10.1371/journal.pntd.0005791

Proteogenomic analysis of the total and surface-exposed proteomes of Plasmodium vivax salivary gland sporozoites
Cited by: 65
Author(s): Kristian E. Swearingen, Scott E. Lindner, Erika L. Flannery, Ashley M. Vaughan, Robert Morrison, Rapatbhorn Patrapuvich, Cristian Koepfli, Ivan Müller, Aaron R. Jex, Robert L. Moritz, Stefan H. I. Kappe, Jetsumon Sattabongkot, Sebastian A. Mikolajczak
Software Mentions: 4
Published: about 9 years ago

10.1038/s41598-019-47363-6

Whole transcriptome analysis reveals correlation of long noncoding RNA ZEB1-AS1 with invasive profile in melanoma
Cited by: 20
Author(s): Ádamo Davi Diógenes Siena, Jéssica Rodrigues Plaça, Luíza Ferreira de Araújo, Isabela Ichihara de Barros, Kamila Chagas Peronni, Greice Andreotti de Molfetta, Carlos Alberto Oliveira de Biagi, Enilza Maria Espreáfico, Josane F. Sousa, Wilson A. Silva
Software Mentions: 4
Published: about 7 years ago

10.1038/s41598-019-47454-4

Glial gene networks associated with alcohol dependence
Cited by: 38
Author(s): Emma K. Erickson, Yuri A. Blednov, R. Adron Harris
Software Mentions: 4
Published: about 7 years ago

10.1186/s12864-018-5184-x

Transcriptome analyses of reprogrammed feather / scale chimeric explants revealed co-expressed epithelial gene networks during organ specification
Cited by: 7
Author(s): Yung-Chih Lai, Ya-Chen Liang, Ting‐Xin Jiang, Randall B. Widelitz, Ping Wu, Cheng‐Ming Chuong
Software Mentions: 4
Published: almost 8 years ago

10.3390/life11070701

RiboNT: A Noise-Tolerant Predictor of Open Reading Frames from Ribosome-Protected Footprints
Cited by: 8
Author(s): Bo Song, Mengyun Jiang, Lei Gao
Software Mentions: 4
Published: about 5 years ago

10.3390/life11050367

Activation of Blood Vessel Development in Endometrial Stromal Cells In Vitro Cocultured with Human Peri-Implantation Embryos Revealed by Single-Cell RNA-Seq
Cited by: 4
Author(s): Bo Lv, Xiaoyu Xu, Xunyi Zhang, Lingbin Qi, He We, Lu Wang, Xian Chen, Luying Peng, Jinfeng Xue, Yao Ji, Zhigang Xue
Software Mentions: 4
Published: over 5 years ago

10.3389/fimmu.2020.00445

Perirenal Adipose Tissue Displays an Age-Dependent Inflammatory Signature Associated With Early Graft Dysfunction of Marginal Kidney Transplants
Cited by: 6
Author(s): Romain Boissier, Pauline François, B. Gondran Tellier, Meunier Maité, Luc Lyonnet, Stéphanie Simoncini, Jéremy Magalon, Tristan Legris, Alexis Laurent, Laurent Guy, Françoise Dignat-George, G. Karsenty, Stéphane Burtey, É. Lechevallier, Florence Sabatier, Pascale Paul
Software Mentions: 4
Published: over 6 years ago

10.3389/fimmu.2021.664249

Over-Generalizing About GC (Hypoxia): Pitfalls of Limiting Breadth of Experimental Systems and Analyses in Framing Informatics Conclusions
Cited by: 7
Author(s): Mark Boothby, Ariel Raybuck, Sung Hoon Cho, Kristy R. Stengel, Volker H. Haase, Scott W. Hiebert, Jingxin Li
Software Mentions: 4
Published: over 5 years ago

10.1016/j.ajhg.2015.11.018

Autosomal-Dominant Corneal Endothelial Dystrophies CHED1 and PPCD1 Are Allelic Disorders Caused by Non-coding Mutations in the Promoter of OVOL2
Cited by: 65
Author(s): Alice E. Davidson, Petra Lišková, Cerys J. Evans, Ľubica Ďuďáková, Lenka Nosková, Nikolas Pontikos, Hana Hartmannová, Kateřina Hodaňová, Viktor Stránecký, Zbyněk Kozmík, Hannah J. Levis, Nwamaka Juliana Idigo, Noriaki Sasai, Geoffrey J. Maher, James Bellingham, Neyme Veli, Neil D. Ebenezer, Michael E. Cheetham, Julie T. Daniels, Caroline Thaung, Kateřina Jirsová, Vincent Plagnol, Martin Filipec, Stanislav Kmoch, Stephen Tuft, Alison J. Hardcastle
Software Mentions: 4
Published: almost 11 years ago

10.1038/s41598-019-46594-x

SREBP1-dependent de novo fatty acid synthesis gene expression is elevated in malignant melanoma and represents a cellular survival trait
Cited by: 27
Author(s): Shi-Fang Wu, Anders M. Näär
Software Mentions: 4
Published: about 7 years ago

10.1038/leu.2016.251

Hemopoietic-specific Sf3b1-K700E knock-in mice display the splicing defect seen in human MDS but develop anemia without ring sideroblasts
Cited by: 99
Author(s): Annalisa Mupo, Monika Seiler, Vijitha Sathiaseelan, Alena Pance, Yi Yang, Anant A. Agrawal, Francesco Iorio, Rubén Bautista, Suruchi Pacharne, Konstantinos Tzelepis, Nicla Manes, Penny Wright, Elli Papaemmanuil, David G. Kent, Peter Campbell, Silvia Buonamici, Niccolò Bolli, George S. Vassiliou
Software Mentions: 4
Published: about 10 years ago

10.1038/s41598-019-43591-y

Apoptotic endothelial cells release small extracellular vesicles loaded with immunostimulatory viral-like RNAs
Cited by: 43
Author(s): Marie-Pierre Hardy, Éric Audemard, Francis Migneault, Albert Feghaly, Sylvie Brochu, Patrick Gendron, Éric Boilard, François Major, Mélanie Dieudé, Marie‐Josée Hébert, Claude Perreault
Software Mentions: 4
Published: over 7 years ago

10.1186/s12711-021-00668-5

A near complete genome for goat genetic and genomic research
Cited by: 11
Author(s): Ran Li, Peng Yang, Xuelei Dai, Hojjat Asadollahpour Nanaei, Wenwen Fang, Zhirui Yang, Yi Cai, Zhuqing Zheng, Xihong Wang, Yu Jiang
Software Mentions: 4
Published: about 5 years ago

10.1016/j.ajhg.2019.03.025

Cell-Type Heterogeneity in Adipose Tissue Is Associated with Complex Traits and Reveals Disease-Relevant Cell-Specific eQTLs
Cited by: 76
Author(s): Craig A. Glastonbury, Alexessander Couto Alves, Julia S. El-Sayed Moustafa, Kerrin S. Small
Software Mentions: 4
Published: over 7 years ago

10.1242/dmm.049044

Comparison of the oncogenomic landscape of canine and feline hemangiosarcoma shows novel parallels with human angiosarcoma
Cited by: 16
Author(s): Kim Wong, Latasha Ludwig, Oscar Krijgsman, David J. Adams, Geoffrey A. Wood, Louise van der Weyden
Software Mentions: 4
Published: over 5 years ago

10.1038/s41598-019-40495-9

Differential gene expression induced by Verteporfin in endometrial cancer cells
Cited by: 8
Author(s): Lisa Bang, Venkata Ramesh Dasari, Dokyoon Kim, Radhika Gogoi
Software Mentions: 4
Published: over 7 years ago

10.12688/f1000research.10221.1

Integration of EGA secure data access into Galaxy
Cited by: 6
Author(s): Youri Hoogstrate, Chao Zhang, Alexander Senf, Jochem Bijlard, Saskia Hiltemann, David van Enckevort, Susanna Repo, Jaap Heringa, Guido Jenster, Remond J.A. Fijneman, Jan-Willem Boiten, Gerrit A. Meijer, Andrew Stubbs, Jordi Rambla, J. Dylan Spalding, Sanne Abeln
Software Mentions: 4
Published: almost 10 years ago

10.1186/s13059-015-0848-1

Transcriptome-wide RNA processing kinetics revealed using extremely short 4tU labeling
Cited by: 59
Author(s): J. David Barrass, Jane E. A. Reid, Yuanhua Huang, Ralph D. Hector, Guido Sanguinetti, Jean D. Beggs, Sander Granneman
Software Mentions: 4
Published: almost 11 years ago

10.1038/s41598-019-39274-3

Genome analysis of the rice coral Montipora capitata
Cited by: 49
Author(s): Alexander Shumaker, Hollie M. Putnam, Huan Qiu, Dana C. Price, Ehud Zelzion, Amnon Harel, Nicole Wagner, Ruth D. Gates, Hwan Su Yoon, Debashish Bhattacharya
Software Mentions: 4
Published: over 7 years ago

10.1002/cam4.3915

The debatable presence of PIWI‐interacting RNAs in invasive breast cancer
Cited by: 11
Author(s): Elisa Kärkkäinen, Sami Heikkinen, Maria Tengström, Veli‐Matti Kosma, Arto Mannermaa, Jaana M. Hartikainen
Software Mentions: 4
Published: over 5 years ago

10.1038/s41598-018-37033-4

Transcriptomics analysis of host liver and meta-transcriptome analysis of rumen epimural microbial community in young calves treated with artificial dosing of rumen content from adult donor cow
Cited by: 14
Author(s): Wenli Li, Andrea Edwards, Christina Riehle, Madison S. Cox, Sarah M Raabis, Joseph H. Skarlupka, Andrew J. Steinberger, Jason G. Walling, Derek M. Bickhart, Garret Suen
Software Mentions: 4
Published: over 7 years ago

10.1038/s41598-018-36912-0

DNA damage and transcriptional regulation in iPSC-derived neurons from Ataxia Telangiectasia patients
Cited by: 10
Author(s): Alessandro Corti, Raina Sota, Matteo Dugo, Raffaele Calogero, Benedetta Terragni, Massimo Mantegazza, Silvana Franceschetti, Michela Restelli, Patrizia Gasparini, Daniele Lecis, Krystyna Chrzanowska, Domenico Delia
Software Mentions: 4
Published: over 7 years ago

10.1186/s12864-017-4362-6

Comparative ribosome profiling uncovers a dominant role for translational control in Toxoplasma gondii
Cited by: 20
Author(s): Musa A. Hassan, Juan J. Vasquez, Guo-Liang Chew, Markus Meissner, T. Nicolai Siegel
Software Mentions: 4
Published: almost 9 years ago

10.1186/s12864-017-3755-x

Drosophila melanogaster positive transcriptional elongation factors regulate metabolic and sex-biased expression in adults
Cited by: 3
Author(s): Haiwang Yang, Denis Basquin, Daniel Pauli, Brian Oliver
Software Mentions: 4
Published: over 9 years ago

10.1016/j.ccell.2017.03.001

Hoxa9 and Meis1 Cooperatively Induce Addiction to Syk Signaling by Suppressing miR-146a in Acute Myeloid Leukemia
Cited by: 85
Author(s): Sebastian Mohr, Carmen Doebele, Federico Comoglio, Tobias Berg, Julia Beck, Hanibal Bohnenberger, Gabriela Alexe, Jasmin Corso, Philipp Ströbel, Astrid Wachter, Tim Beißbarth, Frank Schnütgen, Anjali Cremer, Nadine Haetscher, Stefanie Göllner, A. Maureen Rouhi, Lars Palmqvist, Michael A. Rieger, Timm Schroeder, Halvard Bönig, Carsten Müller‐Tidow, Florian Kuchenbauer, Ekkehard Schütz, Anthony Green, Henning Urlaub, Kimberly Stegmaier, R. Keith Humphries, Hubert Serve, Thomas Oellerich
Software Mentions: 4
Published: over 9 years ago

10.1186/s12864-021-07592-4

RNA sequencing describes both population structure and plasticity-selection dynamics in a non-model fish
Cited by: 8
Author(s): Matt J. Thorstensen, Melinda R. Baerwald, Ken M. Jeffries
Software Mentions: 4
Published: over 5 years ago

10.1038/s41598-018-35086-z

RETRACTED ARTICLE: Non-coding RNAome of RPE cells under oxidative stress suggests unknown regulative aspects of Retinitis pigmentosa etiopathogenesis
Cited by: 16
Author(s): Luigi Donato, Concetta Scimone, Carmela Rinaldi, Rosalia D’Angelo, Antonina Sidoti
Software Mentions: 4
Published: almost 8 years ago

10.1016/j.ebiom.2021.103264

Hyperinsulinemia and insulin resistance in the obese may develop as part of a homeostatic response to elevated free fatty acids: A mechanistic case-control and a population-based cohort study
Cited by: 40
Author(s): Emanuel Fryk, Josefin Olausson, Karin Mossberg, Lena Strindberg, Martin Schmelz, Helén Brogren, Li‐Ming Gan, Silvano Piazza, Alessandro Provenzani, Barbara Becattini, Lars Lind, Giovanni Solinas, Per‐Anders Jansson
Software Mentions: 4
Published: over 5 years ago

10.1186/s13195-020-00598-2

Characterization of the chromatin accessibility in an Alzheimer’s disease (AD) mouse model
Cited by: 24
Author(s): Yaqi Wang, Xiaomin Zhang, Shan Qiao, Yuli Hou, Jing Liu, Yu Sun, Peichang Wang
Software Mentions: 4
Published: over 6 years ago

10.1038/s41598-018-31170-6

Mitochondrial transcription factor A (TFAM) shapes metabolic and invasion gene signatures in melanoma
Cited by: 36
Author(s): Luíza Ferreira de Araújo, Ádamo Davi Diógenes Siena, Jéssica Rodrigues Plaça, Danielle Barbosa Brotto, Isabela Ichihara de Barros, Bruna Rodrigues Muys, Carlos Alberto Oliveira de Biagi, Kamila Chagas Peronni, Josane F. Sousa, Greice Andreotti de Molfetta, Laura Ciaccia West, A. Phillip West, Andréia Machado Leopoldino, Enilza Maria Espreáfico, W. A. Silva
Software Mentions: 4
Published: about 8 years ago

10.12688/f1000research.9037.2

SNPsplit: Allele-specific splitting of alignments between genomes with known SNP genotypes
Cited by: 74
Author(s): Felix Krueger, Simon Andrews
Software Mentions: 4
Published: about 10 years ago

10.15252/embj.2019103790

Microglia promote glioblastoma via mTOR‐mediated immunosuppression of the tumour microenvironment
Cited by: 69
Author(s): Anaëlle Dumas, Nicola Pomella, Gabriel Rosser, Loredana Guglielmi, Claire Vinel, Thomas O Millner, Jeremy Rees, Natasha Aley, Denise Sheer, Jun Wei, Anantha Marisetty, Amy B. Heimberger, Robert L. Bowman, Sebastian Brandner, Johanna A. Joyce, Silvia Marino
Software Mentions: 4
Published: over 6 years ago

10.1186/s13058-020-01318-2

MDM2 inhibition in combination with endocrine therapy and CDK4/6 inhibition for the treatment of ER-positive breast cancer
Cited by: 35
Author(s): Neil Portman, Heloisa Helena Milioli, Sarah Alexandrou, Rhiannon Coulson, Aliza Yong, Kristine J. Fernandez, Karin K.M. Chia, Ensar Halilovic, Davendra Segara, Andrew Parker, Sue Haupt, Ygal Haupt, Wayne D. Tilley, Alexander Swarbrick, C. Elizabeth Caldon, Elgene Lim
Software Mentions: 4
Published: about 6 years ago

10.1186/s12864-018-5393-3

A comparison between whole transcript and 3’ RNA sequencing methods using Kapa and Lexogen library preparation methods
Cited by: 55
Author(s): Feiyang Ma, Brie K. Fuqua, Yehudit Hasin, Clara Yukhtman, Chris D. Vulpe, Aldons J. Lusis, Matteo Pellegrini
Software Mentions: 4
Published: almost 8 years ago

10.1186/s13058-020-01279-6

Investigation of the adolescent female breast transcriptome and the impact of obesity
Cited by: 8
Author(s): Adam Burkholder, Dennis Akrobetu, Arun R. Pandiri, Kiki Ton, Sue Kim, Brian I. Labow, Laura C. Nuzzi, Joseph M. Firriolo, Sallie S. Schneider, Suzanne E. Fenton, Natalie D Shaw
Software Mentions: 4
Published: over 6 years ago

10.1186/s12864-021-07989-1

Global identification of long non-coding RNAs involved in the induction of spinach flowering
Cited by: 11
Author(s): Fatemeh Ghorbani, Reza Abolghasemi, Maryam Haghighi, Nematollah Etemadi, Shui Wang, Marzieh Karimi, Aboozar Soorni
Software Mentions: 4
Published: about 5 years ago

10.1038/s41598-018-29506-3

Analysis of public RNA-sequencing data reveals biological consequences of genetic heterogeneity in cell line populations
Cited by: 18
Author(s): Erik Fasterius, Cristina Al‐Khalili Szigyarto
Software Mentions: 4
Published: about 8 years ago

10.1186/s12859-017-1816-4

mmquant: how to count multi-mapping reads?
Cited by: 29
Author(s): Matthias Zytnicki
Software Mentions: 4
Published: about 9 years ago

10.1038/s41598-018-31659-0

An integrated genomic analysis of anaplastic meningioma identifies prognostic molecular signatures
Cited by: 48
Author(s): Grace Collord, Patrick Tarpey, Natalja Kurbatova, Iñigo Martincorena, Sebastián Morán, Manuel Castro, Tibor Nagy, Graham R. Bignell, Francesco Maura, Matthew D. Young, Jorge Berna, José M. C. Tubío, Christopher E McMurran, Adam M. H. Young, Mathijs A. Sanders, Imran Noorani, Stephen J. Price, Colin Watts, Elke Leipnitz, Matthias Kirsch, Gabriele Schackert, Danita M. Pearson, Abel Devadass, Zvi Ram, V. Peter Collins, Kieren Allinson, Michael D. Jenkinson, Rasheed Zakaria, Khaja Syed, C. Oliver Hanemann, Jemma Dunn, Michael W. McDermott, Ramez Kirollos, George S. Vassiliou, Manel Esteller, Sam Behjati, Alvis Brāzma, Thomas Santarius, Ultan McDermott
Software Mentions: 4
Published: about 8 years ago

10.1186/s12864-019-6147-6

The role of nitric oxide during embryonic wound healing
Cited by: 16
Author(s): Pavel Abaffy, Silvie Tománková, Ravindra Naraine, Mikael Kubista, Radek Šindelka
Software Mentions: 4
Published: almost 7 years ago

10.1111/acer.14259

Chronic Voluntary Ethanol Drinking in Cynomolgus Macaques Elicits Gene Expression Changes in Prefrontal Cortical Area 46
Cited by: 4
Author(s): Nicole A.R. Walter, Christina Zheng, Robert P. Searles, Shannon K. McWeeney, Kathleen A. Grant, Robert Hitzemann
Software Mentions: 4
Published: over 6 years ago

10.1186/s12864-015-1308-8

A comprehensive evaluation of ensembl, RefSeq, and UCSC annotations in the context of RNA-seq read mapping and gene quantification
Cited by: 109
Author(s): Shanrong Zhao, Baohong Zhang
Software Mentions: 4
Published: over 11 years ago

10.1038/s41598-018-26239-1

A 2-transcript host cell signature distinguishes viral from bacterial diarrhea and it is influenced by the severity of symptoms
Cited by: 19
Author(s): Ruth Barral-Arca, Jacobo Pardo‐Seco, Federico Martinón‐Torres, Antonio Salas
Software Mentions: 4
Published: over 8 years ago

10.1038/s41598-018-26416-2

An improved assembly and annotation of the melon (Cucumis melo L.) reference genome
Cited by: 62
Author(s): Valentino Ruggieri, Konstantinos G. Alexiou, Jordi Morata, Jason Argyris, Marta Pujol, Ryoichi Yano, Satoko Nonaka, Hiroshi Ezura, David Latrasse, Adnane Boualem, Moussa Benhamed, Abdelhafid Bendahmane, Riccardo Aiese Cigliano, Walter Sanseverino, Pere Puigdomènech, Josep M. Casacuberta, Jordi García-Más
Software Mentions: 4
Published: over 8 years ago

10.3390/cancers13030527

Radiosensitizing Pancreatic Cancer with PARP Inhibitor and Gemcitabine: An In Vivo and a Whole-Transcriptome Analysis after Proton or Photon Irradiation
Cited by: 7
Author(s): Waisse Waissi, Anaïs Nicol, Matthieu Jung, M. Rousseau, D. Jarnet, Georges Noël, Hélène Burckel
Software Mentions: 4
Published: over 5 years ago

10.12688/f1000research.19426.1

Scavenger: A pipeline for recovery of unaligned reads utilising similarity with aligned reads
Cited by: 2
Author(s): Andrian Yang, Jiangjun Tang, Michael Troup, Joshua W. K. Ho
Software Mentions: 4
Published: about 7 years ago

10.1038/s41598-020-71889-9

Gene expression is stable in a complete CIB1 knockout keratinocyte model
Cited by: 2
Author(s): Elias Imahorn, Magomet Aushev, Stefan Herms, Per Hoffmann, Sven Cichon, Julia Reichelt, Peter Itin, Bettina Burger
Software Mentions: 4
Published: about 6 years ago

10.1038/s41597-020-00719-4

Paired rRNA-depleted and polyA-selected RNA sequencing data and supporting multi-omics data from human T cells
Cited by: 11
Author(s): Li Chen, Ruirui Yang, Tony Kwan, Chao Tang, Stephen Watt, Yiming Zhang, Guillaume Bourque, Bing Ge, Kate Downes, Mattia Frontini, Willem H. Ouwehand, Jing-wen Lin, Nicole Soranzo, Tomi Pastinen, Ciyong Lu
Software Mentions: 4
Published: almost 6 years ago

10.3390/cancers13020208

Interferon Regulatory Factor 9 Promotes Lung Cancer Progression via Regulation of Versican
Cited by: 11
Author(s): David Brunn, Kati Turkowski, Stefan Günther, Andreas Weigert, Thomas Muley, Mark Kriegsmann, Hauke Winter, Reinhard Dammann, Georgios T. Stathopoulos, Michael Thomas, Andreas Güenther, Friedrich Grimminger, Soni Savai Pullamsetti, Werner Seeger, Rajkumar Savai
Software Mentions: 4
Published: almost 6 years ago

10.1093/brain/awaa163

Molecular and cellular correlates of human nerve regeneration: ADCYAP1/PACAP enhance nerve outgrowth
Cited by: 36
Author(s): Georgios Baskozos, Oliver Sandy-Hindmarch, Alex Clark, Katherine Windsor, Páll Karlsson, Greg A. Weir, Lucy A. McDermott, Joanna Burchall, Akira Wiberg, Dominic Furniss, David L.H. Bennett, Annina B. Schmid
Software Mentions: 4
Published: over 6 years ago

10.1186/s13068-021-01895-0

Overexpression of vesicle-associated membrane protein PttVAP27-17 as a tool to improve biomass production and the overall saccharification yields in Populus trees
Cited by: 9
Author(s): Madhavi Latha Gandla, Niklas Mähler, Sacha Escamez, Tomas Skotare, Ogonna Obudulu, Linus Möller, Ilka Nacif Abreu, Joakim Bygdell, Magnus Hertzberg, Torgeir R. Hvidsten, Thomas Moritz, Gunnar Wingsle, Johan Trygg, Hannele Tuominen, Leif J. Jönsson
Software Mentions: 4
Published: over 5 years ago

10.1186/s12864-018-4632-y

Gene co-expression networks in liver and muscle transcriptome reveal sex-specific gene expression in lambs fed with a mix of essential oils
Cited by: 18
Author(s): Marcella Sabino, Victor Adriano Okstoft Carmelo, Gianluca Mazzoni, Katia Cappelli, Stefano Capomaccio, Paolo Ajmone‐Marsan, Andrea Verini-Supplizi, Massimo Trabalza‐Marinucci, Haja N. Kadarmideen
Software Mentions: 4
Published: over 8 years ago

10.1038/s41597-020-00642-8

Large eQTL meta-analysis reveals differing patterns between cerebral cortical and cerebellar brain regions
Cited by: 65
Author(s): Solveig K. Sieberts, Thanneer M. Perumal, Minerva M. Carrasquillo, Mariet Allen, Joseph S. Reddy, Gabriel E. Hoffman, Kristen K. Dang, John N. Calley, Philip J. Ebert, James A. Eddy, X Wang, Anna K. Greenwood, Sara Mostafavi, Schahram Akbarian, Jaroslav Bendl, Michael S. Breen, Kristen J. Brennand, Leanne Brown, Andrew Browne, Joseph D. Buxbaum, Alex Charney, Andrew Chess, Lizette Couto, Greg Crawford, Olivia Devillers, Bernie Devlin, Amanda Dobbyn, Enrico Domenici, Michele Filosi, Elie Flatow, Nancy Francoeur, John F. Fullard, Sergio Espeso-Gil, Kiran Girdhar, Attila Gulyás-Kovács, Ruben C. Gur, Chang Gyu Hahn, Vahram Haroutunian, Mads E. Hauberg, Laura Huckins, Rivka Jacobov, Yonghua Jiang, Jessica Johnson, Bibi Kassim, Y Kim, Lambertus Klei, Robin Kramer, Mario Lauria, Thomas Lehner, David A. Lewis, Barbara K. Lipska, Kelsey S. Montgomery, Royce Park, Chaggai Rosenbluh, Panos Roussos, Douglas M. Ruderfer, Geetha Senthil, Hardik Shah, Laura Sloofman, Song Li, Eli Stahl, Patrick F. Sullivan, Roberto Visintainer, J Wang, Y C Wang, Jennifer Wiseman, Eva Xia, W Zhang, Elizabeth Zharovsky, Laura Addis, Sadiya N. Addo, David Airey, Matthias Arnold, David A. Bennett, Ying Bi, Knut Biber, Colette Blach, E Bradhsaw, Patrick McKinley Brennan, R Canet-Aviles, Shaolong Cao, A Cavalla, Yooree Chae, W W Chen, Joyce Cheng, David A. Collier, Jeffrey L. Dage, Eric B. Dammer, J Davis, J Davis, Derek Drake, Duc Duong, Brian J. Eastwood, Michelle E. Ehrlich, Benjamin M. Ellingson, Brett W. Engelmann, Sahar Esmaeeli-Nieh, Daniel Felsky, Cory C. Funk, Chris Gaiteri
Software Mentions: 4
Published: about 6 years ago

10.1038/s41598-018-28986-7

A monocyte gene expression signature in the early clinical course of Parkinson’s disease
Cited by: 35
Author(s): J Schlachetzki, Iryna Prots, Jenhan Tao, Hyun Bae Chun, Kaoru Saijo, David Gosselin, Beate Winner, Christopher K. Glass
Software Mentions: 4
Published: about 8 years ago

10.3390/cancers13123054

Myeloid-Specific Acly Deletion Alters Macrophage Phenotype In Vitro and In Vivo without Affecting Tumor Growth
Cited by: 6
Author(s): Kyra E. de Goede, Sanne G.S. Verberk, Jeroen Baardman, Karl J. Harber, Yvette van Kooyk, Menno P.J. de Winther, Sjoerd Schetters, Jan Van den Bossche
Software Mentions: 4
Published: over 5 years ago

10.1038/s41597-020-0514-7

Integrated analysis of a compendium of RNA-Seq datasets for splicing factors
Cited by: 2
Author(s): Peng Yu, Li Jin, Su Deng, Feiran Zhang, Petar Grozdanov, Eunice W. M. Chin, Sheree D. Martin, Laurent Vergnes, Mohammad S. Islam, Deqiang Sun, Janine M. LaSalle, Sean L. McGee, Eyleen L. K. Goh, Clinton C. MacDonald, Peng Jin
Software Mentions: 4
Published: over 6 years ago

10.1186/s12864-021-07491-8

A first insight into the genome of Prototheca wickerhamii, a major causative agent of human protothecosis
Cited by: 8
Author(s): Zofia Bakuła, Paweł Siedlecki, Robert Gromadka, Jan Gawor, Agnieszka Gromadka, Jan J. Pomorski, Hanna Panagiotopoulou, Tomasz Jagielski
Software Mentions: 4
Published: over 5 years ago

10.1038/s12276-021-00559-1

Practical prediction model of the clinical response to programmed death-ligand 1 inhibitors in advanced gastric cancer
Cited by: 9
Author(s): Myung‐Giun Noh, Young‐In Yoon, Gihyeon Kim, Hyun Kim, Eulgi Lee, Yeongmin Kim, Chang-Ho Park, Kyung‐Hwa Lee, Hansoo Park
Software Mentions: 4
Published: over 5 years ago

10.1038/s12276-020-00538-y

Tumor-promoting macrophages prevail in malignant ascites of advanced gastric cancer
Cited by: 39
Author(s): Hye Hyeon Eum, Minsuk Kwon, Daeun Ryu, Areum Jo, Wingyan Chung, Nayoung Kim, Yourae Hong, Dae‐Soon Son, Seung Tae Kim, Jeeyun Lee, Hae‐Ock Lee, Woong-Yang Park
Software Mentions: 4
Published: almost 6 years ago

10.1038/srep17901

Identification of Genes Associated with Smad3-dependent Renal Injury by RNA-seq-based Transcriptome Analysis
Cited by: 19
Author(s): Qin Zhou, Yuanyan Xiong, Xiao Ru Huang, Patrick Ming‐Kuen Tang, Xueqing Yu, Hui‐Yao Lan
Software Mentions: 4
Published: almost 11 years ago

10.3390/biom11030449

RNA-seq Characterization of Melanoma Phenotype Switch in 3D Collagen after p38 MAPK Inhibitor Treatment
Cited by: 1
Author(s): Vladimı́r Čermák, Aneta Škarková, Ladislav Merta, Veronika Kolomazníková, Veronika Palušová, Stjepan Uldrijan, Daniel Rösel, Jan Brábek
Software Mentions: 4
Published: over 5 years ago

10.1186/s13059-019-1705-4

Arabidopsis S2Lb links AtCOMPASS-like and SDG2 activity in H3K4me3 independently from histone H2B monoubiquitination
Cited by: 31
Author(s): Anne-Sophie Fiorucci, Clara Bourbousse, Lorenzo Concia, Martin Rougée, Anne-Flore Deton-Cabanillas, Gérald Zabulon, Elodie Layat, David Latrasse, Soon Kap Kim, Nicole Chaumont, Bérangère Lombard, David Stroebel, Sophie Lemoine, Ammara Mohammad, Corinne Blugeon, Damarys Loew, Christophe Bailly, Chris Bowler, Moussa Benhamed, Frédy Barneche
Software Mentions: 4
Published: over 7 years ago

10.1038/sdata.2018.255

Combined RNA-seq and RAT-seq mapping of long noncoding RNAs in pluripotent reprogramming
Cited by: 16
Author(s): Zhonghua Du, Lin Jia, Yichen Wang, Cong Wang, Wei Xue, Jingcheng Chen, Yanbo Zhu, Dehai Yu, Lei Zhou, Naifei Chen, Shilin Zhang, Ilkay Celik, Ferhat Ay, Sujun Gao, Songling Zhang, Wei Li, Andrew R. Hoffman, Jiuwei Cui
Software Mentions: 4
Published: almost 8 years ago

10.3390/biomedicines9070751

AKT Signaling Modifies the Balance between Cell Proliferation and Migration in Neural Crest Cells from Patients Affected with Bosma Arhinia and Microphthalmia Syndrome
Cited by: 5
Author(s): Camille Laberthonnière, Elva María Novoa-del-Toro, Raphaël Chevalier, Natacha Broucqsault, Vanitha Venkoba Rao, Jean Philippe Trani, Karine Nguyen, Shifeng Xue, Bruno Reversade, Jérôme D. Robin, Anaı̈s Baudot, Frédérique Magdinier
Software Mentions: 4
Published: over 5 years ago

10.1186/s12864-020-07141-5

Genomic differences between the new Fusarium oxysporum f. sp. apii (Foa) race 4 on celery, the less virulent Foa races 2 and 3, and the avirulent on celery f. sp. coriandrii
Cited by: 9
Author(s): Peter M. Henry, Sukhwinder Kaur, Quyen Anh Tran Pham, Radwan Barakat, Samuel Brinker, Hannah Haensel, Oleg Daugovish, Lynn Epstein
Software Mentions: 4
Published: almost 6 years ago

10.1155/2017/7183516

PEDF Is Associated with the Termination of Chondrocyte Phenotype and Catabolism of Cartilage Tissue
Cited by: 6
Author(s): Patricia Klinger, Söeren Lukassen, Fulvia Ferrazzi, Arif B. Ekici, Thilo Hotfiel, B. Swoboda, Thomas Aigner, Kolja Gelse
Software Mentions: 4
Published: almost 10 years ago

10.1038/sdata.2017.33

Transcriptomic profiling of 39 commonly-used neuroblastoma cell lines
Cited by: 102
Author(s): Jo Lynne Harenza, Maura Diamond, Rebecca N. Adams, Michael Song, Heather L. Davidson, Lori S. Hart, Maiah H. Dent, Paolo Fortina, C. Patrick Reynolds, John M. Maris
Software Mentions: 4
Published: over 9 years ago

10.1155/2018/1264697

Identification of 170 New Long Noncoding RNAs in<i> Schistosoma mansoni</i>
Cited by: 17
Author(s): Victor Fernandes de Oliveira, Lauro A. G. Moares, Ester Alves Mota, Liana K. Jannotti-Passos, Paulo Marcos Zech Coelho, Ana Carolina Alves de Mattos, Flávia Fernanda Búbula Couto, Brian E. Caffrey, Annalisa Marsico, Renata Guerra‐Sá
Software Mentions: 4
Published: over 8 years ago

10.1126/sciadv.abf9808

Mechanisms underlying divergent responses of genetically distinct macrophages to IL-4
Cited by: 23
Author(s): Marten A. Hoeksema, Zeyang Shen, Inge R. Holtman, An Zheng, Nathan Spann, Isidoro Cobo, Melissa Gymrek, Christopher K. Glass
Software Mentions: 4
Published: over 5 years ago

10.1126/sciadv.abf8660

FUS-ALS mutants alter FMRP phase separation equilibrium and impair protein translation
Cited by: 32
Author(s): Nicol Birsa, Agnieszka M Ule, Maria Giovanna Garone, Brian Tsang, Francesca Mattedi, P. Andrew Chong, Jack Humphrey, Seth Jarvis, Melis Pisiren, Oscar G. Wilkins, Micheal L Nosella, Anny Devoy, Cristian Bodo, Rafaela Fernandez de la Fuente, Elizabeth Fisher, Alessandro Rosa, Gabriella Viero, Julie D. Forman-Kay, Giampietro Schiavo, Pietro Fratta
Software Mentions: 4
Published: about 5 years ago

10.1186/s12870-020-02334-2

The mechanism of potato resistance to Globodera rostochiensis: comparison of root transcriptomes of resistant and susceptible Solanum phureja genotypes
Cited by: 5
Author(s): А. В. Кочетов, А. А. Егорова, Anastasiya Y. Glagoleva, К. В. Стрыгина, Elena K. Khlestkina, С. В. Герасимова, Natalja V. Shatskaya, Gennady V. Vasilyev, Д. А. Афонников, Nikolay A. Shmakov, Olga Antonova, Natalia V. Alpatyeva, А. В. Хютти, Olga Afanasenko, Т. А. Гавриленко
Software Mentions: 4
Published: about 6 years ago

10.1155/2018/2906292

A Simple Guideline to Assess the Characteristics of RNA-Seq Data
Cited by: 21
Author(s): Keun Hong Son, Sungryul Yu, Wonseok Shin, Kyudong Han, Keunsoo Kang
Software Mentions: 4
Published: almost 8 years ago

10.1126/sciadv.abe8215

Dynamics of sex chromosome evolution in a rapid radiation of cichlid fishes
Cited by: 28
Author(s): Athimed El Taher, Fabrizia Ronco, Michael Matschiner, Walter Salzburger, Astrid Böhne
Software Mentions: 4
Published: about 5 years ago

10.1093/bib/bby121

Homeolog expression quantification methods for allopolyploids
Cited by: 24
Author(s): Tony Kuo, Masaomi Hatakeyama, Toshiaki Tameshige, Kentaro Shimizu, Jun Sese
Software Mentions: 4
Published: almost 8 years ago

10.1186/s13059-019-1894-x

Clustered CTCF binding is an evolutionary mechanism to maintain topologically associating domains
Cited by: 76
Author(s): Elissavet Kentepozidou, Sarah J. Aitken, Christine Feig, Klara Stefflova, Ximena Ibarra-Soria, Duncan T. Odom, Maša Roller, Paul Flicek
Software Mentions: 4
Published: almost 7 years ago

10.1038/s41423-019-0218-0

Coexpression of CD163 and CD141 identifies human circulating IL-10-producing dendritic cells (DC-10)
Cited by: 45
Author(s): Michela Comi, Daniele Avancini, Francesca R. Santoni de Sio, Matteo Villa, Molly Javier Uyeda, Matteo Floris, Daniela Tomasoni, Alessandro Bulfone, Maria Grazia Roncarolo, Silvia Gregori
Software Mentions: 4
Published: over 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: over 6 years ago

10.3390/cancers13030548

Identification of RCC Subtype-Specific microRNAs–Meta-Analysis of High-Throughput RCC Tumor microRNA Expression Data
Cited by: 11
Author(s): Arkadiusz Kajdasz, Weronika Majer, Katarzyna Kluzek, Jacek Sobkowiak, Tomasz Milecki, Natalia Derebecka, Zbigniew Kwias, Hans A.R. Bluyssen, Joanna Wesoły
Software Mentions: 4
Published: over 5 years ago

10.1186/s13059-020-01973-w

Multiplexed capture of spatial configuration and temporal dynamics of locus-specific 3D chromatin by biotinylated dCas9
Cited by: 27
Author(s): Xin Liu, Yong Chen, Yuannyu Zhang, Nan Liu, Giovanni A. Botten, Hui Cao, Stuart H. Orkin, Michael Q. Zhang, Jian Xu
Software Mentions: 4
Published: over 6 years ago

10.1530/REP-20-0231

Single cell transcriptome research in human placenta
Cited by: 38
Author(s): Hui Li, Qizhao Huang, Yu Liu, Lana X. Garmire
Software Mentions: 4
Published: almost 6 years ago

10.1186/s12931-021-01743-7

RORγt inhibitors block both IL-17 and IL-22 conferring a potential advantage over anti-IL-17 alone to treat severe asthma
Cited by: 11
Author(s): David Lamb, Dorothy De Sousa, Karsten Quast, Katrin Fundel‐Clemens, Jonas Erjefält, Caroline Sandén, Hans Jürgen Hoffmann, Marc Kästle, RM Schmid, Kevin Menden, Denis Delić
Software Mentions: 4
Published: over 5 years ago

10.1073/pnas.2105968118

Reverse-transcribed SARS-CoV-2 RNA can integrate into the genome of cultured human cells and can be expressed in patient-derived tissues
Cited by: 149
Author(s): Liguo Zhang, Alexsia Richards, M. Inmaculada Barrasa, Stephen H. Hughes, Richard A. Young, Rudolf Jaenisch
Software Mentions: 4
Published: over 5 years ago

10.1186/s12859-020-03888-6

Automated Isoform Diversity Detector (AIDD): a pipeline for investigating transcriptome diversity of RNA-seq data
Cited by: 1
Author(s): Noel‐Marie Plonski, Emily Johnson, Madeline Frederick, Heather Mercer, Gail Fraizer, Richard S. Meindl, Gemma Casadesús, Helen Piontkivska
Software Mentions: 4
Published: almost 6 years ago

10.1186/s13072-020-00341-z

EPIGENE: genome-wide transcription unit annotation using a multivariate probabilistic model of histone modifications
Cited by: 1
Author(s): Anshupa Sahu, Na Li, Ilona Dunkel, Ho‐Ryun Chung
Software Mentions: 4
Published: over 6 years ago

10.1098/rsos.200517

Brain microRNAs among social and solitary bees
Cited by: 12
Author(s): Karen M. Kapheim, Beryl M. Jones, Eirik Søvik, Eckart Stolle, Robert M. Waterhouse, Guy Bloch, Yehuda Ben‐Shahar
Software Mentions: 4
Published: over 6 years ago

10.1371/journal.ppat.1009768

Trichuris muris infection drives cell-intrinsic IL4R alpha independent colonic RELMα+ macrophages
Cited by: 6
Author(s): Ruth Forman, Larisa Logunova, Hannah Smith, Kelly Wemyss, Iris Mair, Louis Boon, Judith E. Allen, Werner Müller, Joanne L. Pennock, Kathryn J. Else
Software Mentions: 4
Published: about 5 years ago

10.1186/s12864-019-6384-8

Chicken adaptive response to low energy diet: main role of the hypothalamic lipid metabolism revealed by a phenotypic and multi-tissue transcriptomic approach
Cited by: 6
Author(s): Frédéric Jehl, Colette Désert, Christophe Klopp, M. Brenet, Andrea Rau, Sophie Leroux, Morgane Boutin, Laëtitia Lagoutte, Kévin Muret, Yuna Blum, Diane Esquerré, David Gourichon, Thierry Burlot, Anne Collin, Frédérique Pitel, Alexandre Bénani, Tatiana Zerjal, Sandrine Lagarrigue
Software Mentions: 4
Published: almost 7 years ago

10.1038/s41419-020-2585-y

Loss of Spry1 reduces growth of BRAFV600-mutant cutaneous melanoma and improves response to targeted therapy
Cited by: 13
Author(s): Barbara Montico, Francesca Colizzi, Giorgio Giurato, Aurora Rizzo, Annamaria Salvati, Lorena Baboci, Dania Benedetti, Eliana Pivetta, Alessia Covre, Michele Dal Bo, Alessandro Weisz, Agostino Steffan, Michele Maio, Luca Sigalotti, Elisabetta Fratta
Software Mentions: 4
Published: over 6 years ago

10.1186/s12864-017-4002-1

Evaluation and comparison of computational tools for RNA-seq isoform quantification
Cited by: 132
Author(s): Chi Zhang, Baohong Zhang, Lih-Ling Lin, Shanrong Zhao
Software Mentions: 4
Published: about 9 years ago

10.1186/s13073-021-00929-4

Haplotype-resolved germline and somatic alterations in renal medullary carcinomas
Cited by: 4
Author(s): Kar Tong Tan, Hyunji Kim, Jian Carrot‐Zhang, Yuxiang Zhang, Won Jun Kim, Guillaume Kugener, Jeremiah A. Wala, Thomas P. Howard, Yueh Yun, Rameen Beroukhim, Heng Li, Gavin Ha, Seth L. Alper, Elizabeth J. Perlman, Elizabeth Mullen, William C. Hahn, Matthew Meyerson, Andrew L. Hong
Software Mentions: 4
Published: about 5 years ago

10.1186/s13059-020-02240-8

Aberrant splicing isoforms detected by full-length transcriptome sequencing as transcripts of potential neoantigens in non-small cell lung cancer
Cited by: 51
Author(s): Miho Oka, Lai Xu, Toshihiro Suzuki, Toshiaki Yoshikawa, Hiromi Sanada, Hayato Uemura, Akiyasu C. Yoshizawa, Yutaka Suzuki, Tetsuya Nakatsura, Yasushi Ishihama, Ayako Suzuki, Masahide Seki
Software Mentions: 4
Published: almost 6 years ago

10.1186/s13073-021-00922-x

High-grade serous tubo-ovarian cancer refined with single-cell RNA sequencing: specific cell subtypes influence survival and determine molecular subtype classification
Cited by: 52
Author(s): Siel Olbrecht, Pieter Busschaert, Jun Qian, Adriaan Vanderstichele, Liselore Loverix, Toon Van Gorp, Els Van Nieuwenhuysen, Sileny Han, Annick Van den Broeck, An Coosemans, Anne‐Sophie Van Rompuy, Diether Lambrechts, Ignace Vergote
Software Mentions: 4
Published: over 5 years ago

10.1186/s12977-020-00544-y

Comparative analysis of human microglial models for studies of HIV replication and pathogenesis
Cited by: 34
Author(s): Ammara Mohammad, J. Hammonds, Mario Pujato, Christopher N. Mayhew, Krishna M. Roskin, Paul Spearman
Software Mentions: 4
Published: almost 6 years ago

10.1186/s13073-021-00884-0

Deletion of a non-canonical regulatory sequence causes loss of Scn1a expression and epileptic phenotypes in mice
Cited by: 14
Author(s): Jessica L Haigh, Anna Adhikari, Nycole A Copping, Tyler W. Stradleigh, A. Ayanna Wade, Rinaldo Catta-Preta, Linda Su-Feher, Iva Zdilar, Sarah Morse, Timothy A. Fenton, Anh B Nguyen, Diana Quintero, Samrawit Agezew, Michael Sramek, Ellie J Kreun, Jasmine Carter, Andrea Gompers, Jason T. Lambert, Cesar P Canales, L Pennacchio, Axel Visel, Diane E. Dickel, Jill L. Silverman, A. Nord
Software Mentions: 4
Published: over 5 years ago

10.5808/GI.2020.18.3.e26

A semi-automatic cell type annotation method for single-cell RNA sequencing dataset
Cited by: 0
Author(s): Wan Kim, Sung Min Yoon, Sang Soo Kim
Software Mentions: 4
Published: about 6 years ago

10.1186/s40170-020-00229-2

Metabolic plasticity of IDH1-mutant glioma cell lines is responsible for low sensitivity to glutaminase inhibition
Cited by: 13
Author(s): Victor Ruiz‐Rodado, Adrian Lita, Tyrone Dowdy, Orieta Celiku, Alejandra Cavazos Saldana, Herui Wang, Chunzhang Yang, Raj Chari, Aiguo Li, Wei Zhang, Hua Song, Meili Zhang, Susie Ahn, Dionne L. Davis, Xiang Chen, Zhengping Zhuang, Christel Herold‐Mende, Kylie J. Walters, Mark R. Gilbert, Mioara Larion
Software Mentions: 4
Published: almost 6 years ago

10.15252/emmm.202013074

Impairment of the ER/mitochondria compartment in human cardiomyocytes with PLN p.Arg14del mutation
Cited by: 25
Author(s): Friederike Cuello, Anika E. Knaust, Umber Saleem, Malte Loos, Janice Raabe, Diogo Mosqueira, Sandra D. Laufer, Michaela Schweizer, Petra van der Kraak, Frederik Flenner, Bärbel Ulmer, Ingke Braren, Xiaoke Yin, Konstantinos Theofilatos, Jorge Ruiz-Orera, Giannino Patone, Birgit Klampe, Thomas G. Schulze, Angelika Piasecki, Yigal M. Pinto, Aryan Vink, Norbert Hübner, Siân E. Harding, Manuel Mayr, Chris Denning, Thomas Eschenhagen, Arne Hansen
Software Mentions: 4
Published: over 5 years ago

10.1186/s12859-016-1276-2

dupRadar: a Bioconductor package for the assessment of PCR artifacts in RNA-Seq data
Cited by: 87
Author(s): Sergi Sayols, Denise Scherzinger, H. Klein
Software Mentions: 4
Published: almost 10 years ago

10.1002/ece3.7401

Transcriptome assembly and differential gene expression of the invasive avian malaria parasite <i>Plasmodium relictum</i> in Hawaiʻi
Cited by: 8
Author(s): Elin Videvall, Kristina L. Paxton, Michael G. Campana, Loren Cassin-Sackett, Carter T. Atkinson, Robert C. Fleischer
Software Mentions: 4
Published: over 5 years ago

10.1038/s41419-020-03020-9

Intracellular amyloid toxicity induces oxytosis/ferroptosis regulated cell death
Cited by: 51
Author(s): Ling Huang, Daniel B. McClatchy, Pamela Maher, Zhibin Liang, Jolene K. Diedrich, David Soriano-Castell, Joshua Goldberg, Maxim N. Shokhirev, John R. Yates, David Schubert, António Currais
Software Mentions: 4
Published: about 6 years ago