10.3390/insects12020167

A Linkage-Based Genome Assembly for the Mosquito Aedes albopictus and Identification of Chromosomal Regions Affecting Diapause
Cited by: 29
Author(s): John H. Boyle, Pasi Rastas, Xin Huang, Austin G. Garner, Indra Vythilingam, Peter Armbruster
Software Mentions: 3
Published: over 5 years ago

10.1038/s42003-020-01118-6

Post-transcriptional air pollution oxidation to the cholesterol biosynthesis pathway promotes pulmonary stress phenotypes
Cited by: 17
Author(s): Juan C. Gonzalez-Rivera, Kevin C. Baldridge, Dongyu Wang, Kanan Patel, Jamie C. L. Chuvalo-Abraham, Lea Hildebrandt Ruiz, Lydia M. Contreras
Software Mentions: 3
Published: about 6 years ago

10.1186/s12915-020-0744-3

A 19-isolate reference-quality global pangenome for the fungal wheat pathogen Zymoseptoria tritici
Cited by: 80
Author(s): Thomas Badet, Ursula Oggenfuss, Leen Nanchira Abraham, Bruce A. McDonald, Daniel Croll
Software Mentions: 3
Published: over 6 years ago

10.18632/oncotarget.13104

Identification of KLK10 as a therapeutic target to reverse trastuzumab resistance in breast cancer
Cited by: 15
Author(s): Zhuo Wang, Beihong Ruan, Y. Jin, Yulong Zhang, Jiaqiu Li, Liyuan Zhu, Wenxia Xu, Lifeng Feng, Hongchuan Jin, Xian Wang
Software Mentions: 3
Published: over 9 years ago

10.1242/bio.046789

Molecular profiling of stem cell-like female germ line cells in <i>Drosophila</i> delineates networks important for stemness and differentiation
Cited by: 5
Author(s): Manu D. Tiwari, Daniela M. Zeitler, Gunter Meister, Andreas Wodarz
Software Mentions: 3
Published: over 7 years ago

10.1016/j.str.2020.01.013

Structure of Microtubule-Trapped Human Kinesin-5 and Its Mechanism of Inhibition Revealed Using Cryoelectron Microscopy
Cited by: 20
Author(s): Alejandro Peña, Aaron Sweeney, Alexander D. Cook, Julia Locke, Maya Topf, Carolyn A. Moores
Software Mentions: 3
Published: over 6 years ago

10.1186/s13041-020-00702-5

Translational changes induced by acute sleep deprivation uncovered by TRAP-Seq
Cited by: 17
Author(s): Lisa C. Lyons, Snehajyoti Chatterjee, Yann Vanrobaeys, Marie E. Gaine, Ted Abel
Software Mentions: 3
Published: over 5 years ago

10.1186/s13041-020-0561-1

Unveiling synapse pathology in spinal bulbar muscular atrophy by genome-wide transcriptome analysis of purified motor neurons derived from disease specific iPSCs
Cited by: 17
Author(s): Kazunari Onodera, Daisuke Shimojo, Yoshio Ishihara, Masato Yano, Fuyuki Miya, Haruhiko Banno, Naoko Kuzumaki, Takuji Ito, Ryosuke Okada, Bruno Herculano, Manabu Ohyama, Mari Yoshida, Tatsuhiko Tsunoda, Masahisa Katsuno, Manabu Doyu, Gen Sobue, Hideyuki Okano, Yohei Okada
Software Mentions: 3
Published: over 6 years ago

10.1186/s12864-021-07934-2

CAMPAREE: a robust and configurable RNA expression simulator
Cited by: 1
Author(s): Nicholas F. Lahens, Thomas G. Brooks, Dimitra Sarantopoulou, Soumyashant Nayak, Cris Lawrence, Antonijo Mrčela, Anand Srinivasan, Jonathan Schug, John B. Hogenesch, Yoseph Barash, Gregory R. Grant
Software Mentions: 3
Published: almost 5 years ago

10.1186/s12943-020-01253-y

Circular RNA CDR1as disrupts the p53/MDM2 complex to inhibit Gliomagenesis
Cited by: 104
Author(s): Jiacheng Lou, Yuchao Hao, Kefeng Lin, Yizhu Lyu, Meiwei Chen, Han Wang, Diao Zou, Xuewen Jiang, Renchun Wang, Di Jin, Eric W.‐F. Lam, Shujuan Shao, Quentin Liu, Jinsong Yan, Xiang Wang, Puxiang Chen, Bo Zhang, Boquan Jin
Software Mentions: 3
Published: almost 6 years ago

10.1186/s12864-019-5579-3

Gene expression profiles at different stages for formation of pearl sac and pearl in the pearl oyster Pinctada fucata
Cited by: 15
Author(s): . Mariom, Saori Take, Yoji Igarashi, Kazutoshi Yoshitake, Shuichi Asakawa, Kaoru Maeyama, Kiyohito Nagai, Shugo Watabe, Shigeharu Kinoshita
Software Mentions: 3
Published: over 7 years ago

10.1186/s12943-019-0977-3

MiR155 sensitized B-lymphoma cells to anti-PD-L1 antibody via PD-1/PD-L1-mediated lymphoma cell interaction with CD8+T cells
Cited by: 60
Author(s): Zhong Zheng, Rui Sun, Hongzheng Zhao, Di Fu, Hui Zhong, Xiang‐Qin Weng, Bin Qu, Yan Zhao, Li Wang, Wei‐Li Zhao
Software Mentions: 3
Published: over 7 years ago

10.1186/s12915-020-00886-1

The CBP KIX domain regulates long-term memory and circadian activity
Cited by: 18
Author(s): Snehajyoti Chatterjee, Christopher C. Angelakos, Ethan Bahl, Joshua D. Hawk, Marie E. Gaine, Shane G. Poplawski, Anne Schneider‐Anthony, Manish Kumar Yadav, Giulia S. Porcari, Jean‐Christophe Cassel, K. Peter Giese, Jacob J. Michaelson, Lisa C. Lyons, Anne‐Laurence Boutillier, Ted Abel
Software Mentions: 3
Published: over 5 years ago

10.1016/j.cub.2018.10.053

Metacognitive Failure as a Feature of Those Holding Radical Beliefs
Cited by: 92
Author(s): Max Rollwage, Raymond J. Dolan, Stephen M. Fleming
Software Mentions: 3
Published: over 7 years ago

10.1016/j.molcel.2019.04.034

Co-transcriptional Loading of RNA Export Factors Shapes the Human Transcriptome
Cited by: 66
Author(s): Nicolas Viphakone, Ian Sudbery, Llywelyn Griffith, Catherine G. Heath, David Sims, Stuart A. Wilson
Software Mentions: 3
Published: about 7 years ago

10.1016/j.molcel.2018.06.032

HuD Is a Neural Translation Enhancer Acting on mTORC1-Responsive Genes and Counteracted by the Y3 Small Non-coding RNA
Cited by: 47
Author(s): Toma Tebaldi, Paola Zuccotti, Daniele Peroni, Marcel Köhn, Lisa Gasperini, Valentina Potrich, Veronica Bonazza, Tatiana Dudnakova, Annalisa Rossi, Guido Sanguinetti, Luciano Conti, Paolo Macchi, Vito D’Agostino, Gabriella Viero, David Tollervey, Stefan Hüttelmaier, Alessandro Quattrone
Software Mentions: 3
Published: about 8 years ago

10.5966/sctm.2015-0401

Human Adipose-Derived Stem Cells Expanded Under Ambient Oxygen Concentration Accumulate Oxidative DNA Lesions and Experience Procarcinogenic DNA Replication Stress
Cited by: 12
Author(s): Rémy Bétous, Marie-Laure Renoud, Claire Hoede, Ignacio González, Natalie Jones, Michel Longy, Luc Sensebé, Christophe Cazaux, Jean-Sébastien Hoffmann
Software Mentions: 3
Published: almost 10 years ago

10.18632/aging.102989

Overexpression of miR-10a-5p facilitates the progression of osteoarthritis
Cited by: 9
Author(s): Huizi Li, Xiaolong Xu, Nan Lin, Dawei Wang, Yiming Lin, Zhongzhen Su, Huading Lu
Software Mentions: 3
Published: over 6 years ago

10.1186/s12864-017-4141-4

Single molecule counting and assessment of random molecular tagging errors with transposable giga-scale error-correcting barcodes
Cited by: 3
Author(s): Billy T. Lau, Hanlee P. Ji
Software Mentions: 3
Published: almost 9 years ago

10.1172/jci.insight.148652

CD40L modulates transcriptional signatures of neutrophils in the bone marrow associated with development and trafficking
Cited by: 1
Author(s): Tábata Takahashi França, Ashraf Al-Sbiei, Ghada Bashir, Yassir A. Mohamed, Ranieri Coelho Salgado, Lucila Akune Barreiros, Sarah Maria da Silva Napoleão, Cristiane Seganfredo Weber, Janáira Fernandes Severo Ferreira, Carolina Sánchez Aranda, Carolina Prando, Mayra B. de Barros Dorna, Igor Jurišica, Maria J. Fernández-Cabezudo, Hans D. Ochs, Antônio Condino‐Neto, Basel K. al-Ramadi, Otávio Cabral-Marques
Software Mentions: 3
Published: almost 5 years ago

10.18632/oncotarget.11356

Zbtb1 prevents default myeloid differentiation of lymphoid-primed multipotent progenitors
Cited by: 6
Author(s): Xianyu Zhang, Ying Lu, Xin Cao, Tao Zhen, Damián Kovalovsky
Software Mentions: 3
Published: almost 10 years ago

10.1016/j.molcel.2021.01.011

Neuronal non-CG methylation is an essential target for MeCP2 function
Cited by: 21
Author(s): Rebekah Tillotson, Justyna Cholewa-Waclaw, Kashyap Chhatbar, John C. Connelly, Sophie A. Kirschner, Shaun Webb, Martha V. Koerner, Jim Selfridge, David A. Kelly, Dina De Sousa, Kyla Brown, Matthew J. Lyst, Skirmantas Kriaucionis, Adrian Bird
Software Mentions: 3
Published: over 5 years ago

10.3390/cells9061406

Cell Type-Specific In Vitro Gene Expression Profiling of Stem Cell-Derived Neural Models
Cited by: 4
Author(s): James A. Gregory, Emily Hoelzli, Rawan Abdelaal, Catherine E. Braine, Miguel Cuevas, Madeline Halpern, Natalie Barretto, Nadine Schrode, Güney Akbalık, Kristy Kang, Esther Cheng, Kathryn R. Bowles, Steven Lotz, Susan K. Goderie, Celeste M. Karch, Sally Temple, Alison Goate, Kristen J. Brennand, Hemali Phatnani
Software Mentions: 3
Published: about 6 years ago

10.7554/eLife.57068

MondoA regulates gene expression in cholesterol biosynthesis-associated pathways required for zebrafish epiboly
Cited by: 7
Author(s): Meltem Weger, Benjamin D. Weger, Andrea Schink, Masanari Takamiya, Johannes Stegmaier, Cédric Gobet, Alice Parisi, Andrei Yu Kobitski, Jonas Mertes, Nils Krone, Uwe Strähle, G. Ulrich Nienhaus, Ralf Mikut, Frédéric Gachon, Philipp Gut, Thomas Dickmeis
Software Mentions: 3
Published: almost 6 years ago

10.3389/fimmu.2019.01624

Activation of the DR3-TL1A Axis in Donor Mice Leads to Regulatory T Cell Expansion and Activation With Reduction in Graft-Versus-Host Disease
Cited by: 13
Author(s): Melissa Mavers, Federico Simonetta, Hidekazu Nishikii, Jessica V. Ribado, Kristina Maas‐Bauer, Maite Álvarez, Toshihito Hirai, Mustafa Turkoz, Jeanette Baker, Robert S. Negrin
Software Mentions: 3
Published: about 7 years ago

10.1371/journal.pone.0231658

A transcriptional regulatory network of Rsv3-mediated extreme resistance against Soybean mosaic virus
Cited by: 8
Author(s): Lindsay C. DeMers, Neelam Redekar, Aardra Kachroo, S. A. Tolin, Li Song, M. A. Saghai Maroof
Software Mentions: 3
Published: over 6 years ago

10.1186/s12864-021-07672-5

Transcriptomics analysis of differentially expressed genes in subcutaneous and perirenal adipose tissue of sheep as affected by their pre- and early postnatal malnutrition histories
Cited by: 4
Author(s): Sharmila Ahmad, Markus Drag, Suraya Mohamad Salleh, Zexi Cai, Mette Olaf Nielsen
Software Mentions: 3
Published: about 5 years ago

10.1186/s12915-021-01011-6

Chromatin accessibility landscapes of immune cells in rheumatoid arthritis nominate monocytes in disease pathogenesis
Cited by: 5
Author(s): Dandan Zong, Beibei Huang, Young Li, Yichen Lu, Nan Xiang, Chuang Guo, Qian Liu, Qing Sha, Pengcheng Du, Qiaoni Yu, Wen Zhang, Pengfei Cai, Yanping Sun, Jin‐Hui Tao, Xiaomei Li, Shanbao Cai, Kun Qu
Software Mentions: 3
Published: over 5 years ago

10.3389/fimmu.2021.695972

Severe COVID-19 Is Characterized by an Impaired Type I Interferon Response and Elevated Levels of Arginase Producing Granulocytic Myeloid Derived Suppressor Cells
Cited by: 43
Author(s): Matthew J. Dean, Juan B. Ochoa, Maria Dulfary Sanchez-Pino, Jovanny Zabaleta, Jone Garai, Luis Del Valle, Dorota Wyczechowska, Lyndsey Buckner Baiamonte, Phaethon Philbrook, Rinku Majumder, Richard S. Vander Heide, Logan Dunkenberger, Ramesh P. Thylur, Bobby D. Nossaman, W. Mark Roberts, Andrew G. Chapple, Jiande Wu, Chindo Hicks, Jack Collins, Brian T. Luke, Randall C. Johnson, Hari K. Koul, Chris A. Rees, Claudia R. Morris, Julia Garcia‐Diaz, Augusto C. Ochoa
Software Mentions: 3
Published: about 5 years ago

10.3389/fimmu.2021.695148

CD32+CD4+ T Cells Sharing B Cell Properties Increase With Simian Immunodeficiency Virus Replication in Lymphoid Tissues
Cited by: 8
Author(s): Nicolas Huot, Philippe Rascle, Cyril Planchais, Vanessa Contreras, Caroline Passaes, Roger Le Grand, Anne-Sophie Beignon, Étienne Kornobis, Rachel Legendre, Hugo Varet, Asier Sáez‐Cirión, Hugo Mouquet, Béatrice Jacquelin, Michaela Müller‐Trutwin
Software Mentions: 3
Published: about 5 years ago

10.1371/journal.pone.0227116

Modeling the effect of prolonged ethanol exposure on global gene expression and chromatin accessibility in normal 3D colon organoids
Cited by: 20
Author(s): Matthew Devall, Lucas T. Jennelle, Jennifer Bryant, Stephanie A. Bien, Ulrike Peters, Steven M. Powell, Graham Casey
Software Mentions: 3
Published: over 6 years ago

10.1371/journal.pone.0217042

RNA sequencing of isolated cell populations expressing human APOL1 G2 risk variant reveals molecular correlates of sickle cell nephropathy in zebrafish podocytes
Cited by: 3
Author(s): Joseph L. Bundy, Blair R. Anderson, Ludmila Francescatto, Melanie E. Garrett, Karen Soldano, Marilyn J. Telen, Erica E. Davis, Allison Ashley‐Koch
Software Mentions: 3
Published: about 7 years ago

10.1016/j.molcel.2017.11.013

hnRNPK Recruits PCGF3/5-PRC1 to the Xist RNA B-Repeat to Establish Polycomb-Mediated Chromosomal Silencing
Cited by: 236
Author(s): Greta Pintacuda, Guifeng Wei, Chloë Roustan, Burcu Anil Kirmizitas, Nicolae Solcan, Andrea Cerase, Alfredo Castelló, Shabaz Mohammed, Benoît Moindrot, Tatyana B. Nesterova, Neil Brockdorff
Software Mentions: 3
Published: over 8 years ago

10.1186/s13062-016-0158-x

CLIP-GENE: a web service of the condition specific context-laid integrative analysis for gene prioritization in mouse TF knockout experiments
Cited by: 1
Author(s): Benjamin Hur, Sangsoo Lim, Han–Jung Chae, Seokjun Seo, Sunwon Lee, Jaewoo Kang, Sun Kim
Software Mentions: 3
Published: over 9 years ago

10.3389/fimmu.2021.535039

Complex Interplay Between MAZR and Runx3 Regulates the Generation of Cytotoxic T Lymphocyte and Memory T Cells
Cited by: 3
Author(s): Alexandra Franziska Gülich, Ramona Rica, Caroline Tizian, Csilla Viczenczová, Kseniya Khamina, Thomas Faux, Daniela Hainberger, Thomas Penz, Rémy Bosselut, Christoph Bock, Asta Laiho, Laura L. Elo, Andréas Bergthaler, Wilfried Ellmeier, Shoji Sakaguchi
Software Mentions: 3
Published: over 5 years ago

10.3390/cells8101169

Aging Triggers H3K27 Trimethylation Hoarding in the Chromatin of Nothobranchius furzeri Skeletal Muscle
Cited by: 14
Author(s): Chiara Cencioni, Johanna Heid, Anna Krepelova, Seyed Mohammad Mahdi Rasa, Carsten Kuenne, Stefan Guenther, Mario Baumgart, Alessandro Cellerino, Francesco Neri, Francesco Spallotta, Carlo Gaetano
Software Mentions: 3
Published: almost 7 years ago

10.1186/s12864-018-5303-8

Higher plane of nutrition pre-weaning enhances Holstein calf mammary gland development through alterations in the parenchyma and fat pad transcriptome
Cited by: 13
Author(s): Mario Vailati-Riboni, Ryan Bucktrout, Siyuan Zhan, Ashley Geiger, Joshua C McCann, R.M. Akers, Juan J. Loor
Software Mentions: 3
Published: over 7 years ago

10.1016/j.molcel.2019.01.027

Selective Roles of Vertebrate PCF11 in Premature and Full-Length Transcript Termination
Cited by: 87
Author(s): Kinga Kamieniarz-Gdula, Michal R. Gdula, Karin Panser, Takayuki Nojima, Joan Monks, Jacek R. Wiśniewski, Joey Riepsaame, Neil Brockdorff, Andrea Pauli, Nick J. Proudfoot
Software Mentions: 3
Published: over 7 years ago

10.18632/oncotarget.13239

Whole-exome and transcriptome sequencing of refractory diffuse large B-cell lymphoma
Cited by: 37
Author(s): Ha Young Park, Seungbok Lee, Hae Young Yoo, Seok Jin Kim, Won Seog Kim, Jong‐Il Kim, Young Hyeh Ko
Software Mentions: 3
Published: over 9 years ago

10.1371/journal.pone.0248796

Evidence that synergism between potassium and nitrate enhances the alleviation of ammonium toxicity in rice seedling roots
Cited by: 12
Author(s): Gen Fang, Jing Yang, Tong Sun, Xiaoxin Wang, Yangsheng Li
Software Mentions: 3
Published: almost 5 years ago

10.1074/mcp.RA117.000400

Proteotranscriptomics Reveal Signaling Networks in the Ovarian Cancer Microenvironment
Cited by: 47
Author(s): Thomas Worzfeld, Florian Finkernagel, Silke Reinartz, Anne Konzer, Till Adhikary, Andrea Nist, Thorsten Stiewe, Uwe Wagner, Mario Looso, Johannes Graumann, Rolf Müller
Software Mentions: 3
Published: over 8 years ago

10.1074/mcp.TIR119.001431

Sensitive Quantitative Proteomics of Human Hematopoietic Stem and Progenitor Cells by Data-independent Acquisition Mass Spectrometry
Cited by: 41
Author(s): Sabine Amon, Fabienne Meier-Abt, Ludovic Gillet, Slavica Dimitrieva, Alexandre Theocharides, Markus G. Manz, Ruedi Aebersold
Software Mentions: 3
Published: about 7 years ago

10.1016/j.mcpro.2021.100092

The C-Mannosylome of Human Induced Pluripotent Stem Cells Implies a Role for ADAMTS16 C-Mannosylation in Eye Development
Cited by: 7
Author(s): Karsten Cirksena, Hermann J. Hütte, Aleksandra Shcherbakova, Thomas Thumberger, Roman Sakson, Stefan Weiß, Lars Riff Jensen, Alina Friedrich, Daniel Todt, Andreas W. Kuß, Thomas Ruppert, Joachim Wittbrodt, Hans Bakker, Falk F. R. Buettner
Software Mentions: 3
Published: over 5 years ago

10.1155/2018/8608327

Transcriptome and DNA Methylome Dynamics during Triclosan-Induced Cardiomyocyte Differentiation Toxicity
Cited by: 7
Author(s): Guizhen Du, Mingming Yu, Lingling Wang, Wu Hu, Song Lee, Chuncheng Lu, Xinru Wang
Software Mentions: 3
Published: over 7 years ago

10.1007/s12015-021-10136-8

C3G Regulates STAT3, ERK, Adhesion Signaling, and Is Essential for Differentiation of Embryonic Stem Cells
Cited by: 4
Author(s): Vijay V Vishnu, Bh Muralikrishna, Archana Verma, Sanjeev Chavan Nayak, Divya Tej Sowpati, Vegesna Radha, P Chandra Shekar
Software Mentions: 3
Published: over 5 years ago

10.1038/s41598-018-24998-5

Genetic mapping identifies loci that influence tomato resistance against Colorado potato beetles
Cited by: 7
Author(s): Erandi Vargas‐Ortiz, Itay Gonda, John R. Smeda, Martha A. Mutschler, James J. Giovannoni, Georg Jander
Software Mentions: 3
Published: about 8 years ago

10.1186/s13287-021-02177-0

The angiogenic potential of CD271+ human adipose tissue-derived mesenchymal stem cells
Cited by: 7
Author(s): Richard J. P. Smith, Alessandro Faroni, James R. Barrow, Jamie Soul, Adam J. Reid
Software Mentions: 3
Published: over 5 years ago

10.1002/glia.23761

Mutant <i>C9orf72</i> human iPSC‐derived astrocytes cause non‐cell autonomous motor neuron pathophysiology
Cited by: 78
Author(s): Chen Zhao, Anna-Claire Devlin, Amit K. Chouhan, Bhuvaneish T. Selvaraj, Maria Stavrou, Karen Burr, Veronica Brivio, Xin He, Arpan R. Mehta, David Story, Christopher E. Shaw, Owen Dando, Giles E. Hardingham, Gareth B. Miles, Siddharthan Chandran
Software Mentions: 3
Published: over 6 years ago

10.1002/mgg3.1381

Deleterious mis‐splicing of <i>STK11</i> caused by a novel single‐nucleotide substitution in the 3′ polypyrimidine tract of intron five
Cited by: 2
Author(s): Thorkild Terkelsen, Ole Halfdan Larsen, Søren Vang, Uffe Birk Jensen, Friedrik P. Wikman
Software Mentions: 3
Published: about 6 years ago

10.3390/insects11110820

Transcriptomics-Based Approach Identifies Spinosad-Associated Targets in the Colorado Potato Beetle, Leptinotarsa decemlineata
Cited by: 10
Author(s): Pierre Bastarache, Gabriel Wajnberg, Pascal Dumas, Simi Chacko, Jacynthe Lacroix, Nicolas Crapoulet, Chandra E. Moffat, Pier Jr Morin
Software Mentions: 3
Published: over 5 years ago

10.3390/cells10071730

Pathophysiological Effects of Overactive STIM1 on Murine Muscle Function and Structure
Cited by: 9
Author(s): Roberto Silva‐Rojas, Anne Charles, Sarah Djeddi, Bernard Gény, Jocelyn Laporte
Software Mentions: 3
Published: about 5 years ago

10.1186/s10020-020-00203-0

Comparison of time and dose dependent gene expression and affected pathways in primary human fibroblasts after exposure to ionizing radiation
Cited by: 14
Author(s): Lara Kim Brackmann, Alicia Schulze, Caine Lucas Grandt, Heike Schwarz, Thomas Hankeln, Steffen Rapp, Sebastian Zahnreich, Danuta Galetzka, Iris Schmitt, Christian Grad, Lukas Eckhard, Johanna Mirsch, Maria Blettner, Peter Scholz-Kreisel, Moritz Hess, Harald Binder, Heinz Schmidberger, Manuela Marron
Software Mentions: 3
Published: almost 6 years ago

10.3389/fphys.2018.01568

Transcriptional Signatures in Liver Reveal Metabolic Adaptations to Seasons in Migratory Blackheaded Buntings
Cited by: 15
Author(s): Devraj Singh, Vivek Swarup, Hiep D. Le, Vinod Kumar
Software Mentions: 3
Published: over 7 years ago

10.1172/jci.insight.149232

Nonredundant, isoform-specific roles of HDAC1 in glioma stem cells
Cited by: 10
Author(s): Costanza Lo Cascio, James B. McNamara, Ernesto Luna Melendez, Erika M. Lewis, Matthew E. Dufault, Nader Sanai, Christopher Plaisier, Shwetal Mehta
Software Mentions: 3
Published: almost 5 years ago

10.1111/acel.13114

Deterioration of hematopoietic autophagy is linked to osteoporosis
Cited by: 17
Author(s): Ye Yuan, Yixuan Fang, Lingjiang Zhu, Yue Gu, Lei Li, Jiawei Qian, Ruijin Zhao, Peng Zhang, Jian Li, Hui Zhang, Na Yuan, Suping Zhang, Quanhong Ma, Jianrong Wang, Youjia Xu
Software Mentions: 3
Published: over 6 years ago

10.1371/journal.pone.0185227

The first transcriptome of Italian wall lizard, a new tool to infer about the Island Syndrome
Cited by: 4
Author(s): Martina Trapanese, Maria Buglione, Valeria Maselli, Simona Petrelli, Serena Aceto, Domenico Fulgione
Software Mentions: 3
Published: almost 9 years ago

10.1038/s42003-021-02051-y

Overlapping roles of spliceosomal components SF3B1 and PHF5A in rice splicing regulation
Cited by: 6
Author(s): Haroon Butt, Jérémie Bazin, Sahar Alshareef, Ayman Eid, Moussa Benhamed, Anireddy S. N. Reddy, Martín Crespi, Magdy M. Mahfouz
Software Mentions: 3
Published: about 5 years ago

10.1186/1745-6150-9-20

A new rhesus macaque assembly and annotation for next-generation sequencing analyses
Cited by: 150
Author(s): Aleksey V. Zimin, Adam Cornish, Mnirnal D Maudhoo, Robert Gibbs, Xiongfei Zhang, Sanjit Pandey, Daniel T. Meehan, Kristin Wipfler, Steven E. Bosinger, Zachary P. Johnson, Gregory K. Tharp, Guillaume Marçais, Michael R. Roberts, Betsy Ferguson, Howard S. Fox, Todd J. Treangen, Steven L. Salzberg, James A. Yorke, Robert B. Norgren
Software Mentions: 3
Published: almost 12 years ago

10.1038/s41597-020-00754-1

Transcriptome dataset of human corneal endothelium based on ribosomal RNA-depleted RNA-Seq data
Cited by: 13
Author(s): Yoshiyuki Tokuda, Naoki Okumura, Yuya Komori, Naoya Hanada, Kei Tashiro, Noriko Koizumi, Masakazu Nakano
Software Mentions: 3
Published: over 5 years ago

10.3389/fphar.2019.00330

Alkylaminophenol Induces G1/S Phase Cell Cycle Arrest in Glioblastoma Cells Through p53 and Cyclin-Dependent Kinase Signaling Pathway
Cited by: 40
Author(s): Phuong L. Doan, Aliyu Musa, Nuno R. Candeias, Frank Emmert‐Streib, Olli Yli‐Harja, Meenakshisundaram Kandhavelu
Software Mentions: 3
Published: over 7 years ago

10.1186/s12885-020-06737-0

RNAseq expression patterns of canine invasive urothelial carcinoma reveal two distinct tumor clusters and shared regions of dysregulation with human bladder tumors
Cited by: 15
Author(s): Heidi G. Parker, Deepika Dhawan, Alex C. Harris, José A. Ramos‐Vara, Brian W. Davis, Deborah W. Knapp, Elaine A. Ostrander
Software Mentions: 3
Published: over 6 years ago

10.1016/j.stemcr.2021.01.013

Unraveling the Developmental Roadmap toward Human Brown Adipose Tissue
Cited by: 9
Author(s): Stefania Carobbio, Anne Claire Guenantin, Myriam Bahri, Sonia Rodríguez-Fdez, Floris Honig, Ioannis Kamzolas, Isabella Samuelson, Kathleen Long, Sherine Awad, Dunja Lukovic, Slaven Erceg, Andrew Bassett, Sasha Mendjan, Ludovic Vallier, Barry Rosen, Davide Chiarugi, António Vidal-Puig
Software Mentions: 3
Published: over 5 years ago

10.1371/journal.ppat.1009723

ACE2-lentiviral transduction enables mouse SARS-CoV-2 infection and mapping of receptor interactions
Cited by: 17
Author(s): Daniel J. Rawle, Thuy T. Le, Troy Dumenil, Kexin Yan, Bing Tang, Wilson Nguyen, Daniel Watterson, Naphak Modhiran, Jody Hobson‐Peters, Cameron Bishop, Andreas Suhrbier
Software Mentions: 3
Published: about 5 years ago

10.1186/s13024-021-00475-y

SRSF1-dependent inhibition of C9ORF72-repeat RNA nuclear export: genome-wide mechanisms for neuroprotection in amyotrophic lateral sclerosis
Cited by: 11
Author(s): Lydia M. Castelli, Luisa Cutillo, Catiane Souza, Álvaro Sánchez-Martínez, Ilaria Granata, Ya-Hui Lin, Monika A. Myszczynska, Paul R. Heath, Matthew R. Livesey, Ke Ning, Mimoun Azzouz, Pamela J. Shaw, Mario Rosario Guarracino, Alexander J. Whitworth, Laura Ferraiuolo, Marta Milo, Guillaume M. Hautbergue
Software Mentions: 3
Published: almost 5 years ago

10.7554/eLife.36278

Support for a clade of Placozoa and Cnidaria in genes with minimal compositional bias
Cited by: 77
Author(s): Christopher E. Laumer, Harald R. Gruber‐Vodicka, Michael G. Hadfield, Vicki B. Pearse, Ana Riesgo, John C. Marioni, Gonzalo Giribet
Software Mentions: 3
Published: over 7 years ago

10.1186/s13024-021-00482-z

The TGFβ/Notch axis facilitates Müller cell-to-epithelial transition to ultimately form a chronic glial scar
Cited by: 15
Author(s): Federica Maria Conedera, Ana Maria Quintela Pousa, Nadia Mercader, Markus Tschopp, Volker Enzmann
Software Mentions: 3
Published: almost 5 years ago

10.1186/s13024-019-0335-3

Microglia affect α-synuclein cell-to-cell transfer in a mouse model of Parkinson’s disease
Cited by: 117
Author(s): Sonia George, Nolwen L. Rey, Trevor Tyson, Corinne R. Esquibel, Lindsay Meyerdirk, Emily Schulz, Steven Pierce, Amanda R. Burmeister, Zachary Madaj, Jennifer A. Steiner, Martha L. Escobar Galvis, Lena Brundin, Patrik Brundin
Software Mentions: 3
Published: almost 7 years ago

10.1371/journal.pone.0209405

Brain transcriptome changes in the aging Drosophila melanogaster accompany olfactory memory performance deficits
Cited by: 22
Author(s): Rodrigo Pacifico, Courtney MacMullen, Erica Walkinshaw, Xiaofan Zhang, Ronald L. Davis
Software Mentions: 3
Published: over 7 years ago

10.1093/bioinformatics/btt731

Oqtans: the RNA-seq workbench in the cloud for complete and reproducible quantitative transcriptome analysis
Cited by: 12
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: 3
Published: over 12 years ago

10.1186/s12885-020-07571-0

Targeted nanopore sequencing for the identification of ABCB1 promoter translocations in cancer
Cited by: 6
Author(s): Mark S. Williams, Naseer J. Basma, Fabio Amaral, Gillian Williams, John Weightman, Wolfgang Breitwieser, Louisa Nelson, Stephen S. Taylor, Daniel H. Wiseman, Tim C. P. Somervaille
Software Mentions: 3
Published: over 5 years ago

10.1186/s13059-020-02053-9

Analysis of transcript-deleterious variants in Mendelian disorders: implications for RNA-based diagnostics
Cited by: 49
Author(s): Sateesh Maddirevula, Hiroyuki Kuwahara, Nour Ewida, Hanan E. Shamseldin, Nisha Patel, Fatema Alzahrani, Tarfa Al‐Sheddi, Eman Alobeid, Mona M. Alenazi, Hessa S. Alsaif, Maha Alqahtani, Maha AlAli, Hatoon Al Ali, Rana Helaby, Niema Ibrahim, Firdous Abdulwahab, Mais Hashem, Nadine Hanna, Dorota Monies, Nada Derar, Afaf Alsagheir, Amal Alhashem, Badr Alsaleem, Hamoud Alhebbi, Sami Wali, Ramzan Umarov, Xin Gao, Fowzan S. Alkuraya
Software Mentions: 3
Published: about 6 years ago

10.1186/s13024-021-00433-8

Altered network properties in C9ORF72 repeat expansion cortical neurons are due to synaptic dysfunction
Cited by: 27
Author(s): Emma M. Perkins, Karen Burr, Poulomi Banerjee, Arpan R. Mehta, Owen Dando, Bhuvaneish T. Selvaraj, Daumante Šuminaite, Jyoti Nanda, Christopher M. Henstridge, Thomas H. Gillingwater, Giles E. Hardingham, David J. A. Wyllie, Siddharthan Chandran, Matthew R. Livesey
Software Mentions: 3
Published: over 5 years ago

10.7554/eLife.36468

Hair follicle dermal condensation forms via Fgf20 primed cell cycle exit, cell motility, and aggregation
Cited by: 53
Author(s): Leah C. Biggs, O. Mäkelä, Satu-Marja Myllymäki, Rishi Das Roy, Katja Närhi, Johanna Pispa, Tuija Mustonen, Marja L. Mikkola
Software Mentions: 3
Published: almost 8 years ago

10.1016/j.stemcr.2019.10.009

Wnt Inhibition Facilitates RNA-Mediated Reprogramming of Human Somatic Cells to Naive Pluripotency
Cited by: 50
Author(s): Nicholas Bredenkamp, Jian Yang, James Clarke, Giuliano Giuseppe Stirparo, Ferdinand von Meyenn, Sabine Dietmann, Duncan Baker, Rosalind Drummond, Yongming Ren, Dongwei Li, Chuman Wu, Maria Rostovskaya, Sarah Eminli-Meissner, Austin Smith, Ge Guo
Software Mentions: 3
Published: over 6 years ago

10.1186/s12974-019-1628-8

Midbrain microglia mediate a specific immunosuppressive response under inflammatory conditions
Cited by: 28
Author(s): Miguel A. Abellanas, Marta Zamarbide, Leyre Basurco, Esther Luquin, Marta Garcı́a-Granero, Pedro Clavero, Patxi San Martín-Úriz, Amaia Vilas, Elisa Mengual, Sandra Hervás-Stubbs, Marta Aymerich
Software Mentions: 3
Published: over 6 years ago

10.1186/s12885-018-4594-0

Chromoanasynthesis is a common mechanism that leads to ERBB2 amplifications in a cohort of early stage HER2+ breast cancer samples
Cited by: 13
Author(s): George Vasmatzis, Xue Wang, James B. Smadbeck, Stephen J. Murphy, Katherine B. Geiersbach, Sarah H. Johnson, Athanasios Gaitatzes, Yan W. Asmann, Farhad Kosari, Mitesh J. Borad, Daniel J. Serie, Sarah A. McLaughlin, Jennifer M. Kachergus, Brian M. Necela, E. Aubrey Thompson
Software Mentions: 3
Published: about 8 years ago

10.3389/fcimb.2020.617998

High-Resolution Mapping of Transcription Initiation in the Asexual Stages of Toxoplasma gondii
Cited by: 9
Author(s): Benedikt M. Markus, Benjamin S. Waldman, Hernan Lorenzi, Sebastian Lourido
Software Mentions: 3
Published: over 5 years ago

10.3389/fphys.2019.00101

Characterization of Endothelial and Smooth Muscle Cells From Different Canine Vessels
Cited by: 19
Author(s): Loes A. Oosterhoff, Hedwig S. Kruitwagen, Monique E. van Wolferen, Bas W. M. van Balkom, Michal Mokrý, Nico Lansu, Noortje A.M. van den Dungen, Louis C. Penning, Talitha C.F. Spanjersberg, Johannes W. de Graaf, Tomas Veenendaal, Flin Zomerdijk, Joost O. Fledderus, Bart Spee, Frank G. van Steenbeek
Software Mentions: 3
Published: over 7 years ago

10.1186/s40478-021-01148-z

TDP-43 proteinopathy alters the ribosome association of multiple mRNAs including the glypican Dally-like protein (Dlp)/GPC6
Cited by: 10
Author(s): Erik M. Lehmkuhl, Suvithanandhini Loganathan, Eric Alsop, Alexander D. Blythe, Tina Kovalik, Nicholas P. Mortimore, Dianne Barrameda, Chuol Kueth, Randall J. Eck, Bhavani Bagevalu Siddegowda, Archi Joardar, Hannah E. Ball, Maria E. Macias, Robert Bowser, Kendall Van Keuren‐Jensen, Daniela C. Zarnescu
Software Mentions: 3
Published: over 5 years ago

10.3389/fpls.2016.00933

Transcriptome Profiling of Huanglongbing (HLB) Tolerant and Susceptible Citrus Plants Reveals the Role of Basal Resistance in HLB Tolerance
Cited by: 45
Author(s): Yunsheng Wang, Lijuan Zhou, Xiaoyue Yu, Ed Stover, Feng Luo, Yongping Duan
Software Mentions: 3
Published: about 10 years ago

10.1002/1878-0261.12797

Optimized low‐dose combinatorial drug treatment boosts selectivity and efficacy of colorectal carcinoma treatment
Cited by: 19
Author(s): Marloes Zoetemelk, George M. Ramzy, Magdalena Rausch, Thibaud Koessler, Judy R. van Beijnum, Andrea Weiss, Valentin Mieville, Sander R. Piersma, Richard R. de Haas, Céline Delucinge-Vivier, Axel Andrès, Christian Toso, Alex A. Henneman, Simone Ragusa, Tatiana V. Petrova, Mylène Docquier, Thomas McKee, Connie R. Jiménez, Youssef Daali, Arjan W. Griffioen, Laura Rubbia‐Brandt, Pierre‐Yves Dietrich, Patrycja Nowak-Śliwińska
Software Mentions: 3
Published: almost 6 years ago

10.1002/1878-0261.12905

IFNβ1 secreted by breast cancer cells undergoing chemotherapy reprograms stromal fibroblasts to support tumour growth after treatment
Cited by: 6
Author(s): Ana Luiza Silva Maia, Zuguang Gu, André Koch, Mireia Berdiel‐Acer, Rainer Will, Matthias Schlesner, Stefan Wiemann
Software Mentions: 3
Published: over 5 years ago

10.1002/1878-0261.12903

REST promotes ETS1‐dependent vascular growth in medulloblastoma
Cited by: 9
Author(s): Shavali Shaik, Satoru Maegawa, Amanda R. Haltom, Feng Wang, Xue Xiao, Tara Dobson, Ajay Sharma, Yanwen Yang, Jyothishmathi Swaminathan, Vikas Kundra, Xiao Nan Li, Keri Schadler, Arif Harmanci, Lin Xu, Vidya Gopalakrishnan
Software Mentions: 3
Published: over 5 years ago

10.1111/mpp.12877

Show me your secret(ed) weapons: a multifaceted approach reveals a wide arsenal of type III‐secreted effectors in the cucurbit pathogenic bacterium <i>Acidovorax citrulli</i> and novel effectors in the <i>Acidovorax</i> genus
Cited by: 26
Author(s): Irene Jiménez‐Guerrero, Francisco Pérez‐Montaño, Gustavo Mateus da Silva, Naama Wagner, Dafna Shkedy, Mei Zhao, Lorena Pizarro, Maya Bar, R. R. Walcott, Guido Sessa, Tal Pupko, Saul Burdman
Software Mentions: 3
Published: almost 7 years ago

10.3390/cells10092289

Comprehensive Characterization of Multitissue Expression Landscape, Co-Expression Networks and Positive Selection in Pikeperch
Cited by: 1
Author(s): Julien Alban Nguinkal, Marieke Verleih, Lidia de los Ríos-Pérez, Ronald M. Brunner, Arne Sahm, Saptarshi Bej, Alexander Rebl, Tom Goldammer
Software Mentions: 3
Published: almost 5 years ago

10.7554/eLife.56086

Enteric glia as a source of neural progenitors in adult zebrafish
Cited by: 37
Author(s): Sarah E. McCallum, Yuichi Obata, Evangelia Fourli, Stefan Boeing, Christopher J. Peddie, Qiling Xu, Stuart Horswell, Robert N. Kelsh, Lucy Collinson, David Wilkinson, Carmen Pin, Vassilis Pachnis, Tiffany A. Heanue
Software Mentions: 3
Published: almost 6 years ago

10.3389/fphys.2020.00653

Rehabilitative Impact of Exercise Training on Human Skeletal Muscle Transcriptional Programs in Parkinson’s Disease
Cited by: 13
Author(s): Kaleen M. Lavin, Yongchao Ge, Stuart C. Sealfon, Venugopalan D. Nair, Katarzyna Wilk, Jeremy McAdam, Samuel T. Windham, Preeti Lakshman Kumar, Merry-Lynn McDonald, Marcas M. Bamman
Software Mentions: 3
Published: about 6 years ago

10.1186/s12885-019-6363-0

The impact of RNA extraction method on accurate RNA sequencing from formalin-fixed paraffin-embedded tissues
Cited by: 26
Author(s): Michał Marczyk, Chunxiao Fu, Rosanna Lau, Lili Du, Alexander J. Trevarton, Bruno Valentin Sinn, Rebekah E. Gould, Lajos Pusztai, Christos Hatzis, W. Fraser Symmans
Software Mentions: 3
Published: over 6 years ago

10.3389/fpls.2021.685416

Transcriptome Responses of Ripe Cherry Tomato Fruit Exposed to Chilling and Rewarming Identify Reversible and Irreversible Gene Expression Changes
Cited by: 8
Author(s): Donald A. Hunter, Nathanael J. Napier, Zoë A. Erridge, Ali Saei, Ronan Chen, Marian J. McKenzie, Erin M. O’Donoghue, Martin Hunt, Laurie Favre, Ross E. Lill, David A. Brummell
Software Mentions: 3
Published: about 5 years ago

10.1093/bioinformatics/btv488

Benchmark analysis of algorithms for determining and quantifying full-length mRNA splice forms from RNA-seq data
Cited by: 75
Author(s): Katharina E. Hayer, Angel Pizarro, Nicholas F. Lahens, John B. Hogenesch, Gregory R. Grant
Software Mentions: 3
Published: almost 11 years ago

10.3389/fpls.2019.01301

Differential Expression of Candidate Salivary Effector Genes in Pea Aphid Biotypes With Distinct Host Plant Specificity
Cited by: 25
Author(s): Hélène Boulain, Fabrice Legeai, Julie Jaquiéry, Endrick Guy, Stéphanie Morlière, Jean‐Christophe Simon, Akiko Sugio
Software Mentions: 3
Published: almost 7 years ago

10.1007/s00401-016-1658-6

Paradoxical antidepressant effects of alcohol are related to acid sphingomyelinase and its control of sphingolipid homeostasis
Cited by: 64
Author(s): Christian P. Müller, L. S. Kalinichenko, Jens Tiesel, Matthias Witt, Thomas Stöckl, Eva Sprenger, Jens Fuchser, Janine Beckmann, Marc Praetner, Sabine Huber, Davide Amato, Christiane Mühle, Christian Büttner, Arif B. Ekici, Irena Smaga, Lucyna Pomierny-Chamioło, Bartosz Pomierny, Małgorzata Filip, Volker Eulenburg, Erich Gulbins, Anbarasu Lourdusamy, Martin Reichel, Johannes Kornhuber
Software Mentions: 3
Published: over 9 years ago

10.18632/oncotarget.17813

Transcriptome profiling in preadipocytes identifies long noncoding RNAs as Sam68 targets
Cited by: 13
Author(s): Naomi Li, Steven C. Hebert, Jingwen Song, Claudia L. Kleinman, Stéphane Richard
Software Mentions: 3
Published: about 9 years ago

10.15252/msb.20177952

Modeling signaling‐dependent pluripotency with Boolean logic to predict cell fate transitions
Cited by: 42
Author(s): Ayako Yachie‐Kinoshita, Kento Onishi, Joel Östblom, Matthew A Langley, Eszter Pósfai, Janet Rossant, Peter W. Zandstra
Software Mentions: 3
Published: over 8 years ago

10.1093/bioinformatics/btz433

CoCo: RNA-seq read assignment correction for nested genes and multimapped reads
Cited by: 27
Author(s): Gabrielle Deschamps-Francoeur, Vincent Boivin, Sherif Abou Elela, Michelle S. Scott
Software Mentions: 3
Published: about 7 years ago

10.1186/s12864-018-4726-6

Evaluation of commercially available small RNASeq library preparation kits using low input RNA
Cited by: 60
Author(s): Ashish Yeri, Amanda Courtright, Kirsty Danielson, Elizabeth Hutchins, Eric Alsop, Elizabeth Carlson, Michael H. Hsieh, Olivia Ziegler, Avash Das, Ravi Shah, Joel Rozowsky, Saumya Das, Kendall Van Keuren‐Jensen
Software Mentions: 3
Published: about 8 years ago

10.7554/eLife.66143

The EMT transcription factor Snai1 maintains myocardial wall integrity by repressing intermediate filament gene expression
Cited by: 8
Author(s): Alessandra Gentile, Anabela Bensimon-Brito, Rashmi Priya, Hans-Martin Maischein, Janett Piesker, Stefan Guenther, Felix Gunawan, Didier Y.R. Stainier
Software Mentions: 3
Published: about 5 years ago

10.3389/fpls.2021.640163

A 598-bp InDel Variation in the Promoter Region of Bna.SOC1.A05 Is Predominantly Present in Winter Type Rapeseeds
Cited by: 1
Author(s): Sarah Matar, Siegbert Melzer
Software Mentions: 3
Published: over 5 years ago

10.3389/fgene.2020.567262

A Recently Formed Triploid Cardamine insueta Inherits Leaf Vivipary and Submergence Tolerance Traits of Parents
Cited by: 5
Author(s): Jianqiang Sun, Rie Shimizu‐Inatsugi, Hugo Hofhuis, Kentaro Shimizu, Angela Hay, Kentaro Shimizu, Jun Sese
Software Mentions: 3
Published: almost 6 years ago

10.1186/s12931-019-0981-6

Whole blood RNA sequencing reveals a unique transcriptomic profile in patients with ARDS following hematopoietic stem cell transplantation
Cited by: 14
Author(s): Joshua A. Englert, Michael H. Cho, Andrew Lamb, Maya Shumyatcher, Diana Barragan-Bradford, Maria C. Basil, Angelica Higuera, Colleen Isabelle, Mayra Pinilla Vera, Paul B. Dieffenbach, Laura E. Fredenburgh, Joyce B. Kang, Ami S. Bhatt, Joseph H. Antin, Vincent T. Ho, Robert J. Soiffer, Judie A. Howrylak, Blanca E. Himes, Rebecca M. Baron
Software Mentions: 3
Published: over 7 years ago