10.1186/s13072-021-00395-7

Loss of EZH2-like or SU(VAR)3–9-like proteins causes simultaneous perturbations in H3K27 and H3K9 tri-methylation and associated developmental defects in the fungus Podospora anserina
Cited by: 13
Author(s): Florian Carlier, M. Li, Laetitia Maroc, Robert Debuchy, Charbel Souaid, Daan Noordermeer, Pierre Grognet, Fabienne Malagnac
Software Mentions: 4
Published: over 5 years ago

10.1186/s12885-021-07911-8

Construction of the optimization prognostic model based on differentially expressed immune genes of lung adenocarcinoma
Cited by: 6
Author(s): Yuanliang Zhai, Bin Zhao, Yuzhen Wang, Lina Li, Jingjin Li, Li Xu, Linhan Chang, Qian Chen, Zhijun Liao
Software Mentions: 4
Published: over 5 years ago

10.1186/s12866-018-1154-3

A microbiome case-control study of recurrent acute otitis media identified potentially protective bacterial genera
Cited by: 108
Author(s): Rachael Lappan, Kara Imbrogno, Chisha Sikazwe, Denise Anderson, D. Mok, Harvey Coates, Shyan Vijayasekaran, Paul Bumbak, Christopher C Blyth, Sarra E. Jamieson, Christopher Peacock
Software Mentions: 4
Published: over 8 years ago

10.1186/s40168-021-01055-4

Whole lung tissue is the preferred sampling method for amplicon-based characterization of murine lung microbiota
Cited by: 18
Author(s): Jennifer M. Baker, Kevin J. Hinkle, Roderick A. McDonald, Christopher Brown, Nicole R. Falkowski, Gary B. Huffnagle, Robert P. Dickson
Software Mentions: 4
Published: over 5 years ago

10.1186/s12864-016-2694-2

RNA-Seq following PCR-based sorting reveals rare cell transcriptional signatures
Cited by: 21
Author(s): Maurizio Pellegrino, Adam Sciambi, Jamie Yates, Joshua D. Mast, Charles Silver, Dennis J. Eastburn
Software Mentions: 4
Published: about 10 years ago

10.1186/s12864-018-4505-4

Transcriptome profiles in peripheral white blood cells at the time of artificial insemination discriminate beef heifers with different fertility potential
Cited by: 28
Author(s): Sarah Dickinson, Brock A. Griffin, Michelle F Elmore, L. A. Kriese-Anderson, J. Bradford Elmore, Paul W. Dyce, Soren P. Rodning, Fernando H. Biase
Software Mentions: 4
Published: over 8 years ago

10.1016/j.comtox.2021.100175

COSMOS next generation – A public knowledge base leveraging chemical and biological data to support the regulatory assessment of chemicals
Cited by: 13
Author(s): Chihae Yang, Mark T.D. Cronin, Kirk Arvidson, Bruno Bienfait, Steven J. Enoch, Bart Heldreth, Bryan Hobocienski, Kristi Muldoon-Jacobs, Y. Lan, Judith C. Madden, Tomasz Magdziarz, J. Marusczyk, Aleksandra Mostrąg, Mark Nelms, Daniel Neagu, Katarzyna R. Przybylak, James F. Rathman, J. Park, A.N. Richarz, Ann M. Richard, J.V. Ribeiro, Oliver Sacher, Christof H. Schwab, Vessela Vitcheva, Patra Volarath, Andrew Worth
Software Mentions: 4
Published: about 5 years ago

10.1186/s13072-018-0252-7

Global distribution of DNA hydroxymethylation and DNA methylation in chronic lymphocytic leukemia
Cited by: 14
Author(s): Sara Wernig-Zorc, Mukesh Yadav, Pradeep Kumar Kopparapu, Mats Bemark, Hallgerður Lind Kristjánsdóttir, Per‐Ola Andersson, Chandrasekhar Kanduri, Meena Kanduri
Software Mentions: 4
Published: over 7 years ago

10.1038/s41598-021-96886-4

Multiple strain analysis of Streptomyces species from Philippine marine sediments reveals intraspecies heterogeneity in antibiotic activities
Cited by: 11
Author(s): Chuckcris P. Tenebro, Dana Joanne Von L. Trono, Carmela Vannette B. Vicera, Edna M. Sabido, Jovito A. Ysulat, Aaron Joseph M. Macaspac, Kimberly A. Tampus, Trisha Alexis P. Fabrigar, Jonel P. Saludes, Doralyn S. Dalisay
Software Mentions: 4
Published: almost 5 years ago

10.1186/s12898-016-0106-8

Palaeoenvironmental drivers of vertebrate community composition in the Belly River Group (Campanian) of Alberta, Canada, with implications for dinosaur biogeography
Cited by: 22
Author(s): Thomas M. Cullen, David C. Evans
Software Mentions: 4
Published: over 9 years ago

10.1111/jcmm.14830

Identification of immune‐enhanced molecular subtype associated with BRCA1 mutations, immune checkpoints and clinical outcome in ovarian carcinoma
Cited by: 23
Author(s): Mingjun Zheng, Yuexin Hu, Rui Gou, Ouxuan Liu, Xin Nie, Xiao Li, Qing Liu, Yingying Hao, Juanjuan Liu, Bei Lin
Software Mentions: 4
Published: over 6 years ago

10.1186/s40168-020-00981-z

Discovery of novel community-relevant small proteins in a simplified human intestinal microbiome
Cited by: 17
Author(s): Hannes Petruschke, Christian Schori, Sebastian Canzler, Sarah Riesbeck, Anja Poehlein, Rolf Daniel, Daniel Frei, Tina Segessemann, Johannes Zimmerman, Γεώργιος Μαρίνος, Christoph Kaleta, Nico Jehmlich, Christian H. Ahrens, Martin von Bergen
Software Mentions: 4
Published: over 5 years ago

10.1186/s13029-015-0040-8

TRX-LOGOS - a graphical tool to demonstrate DNA information content dependent upon backbone dynamics in addition to base sequence
Cited by: 3
Author(s): Connor H. Fortin, Katharina Schulze, Gregory A. Babbitt
Software Mentions: 4
Published: almost 11 years ago

10.1038/s41598-018-24243-z

Environment-dependent striatal gene expression in the BACHD rat model for Huntington disease
Cited by: 9
Author(s): Arianna Novati, Thomas Hentrich, Zinah Wassouf, Jonasz Jeremiasz Weber, Libo Yu-Taeger, Nicole Déglon, Huu Phuc Nguyen, Julia M. Schulze‐Hentrich
Software Mentions: 4
Published: over 8 years ago

10.1186/s40168-017-0328-9

Blood as a route of transmission of uterine pathogens from the gut to the uterus in cows
Cited by: 73
Author(s): Seong-Jeub Jeon, Federico Cunha, A. Vieira-Neto, R.C. Bicalho, Svetlana Lima, M.L.S. Bicalho, Klibs N. Galvão
Software Mentions: 4
Published: almost 9 years ago

10.1371/journal.pone.0215767

Short-term effect of simulated salt marsh restoration by sand-amendment on sediment bacterial communities
Cited by: 11
Author(s): François Thomas, James T. Morris, Cathleen Wigand, Stefan M. Sievert
Software Mentions: 4
Published: over 7 years ago

10.1111/jcmm.15370

Genome‐Wide Analysis of circular RNAs and validation of hsa_circ_0006719 as a potential novel diagnostic biomarker in congenital scoliosis patients
Cited by: 1
Author(s): Gang Liu, Jianxiong Shen, Chong Chen, Yang Jiao, Zheng Li, Haining Tan, Youxi Lin, Tianhua Rong
Software Mentions: 4
Published: over 6 years ago

10.1186/s12885-020-07058-y

Immune landscape of human prostate cancer: immune evasion mechanisms and biomarkers for personalized immunotherapy
Cited by: 25
Author(s): Mayassa J. Bou‐Dargham, Linlin Sha, Qing‐Xiang Amy Sang, Jinfeng Zhang
Software Mentions: 4
Published: about 6 years ago

10.1371/journal.pone.0178217

Automated prediction of emphysema visual score using homology-based quantification of low-attenuation lung region
Cited by: 8
Author(s): Motohiro Nishio, Kazuaki Nakane, Takeshi Kubo, Masahiro Yakami, Yutaka Emoto, Masaki Nishio, Kaori Togashi
Software Mentions: 4
Published: about 9 years ago

10.1038/s41598-018-23207-7

Comparative High-Resolution Transcriptome Sequencing of Lymphoma Cell Lines and de novo Lymphomas Reveals Cell-Line-Specific Pathway Dysregulation
Cited by: 10
Author(s): Leila Taher, Julia Beck, Wen Li, Catrin Roolf, Jan T. Soller, Barbara C. Rütgen, Sabine E. Hammer, Murali Chodisetti, Sina Sender, Katharina A Sterenczak, Georg Fuellen, Christian Junghanß, Bertram Brenig, Ingo Nolte, Ekkehard Schütz, Hugo Murua Escobar
Software Mentions: 4
Published: over 8 years ago

10.1186/s12885-021-08536-7

SERPINE1 associated with remodeling of the tumor microenvironment in colon cancer progression: a novel therapeutic target
Cited by: 26
Author(s): Shaokun Wang, Li Pang, Zuolong Liu, Xiangchuan Meng
Software Mentions: 4
Published: about 5 years ago

10.3389/fcell.2021.671806

Knockdown of Splicing Complex Protein PCBP2 Reduces Extravillous Trophoblast Differentiation Through Transcript Switching
Cited by: 6
Author(s): Danai Georgiadou, Souad Boussata, Remco Keijser, Dianta Janssen, Gijs B. Afink, Marie van Dijk
Software Mentions: 4
Published: about 5 years ago

10.1371/journal.pone.0160791

Natural Cubic Spline Regression Modeling Followed by Dynamic Network Reconstruction for the Identification of Radiation-Sensitivity Gene Association Networks from Time-Course Transcriptome Data
Cited by: 31
Author(s): Agata Michna, Herbert Braselmann, Martin Selmansberger, Anne Dietz, Julia Heß, Maria Gomolka, Sabine Hornhardt, Nils Blüthgen, Horst Zitzelsberger, Kristian Unger
Software Mentions: 4
Published: about 10 years ago

10.1038/s41431-021-00854-5

Regional heritability mapping identifies several novel loci (STAT4, ULK4, and KCNH5) for primary biliary cholangitis in the Japanese population
Cited by: 6
Author(s): Olivier Gervais, Kazuko Ueno, Yosuke Kawai, Yuki Hitomi, Yoshihiro Aiba, Mayumi Ueta, Minoru Nakamura, Katsushi Tokunaga, Masao Nagasaki
Software Mentions: 4
Published: over 5 years ago

10.1038/s42003-020-01356-8

Machine learning enables improved runtime and precision for bio-loggers on seabirds
Cited by: 20
Author(s): Joseph Korpela, Hirokazu Suzuki, S. Matsumoto, Yuichi Mizutani, Masaki Samejima, Taira Maekawa, Junichi Nakai, Ken Yoda
Software Mentions: 4
Published: almost 6 years ago

10.1186/s12870-019-1968-7

Reconstruction of the full-length transcriptome atlas using PacBio Iso-Seq provides insight into the alternative splicing in Gossypium australe
Cited by: 40
Author(s): Shouli Feng, Min Xu, Fujie Liu, Changjiang Cui, Baoliang Zhou
Software Mentions: 4
Published: almost 7 years ago

10.1111/jcmm.15505

Asiaticoside might attenuate bleomycin‐induced pulmonary fibrosis by activating cAMP and Rap1 signalling pathway assisted by A2AR
Cited by: 18
Author(s): Jing Luo, Ting Zhang, Ce Zhu, Junwei Sun, Wenjing Zhu, Wenxiu Ai, Xiaoying Huang, Xiaobing Wang
Software Mentions: 4
Published: about 6 years ago

10.3389/fmicb.2018.02345

The Endophytic Mycobiome of European Ash and Sycamore Maple Leaves – Geographic Patterns, Host Specificity and Influence of Ash Dieback
Cited by: 44
Author(s): Markus Schlegel, Valentin Queloz, Thomas N. Sieber
Software Mentions: 4
Published: almost 8 years ago

10.3390/antibiotics9040208

Prevalence of Virulence Genes and Antimicrobial Resistances in E. coli Associated with Neonatal Diarrhea, Postweaning Diarrhea, and Edema Disease in Pigs from Austria
Cited by: 13
Author(s): René Renzhammer, Igor Loncaric, Franz-Ferdinand Roch, Beate Pinior, Annemarie Käsbohrer, Joachim Spergser, Andrea Ladinig, Christine Unterweger
Software Mentions: 4
Published: over 6 years ago

10.1038/s41598-018-24830-0

Novel analysis of the Harderian gland transcriptome response to Newcastle disease virus in two inbred chicken lines
Cited by: 21
Author(s): Melissa S. Deist, Rodrigo A. Gallardo, David Bunn, T. Ross Kelly, Jack C. M. Dekkers, Huaijun Zhou, Susan J. Lamont
Software Mentions: 4
Published: over 8 years ago

10.1186/s12915-020-00945-7

Horizontally acquired antibacterial genes associated with adaptive radiation of ladybird beetles
Cited by: 8
Author(s): Hao‐Sen Li, Xiaowen Tang, Yu‐Hao Huang, Zhennan Xu, Meilan Chen, Xue‐Yong Du, Bo-Yuan Qiu, Pei‐Tao Chen, Wei Zhang, Adam Ślipiński, Hermes E. Escalona, Robert M. Waterhouse, Andreas Zwick
Software Mentions: 4
Published: over 5 years ago

10.1186/s12915-019-0677-x

Impact of genome architecture on the functional activation and repression of Hox regulatory landscapes
Cited by: 19
Author(s): Eddie Rodríguez-Carballo, Lucille Lopez-Delisle, Nayuta Yakushiji-Kaminatsui, Asier Ullate-Agote, Denis Duboule
Software Mentions: 4
Published: about 7 years ago

10.1186/s12915-020-00860-x

Spatial and temporal modulation of enterotoxigenic E. coli H10407 pathogenesis and interplay with microbiota in human gut models
Cited by: 15
Author(s): Charlène Roussel, Kim De Paepe, Wessam Galia, Jana De Bodt, Sandrine Chalancon, Françoise Leriche, Nathalie Ballet, Sylvain Denis, Monique Alric, Tom Van de Wiele, Stéphanie Blanquet‐Diot
Software Mentions: 4
Published: almost 6 years ago

10.1186/s12870-018-1602-0

Dual RNA-seq analysis provides new insights into interactions between Norway spruce and necrotrophic pathogen Heterobasidion annosum s.l.
Cited by: 31
Author(s): Andriy Kovalchuk, Zhen Zeng, Rajendra P. Ghimire, Minna Kivimäenpää, Tommaso Raffaello, Mengxia Liu, Mukrimin Mukrimin, Risto Kasanen, Hui Sun, Riitta Julkunen‐Tiitto, Jarmo K. Holopainen, Fred O. Asiegbu
Software Mentions: 4
Published: over 7 years ago

10.1186/s12864-018-5265-x

Corn dried distillers grains with solubles (cDDGS) in the diet of pigs change the expression of adipose genes that are potential therapeutic targets in metabolic and cardiovascular diseases
Cited by: 6
Author(s): Maria Oczkowicz, Tomasz Szmatoła, Małgorzata Świątkiewicz, Klaudia Pawlina-Tyszko, Artur Gurgul, Tomasz Ząbek
Software Mentions: 4
Published: over 7 years ago

10.1371/journal.pgen.1006778

Gene duplication and co-evolution of G1/S transcription factor specificity in fungi are essential for optimizing cell fitness
Cited by: 11
Author(s): Adi Hendler, Edgar M. Medina, Anastasiya Kishkevich, Mehtap Abu-Qarn, Steffi Klier, Nicolas E. Buchler, Robertus A.M. de Bruin, Amir Aharoni
Software Mentions: 4
Published: about 9 years ago

10.3389/fmicb.2020.579072

Soil Fungal Community Composition, Not Assembly Process, Was Altered by Nitrogen Addition and Precipitation Changes at an Alpine Steppe
Cited by: 12
Author(s): Yuanming Xiao, Changbin Li, Yang Yang, Yunfeng Peng, Yuanhe Yang, Guoying Zhou
Software Mentions: 4
Published: almost 6 years ago

10.1186/1471-2164-14-283

Unscrambling butterfly oogenesis
Cited by: 38
Author(s): Jean-Michel Carter, Susan C. Baker, Ryan C. Pink, David R. F. Carter, Aiden Collins, Jeremie Tomlin, Melanie Gibbs, Casper J. Breuker
Software Mentions: 4
Published: over 13 years ago

10.7554/eLife.60645

Simultaneous quantification of mRNA and protein in single cells reveals post-transcriptional effects of genetic variation
Cited by: 28
Author(s): Christian Brion, Sheila Lutz, Frank W. Albert
Software Mentions: 4
Published: over 5 years ago

10.1111/jcmm.16221

Expression and prognostic characteristics of m ⁵ C regulators in low‐grade glioma
Cited by: 11
Author(s): Xiaozhi Li, Yutong Meng
Software Mentions: 4
Published: over 5 years ago

10.1186/s12870-016-0926-x

Identification of nuclear genes controlling chlorophyll synthesis in barley by RNA-seq
Cited by: 9
Author(s): Nikolay A. Shmakov, Gennady V. Vasiliev, Natalya V. Shatskaya, А. В. Дорошков, Е. И. Гордеева, D. A. Afonnikov, Е. К. Хлесткина
Software Mentions: 4
Published: almost 10 years ago

10.7554/eLife.62731

GTPBP1 resolves paused ribosomes to maintain neuronal homeostasis
Cited by: 22
Author(s): Markus Terrey, Scott I. Adamson, Alana L. Gibson, Tianda Deng, Ryuta Ishimura, Jeffrey H. Chuang, Susan L. Ackerman
Software Mentions: 4
Published: over 5 years ago

10.1186/s12864-020-07327-x

Gene expression patterns of red sea urchins (Mesocentrotus franciscanus) exposed to different combinations of temperature and pCO2 during early development
Cited by: 5
Author(s): Juliet M. Wong, Gretchen E. Hofmann
Software Mentions: 4
Published: over 5 years ago

10.1186/s12864-016-3306-x

Differences in the skeletal muscle transcriptome profile associated with extreme values of fatty acids content
Cited by: 40
Author(s): Aline Silva Mello Cesar, Luciana Correia de Almeida Regitano, Mirele Daiana Poleti, Sónia C. S. Andrade, P. C. Tizioto, P. S. N. Oliveira, Andrezza Maria Felício, Michele Lopes do Nascimento, Amália Saturnino Chaves, Dante Pazzanese Duarte Lanna, R. R. Túllio, R. T. Nassu, James E. Koltes, Eric R. Fritz-Waters, Gérson Barreto Mourão, Adhemar Zerlotini-Neto, James M. Reecy, Luiz Lehmann Coutinho
Software Mentions: 4
Published: over 9 years ago

10.1186/s12915-021-01009-0

Multi-omic profiling of pituitary thyrotropic cells and progenitors
Cited by: 4
Author(s): Alexandre Z. Daly, L Dudley, Michael T. Peel, Stephen A. Liebhaber, Stephen C. J. Parker, Sally A. Camper
Software Mentions: 4
Published: over 5 years ago

10.7554/eLife.55775

Homeostatic plasticity fails at the intersection of autism-gene mutations and a novel class of common genetic modifiers
Cited by: 13
Author(s): Özgür Genç, Joon Yong An, Richard D. Fetter, Yelena Kulik, Giulia Zunino, Stephan J. Sanders, Graeme W. Davis
Software Mentions: 4
Published: about 6 years ago

10.3390/microorganisms9091842

The Rhizobial Microbiome from the Tropical Savannah Zones in Northern Côte d’Ivoire
Cited by: 5
Author(s): Sara Laetitia Elphège Gnangui, Romain Kouakou Fossou, Anicet Ebou, Chiguié Estelle Raïssa Amon, Dominique Koua, Claude Ghislaine Kouadjo, Don A. Cowan, Adolphe Zézé
Software Mentions: 4
Published: almost 5 years ago

10.1371/journal.pone.0192613

NetMiner-an ensemble pipeline for building genome-wide and high-quality gene co-expression network using massive-scale RNA-seq samples
Cited by: 17
Author(s): Hua Yu, Bingke Jiao, Lu Lu, Pengfei Wang, Shuangcheng Chen, Chengzhi Liang, Wei Liu
Software Mentions: 4
Published: over 8 years ago

10.1111/jcmm.16393

TTN/OBSCN ‘Double‐Hit’ predicts favourable prognosis, ‘immune‐hot’ subtype and potentially better immunotherapeutic efficacy in colorectal cancer
Cited by: 33
Author(s): Xinwei Han, Libo Wang, Chunguang Guo, Long Liu, Dechao Jiao, Zhenqiang Sun, Kunpeng Wu, Yanan Zhao
Software Mentions: 4
Published: over 5 years ago

10.1038/s41598-017-18480-x

RNA-Seq analysis and comparison of corneal epithelium in keratoconus and myopia patients
Cited by: 51
Author(s): Jungmok You, Susan M. Corley, Li Wen, Chris Hodge, Roland Hӧllhumer, Michele C. Madigan, Marc R. Wilkins, Gerard Sutton
Software Mentions: 4
Published: over 8 years ago

10.3389/fmicb.2021.718727

Soil Fungal Community in Grazed Inner Mongolian Grassland Adjacent to Coal-Mining Activity
Cited by: 2
Author(s): Liji Xie, Yinli Bi, Xianglei Li, Kun Wang, Peter Christie
Software Mentions: 4
Published: almost 5 years ago

10.3390/microorganisms9081564

An Update on Trichoderma Mitogenomes: Complete De Novo Mitochondrial Genome of the Fungal Biocontrol Agent Trichoderma harzianum (Hypocreales, Sordariomycetes), an Ex-Neotype Strain CBS 226.95, and Tracing the Evolutionary Divergences of Mitogenomes in Trichoderma
Cited by: 6
Author(s): Yunyoung Kwak
Software Mentions: 4
Published: about 5 years ago

10.1186/s12940-020-00608-8

Persistent organic pollutants, pre-pregnancy use of combined oral contraceptives, age, and time-to-pregnancy in the SELMA cohort
Cited by: 13
Author(s): Richelle D. Björvang, Chris Gennings, Ping Lin, Ghada Hussein, Hannu Kiviranta, Panu Rantakokko, Päivi Ruokojärvi, Christian Lindh, Pauliina Damdimopoulou, Carl‐Gustaf Bornehag
Software Mentions: 4
Published: about 6 years ago

10.3389/fmicb.2021.658927

Implications of Climate Change: How Does Increased Water Temperature Influence Biofilm and Water Quality of Chlorinated Drinking Water Distribution Systems?
Cited by: 14
Author(s): Carolina Calero Preciado, Joby Boxall, Víctor Soria‐Carrasco, Santiago Martínez, Isabel Douterelo
Software Mentions: 4
Published: about 5 years ago

10.1186/s12864-019-5910-z

Identification and differential expression analysis of anthocyanin biosynthetic genes in leaf color variants of ornamental kale
Cited by: 24
Author(s): Na Guo, Shuo Han, Ming Zong, Guixiang Wang, Shuning Zheng, Fan Liu
Software Mentions: 4
Published: about 7 years ago

10.1126/sciadv.aaz4012

Three-dimensional chromatin interactions remain stable upon CAG/CTG repeat expansion
Cited by: 13
Author(s): Gustavo A. Ruiz Buendía, Marion Leleu, Flavia Marzetta, Ludovica Vanzan, Jennifer Y. Tan, Victor Ythier, Emma Randall, Ana C. Marques, Tuncay Baubec, Rabih Murr, Ioannis Xénarios, Vincent Dion
Software Mentions: 4
Published: about 6 years ago

10.1186/s12864-016-3286-x

Genomic differentiation among wild cyanophages despite widespread horizontal gene transfer
Cited by: 91
Author(s): Ann C. Gregory, Sergei A. Solonenko, J. Cesar Ignacio‐Espinoza, Kurt LaButti, Alex Copeland, Sebastian Sudek, Ashley Maitland, Lauren Chittick, Filipa Santos, Joshua S. Weitz, Alexandra Z. Worden, Tanja Woyke, Matthew B. Sullivan
Software Mentions: 4
Published: over 9 years ago

10.1128/mBio.01650-17

<i>De Novo</i> Assembly and Phasing of Dikaryotic Genomes from Two Isolates of <i>Puccinia coronata</i> f. sp. <i>avenae</i> , the Causal Agent of Oat Crown Rust
Cited by: 45
Author(s): Marisa E. Miller, Ying Zhang, Vahid Omidvar, Jana Sperschneider, Benjamin Schwessinger, Castle Raley, Jonathan M. Palmer, Diana Garnica, Narayana M. Upadhyaya, John P. Rathjen, Jennifer Taylor, Robert Park, Peter N. Dodds, Cory D. Hirsch, Shahryar F. Kianian, Melania Figueroa
Software Mentions: 4
Published: over 8 years ago

10.1186/s12864-020-07072-1

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

10.1186/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: about 6 years ago

10.1128/AEM.01003-19

Genomic and Seasonal Variations among Aquatic Phages Infecting the Baltic Sea Gammaproteobacterium <i>Rheinheimera</i> sp. Strain BAL341
Cited by: 20
Author(s): Emelie Nilsson, K. Li, Jimmy Fridlund, Sigitas Šulčius, Carina Bunse, Christofer M. G. Karlsson, Markus V. Lindh, Daniel Lundin, Jarone Pinhassi, Karin Holmfeldt
Software Mentions: 4
Published: almost 7 years ago

10.3389/fmicb.2015.00966

Metagenomic analysis reveals that modern microbialites and polar microbial mats have similar taxonomic and functional potential
Cited by: 39
Author(s): Richard Allen White, Ian M. Power, Gregory M. Dipple, Gordon Southam, Curtis A. Suttle
Software Mentions: 4
Published: almost 11 years ago

10.1002/edm2.140

Prevalence of admission plasma glucose in 'diabetes' or 'at risk' ranges in hospital emergencies with no prior diagnosis of diabetes by gender, age and ethnicity
Cited by: 5
Author(s): Sandip Ghosh, Susan E. Manley, Peter Nightingale, John A. Williams, Radhika Susarla, Irene Alonso‐Perez, I M Stratton, Georgios V. Gkoutos, Jonathan Webber, Stephen Denis Luzio, Wasim Hanif, Graham Roberts
Software Mentions: 4
Published: about 6 years ago

10.1186/s12864-017-4359-1

A next generation sequencing based approach to identify extracellular vesicle mediated mRNA transfers between cells
Cited by: 19
Author(s): Jialiang Yang, Jacob Hagen, Kalyani V. P. Guntur, Kimaada Allette, Sarah Schuyler, Jyoti Ranjan, Francesca Petralia, Stéphane Gesta, Robert Sebra, Milind Mahajan, Bin Zhang, Jun Zhu, Sander M. Houten, Andrew Kasarskis, Vivek K. Vishnudas, Viatcheslav R. Akmaev, Rangaprasad Sarangarajan, Niven R. Narain, Eric E. Schadt, Carmen Argmann, Zhidong Tu
Software Mentions: 4
Published: over 8 years ago

10.1186/s40168-018-0610-5

The bacterial community significantly promotes cast iron corrosion in reclaimed wastewater distribution systems
Cited by: 30
Author(s): Guijuan Zhang, Bing Li, Jie Liu, Mingqiang Luan, Yao Long, Xiaotao Jiang, Ke Yu, Yuntao Guan
Software Mentions: 4
Published: over 7 years ago

10.7554/eLife.67312

YAP and TAZ are transcriptional co-activators of AP-1 proteins and STAT3 during breast cellular transformation
Cited by: 43
Author(s): Lizhi He, Henry E. Pratt, Mingshi Gao, Fengxiang Wei, Zhiping Weng, Kevin Struhl
Software Mentions: 4
Published: almost 5 years ago

10.1111/jcmm.16831

Bioinformatics analysis of the prognostic value of NEK8 and its effects on immune cell infiltration in glioma
Cited by: 7
Author(s): Meng Xiao, Chuang Du, Chuanbo Zhang, Xinzhong Zhang, Shaomin Li, Dainan Zhang, Wang Jia
Software Mentions: 4
Published: about 5 years ago

10.1186/s12864-017-3675-9

Transcriptome analysis reveals potential mechanisms underlying differential heart development in fast- and slow-growing broilers under heat stress
Cited by: 23
Author(s): J. Zhang, Carl J. Schmidt, Susan J. Lamont
Software Mentions: 4
Published: over 9 years ago

10.1186/s12870-021-02997-5

Low nitrogen availability inhibits the phosphorus starvation response in maize (Zea mays ssp. mays L.)
Cited by: 10
Author(s): J. Vladimir Torres-Rodríguez, M. Nancy Salazar-Vidal, Ricardo A. Chávez Montes, Julio A. Massange‐Sánchez, C. Stewart Gillmor, Ruairidh J. H. Sawers
Software Mentions: 4
Published: about 5 years ago

10.3389/fgene.2021.636419

Five Circular RNAs in Metabolism Pathways Related to Prostate Cancer
Cited by: 6
Author(s): Lili Zhang, Wei Zhang, Hexin Li, Xiaokun Tang, Siyuan Xu, Meng Wu, Li Wan, Fei Su, Yaqun Zhang
Software Mentions: 4
Published: over 5 years ago

10.1038/s41598-021-97158-x

Nanopore sequencing and de novo assembly of a misidentified Camelpox vaccine reveals putative epigenetic modifications and alternate protein signal peptides
Cited by: 3
Author(s): Zack Saud, Matthew D. Hitchings, Tariq M. Butt
Software Mentions: 4
Published: almost 5 years ago

10.3389/fgene.2020.585746

Profiling of H3K27Ac Reveals the Influence of Asthma on the Epigenome of the Airway Epithelium
Cited by: 7
Author(s): Peter McErlean, A. Paul Kelly, Jaideep Dhariwal, Max Kirtland, Julie Watson, Ismael Ranz, Janet L. Smith, Alka Saxena, David J. Cousins, Antoon van Oosterhout, Roberto Solari, Michael R. Edwards, Sebastian L. Johnston, Paul Lavender
Software Mentions: 4
Published: over 5 years ago

10.1186/s12864-017-3797-0

Differentially expressed genes from RNA-Seq and functional enrichment results are affected by the choice of single-end versus paired-end reads and stranded versus non-stranded protocols
Cited by: 20
Author(s): Susan M. Corley, Karen L. MacKenzie, Annemiek Beverdam, Louise F. Roddam, Marc R. Wilkins
Software Mentions: 4
Published: about 9 years ago

10.1038/s41598-021-98008-6

Modelling COVID-19 severity in the Republic of Ireland using patient co-morbidities, socioeconomic profile and geographic location, February to November 2020
Cited by: 6
Author(s): Martin Boudou, Coilín ÓhAiseadha, Patricia Garvey, Jean O’Dwyer, Paul Hynds
Software Mentions: 4
Published: almost 5 years ago

10.3389/fpls.2012.00202

A High-Throughput Method for Illumina RNA-Seq Library Preparation
Cited by: 134
Author(s): Ravi Kumar, Yasunori Ichihashi, Seisuke Kimura, Daniel H. Chitwood, Lauren R. Headland, Jie Peng, Julin N. Maloof, Neelima Sinha
Software Mentions: 4
Published: over 14 years ago

10.3390/jcm10132973

Meteorin Is a Novel Therapeutic Target for Wet Age-Related Macular Degeneration
Cited by: 4
Author(s): Kimberley Delaunay, Alexandre Sellam, Virginie Dinet, Alexandre Moulin, Min Zhao, Emmanuelle Gélizé, Jérémie Canonica, Marie‐Christine Naud, Patricia Crisanti-Lassiaz, Francine Behar‐Cohen
Software Mentions: 4
Published: about 5 years ago

10.1038/s41598-021-89741-z

Differential features of chronic cough according to etiology and the simple decision tree for predicting causes
Cited by: 2
Author(s): Hyeon Kyoung Koo, Woo Kyung Bae, Joon-Shik Moon, Hyun Lee, Jin Woo Kim, Seung Hun Jang, Hyoung Kyu Yoon, Deog Kyeom Kim
Software Mentions: 4
Published: about 5 years ago

10.3389/fgene.2021.659788

RNA-Associated Co-expression Network Identifies Novel Biomarkers for Digestive System Cancer
Cited by: 7
Author(s): Zheng Chen, Zijie Shen, Zilong Zhang, Zhao Da, Lei Xu, Lijun Zhang
Software Mentions: 4
Published: over 5 years ago

10.1371/journal.pone.0247076

Physical and nutrient stimuli differentially modulate gut motility patterns, gut transit rate, and transcriptome in an agastric fish, the ballan wrasse
Cited by: 11
Author(s): Hoang T. M. D. Le, Kai Kristoffer Lie, Angela Etayo, Ivar Rønnestad, Øystein Sæle
Software Mentions: 4
Published: over 5 years ago

10.1371/journal.pmed.1003656

SARS-CoV-2 neutralizing antibodies: Longevity, breadth, and evasion by emerging viral variants
Cited by: 100
Author(s): Marc Charabati, Alberto Ospina Stella, Anupriya Aggarwal, D.R. Darley, Deepti Pilli, Daniele Vitale, Vera Merheb, Fiona X Z Lee, Philip Cunningham, G. J. Walker, Christina Fichter, David A. Brown, William D. Rawlinson, Sonia R Isaacs, Vennila Mathivanan, Markus Hoffmann, Stefan Pöhlman, Ohan Mazigi, Daniel Christ, Dominic E. Dwyer, Rebecca Rockett, Vitali Sintchenko, Veronica C. Hoad, David O. Irving, Gregory J. Dore, Iain B Gosbell, Anthony D. Kelleher, Gail V. Matthews, Fabienne Brilot, Stuart Turville
Software Mentions: 4
Published: about 5 years ago

10.1371/journal.pone.0131548

Genotoxic Evaluation of Mexican Welders Occupationally Exposed to Welding-Fumes Using the Micronucleus Test on Exfoliated Oral Mucosa Cells: A Cross-Sectional, Case-Control Study
Cited by: 14
Author(s): Ana Cecilia Jara-Ettinger, Juan C. López-Tavera, María Guadalupe Zavala-Cerna, Olivia Torres-Bugarı́n
Software Mentions: 4
Published: about 11 years ago

10.1371/journal.pcbi.1003246

dPeak: High Resolution Identification of Transcription Factor Binding Sites from PET and SET ChIP-Seq Data
Cited by: 13
Author(s): Dongjun Chung, Dan Park, Kevin S. Myers, Jeffrey A. Grass, Patricia J. Kiley, Robert Landick, Sündüz Keleş
Software Mentions: 4
Published: almost 13 years ago

10.1038/s41598-019-47089-5

Quantitative Mass Spectrometry Imaging Reveals Mutation Status-independent Lack of Imatinib in Liver Metastases of Gastrointestinal Stromal Tumors
Cited by: 33
Author(s): Denis A. Sammour, Christian Marsching, Alexander Geisel, Katrin Erich, Sandra Schulz, Carina Ramallo Guevara, Jan Rabe, Alexander Marx, Peter Findeisen, Peter Hohenberger, Carsten Hopf
Software Mentions: 4
Published: about 7 years ago

10.1186/s12859-017-1648-2

Power analysis for RNA-Seq differential expression studies
Cited by: 27
Author(s): Lianbo Yu, Soledad Fernández, Guy Brock
Software Mentions: 4
Published: over 9 years ago

10.1038/s41426-018-0195-x

Experimental transmission of Zika virus by <i>Aedes japonicus japonicus</i> from southwestern Germany
Cited by: 32
Author(s): Stéphanie Jansen, Anna Heitmann, Renke Lühken, Hanna Jöst, Michelle Helms, Olli Vapalahti, Jonas Schmidt‐Chanasit, Egbert Tannich
Software Mentions: 4
Published: over 7 years ago

10.1186/s12864-020-6541-0

iREAD: a tool for intron retention detection from RNA-seq data
Cited by: 33
Author(s): Hong Dong Li, Cory C. Funk, Nathan D. Price
Software Mentions: 4
Published: over 6 years ago

10.3389/fimmu.2021.686691

Dynamics of the Magnitude, Breadth and Depth of the Antibody Response at Epitope Level Following Dengue Infection
Cited by: 5
Author(s): Francesca Falconi-Agapito, Karen Kerkhof, Xiomara Merino, Johan Míchiels, Marjan Van Esbroeck, Koen Bartholomeeusen, Michael Talledo, Kevin K. Ariën
Software Mentions: 4
Published: about 5 years ago

10.7717/peerj.11931

Establishment of a ferroptosis-related gene signature for prognosis in lung adenocarcinoma patients
Cited by: 4
Author(s): Jingjing Cai, Chunyan Li, Hongsheng Li, Xiaoxiong Wang, Yunyun Zhou
Software Mentions: 4
Published: about 5 years ago

10.1038/s41598-018-29982-7

The influence of latitude, geographic distance, and habitat discontinuities on genetic variation in a high latitude montane species
Cited by: 13
Author(s): John A. Hindley, Brendan A. Graham, Paulo C. Pulgarín‐R, Theresa M. Burg
Software Mentions: 4
Published: about 8 years ago

10.1155/2021/6672899

Comparative Transcriptome Analysis Reveals Relationship among mRNAs, lncRNAs, and circRNAs of Slow Transit Constipation
Cited by: 2
Author(s): Shuai Yan, Yinzi Yue, Mingming Sun, Yinghui Chen, Xiaopeng Wang, Haihua Qian
Software Mentions: 4
Published: almost 5 years ago

10.3389/fcimb.2017.00317

Global Epidemiology of Dengue Outbreaks in 1990–2015: A Systematic Review and Meta-Analysis
Cited by: 220
Author(s): Congcong Guo, Zixing Zhou, Zihao Wen, Yumei Liu, Chengli Zeng, Di Xiao, Minglin Ou, Yuge Han, Shiqi Huang, Dandan Liu, Xiaohong Ye, Xiaoqian Zou, Jing Wu, Huanyu Wang, Eddy Y. Zeng, Chunxia Jing, Guang Yang
Software Mentions: 4
Published: about 9 years ago

10.1186/s40168-020-00827-8

Disentangling the mechanisms shaping the surface ocean microbiota
Cited by: 131
Author(s): Ramiro Logares, Ina Maria Deutschmann, Pedro C. Junger, Caterina R. Giner, Anders K. Krabberød, Thomas Sebastian Benedikt Schmidt, Laura Rubinat-Ripoll, Mireia Mestre, Guillem Salazar, Clara Ruiz‐González, Marta Sebastián, Colomban de Vargas, Silvia G. Acinas, Carlos M. Duarte, Josep M. Gasol, Ramón Massana
Software Mentions: 4
Published: over 6 years ago

10.1186/s13073-020-00824-4

The identification of novel immunogenic antigens as potential Shigella vaccine components
Cited by: 8
Author(s): Ruklanthi de Alwis, Li Liang, Omid Taghavian, Emma Werner, Trang Nguyen Hoang Thu, Vu Thuy Duong, D. Huw Davies, Philip L. Felgner, Stephen Baker
Software Mentions: 4
Published: over 5 years ago

10.1038/s41598-020-75553-0

Transcriptome wide SSR discovery cross-taxa transferability and development of marker database for studying genetic diversity population structure of Lilium species
Cited by: 13
Author(s): Manosh Kumar Biswas, Mita Bagchi, Ujjal Kumar Nath, Dhiman Biswas, Sathishkumar Natarajan, Denison Michael Immanuel Jesse, Jong-In Park, Ill–Sup Nou
Software Mentions: 4
Published: almost 6 years ago

10.1186/s12866-020-01979-1

Habitat disturbance influences the skin microbiome of a rediscovered neotropical-montane frog
Cited by: 14
Author(s): Randall R. Jiménez, Gilbert Alvarado, José Luís Sandoval, Simone Sommer
Software Mentions: 4
Published: almost 6 years ago

10.1155/2020/4581954

Comprehensive Analysis of Differentially Expressed miRNAs and mRNAs Reveals That miR-181a-5p Plays a Key Role in Diabetic Dermal Fibroblasts
Cited by: 4
Author(s): Peng Liu, Yi Zhu, Qin Li, Biao Cheng
Software Mentions: 4
Published: almost 6 years ago

10.12688/f1000research.15895.2

NovoGraph: Human genome graph construction from multiple long-read de novo assemblies
Cited by: 5
Author(s): Evan Biederstedt, Jeffrey C. Oliver, Nancy F. Hansen, Aarti Jajoo, Nathan Dunn, Andrew Olson, Ben Busby, Alexander Dilthey
Software Mentions: 4
Published: over 7 years ago

10.7554/eLife.67481

SORBS2 is a genetic factor contributing to cardiac malformation of 4q deletion syndrome patients
Cited by: 7
Author(s): Fei Liang, Bo Wang, Juan Geng, Guoling You, Jingjing Fa, Min Zhang, Hunying Sun, Huiwen Chen, Qin Fu, Xiaoqing Zhang, Zhen Zhang
Software Mentions: 4
Published: about 5 years ago

10.1371/journal.ppat.1008502

Ablation of non-coding RNAs affects bovine leukemia virus B lymphocyte proliferation and abrogates oncogenesis
Cited by: 15
Author(s): Roghaiyeh Safari, Jean-Rock Jacques, Yves Brostaux, Luc Willems
Software Mentions: 4
Published: about 6 years ago

10.1186/s12863-019-0790-4

Transcriptome, physiological and biochemical analysis of Triarrhena sacchariflora in response to flooding stress
Cited by: 17
Author(s): Jia Wang, Hao Sun, Jiajin Sheng, Surong Jin, Fangjian Zhou, Zhongli Hu, Youxiang Diao
Software Mentions: 4
Published: over 6 years ago