cran: STAR | Projects | Ecosyste.ms: Papers

10.1186/s13059-017-1335-7

Regulatory remodeling in the allo-tetraploid frog Xenopus laevis
Cited by: 27
Author(s): Dei M. Elurbe, Sarita S. Paranjpe, Γεώργιος Γεωργίου, Ila van Kruijsbergen, Ozren Bogdanović, Romain Gibeaux, Rebecca Heald, Ryan Lister, Martijn A. Huynen, Simon J. van Heeringen, Gert Jan C. Veenstra
Software Mentions: 6
Published: almost 9 years ago

10.3390/ijms22126319

Expression Quantitative Trait Loci (eQTLs) Associated with Retrotransposons Demonstrate their Modulatory Effect on the Transcriptome
Cited by: 6
Author(s): Sulev Kõks, Abigail L Pfaff, Vivien J. Bubb, John P. Quinn
Software Mentions: 6
Published: over 5 years ago

10.1016/j.stem.2019.07.009

Distinct Molecular Trajectories Converge to Induce Naive Pluripotency
Cited by: 27
Author(s): Hannah Stuart, Giuliano Giuseppe Stirparo, Tim Lohoff, Lawrence E. Bates, Masaki Kinoshita, Chee Lim, Elsa Joana Sousa, Katsiaryna Maskalenka, Aliaksandra Radzisheuskaya, Andrew A. Malcolm, Mariana R. P. Alves, Rebecca L. Lloyd, Sonia Nestorowa, Peter Humphreys, William Mansfield, Wolf Reik, Paul Bertone, Jennifer Nichols, Berthold Göttgens, José C.R. Silva
Software Mentions: 6
Published: about 7 years ago

10.7554/eLife.18591

RYBP stimulates PRC1 to shape chromatin-based communication between Polycomb repressive complexes
Cited by: 105
Author(s): Nathan R. Rose, Hamish W King, Neil P. Blackledge, Nadezda A. Fursova, Katherine Ji Ember, Román Fischer, Benedikt M. Kessler, Robert J. Klose
Software Mentions: 6
Published: about 10 years ago

10.7554/eLife.59929

Gene expression variability in human and chimpanzee populations share common determinants
Cited by: 27
Author(s): Benjamin Jung Fair, Lauren E. Blake, Abhishek Sarkar, Bryan J. Pavlovic, Claudia Cuevas, Yoav Gilad
Software Mentions: 6
Published: almost 6 years ago

10.7554/eLife.47898

CTCF confers local nucleosome resiliency after DNA replication and during mitosis
Cited by: 52
Author(s): Nick Owens, Thaleia Papadopoulou, Nicola Festuccia, Alexandra Tachtsidi, Inma González, Agnès Dubois, Sandrine Vandormael-Pournin, Elphège P. Nora, Benoit G. Bruneau, Michel Cohen-Tannoudji, Pablo Navarro
Software Mentions: 6
Published: almost 7 years ago

10.1590/1678-4685-GMB-2018-0259

Genome-wide analysis of the transcriptional response to drought stress in root and leaf of common bean
Cited by: 16
Author(s): Wendell Jacinto Pereira, Arthur Tavares de Oliveira Melo, Alexandre Siqueira Guedes Coelho, Fabiana Aparecida Rodrigues, Sujan Mamidi, Sérgio Amorim de Alencar, Anna Cristina Lanna, P. A. M. R. Valdisser, C. Brondani, Ivanildo Ramalho do Nascimento-Júnior, T. C. de O. Borba, R. P. Vianello
Software Mentions: 6
Published: almost 7 years ago

10.1371/journal.pgen.1009645

An enhancer screen identifies new suppressors of small-RNA-mediated epigenetic gene silencing
Cited by: 1
Author(s): Yukiko Shimada, Sarah H. Carl, Merle Skribbe, Valentin Flury, Tahsin Kuzdere, Georg Kempf, Marc Bühler
Software Mentions: 6
Published: over 5 years ago

10.1186/s12864-018-4670-5

Circular RNA expression and regulatory network prediction in posterior cingulate astrocytes in elderly subjects
Cited by: 28
Author(s): Shobana Sekar, Lori Cuyugan, Jonathan Adkins, Philipp Geiger, Winnie S. Liang
Software Mentions: 6
Published: over 8 years ago

10.1371/journal.pcbi.1008491

Predictive network modeling in human induced pluripotent stem cells identifies key driver genes for insulin responsiveness
Cited by: 14
Author(s): Iván Cárcamo-Orive, Marc Henrion, Kuixi Zhu, Noam D. Beckmann, Paige Cundiff, Sara Moein, Zenan Zhang, Melissa Alamprese, Sunita L. D’Souza, Martin Wabitsch, Eric E. Schadt, Thomas Quertermous, Joshua W. Knowles, Rui Chang
Software Mentions: 6
Published: almost 6 years ago

10.1186/s12711-019-0453-y

Machine learning applied to transcriptomic data to identify genes associated with feed efficiency in pigs
Cited by: 24
Author(s): M. Piles, Carlos Fernández-Lozano, María Velasco-Galilea, Olga González‐Rodríguez, Juan Pablo Sánchez, D. Torrallardona, María Ballester, Raquel Quintanilla
Software Mentions: 6
Published: over 7 years ago

10.3390/ijms22168482

Multicellular Human Cardiac Organoids Transcriptomically Model Distinct Tissue-Level Features of Adult Myocardium
Cited by: 17
Author(s): Charles M. Kerr, Dylan Richards, Donald R. Menick, Kristine Y. DeLeon‐Pennell, Ying Mei
Software Mentions: 6
Published: about 5 years ago

10.1016/j.molcel.2021.02.034

POINT technology illuminates the processing of polymerase-associated intact nascent transcripts
Cited by: 44
Author(s): Rui Sousa-Luís, Geneviève Dujardin, Inna Zukher, Hiroshi Kimurâ, Carika Weldon, Maria Carmo‐Fonseca, Nick J. Proudfoot, Takayuki Nojima
Software Mentions: 6
Published: over 5 years ago

10.1038/s41422-020-00455-9

Discriminating mild from critical COVID-19 by innate and adaptive immune single-cell profiling of bronchoalveolar lavages
Cited by: 203
Author(s): Els Wauters, Pierre Van Mol, Abhishek D. Garg, S.L. Jansen, Yannick Van Herck, Lore Vanderbeke, Ayse Bassez, Bram Boeckx, Bert Malengier‐Devlies, Anna Timmerman, Thomas Van Brussel, Tina Van Buyten, Rogier Schepers, Elisabeth Heylen, Dieter Dauwe, Christophe Dooms, Jan Gunst, Greet Hermans, Philippe Meersseman, Dries Testelmans, Jonas Yserbyt, Sabine Tejpar, Walter De Wever, Patrick Matthys, Maria Bosisio, Michaël P Casaer, Frederik De Smet, Paul De Munter, Stéphanie Humblet-Baron, Adrian Liston, Natalie Lorent, Kim Martinod, Paul Proost, Jeroen Raes, Karin Thevissen, Robin Vos, Birgit Weynand, Carine Wouters, Johan Neyts, Joost Wauters, Junbin Qian, Diether Lambrechts
Software Mentions: 6
Published: over 5 years ago

10.7554/eLife.30860

A high-resolution mRNA expression time course of embryonic development in zebrafish
Cited by: 218
Author(s): Richard White, John Collins, Ian Sealy, Neha Wali, Christopher M. Dooley, Zsofia Digby, Derek L. Stemple, Daniel N. Murphy, Konstantinos Billis, Thibaut Hourlier, Anja Füllgrabe, Matthew P Davis, Anton J. Enright, Elisabeth M Busch-Nentwich
Software Mentions: 6
Published: almost 9 years ago

10.3390/genes11111387

GWAS Based on RNA-Seq SNPs and High-Throughput Phenotyping Combined with Climatic Data Highlights the Reservoir of Valuable Genetic Diversity in Regional Tomato Landraces
Cited by: 10
Author(s): Mónica Rodríguez, Alessandro Scintu, Chiara M. Posadinu, Youqiang Xu, Cuong Nguyen, Honghe Sun, Elena Bitocchi, Elisa Bellucci, Roberto Papa, Zhangjun Fei, James J. Giovannoni, Domenico Rau, Giovanna Attene
Software Mentions: 6
Published: almost 6 years ago

10.3390/genes12010081

Non-Redundant tRNA Reference Sequences for Deep Sequencing Analysis of tRNA Abundance and Epitranscriptomic RNA Modifications
Cited by: 8
Author(s): Florian Pichot, Virginie Marchand, Mark Helm, Yuri Motorin
Software Mentions: 6
Published: over 5 years ago

10.1016/j.celrep.2019.11.026

Splice-Junction-Based Mapping of Alternative Isoforms in the Human Proteome
Cited by: 53
Author(s): Edward Lau, Yu Han, Damon R. Williams, Cody T Thomas, Rajani Shrestha, Joseph C. Wu, Maggie Lam
Software Mentions: 6
Published: almost 7 years ago

10.1016/j.xcrm.2021.100267

Cabozantinib and dasatinib synergize to induce tumor regression in non-clear cell renal cell carcinoma
Cited by: 2
Author(s): Hui Wen Lue, Daniel S. Derrick, Soumya Rao, Ahna Van Gaest, Larry C. Cheng, Jennifer Podolak, Samantha Lawson, Changhui Xue, Devin Garg, Ralph E. White, Christopher W. Ryan, Justin M. Drake, Anna Ritz, Laura M. Heiser, George V. Thomas
Software Mentions: 6
Published: over 5 years ago

10.7554/eLife.55159

Condensin I subunit Cap-G is essential for proper gene expression during the maturation of post-mitotic neurons
Cited by: 9
Author(s): Amira Hassan, Pablo Araguas Rodriguez, Stefan Heidmann, Emma L Walmsley, Gabriel Aughey, Tony D. Southall
Software Mentions: 6
Published: over 6 years ago

10.1016/j.ajhg.2019.05.010

Genetic and Epigenetic Fine Mapping of Complex Trait Associated Loci in the Human Liver
Cited by: 33
Author(s): Minal Çalışkan, Elisabetta Manduchi, Harish Rao, Julian A. Segert, Márcia Holsbach Beltrame, Marco Trizzino, YoSon Park, Samuel White Baker, Alessandra Chesi, Matthew E. Johnson, Kenyaita M. Hodge, Michelle E. Leonard, Bao‐Li Loza, Xin Dong, Andrea M. Berrido, Nicholas J. Hand, Robert C. Bauer, Andrew D. Wells, Kim M. Olthoff, Abraham Shaked, Daniel J. Rader, Struan F.A. Grant, Christopher D. Brown
Software Mentions: 6
Published: over 7 years ago

10.1186/s12864-021-07469-6

WASP: a versatile, web-accessible single cell RNA-Seq processing platform
Cited by: 5
Author(s): Andreas Hoek, Katharina Maibach, Ebru Özmen, Ana Ivonne Vazquez‐Armendariz, Jan Philipp Mengel, Torsten Hain, Susanne Herold, Alexander Goesmann
Software Mentions: 6
Published: over 5 years ago

10.1186/s12859-017-1808-4

QNB: differential RNA methylation analysis for count-based small-sample sequencing data with a quad-negative binomial model
Cited by: 36
Author(s): Lian Liu, Shao Wu Zhang, Yufei Huang, Jia Meng
Software Mentions: 6
Published: about 9 years ago

10.7554/eLife.61461

Phenotypic plasticity underlies local invasion and distant metastasis in colon cancer
Cited by: 29
Author(s): Andrea Sacchetti, Miriam Teeuwssen, Mathijs Verhagen, Rosalie Joosten, Tong Xu, Roberto Stabile, Berdine van der Steen, Martin M. Watson, Alem Gusinac, Won Kyu Kim, Inge Ubink, Harmen J.G. van de Werken, Arianna Fumagalli, Madelon Paauwe, Jacco van Rheenen, Owen J. Sansom, Onno Kranenburg, Riccardo Fodde
Software Mentions: 6
Published: over 5 years ago

10.1093/g3journal/jkab177

New genomic resources and comparative analyses reveal differences in floral gene expression in selfing and outcrossing Collinsia sister species
Cited by: 8
Author(s): Lauren J. Frazee, Joanna L. Rifkin, Dinusha C. Maheepala, Alannie‐Grace Grant, Stephen I. Wright, Susan Kalisz, Amy Litt, Rachel B. Spigler
Software Mentions: 6
Published: over 5 years ago

10.7554/eLife.65557

Dimerisation of the PICTS complex via LC8/Cut-up drives co-transcriptional transposon silencing in Drosophila
Cited by: 24
Author(s): Evelyn L Eastwood, Kayla A Jara, Susanne Bornelöv, Marzia Munafò, Vasileios Frantzis, Emma Kneuss, Elisar Barbar, Benjamin Czech, Gregory J. Hannon
Software Mentions: 6
Published: over 5 years ago

10.7554/eLife.65369

Surprising phenotypic diversity of cancer-associated mutations of Gly 34 in the histone H3 tail
Cited by: 18
Author(s): Brandon R Lowe, Rajesh K Yadav, Ryan A. Henry, Patrick Schreiner, Atsushi Matsuda, Alfonso G. Fernandez, David Finkelstein, Margaret Campbell, Satish Kallappagoudar, Carolyn M Jablonowski, Andrew J. Andrews, Yasushi Hiraoka, Janet F. Partridge
Software Mentions: 6
Published: over 5 years ago

10.1371/journal.pcbi.1007625

XPRESSyourself: Enhancing, standardizing, and automating ribosome profiling computational analyses yields improved insight into data
Cited by: 14
Author(s): Jordan A. Berg, Jonathan R Belyeu, Jeffrey T. Morgan, Yeyun Ouyang, Alex J. Bott, Aaron R. Quinlan, Jason Gertz, Jared Rutter
Software Mentions: 6
Published: over 6 years ago

10.1093/g3journal/jkaa043

Global translational landscape of the Candida albicans morphological transition
Cited by: 8
Author(s): Vasanthakrishna Mundodi, Saket Choudhary, Andrew D. Smith, David Kadosh
Software Mentions: 6
Published: almost 6 years ago

10.1186/s12864-020-6714-x

DolphinNext: a distributed data processing platform for high throughput genomics
Cited by: 61
Author(s): Onur Yukselen, Osman Turkyilmaz, Ahmet Öztürk, Manuel Garber, Alper Küçükural
Software Mentions: 6
Published: over 6 years ago

10.1186/s12859-020-03818-6

Calculating the most likely intron splicing orders in S. pombe, fruit fly, Arabidopsis thaliana, and humans
Cited by: 2
Author(s): Meng Li
Software Mentions: 6
Published: almost 6 years ago

10.1186/s13578-021-00691-5

A single-cell interactome of human tooth germ from growing third molar elucidates signaling networks regulating dental development
Cited by: 7
Author(s): Yueqi Shi, Yinglan Yu, Yuqiong Zhou, Jing Zhao, Wenjie Zhang, Duohong Zou, Weichen Song, Shaoyi Wang
Software Mentions: 6
Published: about 5 years ago

10.1371/journal.pcbi.1005420

A comprehensive overview and evaluation of circular RNA detection tools
Cited by: 285
Author(s): Xiangxiang Zeng, Wei Lin, Maozu Guo, Quan Zou
Software Mentions: 6
Published: over 9 years ago

10.7554/eLife.66398

Tetrahydroxanthohumol, a xanthohumol derivative, attenuates high-fat diet-induced hepatic steatosis by antagonizing PPARγ
Cited by: 7
Author(s): Yang Zhang, Gerd Bobe, Cristobal L. Miranda, Malcolm B. Lowry, Victor L. Hsu, Christiane V. Löhr, Carmen P. Wong, Donald Β. Jump, Matthew M. Robinson, Thomas J. Sharpton, Claudia S. Maier, Jan F. Stevens, Adrian F. Gombart
Software Mentions: 6
Published: over 5 years ago

10.1186/s12864-021-07571-9

Prunus persica plant endogenous peptides PpPep1 and PpPep2 cause PTI-like transcriptome reprogramming in peach and enhance resistance to Xanthomonas arboricola pv. pruni
Cited by: 7
Author(s): Laura Foix, Anna Nadal, Maja Zagorščak, Živa Ramšak, Anna Esteve‐Codina, Kristina Gruden, María Pla
Software Mentions: 6
Published: over 5 years ago

10.1534/g3.118.200965

Identification of Gene Variants Associated with Melanocyte Stem Cell Differentiation in Mice Predisposed for Hair Graying
Cited by: 3
Author(s): Allison Fialkowski, Denise J. Levy, Dawn E. Watkins‐Chow, Joseph W. Palmer, Roshan Darji, Hemant K. Tiwari, William J. Pavan, Melissa L. Harris
Software Mentions: 6
Published: over 7 years ago

10.7554/eLife.57189

Repurposing of KLF5 activates a cell cycle signature during the progression from a precursor state to oesophageal adenocarcinoma
Cited by: 11
Author(s): Connor Rogerson, Samuel Ogden, Edward Britton, Yeng Ang, Andrew D. Sharrocks
Software Mentions: 6
Published: about 6 years ago

10.1371/journal.pbio.3000741

Cell-based and multi-omics profiling reveals dynamic metabolic repurposing of mitochondria to drive developmental progression of Trypanosoma brucei
Cited by: 32
Author(s): Eva Doleželová, Michaela Kunzová, Mario Dejung, Michal Levin, Brian Panicucci, Clément Regnault, Christian J. Janzen, Michael P. Barrett, Falk Butter, Alena Zı́ková
Software Mentions: 6
Published: over 6 years ago

10.7554/eLife.53933

Heterogeneous T cell motility behaviors emerge from a coupling between speed and turning in vivo
Cited by: 33
Author(s): Elizabeth R. Jerison, Stephen R. Quake
Software Mentions: 6
Published: over 6 years ago

10.7554/eLife.55249

Generation of inner ear hair cells by direct lineage conversion of primary somatic cells
Cited by: 49
Author(s): Louise Menendez, Talon Trecek, Suhasni Gopalakrishnan, Litao Tao, Alexander L. Markowitz, Haoze V Yu, Xizi Wang, Juan Llamas, Chi‐Chou Huang, James Lee, Radha Kalluri, Justin K. Ichida, Neil Segil
Software Mentions: 6
Published: over 6 years ago

10.1186/s12864-018-4902-8

Genome variants associated with RNA splicing variations in bovine are extensively shared between tissues
Cited by: 30
Author(s): Ruidong Xiang, Ben J. Hayes, Christy J. Vander Jagt, Iona M. MacLeod, Majid Khansefid, P.J. Bowman, Zehu Yuan, Claire P. Prowse-Wilkins, Coralie M. Reich, Brett Mason, Josie B. Garner, L. C. Marett, Yizhou Chen, Sunduimijid Bolormaa, Hans D. Daetwyler, Amanda J. Chamberlain, Michael E. Goddard
Software Mentions: 6
Published: over 8 years ago

10.1371/journal.pbio.2003903

Genome-wide maps of ribosomal occupancy provide insights into adaptive evolution and regulatory roles of uORFs during Drosophila development
Cited by: 62
Author(s): Hong Zhang, Shengqian Dou, Feng He, Junjie Luo, Liping Wei, Jian Lü
Software Mentions: 6
Published: about 8 years ago

10.1371/journal.pbio.3001022

A novel terpene synthase controls differences in anti-aphrodisiac pheromone production between closely related Heliconius butterflies
Cited by: 27
Author(s): Kathy Darragh, Anna Orteu, Daniella Black, Kelsey J. R. P. Byers, Daiane Szczerbowski, Ian A. Warren, Pasi Rastas, Ana Pinharanda, John W. Davey, Sylvia Fernanda Garza, Diana Abondano Almeida, Richard M. Merrill, W. Owen McMillan, Stefan Schulz, Chris D. Jiggins
Software Mentions: 6
Published: over 5 years ago

10.3389/fvets.2019.00214

Transcriptomic Profiling of Duodenal Epithelium Reveals Temporally Dynamic Impacts of Direct Duodenal Starch-Infusion During Dry Period of Dairy Cattle
Cited by: 2
Author(s): Congjun Li, Shudai Lin, María Jose Ranilla-García, VI Ransom L. Baldwin
Software Mentions: 6
Published: over 7 years ago

10.7554/eLife.59388

Gene regulation gravitates toward either addition or multiplication when combining the effects of two signals
Cited by: 10
Author(s): Eric M. Sanford, Benjamin Emert, Allison Coté, Arjun Raj
Software Mentions: 6
Published: almost 6 years ago

10.7554/eLife.66321

Channel nuclear pore complex subunits are required for transposon silencing in Drosophila
Cited by: 10
Author(s): Marzia Munafò, Victoria R Lawless, Alessandro Passera, Serena MacMillan, Susanne Bornelöv, Irmgard U. Haussmann, Matthias Soller, Gregory J. Hannon, Benjamin Czech
Software Mentions: 6
Published: over 5 years ago

10.3389/fpls.2021.642828

Natural Genetic Diversity in Tomato Flavor Genes
Cited by: 12
Author(s): Lara Pereira, Manoj Sapkota, Michael Alonge, Yi Zheng, Youjun Zhang, Hamid Razifard, Nathan K Taitano, Michael C. Schatz, Alisdair R. Fernie, Ying Wang, Zhangjun Fei, Ana L. Caicedo, Denise M. Tieman, Esther van der Knaap
Software Mentions: 6
Published: over 5 years ago

10.1016/j.cell.2020.05.039

Multimodal Analysis of Composition and Spatial Architecture in Human Squamous Cell Carcinoma
Cited by: 438
Author(s): Andrew L. Ji, Adam J. Rubin, Kim Thrane, Sizun Jiang, David L. Reynolds, Robin M. Meyers, Margaret Guo, Benson M. George, Annelie Mollbrink, Joseph Bergenstråhle, Ludvig Larsson, Yunhao Bai, Bokai Zhu, Aparna Bhaduri, Jordan M. Meyers, Xavier Rovira-Clavé, S. Tyler Hollmig, Sumaira Z. Aasi, Garry P. Nolan, Joakim Lundeberg, Paul A. Khavari
Software Mentions: 6
Published: over 6 years ago

10.1186/s12859-021-04128-1

Paired-end small RNA sequencing reveals a possible overestimation in the isomiR sequence repertoire previously reported from conventional single read data analysis
Cited by: 4
Author(s): José Francisco Sánchez-Herrero, Raquel Pluvinet, Antonio Luna de Haro, Lauro Sumoy
Software Mentions: 6
Published: over 5 years ago

10.1186/s12864-021-07930-6

Choice of pre-processing pipeline influences clustering quality of scRNA-seq datasets
Cited by: 4
Author(s): Inbal Shainer, Manuel Stemmer
Software Mentions: 6
Published: about 5 years ago

10.1007/s00439-020-02228-1

A CRISPR and high-content imaging assay compliant with ACMG/AMP guidelines for clinical variant interpretation in ciliopathies
Cited by: 5
Author(s): Liliya Nazlamova, N. Simon Thomas, Man‐Kim Cheung, Jelmer Legebeke, Jenny Lord, Reuben J. Pengelly, William Tapper, Gabrielle Wheway
Software Mentions: 6
Published: almost 6 years ago

10.1016/j.stem.2021.04.031

Naive stem cell blastocyst model captures human embryo lineage segregation
Cited by: 139
Author(s): Akira Yanagida, Daniel Spindlow, Jennifer Nichols, Anish Dattani, Austin Smith, Ge Guo
Software Mentions: 6
Published: over 5 years ago

10.3389/fpls.2021.613059

Identification of ABA-Mediated Genetic and Metabolic Responses to Soil Flooding in Tomato (Solanum lycopersicum L. Mill)
Cited by: 24
Author(s): Vicent Arbona, Miguel González-Guzmán, Zara Pitarch, José Tomás Matus, Héctor Candela, José L. Rambla, Antonio Granell, Aurelio Gómez‐Cadenas
Software Mentions: 6
Published: over 5 years ago

10.1007/s00239-021-10012-6

Dynamic Molecular Evolution of Mammalian Homeobox Genes: Duplication, Loss, Divergence and Gene Conversion Sculpt PRD Class Repertoires
Cited by: 8
Author(s): Thomas D. Lewin, Amy H. Royall, Peter W.H. Holland
Software Mentions: 6
Published: over 5 years ago

10.3389/fpls.2021.675208

Differential Regulation of Maize and Sorghum Orthologs in Response to the Fungal Pathogen Exserohilum turcicum
Cited by: 5
Author(s): Pragya Adhikari, Santiago X. Mideros, Tiffany M. Jamann
Software Mentions: 6
Published: over 5 years ago

10.3389/fpls.2021.714393

Transcriptome Profiling Reveals Differential Gene Expression of Secreted Proteases and Highly Specific Gene Repertoires Involved in Lactarius–Pinus Symbioses
Cited by: 7
Author(s): Nianwu Tang, Annie Lebreton, Wenjun Xu, Yu-Cheng Dai, Fuqiang Yu, Francis Martin
Software Mentions: 6
Published: about 5 years ago

10.3389/fpls.2021.683681

Insertion of Badnaviral DNA in the Late Blight Resistance Gene (R1a) of Brinjal Eggplant (Solanum melongena)
Cited by: 9
Author(s): Saad Serfraz, Vikas Sharma, Florian Maumus, Xavier Aubriot, Andrew D. W. Geering, Pierre‐Yves Teycheney
Software Mentions: 6
Published: about 5 years ago

10.1016/j.stem.2020.11.005

Capture of Mouse and Human Stem Cells with Features of Formative Pluripotency
Cited by: 125
Author(s): Masaki Kinoshita, M. Barber, William Mansfield, Yingzhi Cui, Daniel Spindlow, Giuliano Giuseppe Stirparo, Sabine Dietmann, Jennifer Nichols, Austin Smith
Software Mentions: 6
Published: over 5 years ago

10.1186/s12864-020-07182-w

nanotatoR: a tool for enhanced annotation of genomic structural variants
Cited by: 4
Author(s): Surajit Bhattacharya, Hayk Barseghyan, Emmanuèle C. Délot, Éric Vilain
Software Mentions: 6
Published: almost 6 years ago

10.1371/journal.pgen.1006750

TCF21 and the environmental sensor aryl-hydrocarbon receptor cooperate to activate a pro-inflammatory gene expression program in coronary artery smooth muscle cells
Cited by: 50
Author(s): Juyong Brian Kim, Milos Pjanic, Trieu Nguyen, Clint L. Miller, Dharini Iyer, Boxiang Liu, Ting Wang, Olga V. Sazonova, Iván Cárcamo-Orive, Ljubica Matic, Lars Maegdefessel, Ulf Hedin, Thomas Quertermous
Software Mentions: 6
Published: over 9 years ago

10.1371/journal.pgen.1008749

Genome-wide DNA methylation and gene expression patterns reflect genetic ancestry and environmental differences across the Indonesian archipelago
Cited by: 29
Author(s): Heini M. Natri, Katalina Bobowik, Pradiptajati Kusuma, Chelzie Crenna Darusallam, Guy S. Jacobs, Georgi Hudjashov, J. Stephen Lansing, Herawati Sudoyo, Nicholas E. Banovich, Murray P. Cox, Irene Gallego Romero
Software Mentions: 6
Published: over 6 years ago

10.1242/dev.195883

The BMP antagonist gremlin 1 contributes to the development of cortical excitatory neurons, motor balance and fear responses
Cited by: 4
Author(s): Mari Ichinose, Nobumi Suzuki, Tongtong Wang, Hiroki Kobayashi, Laura Vrbanac, Joseph Kim Fai Ng, Josephine Wright, Tamsin R.M. Lannagan, Krystyna A. Gieniec, Martin Lewis, Ryosuke Ando, Atsushi Enomoto, Simon Koblar, Paul Q. Thomas, Daniel L. Worthley, Susan L. Woods
Software Mentions: 6
Published: about 5 years ago

10.1101/2021.09.08.21263284

Robust immune response to the BNT162b mRNA vaccine in an elderly population vaccinated 15 months after recovery from COVID-19
Cited by: 12
Author(s): Hye Kyung Lee, Ludwig Knabl, Ludwig Knabl, Sebastian Kapferer, Birgit Pateter, Mary Walter, Priscilla A. Furth, Lothar Hennighausen
Software Mentions: 6
Published: about 5 years ago

10.7554/eLife.40197

Global DNA methylation remodeling during direct reprogramming of fibroblasts to neurons
Cited by: 61
Author(s): Chongyuan Luo, Qian Yi Lee, Orly L. Wapinski, Rosa Castanon, Joseph R. Nery, Moritz Mall, Michael S. Kareta, Shay Cullen, Margaret A. Goodell, Howard Y. Chang, Marius Wernig, Joseph R. Ecker
Software Mentions: 6
Published: over 7 years ago

10.1371/journal.pone.0238497

Signatures of somatic mutations and gene expression from p16INK4A positive head and neck squamous cell carcinomas (HNSCC)
Cited by: 2
Author(s): Nabil F. Saba, Ashok R. Dinasarapu, Kelly R. Magliocca, Bhakti Dwivedi, Sandra Seby, Zhaohui S. Qin, Mihir R. Patel, Christopher C. Griffith, Xu Wang, Mark W. El‐Deiry, Conor E. Steuer, Jeanne Kowalski, Dong M. Shin, Michael E. Zwick, Zhuo Georgia Chen
Software Mentions: 6
Published: about 6 years ago

10.1128/mBio.02683-20

The Zinc Finger Antiviral Protein ZAP Restricts Human Cytomegalovirus and Selectively Binds and Destabilizes Viral UL4 / UL5 Transcripts
Cited by: 23
Author(s): Ana Cristina Gonzalez-Perez, Markus Stempel, Emanuel Wyler, Christian Urban, Antonio Piras, Thomas Hennig, Sabina Ganskih, Yuanjie Wei, Albert Heim, Markus Landthaler, Andreas Pichlmair, Lars Dölken, Mathias Munschauer, Florian Erhard, Melanie M. Brinkmann
Software Mentions: 6
Published: over 5 years ago

10.1371/journal.pbio.3000948

Absence of nuclear receptors LXRs impairs immune response to androgen deprivation and leads to prostate neoplasia
Cited by: 3
Author(s): Laura Bousset, Amandine Septier, Julio Buñay, Allison Voisin, Rachel Guiton, Christelle Damon-Soubeyrant, Yoan Renaud, Angélique De Haze, Vincent Sapin, Anne Fogli, Amandine Rambur, Cyrille de Joussineau, Ayhan Kocer, Amalia Trousson, Joëlle Henry-Berger, Marcus Höring, Gerhard Liebisch, Silke Matysik, Jean-Marc A. Lobaccaro, Laurence Morel, Silvère Baron
Software Mentions: 6
Published: almost 6 years ago

10.1128/mBio.01714-20

Repetitive Elements Contribute to the Diversity and Evolution of Centromeres in the Fungal Genus Verticillium
Cited by: 20
Author(s): Michael Seidl, Holger Kramer, David E. Cook, Gabriel Lorencini Fiorin, Grardy C. M. van den Berg, Luigi Faino, B.P.H.J. Thomma
Software Mentions: 6
Published: almost 6 years ago

10.1128/mSystems.00329-20

Selective Translation of Low Abundance and Upregulated Transcripts in Halobacterium salinarum
Cited by: 8
Author(s): Adrián López García de Lomana, Ulrike Kusebauch, Arjun V. Raman, Min Pan, Serdar Turkarslan, Alan Péricles Rodrigues Lorenzetti, Robert L. Moritz, Nitin S. Baliga
Software Mentions: 6
Published: about 6 years ago

10.1186/1471-2105-14-370

Blind spots of quantitative RNA-seq: the limits for assessing abundance, differential expression, and isoform switching
Cited by: 36
Author(s): Hubert Rehrauer, Lennart Opitz, Ge Tan, Lina Sieverling, Ralph Schlapbach
Software Mentions: 6
Published: almost 13 years ago

10.1371/journal.pbio.3000378

Changes in chromatin accessibility ensure robust cell cycle exit in terminally differentiated cells
Cited by: 33
Author(s): Yiqin Ma, Daniel J. McKay, Laura Buttitta
Software Mentions: 6
Published: about 7 years ago

10.1002/advs.201903200

Size‐Dependent Pulmonary Impact of Thin Graphene Oxide Sheets in Mice: Toward Safe‐by‐Design
Cited by: 34
Author(s): Artur Filipe Rodrigues, Leon Newman, Dhifaf Jasim, Sourav P. Mukherjee, Jun Wang, Isabella Anna Vacchi, Cécilia Ménard‐Moyon, Alberto Bianco, Bengt Fadeel, Kostas Kostarelos, Cyrill Bussy
Software Mentions: 6
Published: over 6 years ago

10.1128/mBio.01037-19

Reprogramming of Small Noncoding RNA Populations in Peripheral Blood Reveals Host Biomarkers for Latent and Active Mycobacterium tuberculosis Infection
Cited by: 24
Author(s): Leonardo Silva de Araujo, Marcelo Ribeiro-Alves, Thyago Leal-Calvo, Janaina Aparecida Medeiros Leung, Verónica Durán, Mohamed Samir, Steven R. Talbot, Aravind Tallam, Fernanda Carvalho de Queiroz Mello, Robert Geffers, Maria Helena Féres Saad, Frank Peßler
Software Mentions: 6
Published: almost 7 years ago

10.1186/1471-2105-15-S3-A7

Oqtans: a multifunctional workbench for RNA-seq data analysis
Cited by: 0
Author(s): Vipin T. Sreedharan, Sebastian J. Schultheiß, Géraldine Jean, André Kahles, Regina Bohnert, Philipp Drewe, Pramod Kaushik Mudrakarta, Nico Görnitz, Georg Zeller, Gunnar Rätsch
Software Mentions: 6
Published: over 12 years ago

10.3390/cancers12041028

Changes in the Expression of Pre-Replicative Complex Genes in hTERT and ALT Pediatric Brain Tumors
Cited by: 8
Author(s): Aurora Idilli, Francesca Pagani, Emanuela Kerschbamer, Francesco Berardinelli, Manuel Bernabé, María L. Cayuela, Silvano Piazza, Pietro Luigi Poliani, Emilio Cusanelli, Marina Mione
Software Mentions: 6
Published: over 6 years ago

10.1101/2020.07.19.210955

Interferons and viruses induce a novel primate-specific isoform dACE2 and not the SARS-CoV-2 receptor ACE2
Cited by: 19
Author(s): Olusegun O. Onabajo, Abdul Rouf Banday, Wusheng Yan, Adeola Obajemu, Megan L. Stanifer, Deanna M. Santer, Óscar Flórez-Vargas, Helen Piontkivska, Joselin M. Vargas, Carmon Kee, D. Lorne Tyrrell, Juan L. Mendoza, Steeve Boulant, Ludmila Prokunina‐Olsson
Software Mentions: 6
Published: about 6 years ago

10.1371/journal.pbio.2006092

Refined RIP-seq protocol for epitranscriptome analysis with low input materials
Cited by: 97
Author(s): Yong Zeng, Shiyan Wang, Shanshan Gao, Fraser Soares, Musadeqque Ahmed, Haiyang Guo, Miranda Wang, Junjie Hua, Jiansheng Guan, Michael F. Moran, Ming‐Sound Tsao, Housheng Hansen He
Software Mentions: 6
Published: about 8 years ago

10.3390/plants9040545

Transcriptional Dynamics and Candidate Genes Involved in Pod Maturation of Common Bean (Phaseolus vulgaris L.)
Cited by: 3
Author(s): Cristina Gómez-Martín, Carmen Capel, Ana M. González, Ricardo Lebrón, Fernando J. Yuste‐Lisbona, Michael Hackenberg, José Luis Tejera Oliver, Marta Santalla, Rafael Lozano
Software Mentions: 6
Published: over 6 years ago

10.3390/cancers12113311

Role of miRNAs in Sigmoid Colon Cancer: A Search for Potential Biomarkers
Cited by: 2
Author(s): Denílson Bezerra Marques, Layse Raynara Ferreira-Costa, Lorenna Larissa Ferreira-Costa, Ana Beatriz Bezerra-Oliveira, Romualdo da Silva Corrêa, Carlos César de Oliveira Ramos, Tatiana Vinasco-Sandoval, Kátia de Paiva Lopes, Ricardo Assunção Vialle, Amanda Ferreira Vidal, Vivian Nogueira Silbiger, Ândrea Ribeiro-dos-Santos
Software Mentions: 6
Published: almost 6 years ago

10.1101/2020.09.01.20185884

Immune transcriptomes of highly exposed SARS-CoV-2 asymptomatic seropositive versus seronegative individuals from the Ischgl community
Cited by: 0
Author(s): Hye Kyung Lee, Ludwig Knabl, Lisa Pipperger, André Volland, Priscilla A. Furth, Keunsoo Kang, Harold E. Smith, Romuald Bellmann, Christina Bernhard, Norbert Kaiser, Hannes Gänzer, Mathias Ströhle, Andreas Walser, Dorothee von Laer, Lothar Hennighausen
Software Mentions: 6
Published: about 6 years ago

10.1186/s12864-017-4386-y

Global accumulation of circRNAs during aging in Caenorhabditis elegans
Cited by: 127
Author(s): Mariela Cortés-López, Matthew Gruner, Daphne A. Cooper, Hannah N. Gruner, Alexandru-Ioan Voda, Alexander M. van der Linden, Pedro Miura
Software Mentions: 6
Published: almost 9 years ago

10.7150/thno.56141

Distinct placental molecular processes associated with early-onset and late-onset preeclampsia
Cited by: 31
Author(s): Zhonglu Ren, Yunfei Gao, Yue Gao, Guanmei Liang, Qian Chen, Sijia Jiang, Xiaoxue Yang, Cui-Xia Fan, Haizhen Wang, Jing Wang, Yi‐Wu Shi, Chaoqun Xiao, Ming Zhong, Xinping Yang
Software Mentions: 6
Published: almost 6 years ago

10.7150/thno.47390

Upregulation of amplified in breast cancer 1 contributes to pancreatic ductal adenocarcinoma progression and vulnerability to blockage of hedgehog activation
Cited by: 2
Author(s): Licen Li, Jiaolin Bao, Haitao Wang, Josh Haipeng Lei, Cheng Peng, Jianming Zeng, Hao Wu, Xu Zhang, Xiaoling Xu, Chundong Yu, Chu Xia Deng, Qiang Chen
Software Mentions: 6
Published: almost 6 years ago

10.1038/s41398-021-01447-y

Essential genes from genome-wide screenings as a resource for neuropsychiatric disorders gene discovery
Cited by: 2
Author(s): Wei Zhang, Joao L De Quevedo, Gabriel R. Fries
Software Mentions: 6
Published: over 5 years ago

10.3389/fnins.2021.591122

Single-Cell Transcriptomics: Current Methods and Challenges in Data Acquisition and Analysis
Cited by: 40
Author(s): Asif Adil, Vijay Kumar, Arif Tasleem Jan, M. Asger
Software Mentions: 6
Published: over 5 years ago

10.1186/s12864-019-6034-1

De novo profiling of RNA viruses in Anopheles malaria vector mosquitoes from forest ecological zones in Senegal and Cambodia
Cited by: 19
Author(s): Eugeni Belda, Ferdinand Nanfack-Minkeu, Karin Eiglmeier, Guillaume Carissimo, Inge Holm, Mawlouth Diallo, Diawo Diallo, Amélie Vantaux, Saorin Kim, Igor V. Sharakhov, Kenneth D. Vernick
Software Mentions: 6
Published: about 7 years ago

10.1038/s41598-021-87384-8

Field multi-omics analysis reveals a close association between bacterial communities and mineral properties in the soybean rhizosphere
Cited by: 11
Author(s): Shinichi Yamazaki, Hossein Mardani-Korrani, Rumi Kaida, Kumiko Ochiai, Masaru Kobayashi, Atsushi J. Nagano, Yoshiharu Fujii, Akifumi Sugiyama, Yosuke Aoki
Software Mentions: 6
Published: over 5 years ago

10.1038/s41398-021-01561-x

Comparison of mouse models reveals a molecular distinction between psychotic illness in PWS and schizophrenia
Cited by: 5
Author(s): Simona Zahova, Trevor Humby, Jennifer R. Davies, Joanne Morgan, Anthony R Isles
Software Mentions: 6
Published: about 5 years ago

10.1101/2020.08.11.20171108

ACE2 expression in adipose tissue is associated with COVID-19 cardio-metabolic risk factors and cell type composition
Cited by: 8
Author(s): Julia S. El-Sayed Moustafa, Anne Jackson, Sarah M. Brotman, Li Guan, Sergio Villicaña, Amy L. Roberts, Antonino Zito, Lori L. Bonnycastle, Michael R. Erdos, Narisu Narisu, Heather M. Stringham, Ryan Welch, Tingfen Yan, Timo A. Lakka, Stephen C. J. Parker, Jaakko Tuomilehto, Francis S. Collins, Päivi Pajukanta, Michael Boehnke, Heikki A. Koistinen, Markku Laakso, Mario Falchi, Jordana T. Bell, Laura J. Scott, Karen L. Mohlke, Kerrin S. Small
Software Mentions: 6
Published: about 6 years ago

10.1038/s41598-021-82429-4

Molecular characterization of atherosclerosis in HIV positive persons
Cited by: 5
Author(s): Adam Cornwell, Rohith Palli, Meera V. Singh, Lauren Benoodt, Alicia Tyrell, Jun Abe, Giovanni Schifitto, Sanjay B. Maggirwar, Juilee Thakar
Software Mentions: 6
Published: over 5 years ago

10.1038/s41598-021-83110-6

Immune transcriptomes of highly exposed SARS-CoV-2 asymptomatic seropositive versus seronegative individuals from the Ischgl community
Cited by: 13
Author(s): Hye Kyung Lee, Ludwig Knabl, Lisa Pipperger, André Volland, Priscilla A. Furth, Keunsoo Kang, Harold E. Smith, Ludwig Knabl, Romuald Bellmann, Christina Bernhard, Norbert Kaiser, Hannes Gänzer, Mathias Ströhle, Andreas Walser, Dorotheé von Laer, Lothar Hennighausen
Software Mentions: 6
Published: over 5 years ago

10.3389/fnmol.2021.637143

Estimating and Correcting for Off-Target Cellular Contamination in Brain Cell Type Specific RNA-Seq Data
Cited by: 7
Author(s): Jordan Sicherman, Dwight F. Newton, Paul Pavlidis, Etienne Sibille, Shreejoy J. Tripathy
Software Mentions: 6
Published: over 5 years ago

10.3389/fmicb.2018.00381

The Impact of Maltitol-Sweetened Chewing Gum on the Dental Plaque Biofilm Microbiota Composition
Cited by: 16
Author(s): Bart J. F. Keijser, Tim J. van den Broek, Dagmar Else Slot, Lodewic van Twillert, Jolanda Kool, Clémentine Thabuis, Michel Ossendrijver, Fridus A. Van der Weijden, R.C. Montijn
Software Mentions: 6
Published: over 8 years ago

10.1038/s41598-021-81933-x

Cell type-specific changes in transcriptomic profiles of endothelial cells, iPSC-derived neurons and astrocytes cultured on microfluidic chips
Cited by: 15
Author(s): Heleen H.T. Middelkamp, Anouk H.A. Verboven, Aisen Vivas, Chantal Schoenmaker, Teun Klein Gunnewiek, Robert Passier, Cornelis A. Albers, Peter-Bram A.C. ’t Hoen, Nael Nadif Kasri, Andries D. van der Meer
Software Mentions: 6
Published: over 5 years ago

10.1038/s41598-021-85256-9

Creation and validation of models to predict response to primary treatment in serous ovarian cancer
Cited by: 11
Author(s): Jesús González Bosquet, Eric J. Devor, A.M. Newtson, Brian J. Smith, David Bender, Michael J. Goodheart, Megan McDonald, Terry A. Braun, Kristina W. Thiel, Kimberly K. Leslie
Software Mentions: 6
Published: over 5 years ago

10.1038/s41598-020-74567-y

Impact of RNA-seq data analysis algorithms on gene expression estimation and downstream prediction
Cited by: 11
Author(s): Tong Li, Po-Yen Wu, John H. Phan, Hamid R Hassazadeh, Weida Tong, May D. Wang
Software Mentions: 6
Published: almost 6 years ago

10.15252/msb.202110253

Model‐guided development of an evolutionarily stable yeast chassis
Cited by: 5
Author(s): Filipa Pereira, Helena Lopes, Paulo Maia, Britta Meyer, Justyna Nocon, Paula Jouhten, D. Konstantinidis, Eleni Kafkia, Miguel Rocha, Peter Kötter, Isabel Rocha, Kiran R. Patil
Software Mentions: 6
Published: over 5 years ago

10.1038/s41598-020-75998-3

Transcriptomic profiling of feline teeth highlights the role of matrix metalloproteinase 9 (MMP9) in tooth resorption
Cited by: 8
Author(s): S. Lee, Stephen J. Bush, Susan Thorne, Nicola Mawson, Colin Farquharson, Guraa Bergkvist
Software Mentions: 6
Published: almost 6 years ago

10.1186/s12864-019-5927-3

Alternative polyadenylation produces multiple 3’ untranslated regions of odorant receptor mRNAs in mouse olfactory sensory neurons
Cited by: 5
Author(s): Mohamed Doulazmi, Cyril Cros, Isabelle Dusart, Alain Trembleau, Caroline Dubacq
Software Mentions: 6
Published: about 7 years ago

10.15252/msb.20156520

Environment‐induced epigenetic reprogramming in genomic regulatory elements in smoking mothers and their children
Cited by: 93
Author(s): Tobias Bauer, Saskia Trump, Naveed Ishaque, Loreen Thürmann, Lei Gu, Mario Bauer, Matthias Bieg, Zuguang Gu, Dieter Weichenhan, Jan‐Philipp Mallm, Stefan Röder, Gunda Herberth, Eiko Takada, Oliver Mücke, Marcus Winter, Kristin M. Junge, Konrad Grützmann, Ulrike Rolle-Kampczyk, Qi Wang, Christian Lawerenz, Michael Borte, Tobias Polte, Matthias Schlesner, Michaela Schanné, Stefan Wiemann, Christina Geörg, Hendrik G. Stunnenberg, Christoph Plass, Karsten Rippe, Junichiro Mizuguchi, Carl Herrmann, Roland Eils, Irina Lehmann
Software Mentions: 6
Published: over 10 years ago

Projects: cran: STAR

Science Score: 100/100

Bonuses:

Papers Mentioning STAR 5,759