli O157:H7 in bovine digestive contents
Cited by: 13
Author(s): Audrey Segura, Marine Bertoni, Pauline Auffret, Christophe Klopp, Olivier Bouchez, Clémence Genthon, Alexandra Durand, Yolande Bertin, Evelyne Forano
Software Mentions: 3
Published: about 6 years ago

10.1038/s41598-018-33627-0

Blood immune transcriptome analysis of artificially fed dairy calves and naturally suckled beef calves from birth to 7 days of age
Cited by: 8
Author(s): Carla Surlis, Bernadette Earley, M. McGee, Kate Keogh, Paul Cormican, Gordon Blackshields, K. Tiernan, Amanda Dunn, Steven Morrison, A. Argüello, Sinéad M. Waters
Software Mentions: 3
Published: about 6 years ago

10.1186/s12864-015-2252-3

Construction of relatedness matrices using genotyping-by-sequencing data
Cited by: 104
Author(s): K. G. Dodds, John C. McEwan, Rüdiger Bräuning, R. M. Anderson, Tracey C. van Stijn, Theódór Kristjánsson, Shannon Clarke
Software Mentions: 3
Published: almost 9 years ago

10.1371/journal.pone.0095633

Hybridization Capture Reveals Evolution and Conservation across the Entire Koala Retrovirus Genome
Cited by: 39
Author(s): Kyriakos Tsangaras, Matthew C. Siracusa, Nikolas Nikolaidis, Yasuko Ishida, Pin Cui, Hanna Vielgrader, Kristofer M. Helgen, Alfred L. Roca, Alex D. Greenwood
Software Mentions: 3
Published: over 10 years ago

10.3390/ijms22010296

Distinct Regulation of the Expression of Satellite DNAs in the Beetle Tribolium castaneum
Cited by: 4
Author(s): Antonio Sermek, Isidoro Feliciello, Đurđica Ugarković
Software Mentions: 3
Published: almost 4 years ago

10.1371/journal.pone.0211978

Testing of library preparation methods for transcriptome sequencing of real life glioblastoma and brain tissue specimens: A comparative study with special focus on long non-coding RNAs
Cited by: 7
Author(s): Marek Večeřa, Jiří Šána, Jan Oppelt, Boris Tichý, Alena Kopková, Radim Lipina, Martin Smrčka, Radim Jančálek, Markéta Hermanová, Leoš Křen, Ondřej Slabý
Software Mentions: 3
Published: almost 6 years ago

10.1038/s41598-018-26453-x

Blood lipid-related low-frequency variants in LDLR and PCSK9 are associated with onset age and risk of myocardial infarction in Japanese
Cited by: 14
Author(s): Tomoyuki Tajima, Hiroyuki Morita, Kei Ito, Tsutomu Yamazaki, Michiaki Kubo, Issei Komuro, Yukihide Momozawa
Software Mentions: 3
Published: over 6 years ago

10.1371/journal.pone.0194023

ER-positive breast cancer cells are poised for RET-mediated endocrine resistance
Cited by: 18
Author(s): Sachi Horibata, Edward J. Rice, Chinatsu Mukai, Brooke A. Marks, Kelly L. Sams, Hui Zheng, Lynne J. Anguish, Scott A. Coonrod, Charles G. Danko
Software Mentions: 3
Published: over 6 years ago

10.1371/journal.pone.0201851

Small RNAs detected in exosomes derived from the MH7A synovial fibroblast cell line with TNF-α stimulation
Cited by: 19
Author(s): Yosuke Takamura, Wataru Aoki, Atsushi Satomura, Seiji Shibasaki
Software Mentions: 3
Published: over 6 years ago

10.1186/s12864-015-2111-2

Identification and annotation of conserved promoters and macrophage-expressed genes in the pig genome
Cited by: 15
Author(s): Christelle Robert, Ronan Kapétanovic, Dario Beraldi, Michael Watson, Alan Archibald, David Hume
Software Mentions: 3
Published: about 9 years ago

10.1371/journal.pone.0194036

Allele-specific DNA methylation of disease susceptibility genes in Japanese patients with inflammatory bowel disease
Cited by: 11
Author(s): Hirofumi Chiba, Yoichi Kakuta, Yoshitaka Kinouchi, Yosuke Kawai, Kazuhiro Watanabe, Munenori Nagao, Takeo Naito, Motoyuki Onodera, Rintaro Moroi, Masatake Kuroha, Yoshitake Kanazawa, Tsutomu Kimura, Hisashi Shiga, Katsuya Endo, Kenichi Negoro, Masao Nagasaki, Michiaki Unno, Tooru Shimosegawa
Software Mentions: 3
Published: over 6 years ago

10.1371/journal.pone.0242880

A shotgun metagenomic investigation of the microbiota of udder cleft dermatitis in comparison to healthy skin in dairy cows
Cited by: 7
Author(s): Lisa Ekman, Elisabeth Bagge, Ann-Kristin Nyman, Karin Persson Waller, Märit Pringle, Bo Segerman
Software Mentions: 3
Published: almost 4 years ago

10.1371/journal.pone.0182638

Epigenetic differences between monozygotic twins discordant for amyotrophic lateral sclerosis (ALS) provide clues to disease pathogenesis
Cited by: 35
Author(s): Paul E. Young, Stephen Kum Jew, Michael E. Buckland, Roger Pamphlett, Catherine M. Suter
Software Mentions: 3
Published: over 7 years ago

10.1038/s41598-017-16193-9

PinAPL-Py: A comprehensive web-application for the analysis of CRISPR/Cas9 screens
Cited by: 66
Author(s): Philipp N. Spahn, Tyler Bath, Ryan J. Weiss, Jihoon Kim, Jeffrey D. Esko, Nathan E. Lewis, Olivier Harismendy
Software Mentions: 3
Published: about 7 years ago

10.1038/s41598-017-14301-3

Exosomal microRNA signatures in multiple sclerosis reflect disease status
Cited by: 178
Author(s): Saeideh Ebrahimkhani, Fatemeh Vafaee, Paul E. Young, Suzy S J Hur, Simon Hawke, Emma Devenney, Heidi Beadnall, Michael Barnett, Catherine M. Suter, Michael E. Buckland
Software Mentions: 3
Published: about 7 years ago

10.3390/ijms21218252

Aging Induces Profound Changes in sncRNA in Rat Sperm and These Changes Are Modified by Perinatal Exposure to Environmental Flame Retardant
Cited by: 9
Author(s): Alexander Suvorov, J. Richard Pilsner, В. А. Наумов, Victoria Shtratnikova, Anna Zheludkevich, Evgeny S. Gerasimov, Maria D. Logacheva, Oleg Sergeyev
Software Mentions: 3
Published: about 4 years ago

10.1371/journal.pone.0114598

Impact of the Genetic Background on the Composition of the Chicken Plasma MiRNome in Response to a Stress
Cited by: 14
Author(s): Marie-Laure Endale Ahanda, Tatiana Zerjal, Sophie Dhorne–Pollet, Andrea Rau, Amanda M. Cooksey, Elisabetta Giuffra
Software Mentions: 3
Published: almost 10 years ago

10.1038/srep37814

Environmental Intervention as a Therapy for Adverse Programming by Ancestral Stress
Cited by: 46
Author(s): J. Keiko McCreary, Zachary T. Erickson, Yongxin Hao, Yaroslav Ilnytskyy, Igor Kovalchuk, Gerlinde A. S. Metz
Software Mentions: 3
Published: almost 8 years ago

10.3390/ijms21197120

Transcriptome and Gene Fusion Analysis of Synchronous Lesions Reveals lncMRPS31P5 as a Novel Transcript Involved in Colorectal Cancer
Cited by: 2
Author(s): Anna Panza, Stefano Castellana, Giuseppe Biscaglia, Ada Piepoli, Luca Parca, Annamaria Gentile, Anna Latiano, Tommaso Mazza, Francesco Perri, Angelo Andriulli
Software Mentions: 3
Published: about 4 years ago

10.1038/srep35436

Integrating Candida albicans metabolism with biofilm heterogeneity by transcriptome mapping
Cited by: 34
Author(s): Ranjith Rajendran, Ali May, Leighann Sherry, Ryan Kean, Craig Williams, Brian Jones, Karl Burgess, Jaap Heringa, Sanne Abeln, Bernd W. Brandt, Carol A. Munro, Gordon Ramage
Software Mentions: 3
Published: about 8 years ago

10.1038/srep28984

An emerging zoonotic clone in the Netherlands provides clues to virulence and zoonotic potential of Streptococcus suis
Cited by: 37
Author(s): Niels Willemse, Kate J. Howell, Lucy A. Weinert, Annet Heuvelink, Yvonne Pannekoek, Jaap A. Wagenaar, Hilde E. Smith, Arie van der Ende, Constance Schultsz
Software Mentions: 3
Published: over 8 years ago

10.1038/srep29235

A highly diverse, desert-like microbial biocenosis on solar panels in a Mediterranean city
Cited by: 31
Author(s): Pedro Dorado-Morales, Cristina Vilanova, Juli Peretó, Francisco M. Codoñer, Daniel Ramón, Manuel Porcar
Software Mentions: 3
Published: over 8 years ago

10.1371/journal.pone.0209846

Bioinformatic analysis of long-lasting transcriptional and translational changes in the basolateral amygdala following acute stress
Cited by: 19
Author(s): Stephanie E. Sillivan, Meghan E. Jones, Sarah E. Jamieson, Gavin Rumbaugh, Courtney A. Miller
Software Mentions: 3
Published: almost 6 years ago

10.1038/srep08957

Systematic identification and characterization of long intergenic non-coding RNAs in fetal porcine skeletal muscle development
Cited by: 84
Author(s): Weimin Zhao, Yulian Mu, Lei Ma, Chen Wang, Zhonglin Tang, Shulin Yang, Rong Zhou, Xiaoju Hu, Menghua Li, Kui Li
Software Mentions: 3
Published: over 9 years ago

10.1186/s12864-016-2704-4

Characterization of the watercress (Nasturtium officinale R. Br.; Brassicaceae) transcriptome using RNASeq and identification of candidate genes for important phytonutrient traits linked to human health
Cited by: 30
Author(s): Nikol Voutsina, Adrienne Payne, Robert D. Hancock, Graham J. J. Clarkson, Steve D. Rothwell, Mark A. Chapman, Gail Taylor
Software Mentions: 3
Published: over 8 years ago

10.1371/journal.pone.0222531

Pathogen surveillance in the informal settlement, Kibera, Kenya, using a metagenomics approach
Cited by: 22
Author(s): René S. Hendriksen, Oksana Lukjancenko, Patrick Munk, Mathis Hjort Hjelmsø, Jennifer R. Verani, Eric Ng’eno, Godfrey Bigogo, Samuel Kiplangat, Traoré Soumana Oumar, Lasse Bergmark, Timo Röder, John Neatherlin, Clayton Onyango, Tine Hald, Susanne Karlsmose, Sünje Johanna Pamp, Barry S. Fields, Joel M. Montgomery, Frank Møller Aarestrup
Software Mentions: 3
Published: about 5 years ago

10.1038/s41597-020-0556-x

Chromatin accessibility and transcriptome landscapes of Monomorium pharaonis brain
Cited by: 9
Author(s): Mingyue Wang, Yang Liu, Tinggang Wen, Weiwei Liu, Qionghua Gao, Jie Zhao, Zijun Xiong, Zhifeng Wang, Wei Jiang, Yeya Yu, Liang Wu, Yue Yuan, Xiaoyü Wei, Jiangshan Xu, Mengnan Cheng, Pei Zhang, Panyi Li, Yong Hou, Huanming Yang, Guojie Zhang, Qiye Li, Chuanyu Liu, Longqi Liu
Software Mentions: 3
Published: over 4 years ago

10.1371/journal.pone.0145575

Effects of Fertilization and Sampling Time on Composition and Diversity of Entire and Active Bacterial Communities in German Grassland Soils
Cited by: 35
Author(s): Sarah Herzog, Franziska Wemheuer, Bernd Wemheuer, Rolf Daniel
Software Mentions: 3
Published: almost 9 years ago

10.1371/journal.pone.0157783

De Novo Transcriptome Analysis of the Common New Zealand Stick Insect Clitarchus hookeri (Phasmatodea) Reveals Genes Involved in Olfaction, Digestion and Sexual Reproduction
Cited by: 15
Author(s): Chen Wu, Ross N. Crowhurst, Alice B. Dennis, Victoria Twort, Shanlin Liu, Richard D. Newcomb, Howard A. Ross, Thomas R. Buckley
Software Mentions: 3
Published: over 8 years ago

10.1038/s41597-019-0140-4

Transcriptome profiling of interaction effects of soybean cyst nematodes and soybean aphids on soybean
Cited by: 11
Author(s): Surendra Neupane, Febina M. Mathew, Adam J. Varenhorst, Madhav P. Nepal
Software Mentions: 3
Published: over 5 years ago

10.1038/sdata.2019.6

RNA-Seq profiling in peripheral blood mononuclear cells of amyotrophic lateral sclerosis patients and controls
Cited by: 21
Author(s): Susanna Zucca, Stella Gagliardi, Cecilia Pandini, Luca Diamanti, Matteo Bordoni, Daisy Sproviero, Maddalena Arigoni, Martina Olivero, Orietta Pansarasa, Mauro Ceroni, Raffaele Calogero, Cristina Cereda
Software Mentions: 3
Published: almost 6 years ago

10.1038/sdata.2018.146

BARM and BalticMicrobeDB, a reference metagenome and interface to meta-omic data for the Baltic Sea
Cited by: 33
Author(s): Johannes Alneberg, John Sundh, Christin M. Bennke, Sara Beier, Daniel Lundin, Luisa W. Hugerth, Jarone Pinhassi, Veljo Kisand, Lasse Riemann, Klaus Jürgens, Matthias Labrenz, Anders F. Andersson
Software Mentions: 3
Published: over 6 years ago

10.1038/sdata.2017.67

Single-cell transcriptome of early embryos and cultured embryonic stem cells of cynomolgus monkeys
Cited by: 40
Author(s): Tomonori Nakamura, Yukihiro Yabuta, Ikuhiro Okamoto, Kotaro Sasaki, Chizuru Iwatani, Hideaki Tsuchiya, Mitinori Saitou
Software Mentions: 3
Published: over 7 years ago

10.1371/journal.pone.0128022

Chamber Bioaerosol Study: Outdoor Air and Human Occupants as Sources of Indoor Airborne Microbes
Cited by: 148
Author(s): Rachel I. Adams, Seema Bhangar, Wilmer Pasut, Edward Arens, John W. Taylor, Steven E. Lindow, William W. Nazaroff, Thomas D. Bruns
Software Mentions: 3
Published: over 9 years ago

10.1371/journal.pone.0131787

Quantitative Analysis of MicroRNAs in Vaccinia virus Infection Reveals Diversity in Their Susceptibility to Modification and Suppression
Cited by: 5
Author(s): Amy H. Buck, Alasdair Ivens, Katrina Gordon, Nicky Craig, Alexandre Houzelle, Alice Roche, Neil Turnbull, Philippa M. Beard
Software Mentions: 3
Published: over 9 years ago

10.21203/rs.3.rs-86169/v1

Clofazimine is a broad-spectrum coronavirus inhibitor that antagonizes SARS-CoV-2 replication in primary human cell culture and hamsters
Cited by: 11
Author(s): Shuofeng Yuan, Xin Yin, Xiangzhi Meng, Jasper Fuk Woo Chan, Zi‐Wei Ye, Laura Riva, Lars Pache, Chris Chun-Yiu Chan, Pok-Man Lai, Chris Chun Yiu Chan, Vincent Kwok Man Poon, Naoko Matsunaga, Yuan Pu, Chun-Kit Yuen, Jianli Cao, Ronghui Liang, Kaiming Tang, Sheng Li, Yushen Du, Wan Xu, Kong-Hung Sze, Jinxia Zhang, Hin Chu, Kin‐Hang Kok, Kelvin Kai-Wang To, Dong-Yan Jin, Ren Sun, Sumit K. Chanda, Kwok‐Yung Yuen
Software Mentions: 3
Published: about 4 years ago

10.1371/journal.pone.0210675

Murine trophoblast-derived and pregnancy-associated exosome-enriched extracellular vesicle microRNAs: Implications for placenta driven effects on maternal physiology
Cited by: 27
Author(s): Adrianne L. Stefanski, Nadine Martinez, Lisa K. Peterson, Tiffany J. Callahan, Eileen P. Treacy, Marisa E. Luck, Samantha F. Friend, Amy Hermesch, Emin Maltepe, Tzu L. Phang, Leonard L. Dragone, Virginia D. Winn
Software Mentions: 3
Published: almost 6 years ago

10.1098/rsos.170988

The York Gospels: a 1000-year biological palimpsest
Cited by: 60
Author(s): Matthew D. Teasdale, Sarah Fiddyment, Jiří Vnouček, Valeria Mattiangeli, Camilla Speller, Annelise Binois, Martin Carver, Catherine Dand, Timothy P. Newfield, Christopher C. Webb, Daniel G. Bradley, Matthew J. Collins
Software Mentions: 3
Published: about 7 years ago

10.1371/journal.pone.0239528

Regulatory and evolutionary adaptation of yeast to acute lethal ethanol stress
Cited by: 9
Author(s): Jiping Yang, Saeed Tavazoie
Software Mentions: 3
Published: about 4 years ago

10.1371/journal.pone.0066086

Distinct MicroRNAs Expression Profile in Primary Biliary Cirrhosis and Evaluation of miR 505-3p and miR197-3p as Novel Biomarkers
Cited by: 81
Author(s): Masashi Ninomiya, Yasuteru Kondo, Ryo Funayama, Takeshi Nagashima, Takayuki Kogure, Eiji Kakazu, Osamu Kimura, Yoshiyuki Ueno, Keiko Nakayama, Tooru Shimosegawa
Software Mentions: 3
Published: over 11 years ago

10.3390/cancers12051178

The Impact of Whole Genome Data on Therapeutic Decision-Making in Metastatic Prostate Cancer: A Retrospective Analysis
Cited by: 10
Author(s): Megan Crumbaker, Eva Chan, Ting-Ting Gong, Niall M. Corcoran, Weerachai Jaratlerdsiri, Ruth J. Lyons, Anne‐Maree Haynes, Anna Kulidjian, Anton M.F. Kalsbeek, Desiree C. Petersen, Phillip D. Stricker, Christina Jamieson, Peter I. Croucher, Christopher M. Hovens, Anthony M. Joshua, Vanessa M. Hayes
Software Mentions: 3
Published: over 4 years ago

10.3390/cancers13071497

An Evaluation of the Diagnostic Accuracy of a Panel of Variants in DPYD and a Single Variant in ENOSF1 for Predicting Common Capecitabine Related Toxicities
Cited by: 12
Author(s): Claire Palles, Susan Fotheringham, Laura Chegwidden, Marie Madeleine Lucas, Rachel Kerr, Guy Mozolowski, Dan Rosmarin, Jenny C. Taylor, Ian Tomlinson, David Kerr
Software Mentions: 3
Published: over 3 years ago

10.3390/cancers13102341

Pharmacological or TRIB3-Mediated Suppression of ATF4 Transcriptional Activity Promotes Hepatoma Cell Resistance to Proteasome Inhibitor Bortezomib
Cited by: 7
Author(s): Tiit Örd, Daima Örd, Minna U. Kaikkonen, Tônis Örd
Software Mentions: 3
Published: over 3 years ago

10.1098/rspb.2020.3169

Conservation and turnover of miRNAs and their highly complementary targets in early branching animals
Cited by: 5
Author(s): Daniela Praher, Bob Zimmermann, Rohit Dnyansagar, David J. Miller, Aurélie Moya, Vengamanaidu Modepalli, Arie Fridrich, Daniel Sher, Lene Friis-Møller, Per Sundberg, Sylvain Forêt, Regan Ashby, Yehu Moran, Ulrich Technau
Software Mentions: 3
Published: over 3 years ago

10.1016/j.cell.2019.06.006

Human Artificial Chromosomes that Bypass Centromeric DNA
Cited by: 71
Author(s): Glennis A. Logsdon, Craig W. Gambogi, Mikhail Liskovykh, Evelyne J. Barrey, Vladimir Larionov, Karen H. Miga, Patrick Heun, Ben E. Black
Software Mentions: 3
Published: over 5 years ago

Projects: pypi: cutadapt

Papers Mentioning cutadapt 1,562