10.1016/j.celrep.2021.109423

RHOX10 drives mouse spermatogonial stem cell establishment through a transcription factor signaling cascade
Cited by: 11
Author(s): Kun Tan, H. C. Song, Miles Wilkinson
Software Mentions: 5
Published: about 5 years ago

10.1038/s41598-021-97258-8

Novel interferon-sensitive genes unveiled by correlation-driven gene selection and systems biology
Cited by: 3
Author(s): Cristina Cheroni, Lara Manganaro, Lorena Donnici, Valeria Bevilacqua, Raoul J. P. Bonnal, Riccardo Rossi, Raffaele De Francesco
Software Mentions: 5
Published: almost 5 years ago

10.1038/s41598-021-96966-5

Molecular characterization and cell type composition deconvolution of fibrosis in NAFLD
Cited by: 26
Author(s): Lorena Pantano, George Agyapong, Yang Shen, Zhuo Zhu, Francesc Fernández-Albert, Werner Rust, Dagmar Knebel, Jon Hill, Carine M. Boustany-Kari, Julia F. Doerner, Jörg F. Rippmann, Raymond T. Chung, Shannan Ho Sui, Eric J. Simon, Kathleen E. Corey
Software Mentions: 5
Published: almost 5 years ago

10.1371/journal.pgen.1007631

Spatially varying cis-regulatory divergence in Drosophila embryos elucidates cis-regulatory logic
Cited by: 16
Author(s): Peter A. Combs, Hunter B. Fraser
Software Mentions: 5
Published: almost 8 years ago

10.1038/s41598-021-93297-3

Zfp57 inactivation illustrates the role of ICR methylation in imprinted gene expression during neural differentiation of mouse ESCs
Cited by: 7
Author(s): Basilia Acurzio, Ankit Verma, Alessia Polito, Carlo Giaccari, Francesco Cecere, Salvatore Fioriniello, Floriana Della Ragione, Annalisa Fico, Flavia Cerrato, Claudia Angelini, Robert Feil, Andrea Riccio
Software Mentions: 5
Published: about 5 years ago

10.3389/fimmu.2021.670309

Comparative Immunogenomics of Canine Natural Killer Cells as Immunotherapy Target
Cited by: 7
Author(s): Alicia A. Gingrich, Taylor Reiter, Sean J Judge, Daniel York, Mio Yanagisawa, Aryana Razmara, Ian R. Sturgill, Ugur Nur Basmaci, Rachel Brady, Kevin Stoffel, William J. Murphy, Robert B. Rebhun, C. Titus Brown, Robert J. Canter
Software Mentions: 5
Published: almost 5 years ago

10.1016/j.cmet.2020.03.003

Microbiota-Derived Metabolites Suppress Arthritis by Amplifying Aryl-Hydrocarbon Receptor Activation in Regulatory B Cells
Cited by: 247
Author(s): Elizabeth C. Rosser, Christopher Piper, Diana E. Matei, Paul A. Blair, André F. Rendeiro, Michael Orford, Dagmar Alber, Thomas Krausgruber, Diego Catalán, Nigel Klein, Jessica Manson, Ignat Drozdov, Christoph Bock, Lucy R. Wedderburn, Simon Eaton, Claudia Mauri
Software Mentions: 5
Published: over 6 years ago

10.1172/JCI133187

Mesenchymal niche remodeling impairs hematopoiesis via stanniocalcin 1 in acute myeloid leukemia
Cited by: 45
Author(s): Alexander Waclawiczek, Ashley Hamilton, Kevin Rouault-Pierre, Ander Abarrategi, Manuel Garcia-Albornoz, Farideh Miraki-Moud, Nourdine Bah, John G. Gribben, Jude Fitzgibbon, David Taussig, Dominique Bonnet
Software Mentions: 5
Published: over 6 years ago

10.1038/s41598-021-93863-9

MYCN-induced nucleolar stress drives an early senescence-like transcriptional program in hTERT-immortalized RPE cells
Cited by: 6
Author(s): Sofia Zanotti, Suzanne Vanhauwaert, Christophe Van Neste, Volodimir Olexiouk, Jolien Van Laere, Marlies Verschuuren, Joni Van der Meulen, Liselot Mus, Kaat Durinck, Laurentijn Tilleman, Dieter Deforce, Filip Van Nieuwerburgh, Michael D. Hogarty, Bieke Decaesteker, Winnok H. De Vos, Frank Speleman
Software Mentions: 5
Published: about 5 years ago

10.1016/j.isci.2021.102847

High glucose macrophage exosomes enhance atherosclerosis by driving cellular proliferation & hematopoiesis
Cited by: 25
Author(s): Laura Bouchareychas, Phat Duong, Tuan Anh Phu, Eric Alsop, Bessie Meechoovet, Rebecca Reiman, M. Ng, Ryō Yamamoto, Hiromitsu Nakauchi, Warren J. Gasper, Kendall Van Keuren‐Jensen, Robert L. Raffaı̈
Software Mentions: 5
Published: about 5 years ago

10.1371/journal.ppat.1009674

Tissue-specific transcriptional profiling of plasmacytoid dendritic cells reveals a hyperactivated state in chronic SIV infection
Cited by: 5
Author(s): Michelle Y.H. Lee, Amit A. Upadhyay, Hasse Walum, Chi N. Chan, Reem A. Dawoud, Christine Grech, Justin Harper, Kirti A. Karunakaran, Sydney A. Nelson, Ernestine Mahar, Kyndal Goss, Diane G. Carnathan, Barbara Cervasi, Kiran Gill, Gregory K. Tharp, Elizabeth R. Wonderlich, Vijayakumar Velu, Simon M. Barratt‐Boyes, Mirko Paiardini, Guido Silvestri, Jacob D. Estes, Steven E. Bosinger
Software Mentions: 5
Published: about 5 years ago

10.1002/evl3.129

Methylation and gene expression differences between reproductive and sterile bumblebee workers
Cited by: 48
Author(s): Hollie Marshall, Zoë N. Lonsdale, Eamonn B. Mallon
Software Mentions: 5
Published: almost 7 years ago

10.18632/oncotarget.13062

Genomic profiling is predictive of response to cisplatin treatment but not to PI3K inhibition in bladder cancer patient-derived xenografts
Cited by: 29
Author(s): Lei Wei, Sreenivasulu Chintala, Eric Ciamporcero, Swathi Ramakrishnan, May Elbanna, Jianmin Wang, Qiang Hu, Sean T. Glenn, Mitsuko Murakami, Lu Liu, Eduardo Cortes Gomez, Yuchen Sun, Jacob Conroy, Kiersten Marie Miles, Malathi Kullappan, Sudha Ramaiah, Anand Anbarasu, Anna Woloszynska‐Read, Candace S. Johnson, Jeffrey M. Conroy, Song Liu, Carl Morrison, Роберто Пили
Software Mentions: 5
Published: almost 10 years ago

10.1371/journal.ppat.1009256

A murine model of Lyme disease demonstrates that Borrelia burgdorferi colonizes the dura mater and induces inflammation in the central nervous system
Cited by: 23
Author(s): Timothy Casselli, Ali Divan, Emilie E. Vomhof-DeKrey, Yvonne Tourand, Heidi L. Pecoraro, Catherine A. Brissette
Software Mentions: 5
Published: over 5 years ago

10.1002/eji.201948432

CD73 contributes to anti‐inflammatory properties of afferent lymphatic endothelial cells in humans and mice
Cited by: 10
Author(s): Dominik Eichin, Alberto Pessia, Akiko Takeda, Joni Laakkonen, Lydia Bellmann, Matti Kankainen, Beat A. Imhof, Patrizia Stoitzner, Jing Tang, Marko Salmi, Sirpa Jalkanen
Software Mentions: 5
Published: almost 6 years ago

10.15252/embr.202050932

Foxm1 regulates neural progenitor fate during spinal cord regeneration
Cited by: 6
Author(s): Diane Pelzer, Lauren S. Phipps, Raphaël Thuret, Carlos J Gallardo-Dodd, Syed Murtuza Baker, Karel Dorey
Software Mentions: 5
Published: almost 5 years ago

10.1371/journal.ppat.1009349

PD-1 is imprinted on cytomegalovirus-specific CD4+ T cells and attenuates Th1 cytokine production whilst maintaining cytotoxicity
Cited by: 15
Author(s): Helen Parry, Alexander C. Dowell, Jianmin Zuo, Kriti Verma, Francesca Kinsella, Jusnara Begum, Wayne Croft, Archana Sharma-Oates, Guy Pratt, Paul Moss
Software Mentions: 5
Published: over 5 years ago

10.1002/eji.201847897

Expression of IL‐7Rα and KLRG1 defines functionally distinct CD8 ⁺ T‐cell populations in humans
Cited by: 24
Author(s): Ester B. M. Remmerswaal, Pleun Hombrink, Benjamin Nota, Hanspeter Pircher, Ineke J. M. ten Berge, René A. W. van Lier, Michiel C. van Aalderen
Software Mentions: 5
Published: over 7 years ago

10.1186/s13059-021-02298-y

SRSF3 and SRSF7 modulate 3′UTR length through suppression or activation of proximal polyadenylation sites and regulation of CFIm levels
Cited by: 26
Author(s): Oliver D. Schwich, Nicole Blümel, Mario Keller, Marius Wegener, Samarth Thonta Setty, Melinda Elaine Brunstein, Ina Poser, Igor Ruiz de los Mozos, Beatrix Suess, Christian Münch, François McNicoll, Kathi Zarnack, Michaela Müller-McNicoll
Software Mentions: 5
Published: over 5 years ago

10.1038/s41598-019-40375-2

Transcriptome analysis of rumen epithelium and meta-transcriptome analysis of rumen epimural microbial community in young calves with feed induced acidosis
Cited by: 21
Author(s): Wenli Li, S.L. Gelsinger, Andrea Edwards, Christina Riehle, Daniel C. Koch
Software Mentions: 5
Published: over 7 years ago

10.1186/s13059-021-02334-x

The impact of cell type and context-dependent regulatory variants on human immune traits
Cited by: 27
Author(s): Zepeng Mu, Wei Wei, Benjamin Jung Fair, Jinlin Miao, Ping Zhu, Yang Li
Software Mentions: 5
Published: over 5 years ago

10.1186/s13059-021-02296-0

2passtools: two-pass alignment using machine-learning-filtered splice junctions increases the accuracy of intron detection in long-read RNA sequencing
Cited by: 12
Author(s): Matthew T Parker, Katarzyna Knop, Geoffrey J. Barton, Gordon G. Simpson
Software Mentions: 5
Published: over 5 years ago

10.1038/s41419-021-03739-z

WNT/β-catenin-suppressed FTO expression increases m6A of c-Myc mRNA to promote tumor cell glycolysis and tumorigenesis
Cited by: 61
Author(s): Xueying Yang, Fei Shao, Dong Guo, Wei Wang, Juhong Wang, Rongxuan Zhu, Yibo Gao, Jie He, Zhimin Lu
Software Mentions: 5
Published: over 5 years ago

10.1016/j.celrep.2019.07.039

Activation and In Vivo Evolution of the MAIT Cell Transcriptome in Mice and Humans Reveals Tissue Repair Functionality
Cited by: 130
Author(s): Timothy S C Hinks, Emanuele Marchi, Maisha Jabeen, Moshe Olshansky, Ayako Kurioka, Troi Pediongco, Bronwyn S. Meehan, Lyudmila Kostenko, Stephen J. Turner, Alexandra J. Corbett, Zhenjun Chen, Paul Klenerman, James McCluskey
Software Mentions: 5
Published: almost 7 years ago

10.1371/journal.pbio.3000710

The pregnant myometrium is epigenetically activated at contractility-driving gene loci prior to the onset of labor in mice
Cited by: 18
Author(s): Virlana M. Shchuka, Luis E. Abatti, Huayun Hou, Nawrah Khader, Anna Dorogin, Michael D. Wilson, Oksana Shynlova, Jennifer A. Mitchell
Software Mentions: 5
Published: about 6 years ago

10.1038/s41598-019-40867-1

Loss of the Polycomb group protein Rnf2 results in derepression of tbx-transcription factors and defects in embryonic and cardiac development
Cited by: 17
Author(s): Naomi D. Chrispijn, Dei M. Elurbe, Michaela Mickoleit, Marco Aben, Dennis E. M. de Bakker, Karolina M. Andralojc, Jan Huisken, Jeroen Bakkers, Leonie M. Kamminga
Software Mentions: 5
Published: over 7 years ago

10.1371/journal.pcbi.1004105

Transcriptome Sequencing Reveals Potential Mechanism of Cryptic 3’ Splice Site Selection in SF3B1-mutated Cancers
Cited by: 173
Author(s): Christopher DeBoever, Emanuela M. Ghia, Peter J. Shepard, Laura Z. Rassenti, Christian Barrett, Kristen Jepsen, Catriona Jamieson, Dennis A. Carson, Thomas J. Kipps, Kelly A. Frazer
Software Mentions: 5
Published: over 11 years ago

10.1007/s00122-020-03712-y

The Aegilops ventricosa 2NvS segment in bread wheat: cytology, genomics and breeding
Cited by: 38
Author(s): Liangliang Gao, Dal Hoe Koo, Philomin Juliana, Trevor W. Rife, Daljit Singh, Cristiano Lemes da Silva, Thomas Lux, Kevin M. Dorn, Marshall Clinesmith, Paula Silva, Xu Wang, Manuel Spannagl, Cécile Monat, Bernd Friebe, Burkhard Steuernagel, Gary J. Muehlbauer, Sean Walkowiak, Curtis Pozniak, Ravi P. Singh, Nils Stein, Martin Mascher, Allan K. Fritz, Jesse Poland
Software Mentions: 5
Published: almost 6 years ago

10.1186/s13059-021-02348-5

Genetic and environmental modulation of transposition shapes the evolutionary potential of Arabidopsis thaliana
Cited by: 65
Author(s): Pierre Baduel, Basile Leduque, Amandine Ignace, Isabelle Gy, José Pedro Gil, Olivier Loudet, Vincent Colot, Leandro Quadrana
Software Mentions: 5
Published: over 5 years ago

10.7554/eLife.63324

Adipocyte NR1D1 dictates adipose tissue expansion during obesity
Cited by: 20
Author(s): Louise Hunter, Charlotte E Pelekanou, Nichola J Barron, Rebecca C Northeast, M Grudzień, Antony Adamson, Polly Downton, Thomas Cornfield, Peter Cunningham, Jean-Noël Billaud, Leanne Hodson, Andrew S. I. Loudon, Richard D. Unwin, Mudassar Iqbal, David Ray, David A. Bechtold
Software Mentions: 5
Published: about 5 years ago

10.1038/s41598-018-38458-7

High-throughput, Efficient, and Unbiased Capture of Small RNAs from Low-input Samples for Sequencing
Cited by: 15
Author(s): Cassandra D. Belair, Hu Tao, Brandon Chu, Jacob W. Freimer, Matthew R. Cooperberg, Robert Blelloch
Software Mentions: 5
Published: over 7 years ago

10.1186/s13059-021-02263-9

Optimized RNA-targeting CRISPR/Cas13d technology outperforms shRNA in identifying functional circRNAs
Cited by: 62
Author(s): Yang Zhang, Tuan M. Nguyen, Xiao‐Ou Zhang, Limei Wang, Tin Phan, John G. Clohessy, Pier Paolo Pandolfi
Software Mentions: 5
Published: over 5 years ago

10.1038/s41598-018-38209-8

Differentially expressed gene networks, biomarkers, long noncoding RNAs, and shared responses with cocaine identified in the midbrains of human opioid abusers
Cited by: 30
Author(s): Manal H. Saad, Matthew Rumschlag, Michael H. Guerra, Candace Savonen, Alaina M Jaster, Philip D. Olson, Adnan Alazizi, Francesca Luca, Roger Piqué-Regi, Carl J. Schmidt, Michael J. Bannon
Software Mentions: 5
Published: over 7 years ago

10.1038/s41598-018-36768-4

Consistent Reanalysis of Genome-wide Imprinting Studies in Plants Using Generalized Linear Models Increases Concordance across Datasets
Cited by: 10
Author(s): Stefan Wyder, Michael T. Raissig, Ueli Grossniklaus
Software Mentions: 5
Published: over 7 years ago

10.1371/journal.ppat.1007050

Isolation of a natural DNA virus of Drosophila melanogaster, and characterisation of host resistance and immune responses
Cited by: 48
Author(s): William H. Palmer, Nathan Medd, Philippa M. Beard, Darren J. Obbard
Software Mentions: 5
Published: about 8 years ago

10.1002/evl3.166

Artificial selection reveals the role of transcriptional constraints in the maintenance of life history variation
Cited by: 6
Author(s): Joel L. Pick, Masaomi Hatakeyama, Kate E. Ihle, Julien Gasparini, Claudy Haussy, Satoshi Ishishita, Yoichi Matsuda, Takashi Yoshimura, Masahiro M. Kanaoka, Rie Shimizu‐Inatsugi, Kentaro Shimizu, Barbara Tschirren
Software Mentions: 5
Published: about 6 years ago

10.7554/eLife.63856

Single-cell transcriptomes of developing and adult olfactory receptor neurons in Drosophila
Cited by: 60
Author(s): Colleen N. McLaughlin, Maria Brbić, Qijing Xie, Tongchao Li, Felix Horns, Sai Saroja Kolluru, Justus M. Kebschull, David Vacek, Anthony Xie, Jiefu Li, Robert C. Jones, Jure Leskovec, Stephen R. Quake, Liqun Luo, Hongjie Li
Software Mentions: 5
Published: over 5 years ago

10.18632/oncotarget.26929

Deregulated expression of NKL homeobox genes in T-cell lymphomas
Cited by: 10
Author(s): Stefan Nagel, Claudia Pommerenke, Roderick A.F. MacLeod, Corinna Meyer, Maren Kaufmann, Silke Fähnrich, Hans Drexler
Software Mentions: 5
Published: over 7 years ago

10.1186/s13059-020-02129-6

sn-spMF: matrix factorization informs tissue-specific genetic regulation of gene expression
Cited by: 16
Author(s): Yuan He, Surya B. Chhetri, Marios Arvanitis, Kaushik Srinivasan, François Aguet, Kristin Ardlie, Alvaro N. Barbeira, Rodrigo Bonazzola, Hae Kyung Im, Christopher D. Brown, Alexis Battle
Software Mentions: 5
Published: almost 6 years ago

10.1186/s13059-021-02397-w

A trans locus causes a ribosomopathy in hypertrophic hearts that affects mRNA translation in a protein length-dependent fashion
Cited by: 4
Author(s): Franziska Witte, Jorge Ruiz-Orera, Camilla Ciolli Mattioli, Susanne Blachut, Eleonora Adami, Jana Felicitas Schulz, Valentin Schneider-Lunitz, Oliver Hummel, Giannino Patone, Michael Mücke, Jan Šilhavý, Matthias Heinig, Leonardo Bottolo, Daniel Sanchı́s, Martin Vingron, Marina Chekulaeva, Michal Pravenec, Norbert Hübner, Sebastiaan van Heesch
Software Mentions: 5
Published: about 5 years ago

10.1093/femsyr/foab011

Transcriptomic response of Saccharomyces cerevisiae to octanoic acid production
Cited by: 2
Author(s): Leonie Baumann, Tyler W. Doughty, Verena Siewers, Jens Nielsen, Eckhard Boles, Mislav Oreb
Software Mentions: 5
Published: over 5 years ago

10.3389/fimmu.2020.575488

Integrated Analysis of Transcriptome and Secretome From Umbilical Cord Mesenchymal Stromal Cells Reveal New Mechanisms for the Modulation of Inflammation and Immune Activation
Cited by: 18
Author(s): Mónica Cruz-Barrera, Nathalia Flórez-Zapata, Nicolás Lemus-Diaz, Carlos O. Medina, Cristian Camilo Galindo, Lorena-Xiomara González-Acero, Luz Correa, Bernardo Camacho, Jens Gruber, Gustavo Salguero
Software Mentions: 5
Published: almost 6 years ago

10.7554/eLife.44161

Renal medullary carcinomas depend upon SMARCB1 loss and are sensitive to proteasome inhibition
Cited by: 30
Author(s): Andrew L. Hong, Yuen-Yi Tseng, Jeremiah A. Wala, Won-Jun Kim, Bryan D. Kynnap, Mihir B. Doshi, Guillaume Kugener, Gabriel J. Sandoval, Thomas P. Howard, Ji Li, Xiaoping Yang, Michelle Tillgren, Mahmhoud Ghandi, Abeer Sayeed, Rebecca Deasy, Abigail Ward, Brian McSteen, Katherine Labella, Paula Keskula, Adam Tracy, Cora Connor, Catherine Clinton, Alanna J. Church, Brian D. Crompton, Katherine A. Janeway, Barbara Van Hare, David Sandak, Ole Gjoerup, Pratiti Bandopadhayay, Paul A. Clemons, Stuart L. Schreiber, David E. Root, Prafulla C. Gokhale, N. Susan, Elizabeth Mullen, Charles W.M. Roberts, Cigall Kadoch, Rameen Beroukhim, Keith L. Ligon, Jesse S. Boehm, William C. Hahn
Software Mentions: 5
Published: over 7 years ago

10.1002/ece3.6930

Immunogenetic and tolerance strategies against a novel parasitoid of wild field crickets
Cited by: 0
Author(s): Kristin L. Sikkink, Nathan W. Bailey, Marlene Zuk, Susan L. Balenger
Software Mentions: 5
Published: almost 6 years ago

10.1186/s13059-021-02446-4

Retrotransposons as pathogenicity factors of the plant pathogenic fungus Botrytis cinerea
Cited by: 20
Author(s): Antoine Porquier, Constance Tisserant, F. Salinas, Carla Glassl, Lucas E. Wange, Wolfgang Enard, Andreas Hauser, Matthias Hahn, Arne Weiberg
Software Mentions: 5
Published: about 5 years ago

10.1371/journal.pgen.1005952

Evolution of Social Insect Polyphenism Facilitated by the Sex Differentiation Cascade
Cited by: 46
Author(s): Antonia Klein, Eva Schultner, Helena Lowak, Lukas Schrader, Juergen Heinze, Luke Holman, Jan Oettler
Software Mentions: 5
Published: over 10 years ago

10.1186/s13059-021-02464-2

Systematic functional interrogation of human pseudogenes using CRISPRi
Cited by: 11
Author(s): Ming Sun, Yunfei Wang, Caishang Zheng, Yanjun Wei, Jiakai Hou, Peng Zhang, Wei He, Xiangdong Lv, Yao Ding, Han Liang, Chung-Chau Hon, Xi Chen, Xu Han, Yiwen Chen
Software Mentions: 5
Published: almost 5 years ago

10.1038/s41419-019-1821-9

C-Jun drives melanoma progression in PTEN wild type melanoma cells
Cited by: 21
Author(s): Melanie Kappelmann‐Fenzl, Claudia Gebhard, Alexander Matthies, Silke Kuphal, Michael Rehli, Anja Boßerhoff
Software Mentions: 5
Published: about 7 years ago

10.1186/s13567-021-00972-4

Transcriptomic analysis of equine chorioallantois reveals immune networks and molecular mechanisms involved in nocardioform placentitis
Cited by: 8
Author(s): Hesham A. Ali, Shavahn C. Loux, Laura Kennedy, Kirsten E. Scoggin, Pouya Dini, Carleigh E. Fedorka, Theodore S. Kalbfleisch, A. Esteller-Vico, David W. Horohov, Erdal Erol, Craig N. Carter, Jon J. Smith, Barry A. Ball
Software Mentions: 5
Published: about 5 years ago

10.12688/wellcomeopenres.14735.2

Mapping targets for small nucleolar RNAs in yeast
Cited by: 16
Author(s): Tatiana Dudnakova, Hywel Dunn-Davies, Rosie Peters, David Tollervey
Software Mentions: 5
Published: over 7 years ago

10.1016/j.cell.2021.03.062

Splice site m6A methylation prevents binding of U2AF35 to inhibit RNA splicing
Cited by: 88
Author(s): Mateusz Mendel, Kamila Delaney, Radha Raman Pandey, Kuan-Ming Chen, Joanna M. Wenda, Cathrine Broberg Vågbø, Florian Steiner, David Homolka, Ramesh S. Pillai
Software Mentions: 5
Published: about 5 years ago

10.1371/journal.pgen.1007661

Balancing selection on a recessive lethal deletion with pleiotropic effects on two neighboring genes in the porcine genome
Cited by: 29
Author(s): Martijn F.L. Derks, Marcos S. Lopes, Mirte Bosse, Ole Madsen, Bert Dibbits, B. Harlizius, M.A.M. Groenen, Hendrik Jan Megens
Software Mentions: 5
Published: almost 8 years ago

10.1186/s13068-020-01838-1

Genome-scale metabolic modeling underscores the potential of Cutaneotrichosporon oleaginosus ATCC 20509 as a cell factory for biofuel production
Cited by: 16
Author(s): Nhung Pham, Maarten J.M.F. Reijnders, María Suárez-Diez, Bart Nijsse, Jan Springer, Gerrit Eggink, Peter J. Schaap
Software Mentions: 5
Published: over 5 years ago

10.1371/journal.pgen.1007559

Transcriptome analysis of adult Caenorhabditis elegans cells reveals tissue-specific gene and isoform expression
Cited by: 141
Author(s): Rachel Kaletsky, Victoria Yao, April Williams, Alexi Runnels, Alicja Tadych, Shaoqiang Zhou, Olga G. Troyanskaya, Coleen T. Murphy
Software Mentions: 5
Published: about 8 years ago

10.1371/journal.pgen.1007268

Activation of DAF-16/FOXO by reactive oxygen species contributes to longevity in long-lived mitochondrial mutants in Caenorhabditis elegans
Cited by: 106
Author(s): Megan M. Senchuk, Dylan J. Dues, Claire E. Schaar, Benjamin K. Johnson, Zachary Madaj, Megan J. Bowman, Mary E. Winn, Jeremy M. Van Raamsdonk
Software Mentions: 5
Published: over 8 years ago

10.1016/j.cell.2016.09.006

Inheritable Silencing of Endogenous Genes by Hit-and-Run Targeted Epigenetic Editing
Cited by: 349
Author(s): Angelo Amabile, Alessandro Migliara, Paola Capasso, Mauro Biffi, Davide Cittaro, Luigi Naldini, Angelo Lombardo
Software Mentions: 5
Published: almost 10 years ago

10.1371/journal.pgen.1008611

A non-canonical RNAi pathway controls virulence and genome stability in Mucorales
Cited by: 17
Author(s): Carlos Pérez-Arques, María Isabel Navarro-Mendoza, Laura Murcia, Eusebio Navarro, Victoriano Garre
Software Mentions: 5
Published: about 6 years ago

10.1186/s13293-018-0205-7

Tissue-specific pathways and networks underlying sexual dimorphism in non-alcoholic fatty liver disease
Cited by: 55
Author(s): Zeyneb Kurt, Rio Barrere‐Cain, Jonnby LaGuardia, Margarete Mehrabian, Calvin Pan, Simon T. Hui, Frode Norheim, Zhiqiang Zhou, Yehudit Hasin, Aldons J. Lusis, Xia Yang
Software Mentions: 5
Published: almost 8 years ago

10.1371/journal.pgen.1007830

Global transcriptional regulation of innate immunity by ATF-7 in C. elegans
Cited by: 46
Author(s): Marissa Fletcher, Erik J. Tillman, Vincent Butty, Stuart S. Levine, Dennis H. Kim
Software Mentions: 5
Published: over 7 years ago

10.3389/fnins.2021.620899

Integrated miRNA-Seq and mRNA-Seq Study to Identify miRNAs Associated With Alzheimer’s Disease Using Post-mortem Brain Tissue Samples
Cited by: 21
Author(s): Qingqin Li, Diana Cai
Software Mentions: 5
Published: over 5 years ago

10.1371/journal.pgen.1006648

Adaptation of A-to-I RNA editing in Drosophila
Cited by: 56
Author(s): Yuange Duan, Shengqian Dou, Shiqi Luo, Hong Zhang, Jian Lü
Software Mentions: 5
Published: over 9 years ago

10.7554/eLife.32332

Evolution and cell-type specificity of human-specific genes preferentially expressed in progenitors of fetal neocortex
Cited by: 131
Author(s): Marta Florio, Michael Heide, Anneline Pinson, Holger Brandl, Mareike Albert, Sylke Winkler, Pauline Wimberger, Wieland B. Huttner, Michael Hiller
Software Mentions: 5
Published: over 8 years ago

10.3389/fnins.2018.00136

Neurogenomic Profiling Reveals Distinct Gene Expression Profiles Between Brain Parts That Are Consistent in Ophthalmotilapia Cichlids
Cited by: 4
Author(s): Sofie Derycke, Loïc Kéver, Koen Herten, Koen Van Den Berge, Maarten Van Steenberge, Jeroen Van Houdt, Lieven Clement, Pascal Poncin, Éric Parmentier, Erik Verheyen
Software Mentions: 5
Published: over 8 years ago

10.1371/journal.pntd.0009587

Transcriptomic analysis and molecular docking reveal genes involved in the response of Aedes aegypti larvae to an essential oil extracted from Eucalyptus
Cited by: 9
Author(s): Ivana Sierra, José Manuel Latorre-Estivalis, Lucila Traverso, Paula Valeria Gonzalez, Ariel A Aptekmann, Alejandro D. Nadra, Héctor Mario Masuh, Sheila Ons
Software Mentions: 5
Published: about 5 years ago

10.3390/genes12081291

Regional Specific Differentiation of Integumentary Organs: Regulation of Gene Clusters within the Avian Epidermal Differentiation Complex and Impacts of SATB2 Overexpression
Cited by: 3
Author(s): Gee-Way Lin, Yung-Chih Lai, Ya-Chen Liang, Randall B. Widelitz, Ping Wu, Cheng‐Ming Chuong
Software Mentions: 5
Published: almost 5 years ago

10.3389/fmolb.2021.612881

Genome-Wide Changes of Regulatory Non-Coding RNAs Reveal Pollen Development Initiated at Ecodormancy in Peach
Cited by: 7
Author(s): Jiali Yu, Dennis Bennett, Christopher Dardick, Tetyana Zhebentyayeva, Albert G. Abbott, Zongrang Liu, Margaret Staton
Software Mentions: 5
Published: over 5 years ago

10.1186/s13045-020-01005-x

RNA sequencing: new technologies and applications in cancer research
Cited by: 187
Author(s): Mingye Hong, Shuangping Tao, Ling Zhang, Li-Ting Diao, Xuanmei Huang, Shaohui Huang, Shu‐Juan Xie, Zhilong Xiao, Hua Zhang
Software Mentions: 5
Published: over 5 years ago

10.3390/cancers12113208

Impact of Genetic Ancestry on Prognostic Biomarkers in Uveal Melanoma
Cited by: 2
Author(s): Daniel A. Rodriguez, Margarita Dorantes Sánchez, Christina L. Decatur, Zélia M. Corrêa, Eden R. Martin, J. William Harbour
Software Mentions: 5
Published: almost 6 years ago

10.1093/bib/bbaa339

FR-Match: robust matching of cell type clusters from single cell RNA sequencing data using the Friedman–Rafsky non-parametric test
Cited by: 9
Author(s): Yun Zhang, Brian D. Aevermann, Trygve E. Bakken, Jeremy A. Miller, Rebecca D. Hodge, Ed Lein, Richard H. Scheuermann
Software Mentions: 5
Published: over 5 years ago

10.1371/journal.pone.0232963

Identifying the key regulators that promote cell-cycle activity in the hearts of early neonatal pigs after myocardial injury
Cited by: 11
Author(s): Eric Zhang, Thanh Nguyen, Meng Zhao, Son Do Hai Dang, Jake Y. Chen, Weihua Bian, Gregory P. Walcott
Software Mentions: 5
Published: about 6 years ago

10.1038/s41389-020-0224-1

Desmoplastic small round cell tumor is dependent on the EWS-WT1 transcription factor
Cited by: 24
Author(s): Jenna M. Gedminas, Maggie H. Chassé, Mitchell McBrairty, Ian Beddows, Susan M. Kitchen-Goosen, Patrick J. Grohar
Software Mentions: 5
Published: over 6 years ago

10.3390/cancers12061487

Only Hematopoietic Stem and Progenitor Cells from Cord Blood Are Susceptible to Malignant Transformation by MLL-AF4 Translocations
Cited by: 12
Author(s): Kathy-Ann Secker, Lukas Bruns, Hildegard Keppeler, Johan Jeong, Thomas Hentrich, Julia M. Schulze‐Hentrich, Barbara Mankel, Falko Fend, Dominik Schneidawind, Corina Schneidawind
Software Mentions: 5
Published: about 6 years ago

10.1167/iovs.18-24101

Ascorbate Suppresses VEGF Expression in Retinal Pigment Epithelial Cells
Cited by: 20
Author(s): David W. Sant, Vladimir Camarena, Sushmita Mustafi, Yiwen Li, Zachary Wilkes, Derek Van Booven, Rong Wen, Gaofeng Wang
Software Mentions: 5
Published: about 8 years ago

10.1038/s41598-017-14451-4

Expression and regulation of long noncoding RNAs during the osteogenic differentiation of periodontal ligament stem cells in the inflammatory microenvironment
Cited by: 13
Author(s): Qingbin Zhang, Li Chen, Shiman Cui, Yan Li, Qi Zhao, Weimin Cao, Shixiang Lai, Sanjun Yin, Zhixiang Zuo
Software Mentions: 5
Published: almost 9 years ago

10.1038/s41388-021-02005-y

Intron retention-induced neoantigen load correlates with unfavorable prognosis in multiple myeloma
Cited by: 19
Author(s): Chuanpeng Dong, Annamaria Cesarano, Giuseppe Bombaci, Jill L. Reiter, Christina Y. Yu, Yue Wang, Zhaoyang Jiang, Mohammad Abu Zaid, Kun Huang, Xiongbin Lu, Brian A Walker, Fabiana Perna, Yunlong Liu
Software Mentions: 5
Published: almost 5 years ago

10.1186/s13058-019-1230-0

Elacestrant (RAD1901) exhibits anti-tumor activity in multiple ER+ breast cancer models resistant to CDK4/6 inhibitors
Cited by: 44
Author(s): Hemang Patel, Nianjun Tao, Kyung Min Lee, Mariela Huerta, Heike Arlt, Tara Mullarkey, Steven Troy, Carlos L. Arteaga, Teeru Bihani
Software Mentions: 5
Published: over 6 years ago

10.3390/brainsci10050275

Transcriptome Analysis of Alcohol Drinking in Non-Dependent and Dependent Mice Following Repeated Cycles of Forced Swim Stress Exposure
Cited by: 10
Author(s): Sean P. Farris, Gayatri R. Tiwari, Olga N. Ponomareva, Marcelo F. López, R. Dayne Mayfield, Howard C. Becker
Software Mentions: 5
Published: over 6 years ago

10.3390/ijms21020471

The Influence of Met Receptor Level on HGF-Induced Glycolytic Reprogramming in Head and Neck Squamous Cell Carcinoma
Cited by: 17
Author(s): Verena Boschert, Nicola Klenk, Alexander Abt, Sudha Janaki Raman, Markus Fischer, Roman C. Brands, Axel Seher, Christian Linz, Urs Müller‐Richter, Thorsten Bischler, Stefan Hartmann
Software Mentions: 5
Published: over 6 years ago

10.3390/cancers12010037

Molecular Signature of Subtypes of Non-Small-Cell Lung Cancer by Large-Scale Transcriptional Profiling: Identification of Key Modules and Genes by Weighted Gene Co-Expression Network Analysis (WGCNA)
Cited by: 158
Author(s): Magdalena Niemira, François Collin, Anna Szałkowska, Agnieszka Bielska, Karolina Chwiałkowska, Joanna Reszeć, Jacek Nikliński, Mirosław Kwaśniewski, Adam Krętowski
Software Mentions: 5
Published: over 6 years ago

10.1093/brain/awaa242

Functional gene networks reveal distinct mechanisms segregating in migraine families
Cited by: 14
Author(s): Anne Marie Rasmussen, Lisette J. A. Kogelman, David M. Kristensen, Mona Ameri Chalmer, Jes Olesen, Thomas Folkmann Hansen
Software Mentions: 5
Published: almost 6 years ago

10.1136/jitc-2020-001657

Regorafenib enhances antitumor immunity via inhibition of p38 kinase/Creb1/Klf4 axis in tumor-associated macrophages
Cited by: 52
Author(s): Da-Liang Ou, Chia Wei Chen, Chia‐Lang Hsu, Chih‐Hung Chung, Zi Rui Feng, Bin Shyun Lee, Ann Lii Cheng, Muh Hwa Yang, Chiun Hsu
Software Mentions: 5
Published: over 5 years ago

10.1007/s00442-019-04499-6

Resistance is futile: RNA-sequencing reveals differing responses to bat fungal pathogen in Nearctic Myotis lucifugus and Palearctic Myotis myotis
Cited by: 20
Author(s): Thomas M. Lilley, Jenni M. Prokkola, Anna Blomberg, Steve Paterson, Joseph S. Johnson, Gregory G. Turner, Tomáš Bartonička, Erik Bachorec, DeeAnn M. Reeder, Kenneth A. Field
Software Mentions: 5
Published: almost 7 years ago

10.1155/2021/8880585

Gene Regulatory Network of Human GM-CSF-Secreting T Helper Cells
Cited by: 3
Author(s): Szabolcs Éliás, Angelika Schmidt, David Green, Jesper Tegnér
Software Mentions: 5
Published: about 5 years ago

10.1038/s41598-017-14595-3

UClncR: Ultrafast and comprehensive long non-coding RNA detection from RNA-seq
Cited by: 27
Author(s): Zhifu Sun, Asha Nair, Xianfeng Chen, Naresh Prodduturi, Junwen Wang, Jean Pierre A. Kocher
Software Mentions: 5
Published: almost 9 years ago

10.1186/s12711-021-00602-9

Expression quantitative trait loci in sheep liver and muscle contribute to variations in meat traits
Cited by: 12
Author(s): Zehu Yuan, Sunduimijid Bolormaa, Ruidong Xiang, R. Behrendt, Matthew I. Knight, Brett Mason, Coralie M. Reich, Claire P. Prowse-Wilkins, Christy J. Vander Jagt, Amanda J. Chamberlain, Iona M. MacLeod, Fadi Li, Xiangpeng Yue, Hans D. Daetwyler
Software Mentions: 5
Published: over 5 years ago

10.7717/peerj.3720

Atropos: specific, sensitive, and speedy trimming of sequencing reads
Cited by: 168
Author(s): John P. Didion, Marcel Martin, Francis S. Collins
Software Mentions: 5
Published: almost 9 years ago

10.7717/peerj.4619

Sheep skeletal muscle transcriptome analysis reveals muscle growth regulatory lncRNAs
Cited by: 6
Author(s): Tianle Chao, Zhibin Ji, Lei Hou, Jin Wang, Chunlan Zhang, Guizhi Wang
Software Mentions: 5
Published: over 8 years ago

10.1038/s41598-017-14942-4

Genome-wide profiling of nardilysin target genes reveals its role in epigenetic regulation and cell cycle progression
Cited by: 6
Author(s): Yusuke Morita, Mikiko Ohno, Kiyoto Nishi, Yutaka Hiraoka, Sayaka Saijo, Shintaro Matsuda, Toru Kita, Takeshi Kimura, Eiichiro Nishi
Software Mentions: 5
Published: almost 9 years ago

10.1186/s13059-015-0685-2

Distinct roles of DNMT1-dependent and DNMT1-independent methylation patterns in the genome of mouse embryonic stem cells
Cited by: 64
Author(s): Chi Kong Li, Hongzheng Dai, Suzanne N. Martos, Beisi Xu, Yang Gao, Li Teng, Guangjing Zhu, Dustin E. Schones, Zhibin Wang
Software Mentions: 5
Published: about 11 years ago

10.3389/fcell.2021.652408

Integrating Spatial Transcriptomics and Single-Cell RNA-seq Reveals the Gene Expression Profling of the Human Embryonic Liver
Cited by: 21
Author(s): Xianliang Hou, Yane Yang, Ping Li, Zhipeng Zeng, Wenlong Hu, Ruilian Zhe, Xinqiong Liu, Donge Tang, Minglin Ou, Yong Dai
Software Mentions: 5
Published: about 5 years ago

10.1186/s13059-015-0720-3

BioWardrobe: an integrated platform for analysis of epigenomics and transcriptomics data
Cited by: 70
Author(s): Andrey V. Kartashov, Artem Barski
Software Mentions: 5
Published: about 11 years ago

10.3389/fcell.2020.00639

DNA Methyltransferase 1 (DNMT1) Function Is Implicated in the Age-Related Loss of Cortical Interneurons
Cited by: 14
Author(s): Anne M. Hahn, Daniel Pensold, Cathrin Bayer, Jessica Tittelmeier, Lourdes González-Bermúdez, Lisa Marx-Blümel, Jenice Linde, Jonas Groß, Gabriela Salinas-Riester, Thomas Lingner, Julia von Maltzahn, Marc Spehr, Tomas Pieler, Anja Urbach, Geraldine Zimmer-Bensch
Software Mentions: 5
Published: about 6 years ago

10.1186/s13059-015-0734-x

Errors in RNA-Seq quantification affect genes of relevance to human disease
Cited by: 128
Author(s): Christelle Robert, Michael Watson
Software Mentions: 5
Published: almost 11 years ago

10.7717/peerj.11237

NGScloud2: optimized bioinformatic analysis using Amazon Web Services
Cited by: 4
Author(s): Fernando Mora‐Márquez, José Luis Vázquez-Poletti, Unai López de Heredia
Software Mentions: 5
Published: over 5 years ago

10.3389/fgene.2020.01009

RNA-Seq Analysis Reveals Hub Genes Involved in Chicken Intramuscular Fat and Abdominal Fat Deposition During Development
Cited by: 22
Author(s): Siyuan Xing, Ranran Liu, Guiping Zhao, Lu Liu, M.A.M. Groenen, Ole Madsen, Maiqing Zheng, Xinting Yang, R.P.M.A. Crooijmans, Jie Wen
Software Mentions: 5
Published: almost 6 years ago

10.3389/fcell.2021.669354

Transcriptomic Signature of Human Embryonic Thyroid Reveals Transition From Differentiation to Functional Maturation
Cited by: 7
Author(s): Geert Dom, Petr Dmitriev, Marie-Alexandra Lambot, Guy Van Vliet, Daniel Glinoer, Frédérick Libert, Anne Lefort, Jacques Emile Dumont, Carine Maenhaut
Software Mentions: 5
Published: about 5 years ago

10.1186/s13059-016-1010-4

GiniClust: detecting rare cell types from single-cell gene expression data with Gini index
Cited by: 229
Author(s): Lan Jiang, Huidong Chen, Luca Pinello, Guo‐Cheng Yuan
Software Mentions: 5
Published: about 10 years ago

10.1002/pld3.320

High resolution RNA‐seq profiling of genes encoding ribosomal proteins across different organs and developmental stages in <i>Arabidopsis thaliana</i>
Cited by: 5
Author(s): Wei Xiong, Jiancong Zhang, Ting Lan, Wenwen Kong, Xiaoyan Wang, Lin Liu, Xuemei Chen, Beixin Mo
Software Mentions: 5
Published: over 5 years ago

10.3389/fcell.2020.00552

Id Proteins Promote a Cancer Stem Cell Phenotype in Mouse Models of Triple Negative Breast Cancer via Negative Regulation of Robo1
Cited by: 15
Author(s): Wee Siang Teo, Holly Holliday, N. Karthikeyan, Aurélie Cazet, Daniel Roden, Kate Harvey, Christina Valbirk Konrad, Reshma Murali, Binitha Anu Varghese, Archana P. Thankamony, Chia-Ling Chan, Andrea McFarland, Simon Junankar, Sunny Ye, Jessica Yang, Iva Nikolić, Jaynish S. Shah, Laura A. Baker, Ewan K.A. Millar, Matthew J. Naylor, Christopher J. Ormandy, Sunil R. Lakhani, Warren Kaplan, Albert S. Mellick, Sandra A. O’Toole, Alexander Swarbrick, Radhika Nair
Software Mentions: 5
Published: about 6 years ago

10.3389/fcell.2021.719192

PARP1 Inhibitor Combined With Oxaliplatin Efficiently Suppresses Oxaliplatin Resistance in Gastric Cancer-Derived Organoids via Homologous Recombination and the Base Excision Repair Pathway
Cited by: 1
Author(s): Huafu Li, Chunming Wang, Linxiang Lan, Wenhui Wu, Ian M. Evans, E Josue Ruiz, Le-Ping Yan, Zhijun Zhou, Joaquím M. Oliveira, Rui L. Reis, Zhenran Hu, Wei Chen, Axel Behrens, Yulong He, Changhua Zhang
Software Mentions: 5
Published: almost 5 years ago