10.1016/j.cmet.2018.04.013

The Polycomb-Dependent Epigenome Controls β Cell Dysfunction, Dedifferentiation, and Diabetes
Cited by: 104
Author(s): Tess Tsai-Hsiu Lu, Steffen Heyne, Erez Dror, Eduard Casas, Laura Leonhardt, Thorina Boenke, Ching‐Yao Yang, Sagar, Laura Arrigoni, Kevin Dalgaard, Raffaele Teperino, Lennart Enders, Madhan Selvaraj, Marius Ruf, Sunil Jayaramaiah Raja, Huafeng Xie, Ulrike Boenisch, Stuart H. Orkin, Francis C. Lynn, Brad G. Hoffman, Dominic Grün, Tanya Vavouri, Adelheid Lempradl, J. Andrew Pospisilik
Software Mentions: 7
Published: about 8 years ago

10.1038/s42003-021-02095-0

Genome-wide bioinformatic analyses predict key host and viral factors in SARS-CoV-2 pathogenesis
Cited by: 28
Author(s): Mariana Galvão Ferrarini, Avantika Lal, Rita Rebollo, Andreas J. Gruber, Andrea Guarracino, Itziar Martinez Gonzalez, Taylor Floyd, Daniel Siqueira de Oliveira, Justin Shanklin, Ethan Beausoleil, Taneli Pusa, Brett E. Pickett, Vanessa Aguiar‐Pulido
Software Mentions: 7
Published: about 5 years ago

10.1038/s42003-020-01318-0

Lung gene expression signatures suggest pathogenic links and molecular markers for pulmonary tuberculosis, adenocarcinoma and sarcoidosis
Cited by: 15
Author(s): Qiyao Chai, Zhe Lü, Zhidong Liu, Yanzhao Zhong, Fuzhen Zhang, Changgen Qiu, Bingxi Li, Jing Wang, Lingqiang Zhang, Yu Pang, Cui Hua Liu
Software Mentions: 7
Published: over 5 years ago

10.1186/s13195-020-00654-x

Identification of potential blood biomarkers for early diagnosis of Alzheimer’s disease through RNA sequencing analysis
Cited by: 44
Author(s): Daichi Shigemizu, Tomohisa Mori, Shintaro Akiyama, Sayuri Higaki, Hiroshi Watanabe, Takashi Sakurai, Shumpei Niida, Kouichi Ozaki
Software Mentions: 7
Published: almost 6 years ago

10.1186/1471-2105-16-S9-S2

Alternative splicing detection workflow needs a careful combination of sample prep and bioinformatics analysis
Cited by: 17
Author(s): Matteo Carrara, Josephine Lum, Francesca Cordero, Marco Beccuti, Michael Poidinger, Susanna Donatelli, Raffaele Calogero, Francesca Zolezzi
Software Mentions: 7
Published: about 11 years ago

10.1186/s13059-020-1930-x

CUBIC: an atlas of genetic architecture promises directed maize improvement
Cited by: 49
Author(s): Haijun Liu, Xiaqing Wang, Yingjie Xiao, Jingyun Luo, Feng Qiao, Wenyu Yang, Ruyang Zhang, Yijiang Meng, Jiamin Sun, Shijuan Yan, Yong Peng, Luyao Niu, Liumei Jian, Wei Song, Jiali Yan, Chunhui Li, Yanxin Zhao, Liu Ya, Marilyn L. Warburton, Jiuran Zhao
Software Mentions: 7
Published: over 6 years ago

10.1186/s13059-020-1948-0

Regenerating zebrafish fin epigenome is characterized by stable lineage-specific DNA methylation and dynamic chromatin accessibility
Cited by: 42
Author(s): Hyung Joo Lee, Yiran Hou, Yujie Chen, Zea Z. Dailey, Aiyana Riddihough, Hyo Sik Jang, Ting Wang, Stephen L. Johnson
Software Mentions: 7
Published: over 6 years ago

10.1186/s13059-020-02024-0

Defining the relative and combined contribution of CTCF and CTCFL to genomic regulation
Cited by: 33
Author(s): Mayilaadumveettil Nishana, Caryn Ha, Javier Rodriguez-Hernaez, Ali Ranjbaran, Erica Chio, Elphège P. Nora, Sana Badri, Andreas Kloetgen, Benoit G. Bruneau, Aristotelis Tsirigos, Jane A. Skok
Software Mentions: 7
Published: about 6 years ago

10.1186/s12864-021-07735-7

Non-coding RNAs in the interaction between rice and Meloidogyne graminicola
Cited by: 11
Author(s): Bruno Verstraeten, Mohammad Reza Atighi, Virginia Ruiz‐Ferrer, Carolina Escobar, Tim De Meyer, Tina Kyndt
Software Mentions: 7
Published: almost 5 years ago

10.1097/j.pain.0000000000001416

Comprehensive analysis of long noncoding RNA expression in dorsal root ganglion reveals cell-type specificity and dysregulation after nerve injury
Cited by: 41
Author(s): Georgios Baskozos, J. D. K. Dawes, Jean-Sébastien Austin, Ana Antunes-Martins, Lucy A. McDermott, Alex Clark, Teodora Trendafilova, Jon Lees, Stephen B. McMahon, Jeffrey S. Mogil, Christine Orengo, David L.H. Bennett
Software Mentions: 7
Published: over 7 years ago

10.1186/s12864-021-07744-6

The effect of methanol fixation on single-cell RNA sequencing data
Cited by: 19
Author(s): Xinlei Wang, Yu Liu, Angela Ruohao Wu
Software Mentions: 7
Published: about 5 years ago

10.3390/microorganisms8101528

Metabolic Response of Faecalibacterium prausnitzii to Cell-Free Supernatants from Lactic Acid Bacteria
Cited by: 14
Author(s): Mathilde Lebas, Peggy Garault, Daniel Carrillo, Francisco M. Codoñer, Muriel Derrien
Software Mentions: 7
Published: over 5 years ago

10.1371/journal.ppat.1005438

Transcriptome-Wide Analysis of Hepatitis B Virus-Mediated Changes to Normal Hepatocyte Gene Expression
Cited by: 42
Author(s): Jason Lamontagne, Joshua Chang Mell, Michael J. Bouchard
Software Mentions: 7
Published: over 10 years ago

10.1186/s12859-018-2445-2

Empirical assessment of the impact of sample number and read depth on RNA-Seq analysis workflow performance
Cited by: 44
Author(s): Alyssa Baccarella, Claire Williams, Jay Z. Parrish, Charles C. Kim
Software Mentions: 7
Published: over 7 years ago

10.1093/molbev/msz154

Ancient Hybridization and Adaptive Introgression of an Invadolysin Gene in Schistosome Parasites
Cited by: 51
Author(s): Roy N. Platt, Marina McDew-White, Winka Le Clec’h, Frédéric D. Chevalier, Fiona Allan, Aidan M. Emery, Amadou Garba, Amina Amadou Hamidou, M. Shaali, Joanne P. Webster, David Rollinson, Bonnie L. Webster, Timothy J. Anderson
Software Mentions: 7
Published: about 7 years ago

10.1186/1471-2105-16-S13-S7

Enhancing cancer clonality analysis with integrative genomics
Cited by: 6
Author(s): Erich A. Peterson, Michael Bauer, Shweta S. Chavan, Cody Ashby, Niels Weinhold, Christoph Heuck, Gareth J. Morgan, Donald J. Johann
Software Mentions: 7
Published: over 10 years ago

10.1371/journal.ppat.1009130

Infection of human Nasal Epithelial Cells with SARS-CoV-2 and a 382-nt deletion isolate lacking ORF8 reveals similar viral kinetics and host transcriptional profiles
Cited by: 90
Author(s): Akshamal M Gamage, Kai Sen Tan, Wharton Chan, Jing Liu, Chee Wah Tan, Yew Kwang Ong, Mark Thong, Anand Kumar Andiappan, Danielle E. Anderson, De Yun Wang, Lin‐Fa Wang
Software Mentions: 7
Published: over 5 years ago

10.1186/s12859-016-1274-4

ChiLin: a comprehensive ChIP-seq and DNase-seq quality control and analysis pipeline
Cited by: 95
Author(s): Qian Qin, Shenglin Mei, Qiu Liang Wu, Hanfei Sun, Lewyn Li, Len Taing, Sujun Chen, Fugen Li, Tao Liu, Chongzhi Zang, Xu Han, Yiwen Chen, Clifford A. Meyer, Yong Zhang, Myles Brown, Henry W. Long, X. Shirley Liu
Software Mentions: 7
Published: over 9 years ago

10.1186/s12864-018-4835-2

Development and application of an integrated allele-specific pipeline for methylomic and epigenomic analysis (MEA)
Cited by: 15
Author(s): Julien Richard Albert, Takao Koike, Hamid Younesy, Iain Thompson, Aaron B. Bogutz, Mehdi Karimi, Matthew C. Lorincz
Software Mentions: 7
Published: about 8 years ago

10.26508/lsa.201800085

Transcriptional repression by FACT is linked to regulation of chromatin accessibility at the promoter of ES cells
Cited by: 29
Author(s): Constantine Mylonas, Peter Tessarz
Software Mentions: 7
Published: about 8 years ago

10.1111/1751-7915.13634

Soil microbiota influences clubroot disease by modulating <i>Plasmodiophora brassicae</i> and <i>Brassica napus</i> transcriptomes
Cited by: 19
Author(s): Stéphanie Daval, Kévin Gazengel, Arnaud Belcour, Juliette Linglin, Anne‐Yvonne Guillerm‐Erckelboudt, Alain Sarniguet, Maria Manzanares-Dauleux, Lionel Lebreton, Christophe Mougel
Software Mentions: 7
Published: almost 6 years ago

10.1038/s41598-018-26592-1

Asymmetric distribution of biomolecules of maternal origin in the Xenopus laevis egg and their impact on the developmental plan
Cited by: 13
Author(s): Radek Šindelka, Pavel Abaffy, Yanyan Qu, Silvie Tománková, Monika Šídová, Ravindra Naraine, Michal Kolář, Elizabeth H. Peuchen, Liangliang Sun, Norman J. Dovic̀hi, Mikael Kubista
Software Mentions: 7
Published: about 8 years ago

10.1186/s13059-019-1912-z

cis-regulatory variation modulates susceptibility to enteric infection in the Drosophila genetic reference panel
Cited by: 14
Author(s): Michael Frochaux, Maroun Bou Sleiman, Vincent Gardeux, Riccardo Dainese, Brian Hollis, Maria Litovchenko, Virginie Braman, Tommaso Andreani, Dani Osman, Bart Deplancke
Software Mentions: 7
Published: over 6 years ago

10.1002/jcsm.12665

Myogenesis modelled by human pluripotent stem cells: a multi‐omic study of Duchenne myopathy early onset
Cited by: 28
Author(s): Virginie Mournetas, Emmanuelle Massouridès, Jean-Baptiste Dupont, Étienne Kornobis, Hélène Polveche, Margot Jarrige, Alan R L Dorval, Maxime R. F. Gosselin, Antigoni Manousopoulou, Spiros D. Garbis, Dariusz C. Górecki, Christian Pinset
Software Mentions: 7
Published: over 5 years ago

10.1186/s13059-018-1521-2

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

10.1186/s12859-018-2353-5

XenofilteR: computational deconvolution of mouse and human reads in tumor xenograft sequence data
Cited by: 81
Author(s): Roelof J.C. Kluin, Kristel Kemper, Thomas Kuilman, Julian R. de Ruiter, Vivek Iyer, Josep V. Forment, Paulien Cornelissen-Steijger, Iris de Rink, Petra ter Brugge, Ji‐Ying Song, Sjoerd Klarenbeek, Ultan McDermott, Jos Jonkers, Arno Velds, David J. Adams, Daniel S. Peeper, Oscar Krijgsman
Software Mentions: 7
Published: over 7 years ago

10.1016/j.virol.2021.03.019

Zika virus infection during pregnancy protects against secondary infection in the absence of CD8+ cells
Cited by: 3
Author(s): Blake Schouest, Brandon J Beddingfield, Margaret H. Gilbert, Rudolf P. Bohm, Faith Schiro, Pyone P. Aye, Antonito T. Panganiban, Diogo M. Magnani, Nicholas J. Maness
Software Mentions: 7
Published: almost 5 years ago

10.1016/j.celrep.2020.107694

A Landscape of Murine Long Non-Coding RNAs Reveals the Leading Transcriptome Alterations in Adipose Tissue during Aging
Cited by: 24
Author(s): Qi Zhou, Qianfen Wan, Yuxi Jiang, Jin Liu, Qiang Li, Li Sun
Software Mentions: 7
Published: about 6 years ago

10.1007/s00572-020-01001-6

Phosphate availability and ectomycorrhizal symbiosis with Pinus sylvestris have independent effects on the Paxillus involutus transcriptome
Cited by: 6
Author(s): Christina Paparokidou, Jonathan R. Leake, David J. Beerling, Stephen A. Rolfe
Software Mentions: 7
Published: over 5 years ago

10.1038/s41598-019-44491-x

The LL-100 panel: 100 cell lines for blood cancer studies
Cited by: 67
Author(s): Hilmar Quentmeier, Claudia Pommerenke, Wilhelm G. Dirks, Sonja Eberth, Max Koeppel, Roderick A.F. MacLeod, Stefan Nagel, Klaus G. Steube, Cord C. Uphoff, Hans G. Drexler
Software Mentions: 7
Published: about 7 years ago

10.1186/s13059-016-0940-1

A benchmark for RNA-seq quantification pipelines
Cited by: 146
Author(s): Mingxiang Teng, Michael I. Love, Carrie A. Davis, Sarah Djebali, Alexander Dobin, Brenton R. Graveley, Sheng Li, Christopher E. Mason, Sara Olson, Dmitri D. Pervouchine, Cricket A. Sloan, Xintao Wei, Lijun Zhan, Rafael A. Irizarry
Software Mentions: 7
Published: about 10 years ago

10.1038/s42003-021-01897-6

Identification of a targetable KRAS-mutant epithelial population in non-small cell lung cancer
Cited by: 9
Author(s): Giorgia Maroni, Mahmoud A. Bassal, Indira Krishnan, Chee Wai Fhu, Virginia Savova, Rapolas Žilionis, Valerie A. Maymi, Nicole Pandell, Eva Csizmadia, Junyan Zhang, Barbara Storti, Julio Castaño, Riccardo Panella, Jia Li, Corinne E. Gustafson, Sam Fox, Rachel Levy, Claire Meyerovitz, Peter J. Tramontozzi, Kimberly Vermilya, Assunta De Rienzo, Stefania Crucitta, Daniela S. Bassères, Marla Weetall, Art Branstrom, Alessandra Giorgetti, Raffaele Ciampi, Marzia Del Re, Romano Danesi, Ranieri Bizzarri, Henry Yang, Olivier Kocher, Allon M. Klein, Robert S. Welner, Raphael Bueno, Maria Cristina Magli, John G. Clohessy, Azhar Ali, Daniel G. Tenen, Elena Levantini
Software Mentions: 7
Published: about 5 years ago

10.1186/s12967-021-02936-w

TPM, FPKM, or Normalized Counts? A Comparative Study of Quantification Measures for the Analysis of RNA-seq Data from the NCI Patient-Derived Models Repository
Cited by: 114
Author(s): Yingdong Zhao, Ming-Chung Li, Mariam M. Konaté, Li Chen, Biswajit Das, Chris Karlovich, P. Mickey Williams, Yvonne A. Evrard, James H. Doroshow, Lisa M. McShane
Software Mentions: 7
Published: about 5 years ago

10.1186/s12859-020-3433-x

RASflow: an RNA-Seq analysis workflow with Snakemake
Cited by: 30
Author(s): Xiaokang Zhang, Inge Jonassen
Software Mentions: 7
Published: over 6 years ago

10.1016/j.isci.2021.102870

Single paternal dexamethasone challenge programs offspring metabolism and reveals multiple candidates in RNA-mediated inheritance
Cited by: 14
Author(s): Katharina Gapp, Guillermo E. Parada, Fridolin Groß, Alberto Corcoba, Jasmine Kaur, Evelyn Grau, Martin Hemberg, Johannes Bohacek, Eric A. Miska
Software Mentions: 7
Published: almost 5 years ago

10.1038/s41418-021-00751-w

Bromodomain protein BRDT directs ΔNp63 function and super-enhancer activity in a subset of esophageal squamous cell carcinomas
Cited by: 17
Author(s): Xin Wang, Ana P. Kutschat, Mitsuko Yamada, Evangelos Prokakis, Patricia Böttcher, Koji Tanaka, Yuichiro Doki, Feda H. Hamdan, Steven A. Johnsen
Software Mentions: 7
Published: over 5 years ago

10.1038/s41435-020-00118-0

Genomic profiling of T-cell activation suggests increased sensitivity of memory T cells to CD28 costimulation
Cited by: 13
Author(s): Dafni A. Glinos, Blagoje Soskic, Cayman Williams, Alan Kennedy, Luke Jostins, David M. Sansom, Gosia Trynka
Software Mentions: 7
Published: over 5 years ago

10.1186/s13040-016-0099-z

SePIA: RNA and small RNA sequence processing, integration, and analysis
Cited by: 22
Author(s): Katherine Icay, Ping Chen, Alejandra Cervera, Ville Rantanen, Rainer Lehtonen, Sampsa Hautaniemi
Software Mentions: 7
Published: about 10 years ago

10.7554/eLife.55794

Intra-species differences in population size shape life history and genome evolution
Cited by: 31
Author(s): David Willemsen, Rongfeng Cui, Martin Reichard, Dario Riccardo Valenzano
Software Mentions: 7
Published: almost 6 years ago

10.3389/fmolb.2020.565530

Cross-Sectional Transcriptional Analysis of the Aging Murine Heart
Cited by: 4
Author(s): Matthew Greenig, Andrew Melville, Derek Huntley, Mark Isalan, Michał Mielcarek
Software Mentions: 7
Published: almost 6 years ago

10.7554/eLife.49658

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

10.1186/s13007-019-0440-x

Comparing time series transcriptome data between plants using a network module finding algorithm
Cited by: 6
Author(s): Jiyoung Lee, Lenwood S. Heath, Ruth Grene, Song Li
Software Mentions: 7
Published: about 7 years ago

10.3389/fgene.2021.684002

Regulation of Long Non-coding RNA KCNQ1OT1 Network in Colorectal Cancer Immunity
Cited by: 5
Author(s): Junjie Liu, Wei Lv, Shuling Li, Jingwen Deng
Software Mentions: 7
Published: almost 5 years ago

10.1186/s12864-021-07509-1

Transcriptome analyses of 7-day-old zebrafish larvae possessing a familial Alzheimer’s disease-like mutation in psen1 indicate effects on oxidative phosphorylation, ECM and MCM functions, and iron homeostasis
Cited by: 7
Author(s): Yang Dong, Morgan Newman, Stephen Pederson, Karissa Barthelson, Nhi Hin, Michael Lardelli
Software Mentions: 7
Published: over 5 years ago

10.1186/s12870-020-02808-3

Integrated Transcriptomic and Metabolomic analysis reveals a transcriptional regulation network for the biosynthesis of carotenoids and flavonoids in ‘Cara cara’ navel Orange
Cited by: 18
Author(s): Haipeng Zhang, Jiajing Chen, Zhaoxin Peng, Meiyan Shi, Xiao Liu, Wen Huang, Youwu Jiang, Yunjiang Cheng, Juan Xu, Hongyan Zhang
Software Mentions: 7
Published: over 5 years ago

10.1002/cti2.1173

Systematic analysis of the transcriptome in small‐cell carcinoma of the oesophagus reveals its immune microenvironment
Cited by: 2
Author(s): Qi Zhao, Yan‐Xing Chen, Qi‐Nian Wu, Chao Zhang, Min Liu, Yingnan Wang, Yan Feng, Jiajia Hu, Jianhua Fu, Hong Yang, Jingjing Qi, Zixian Wang, Yong Lu, Hui Sheng, Zexian Liu, Zhixiang Zuo, Jian Zheng, Jing‐Ping Yun, Jin‐Xin Bei, Wei‐Hua Jia, Dong Lin, Rui‐Hua Xu, Feng Wang
Software Mentions: 7
Published: over 6 years ago

10.3389/fcimb.2021.733619

Antigen Presenting Cells Link the Female Genital Tract Microbiome to Mucosal Inflammation, With Hormonal Contraception as an Additional Modulator of Inflammatory Signatures
Cited by: 8
Author(s): Elizabeth H. Byrne, M Fărcăşanu, Seth M. Bloom, Nondumiso Xulu, Jiawu Xu, Barry L. Hykes, Nomfuneko A. Mafunda, Matthew R. Hayward, Mary Dong, Krista Dong, Thandeka Gumbi, Fransisca Xolisile Ceasar, Nasreen Ismail, Thumbi Ndung’u, Christina Gosmann, Musie Ghebremichael, Scott A. Handley, Caroline Mitchell, Alexandra Chloé Villani, Douglas S. Kwon
Software Mentions: 7
Published: almost 5 years ago

10.1186/s12915-021-01062-9

Exposure to ethanol leads to midfacial hypoplasia in a zebrafish model of FASD via indirect interactions with the Shh pathway
Cited by: 12
Author(s): Alfire Sidik, Groves Dixon, Desirè M. Buckley, Hannah G. Kirby, Suwan Sun, Johann K. Eberhart
Software Mentions: 7
Published: almost 5 years ago

10.3389/fcell.2021.702046

Transcriptomic Drivers of Differentiation, Maturation, and Polyploidy in Human Extravillous Trophoblast
Cited by: 17
Author(s): Robert Morey, Omar Farah, Sampada Kallol, Daniela F. Requena, Morgan Meads, Matteo Moretto-Zita, Francesca Soncin, Louise C. Laurent, Mana M. Parast
Software Mentions: 7
Published: almost 5 years ago

10.1128/mBio.01468-21

Lung Epithelial Signaling Mediates Early Vaccine-Induced CD4⁺T Cell Activation and<i>Mycobacterium tuberculosis</i>Control
Cited by: 9
Author(s): Shibali Das, Nancy D. Marín, Ekaterina Esaulova, Mushtaq Ahmed, Amanda Swain, Bruce A. Rosa, Makedonka Mitreva, Javier Rangel-Moreno, Mihai G. Netea, Luis B. Barreiro, Maziar Divangahi, Maxim N. Artyomov, Deepak Kaushal, Shabaana A. Khader
Software Mentions: 7
Published: almost 5 years ago

10.1186/s13059-020-02082-4

Genome-wide studies reveal the essential and opposite roles of ARID1A in controlling human cardiogenesis and neurogenesis from pluripotent stem cells
Cited by: 22
Author(s): Juli Liu, Sheng Liu, Hongyu Gao, Lei Han, Xun Chu, Sheng Yi, Weinian Shou, Yue Wang, Yunlong Liu, Jun Wan, Lei Yang
Software Mentions: 7
Published: almost 6 years ago

10.1371/journal.pone.0173115

Altered regulation and expression of genes by BET family of proteins in COPD patients
Cited by: 11
Author(s): Rajneesh Malhotra, Nisha Kurian, Xin Zhou, Fang Jiang, Susan J. Monkley, Amy DeMicco, Ib Groth Clausen, Göran Dellgren, Goran Edenro, Miika J. Ahdesmäki, Maryam Clausen, Lisa Öberg, Elisabeth Israelsson, Graham Belfield, Outi Vaarala
Software Mentions: 7
Published: over 9 years ago

10.1186/1472-6807-13-2

Designing and benchmarking the MULTICOM protein structure prediction system
Cited by: 25
Author(s): Jilong Li, Xin Deng, Jesse Eickholt, Jianlin Cheng
Software Mentions: 7
Published: over 13 years ago

10.1038/sdata.2018.21

Small RNA-seq analysis of circulating miRNAs to identify phenotypic variability in Friedreich’s ataxia patients
Cited by: 22
Author(s): Marta Seco-Cervera, Daymé González-Rodríguez, José Santiago Ibáñez-Cabellos, Lorena Peiró-Chova, Federico V. Pallardó, José Luis García-Giménez
Software Mentions: 7
Published: over 8 years ago

10.7554/eLife.61138

The biphasic and age-dependent impact of klotho on hallmarks of aging and skeletal muscle function
Cited by: 15
Author(s): Zachary Clemens, Sruthi Sivakumar, Abish Pius, Amrita Sahu, Sunita Shinde, Hikaru Mamiya, Nathaniel Luketich, Jian Cui, Purushottam D. Dixit, Joerg D. Hoeck, Sebastian Kreuz, Michael Franti, Aaron Barchowsky, Fabrisia Ambrosio
Software Mentions: 7
Published: about 5 years ago

10.1002/jev2.12127

Inflammasome‐induced extracellular vesicles harbour distinct RNA signatures and alter bystander macrophage responses
Cited by: 26
Author(s): Christina F. Budden, Linden J. Gearing, Romina Kaiser, Lena Standke, Paul J. Hertzog, Eicke Latz
Software Mentions: 7
Published: almost 5 years ago

10.1093/bib/bbx143

Bioinformatics for precision oncology
Cited by: 49
Author(s): Jochen Singer, Anja Irmisch, Hans‐Joachim Ruscheweyh, Franziska Singer, Nora C. Toussaint, Mitchell P. Levesque, Daniel J. Stekhoven, Niko Beerenwinkel
Software Mentions: 7
Published: over 8 years ago

10.7554/eLife.22631

The pioneer factor OCT4 requires the chromatin remodeller BRG1 to support gene regulatory element function in mouse embryonic stem cells
Cited by: 184
Author(s): Hamish W King, Robert J. Klose
Software Mentions: 7
Published: over 9 years ago

10.1002/bit.27209

Comparative genome‐scale analysis of <i>Pichia pastoris</i> variants informs selection of an optimal base strain
Cited by: 31
Author(s): Joseph Brady, Charles A. Whittaker, Melody C. Tan, D. Lee Kristensen, Duanduan Ma, Neil C. Dalvie, Kerry R. Love, J. Christopher Love
Software Mentions: 7
Published: over 6 years ago

10.7554/eLife.59654

HNRNPM controls circRNA biogenesis and splicing fidelity to sustain cancer cell fitness
Cited by: 19
Author(s): Jessica Sy Ho, Federico Di Tullio, Megan Schwarz, Diana Low, Danny Incarnato, Tommaso Tabaglio, Jingxian Zhang, Heike Wollmann, Leilei Chen, Ömer An, Tim Chan, Alexander Hall Hickman, Simin Zheng, Vladimir Roudko, Sujun Chen, Alcida Karz, Musaddeque Ahmed, Housheng Hansen He, Benjamin Greenbaum, Salvatore Oliviero, Michela Serresi, Gaetano Gargiulo, Karen Mann, Eva Hernando, David J. Mulholland, Ivan Marazzi, Dave Keng Boon Wee, Ernesto Guccione
Software Mentions: 7
Published: about 5 years ago

10.1016/j.ccell.2019.08.008

An Evolutionarily Conserved Function of Polycomb Silences the MHC Class I Antigen Presentation Pathway and Enables Immune Evasion in Cancer
Cited by: 314
Author(s): Marian L. Burr, Christina E Sparbier, Kah Lok Chan, Yih-Chih Chan, Ariena Kersbergen, Enid Y.N. Lam, Elizabeth Azidis-Yates, Dane Vassiliadis, Charles C. Bell, Omer Gilan, Susan Jackson, Lavinia Tan, Stephen Q. Wong, Sebastian Hollizeck, Ewa M. Michalak, Hannah V. Siddle, Michael T. McCabe, Rab K. Prinjha, Glen R Guerra, Benjamin Solomon, Shahneen Sandhu, Sarah‐Jane Dawson, Paul A. Beavis, Richard W. Tothill, Carleen Cullinane, Paul J. Lehner, Kate D. Sutherland, Mark A. Dawson
Software Mentions: 7
Published: over 6 years ago

10.3389/fmicb.2021.631889

DWV Infection in vitro Using Honey Bee Pupal Tissue
Cited by: 3
Author(s): Yunfei Wu, Xuye Yuan, Jing Li, Tatsuhiko Kadowaki
Software Mentions: 7
Published: over 5 years ago

10.1242/dev.178590

Maintenance of spatial gene expression by Polycomb-mediated repression after formation of a vertebrate body plan
Cited by: 13
Author(s): Julien Rougeot, Naomi D. Chrispijn, Marco Aben, Dei M. Elurbe, Karolina M. Andralojc, Patrick J. Murphy, Pascal W.T.C. Jansen, Michiel Vermeulen, Bradley R. Cairns, Leonie M. Kamminga
Software Mentions: 7
Published: over 7 years ago

10.1534/g3.119.0011

Chromosome-Wide Evolution and Sex Determination in the Three-Sexed Nematode <i>Auanema rhodensis</i>
Cited by: 31
Author(s): Sophie Tandonnet, Georgios Koutsovoulos, Sally Adams, Delphine Cloarec, Manish Parihar, Mark Blaxter, André Pires-daSilva
Software Mentions: 7
Published: about 7 years ago

10.3390/brainsci10020109

Chronic Chemogenetic Stimulation of the Nucleus Accumbens Produces Lasting Reductions in Binge Drinking and Ameliorates Alcohol-Related Morphological and Transcriptional Changes
Cited by: 27
Author(s): Dar'ya Pozhidayeva, Sean P. Farris, Calla M Goeke, Evan Firsick, Kayla G. Townsley, Marina Guizzetti, Angela R. Ozburn
Software Mentions: 7
Published: over 6 years ago

10.3389/fimmu.2018.01553

Single Cell RNA Sequencing of Rare Immune Cell Populations
Cited by: 88
Author(s): Akira Nguyen, Weng Hua Khoo, Imogen Moran, Peter I. Croucher, Tri Giang Phan
Software Mentions: 7
Published: almost 8 years ago

10.1534/g3.114.011759

Genomic Profiling of Collaborative Cross Founder Mice Infected with Respiratory Viruses Reveals Novel Transcripts and Infection-Related Strain-Specific Gene and Isoform Expression
Cited by: 22
Author(s): Hao Xiong, Juliet Morrison, Martin T. Ferris, Lisa E. Gralinski, Alan C. Whitmore, Richard Green, Matthew Thomas, Jennifer Tisoncik-Go, Gary P. Schroth, Fernando P Pardo Manuel De Villena, Ralph S. Baric, Mark T. Heise, Xinxia Peng, Michael G. Katze
Software Mentions: 7
Published: almost 12 years ago

10.1371/journal.pgen.1007784

Maternal and zygotic gene regulatory effects of endogenous RNAi pathways
Cited by: 17
Author(s): Miguel Vasconcelos Almeida, António Miguel de Jesus Domingues, René F. Ketting
Software Mentions: 7
Published: over 7 years ago

10.21203/rs.3.rs-380803/v1

Impaired immune signaling and changes in the lung microbiome precede secondary bacterial pneumonia in COVID-19
Cited by: 9
Author(s): Alexandra Tsitsiklis, Beth Shoshana Zha, Ashley Byrne, Catherine DeVoe, Sophia Levan, Elze Rackaityte, Sara Sunshine, Eran Mick, Rajani Ghale, Alejandra Jauregui, Norma Neff, Aartik Sarma, Paula Hayakawa Serpa, Thomas Deiss, Amy Kistler, Sidney Carrillo, K. Mark Ansel, Aleksandra Leligdowicz, S. Christenson, Nicola L. Jones, Benjamin Wu, Spyros Darmanis, Michael A. Matthay, Susan V. Lynch, Joseph L. DeRisi, Carolyn M. Hendrickson, Kirsten N. Kangelaris, Matthew F. Krummel, Prescott G. Woodruff, David J. Erle, O. A. Rosenberg, Carolyn S. Calfee, Charles Langelier
Software Mentions: 7
Published: about 5 years ago

10.7554/eLife.56689

Genome streamlining in a minute herbivore that manipulates its host plant
Cited by: 30
Author(s): Robert Greenhalgh, Wannes Dermauw, Joris J. Glas, Stéphane Rombauts, Nicky Wybouw, Jainy Thomas, Juan M. Alba, Ellen J. Pritham, Saioa Legarrea, René Feyereisen, Yves Van de Peer, Thomas Van Leeuwen, Richard M. Clark, Merijn R. Kant
Software Mentions: 7
Published: over 5 years ago

10.3389/fimmu.2021.665312

An IRF1-IRF4 Toggle-Switch Controls Tolerogenic and Immunogenic Transcriptional Programming in Human Langerhans Cells
Cited by: 8
Author(s): James Davies, Andrés F. Vallejo, Sofía Sirvent, Gemma Porter, Kalum Clayton, Yamkela Qumbelo, Patrick S. Stumpf, Jonathan West, Clive M. Gray, Nyaradzo T. L. Chigorimbo‐Murefu, Ben D. MacArthur, Marta E. Polak
Software Mentions: 7
Published: about 5 years ago

10.3389/fimmu.2020.580373

Systems Biology Methods Applied to Blood and Tissue for a Comprehensive Analysis of Immune Response to Hepatitis B Vaccine in Adults
Cited by: 13
Author(s): Rym Ben‐Othman, Bing Cai, Aaron C. Liu, Natallia Varankovich, Daniel He, Travis M. Blimkie, Ahwon Lee, Erin E. Gill, M. A. Novotny, Brian D. Aevermann, Sibyl Drissler, Casey P. Shannon, Sarah McCann, Kim Marty, Gordean Bjornson, Rachel D. Edgar, David Lin, Nicole Gladish, Julia L. Maclsaac, Nelly Amenyogbe, Queenie Chan, Alba Llibre, Collin Joyce, Elise Landais, Khoa Le, Samantha M. Reiss, Wayne C. Koff, Colin Havenar-Daughton, Manraj K.S. Heran, Bippan S. Sangha, David R. Walt, Mel Krajden, Shane Crotty, Devin Sok, Bryan Briney, Dennis R. Burton, Darragh Duffy, Leonard J. Foster, William W. Mohn, Michael S. Kobor, Scott J. Tebbutt, Ryan R. Brinkman, Richard H. Scheuermann, Robert E. W. Hancock, Tobias R. Kollmann, Manish Sadarangani
Software Mentions: 7
Published: over 5 years ago

10.1371/journal.pgen.1008482

A transcriptome-based signature of pathological angiogenesis predicts breast cancer patient survival
Cited by: 12
Author(s): Rodrigo Guarischi-Sousa, Jhonatas Sirino Monteiro, Lilian Costa Alecrim, Jussara S. Michaloski, Laura Beatriz da Silva Cardeal, Elisa Napolitano Ferreira, Dirce Maria Carraro, Diana Noronha Nunes, Emmanuel Dias-Neto, Jüri Reimand, Paul C. Boutros, João Carlos Setúbal, Ricardo J. Giordano
Software Mentions: 7
Published: over 6 years ago

10.1371/journal.pgen.1008506

Latent transcriptional variations of individual Plasmodium falciparum uncovered by single-cell RNA-seq and fluorescence imaging
Cited by: 21
Author(s): Katelyn A. Walzer, Hélène Fradin, Liane Y. Emerson, David L. Corcoran, Jen‐Tsan Chi
Software Mentions: 7
Published: over 6 years ago

10.1371/journal.pgen.1008662

Discovery of novel hepatocyte eQTLs in African Americans
Cited by: 19
Author(s): Yi Zhong, Tanima De, Cristina Alárcon, C. Sehwan Park, Bianca Lec, Minoli Perera
Software Mentions: 7
Published: about 6 years ago

10.3389/fimmu.2020.588411

Distinctive Cellular and Metabolic Reprogramming in Porcine Lung Mononuclear Phagocytes Infected With Type 1 PRRSV Strains
Cited by: 6
Author(s): Elisa Crisci, Marco Moroldo, Thien‐Phong Vu Manh, Ammara Mohammad, Laurent Jourdren, Céline Urien, Edwige Bouguyon, Elise Bordet, Claudia Bevilacqua, Mickaël Bourge, Jérémy Pezant, Alexis Pléau, Olivier Boulesteix, Isabelle Schwartz, Nicolas Bertho, Elisabetta Giuffra
Software Mentions: 7
Published: over 5 years ago

10.3389/fimmu.2021.568729

Evolution and Expression of the Immune System of a Facultatively Anadromous Salmonid
Cited by: 7
Author(s): Thomas J. Colgan, Peter Moran, Louise C. Archer, Robert Wynne, Stephen A. Hutton, Philip McGinnity, Thomas E. Reed
Software Mentions: 7
Published: over 5 years ago

10.3389/fimmu.2020.578505

Preparing for Life: Plasma Proteome Changes and Immune System Development During the First Week of Human Life
Cited by: 18
Author(s): Tue Bjerg Bennike, Benoit Fatou, Asimenia Angelidou, Joann Diray‐Arce, Reza Falsafi, Rebecca Ford, Erin E. Gill, Simon D. van Haren, Olubukola T. Idoko, Ahwon Lee, Rym Ben‐Othman, William Pomat, Casey P. Shannon, Kinga K. Smolen, Scott J. Tebbutt, Al Ozonoff, Peter Richmond, Anita H. J. van den Biggelaar, Robert E. W. Hancock, Beate Kampmann, Tobias R. Kollmann, Ofer Levy, Hanno Steen
Software Mentions: 7
Published: over 5 years ago

10.3390/cancers12061453

DSCAM-AS1-Driven Proliferation of Breast Cancer Cells Involves Regulation of Alternative Exon Splicing and 3′-End Usage
Cited by: 16
Author(s): Jamal Elhasnaoui, Valentina Miano, Giulio Ferrero, Elena Doria, Antonette E. Leon, Aline S C Fabrício, Laura Annaratone, Isabella Castellano, Anna Sapino, Michele De Bortoli
Software Mentions: 7
Published: about 6 years ago

10.3390/cancers11060759

Detection of Epstein-Barr Virus Infection in Non-Small Cell Lung Cancer
Cited by: 31
Author(s): Fayez Kheir, Mengmeng Zhao, Michael J. Strong, Yi Yu, Asuka Nanbo, Erik K. Flemington, Gilbert F. Morris, Krzysztof Reiss, Li Li, Zhen Lin
Software Mentions: 7
Published: about 7 years ago

10.1016/j.devcel.2017.07.002

The Helicase Aquarius/EMB-4 Is Required to Overcome Intronic Barriers to Allow Nuclear RNAi Pathways to Heritably Silence Transcription
Cited by: 59
Author(s): Alper Akay, Tomás Di Domenico, Kin Man Suen, Amena Nabih, Guillermo E. Parada, Mark Larance, Ragini Medhi, Ahmet C. Berkyurek, Xinlian Zhang, Christopher J. Wedeles, Konrad L. M. Rudolph, Jan Engelhardt, Martin Hemberg, Ping Ma, Angus I. Lamond, Julie M. Claycomb, Eric A. Miska
Software Mentions: 7
Published: almost 9 years ago

10.1038/sdata.2016.90

Genome-wide chromatin and gene expression profiling during memory formation and maintenance in adult mice
Cited by: 5
Author(s): Tonatiuh Peña Centeno, Orr Shomroni, Magali Hennion, Rashi Halder, Ramón Vidal, Raza-Ur Rahman, Stefan Bonn
Software Mentions: 7
Published: over 9 years ago

10.15252/emmm.202012525

<scp>LSD</scp> 1 inhibition induces differentiation and cell death in Merkel cell carcinoma
Cited by: 36
Author(s): Lukas Leiendecker, Pauline S. Jung, Izabela Krecioch, Tobias Neumann, Alexander Schleiffer, Karl Mechtler, Thomas Wiesner, Anna C. Obenauf
Software Mentions: 7
Published: over 5 years ago

10.1038/sdata.2017.149

Building a locally diploid genome and transcriptome of the diatom Fragilariopsis cylindrus
Cited by: 12
Author(s): Pirita Paajanen, Jan Strauss, Cock van Oosterhout, Mark McMullan, Matt Clark, Thomas Möck
Software Mentions: 7
Published: over 8 years ago

10.1093/g3journal/jkab255

Improved draft reference genome for the Glassy-winged Sharpshooter (<i>Homalodisca vitripennis</i>), a vector for Pierce’s disease
Cited by: 8
Author(s): Cassandra L. Ettinger, Frank J. Byrne, Matthew A. Collin, Derreck Carter-House, Linda L. Walling, Peter W. Atkinson, Rick A Redak, Jason E. Stajich
Software Mentions: 7
Published: almost 5 years ago

10.1371/journal.pgen.1009422

High-resolution genetic mapping reveals cis-regulatory and copy number variation in loci associated with cytochrome P450-mediated detoxification in a generalist arthropod pest
Cited by: 25
Author(s): Seyedeh Masoumeh Fotoukkiaii, Nicky Wybouw, Andre H. Kurlovs, Dimitra Tsakireli, Spiros A. Pergantis, Richard M. Clark, John Vontas, Thomas Van Leeuwen
Software Mentions: 7
Published: about 5 years ago

10.3390/cancers13163929

Maturation State-Specific Alternative Splicing in FLT3-ITD and NPM1 Mutated AML
Cited by: 4
Author(s): Anna Wojtuszkiewicz, Inge van der Werf, Stephan Hütter, Wencke Walter, Constance Baer, Wolfgang Kern, Jeroen Janssen, Gert J. Ossenkoppele, Claudia Haferlach, Jacqueline Cloos, Torsten Haferlach
Software Mentions: 7
Published: almost 5 years ago

10.3390/jof7090700

Trends and Applications of Omics Technologies to Functional Characterisation of Enzymes and Protein Metabolites Produced by Fungi
Cited by: 3
Author(s): Grace N. Ijoma, Sylvie M Heri, Tonderayi Matambo, Memory Tekere
Software Mentions: 7
Published: almost 5 years ago

10.3389/fimmu.2020.596514

Intestinal Transcriptome Analysis Reveals Soy Derivative-Linked Changes in Atlantic Salmon
Cited by: 26
Author(s): Viswanath Kiron, Youngjin Park, Prabhugouda Siriyappagouder, Dalia Dahle, Ghana Kalerammana Vasanth, Jorge Dias, Jorge M. O. Fernandes, Mette Sørensen, Viviane Verlhac Trichet
Software Mentions: 7
Published: over 5 years ago

10.1186/s10194-021-01285-9

Identification of disease- and headache-specific mediators and pathways in migraine using blood transcriptomic and metabolomic analysis
Cited by: 13
Author(s): Tímea Aczél, Tamás Körtési, József Kun, Péter Urbán, Witold Bauer, Róbert Herczeg, Robert Farkaš, K Kovács, Barna Vásárhelyi, Gellért Balázs Karvaly, Attila Gyenesei, Bernadett Tuka, János Tajti, László Vécsei, Kata Bölcskei, Zsuzsanna Helyes
Software Mentions: 7
Published: over 4 years ago

10.1534/g3.120.401579

High-Quality Assemblies for Three Invasive Social Wasps from the <i>Vespula</i> Genus
Cited by: 19
Author(s): Thomas W. R. Harrop, Joseph Guhlin, Gemma M. McLaughlin, Elizabeth Permina, Peter A. Stockwell, Josh Gilligan, Marissa F. Le Lec, Monica A. M. Gruber, Oliver Quinn, Mackenzie Lovegrove, Elizabeth J. Duncan, Emily J. Remnant, Jens Van Eeckhoven, Brittany Graham, Rosemary A Knapp, Kyle W. Langford, Zev Kronenberg, Maximilian O. Press, Stephen Eacker, Erin E. Wilson Rankin, Jessica Purcell, Philip J. Lester, Peter K. Dearden
Software Mentions: 7
Published: over 5 years ago

10.1186/s13062-016-0169-7

Sensitivity, specificity, and reproducibility of RNA-Seq differential expression calls
Cited by: 26
Author(s): Paweł P. Łabaj, David P. Kreil
Software Mentions: 7
Published: over 9 years ago

10.1093/bfgp/ely003

The impact of single-cell RNA sequencing on understanding the functional organization of the immune system
Cited by: 15
Author(s): Péter Végh, Muzlifah Haniffa
Software Mentions: 7
Published: over 8 years ago

10.3390/cancers12030690

Comparative Molecular Analysis of Cancer Behavior Cultured In Vitro, In Vivo, and Ex Vivo
Cited by: 17
Author(s): Nicholas R. Hum, Aimy Sebastian, Sean F. Gilmore, Wei He, Kelly A. Martin, Aubree Hinckley, Karen Dubbin, Monica L. Moya, Elizabeth K. Wheeler, Matthew A. Coleman, Gabriela G. Loots
Software Mentions: 7
Published: over 6 years ago

10.1038/s41598-019-52584-w

Identifying inaccuracies in gene expression estimates from unstranded RNA-seq data
Cited by: 8
Author(s): Mikhail Pomaznoy, Ashu Sethi, Jason A. Greenbaum, Bjoern Peters
Software Mentions: 7
Published: over 6 years ago

10.7554/eLife.63194

Evolutionary dynamics of transposable elements in bdelloid rotifers
Cited by: 21
Author(s): Reuben W. Nowell, Christopher G. Wilson, Pedro Almeida, Philipp H. Schiffer, Diego Fontaneto, Lutz Becks, Fernando Rodríguez, Irina R. Arkhipova, Timothy G. Barraclough
Software Mentions: 7
Published: over 5 years ago

10.1186/s13293-020-00312-9

Reference genome and transcriptome informed by the sex chromosome complement of the sample increase ability to detect sex differences in gene expression from RNA-Seq data
Cited by: 27
Author(s): Kimberly C. Olney, Sarah M. Brotman, Jocelyn P. Andrews, Valeria A. Valverde-Vesling, Melissa A. Wilson
Software Mentions: 7
Published: almost 6 years ago

10.1093/bib/bbz126

Systematic evaluation of differential splicing tools for RNA-seq studies
Cited by: 99
Author(s): Arfa Mehmood, Asta Laiho, Mikko S Venäläinen, Aidan McGlinchey, Ning Wang, Laura L. Elo
Software Mentions: 7
Published: over 6 years ago

10.1016/j.cell.2021.01.002

Meta-analysis of tumor- and T cell-intrinsic mechanisms of sensitization to checkpoint inhibition
Cited by: 412
Author(s): Kevin Litchfield, James L. Reading, Clare Puttick, Krupa Thakkar, Chris Abbosh, Robert Bentham, Thomas B.K. Watkins, Rachel Rosenthal, Dhruva Biswas, Andrew Rowan, Emilia L. Lim, Maise Al Bakir, Virginia Turati, José Afonso Guerra-Assunção, Lucía Conde, Andrew J.S. Furness, Sunil Kumar Saini, Sine Reker Hadrup, Javier Herrero, Se‐Hoon Lee, Peter Van Loo, Tariq Enver, James Larkin, Matthew D. Hellmann, Samra Turajlic, Sergio A. Quezada, Nicholas McGranahan, Charles Swanton
Software Mentions: 7
Published: over 5 years ago

10.1016/j.cell.2020.07.017

Therapy-Induced Evolution of Human Lung Cancer Revealed by Single-Cell RNA Sequencing
Cited by: 319
Author(s): Ashley Maynard, Caroline E. McCoach, Julia Rotow, Lincoln Harris, Franziska Haderk, D. Lucas Kerr, Elizabeth A. Yu, Erin L. Schenk, Weilun Tan, Alexander Zee, Michelle Tan, Philippe Gui, Tasha Lea, Wei Wu, Anatoly Urisman, Kirk D. Jones, Rene Sit, Pallav K. Kolli, E. Scott Seeley, Yaron Gesthalter, Daniel Le, Kevin A. Yamauchi, David M. Naeger, Sourav Bandyopadhyay, Khyati N. Shah, Lauren Cech, Norman Thomas, Anshal Gupta, Mayra A. Gonzalez, Hien Do, Lisa Tan, Bianca Bacaltos, Rafael Gómez-Sjöberg, Matthew A. Gubens, Thierry Jahan, Johannes R. Kratz, David M. Jablons, Norma Neff, Robert C. Doebele, Jonathan S. Weissman, Collin M. Blakely, Spyros Darmanis, Trever G. Bivona
Software Mentions: 7
Published: almost 6 years ago