10.1186/s12859-021-04313-2

The ‘un-shrunk’ partial correlation in Gaussian graphical models
Cited by: 0
Author(s): Victor Bernal, Rainer Bischoff, Péter Horvatovich, Victor Guryev, Marco Grzegorczyk
Software Mentions: 2
Published: almost 5 years ago

10.1186/1471-2105-7-437

STAR: predicting recombination sites from amino acid sequence
Cited by: 6
Author(s): Denis C. Bauer, Mikael Bodén, Ricarda Thier, Elizabeth M. J. Gillam
Software Mentions: 2
Published: almost 20 years ago

10.1186/1471-2105-15-229

SnowyOwl: accurate prediction of fungal genes by using RNA-Seq and homology information to select among ab initio models
Cited by: 27
Author(s): Ian D. Reid, Nicholas O’Toole, Omar Zabaneh, Reza Nourzadeh, Mahmoud Dahdouli, Mostafa Abdellateef, Paul M. Gordon, Jung Soh, Gregory Butler, Christoph Wilhelm Sensen, Adrian Tsang
Software Mentions: 2
Published: about 12 years ago

10.3389/fncel.2019.00310

Comprehensive Evaluation of White Matter Damage and Neuron Death and Whole-Transcriptome Analysis of Rats With Chronic Cerebral Hypoperfusion
Cited by: 9
Author(s): Wenxian Li, Di Wei, Jianye Liang, Xiaomei Xie, Kangping Song
Software Mentions: 2
Published: almost 7 years ago

10.1186/1756-0500-4-121

mmView: a web-based viewer of the mmCIF format
Cited by: 0
Author(s): Petr Čech, Daniel Svozil
Software Mentions: 2
Published: over 15 years ago

10.7150/thno.56737

Small-molecule inhibitor of AF9/ENL-DOT1L/AF4/AFF4 interactions suppresses malignant gene expression and tumor growth
Cited by: 14
Author(s): Feng Wu, Shuang Nie, Yuan Yao, Tong Huo, Xin Li, Xiaowei Wu, Jidong Zhao, Yi-Lun Lin, Zhang Yin-jie, Qianxing Mo, Yuanlin Song
Software Mentions: 2
Published: over 5 years ago

10.7150/thno.61833

Inhibiting microglia proliferation after spinal cord injury improves recovery in mice and nonhuman primates
Cited by: 28
Author(s): Gaëtan Poulen, Emilie Aloy, Claire M. Bringuier, Nadine Mestre‐Francés, Emaëlle V.F. Artus, Maïda Cardoso, Jean‐Christophe Perez, Christophe Goze-Bac, Hassan Boukhaddaoui, Nicolas Lonjon, Yannick Nicolas Gerber, Florence E. Perrin
Software Mentions: 2
Published: over 5 years ago

10.1089/thy.2020.0307

Limitations of Detecting Genetic Variants from the RNA Sequencing Data in Tissue and Fine-Needle Aspiration Samples
Cited by: 15
Author(s): Cihan Kaya, Princesca Dorsaint, Stephanie Mercurio, Alexander M Campbell, Kenneth Eng, Marina N. Nikiforova, Olivier Elemento, Andrea Sboner
Software Mentions: 2
Published: over 5 years ago

10.1093/g3journal/jkaa021

Transcriptome analysis implicates secondary metabolite production, redox reactions, and programmed cell death during allorecognition inCryphonectria parasitica
Cited by: 2
Author(s): Anatoly Belov, Thomas E. Witte, David P. Overy, Myron L. Smith
Software Mentions: 2
Published: over 5 years ago

10.1093/g3journal/jkaa046

Roles for RNA export factor, <i>Nxt1</i>, in ensuring muscle integrity and normal RNA expression in <i>Drosophila</i>
Cited by: 3
Author(s): Kevin van der Graaf, Katia Jindrich, Robert Mitchell, Helen White-Cooper
Software Mentions: 2
Published: over 5 years ago

10.3390/toxins12070429

Insights into Aflatoxin B1 Toxicity in Cattle: An In Vitro Whole-Transcriptomic Approach
Cited by: 22
Author(s): Marianna Pauletto, Roberta Tolosi, Mery Giantin, Giorgia Guerra, Andrea Barbarossa, Anna Zaghini, Mauro Dacasto
Software Mentions: 2
Published: about 6 years ago

10.7554/eLife.42530

Natural depletion of histone H1 in sex cells causes DNA demethylation, heterochromatin decondensation and transposon activation
Cited by: 51
Author(s): Shengbo He, Martin Vickers, Jingyi Zhang, Xiaoqi Feng
Software Mentions: 2
Published: about 7 years ago

10.3389/fevo.2019.00085

Alternative Transcription at Venom Genes and Its Role as a Complementary Mechanism for the Generation of Venom Complexity in the Common House Spider
Cited by: 13
Author(s): Robert A. Haney, Taylor Matte, FitzAnthony S. Forsyth, Jessica E. Garb
Software Mentions: 2
Published: about 7 years ago

10.1186/s12859-018-2589-0

NCLcomparator: systematically post-screening non-co-linear transcripts (circular, trans-spliced, or fusion RNAs) identified from various detectors
Cited by: 16
Author(s): Chia-Ying Chen, Trees‐Juen Chuang
Software Mentions: 2
Published: over 7 years ago

10.1093/g3journal/jkab218

The amino acid substitution affects cellular response to mistranslation
Cited by: 8
Author(s): Matthew D. Berg, Yi Zhu, Bianca Y. Ruiz, Raphaël Loll-Krippleber, Joshua Isaacson, Bryan-Joseph San Luis, Julie Genereaux, Charles Boone, Judit Villén, Grant W. Brown, Christopher J. Brandl
Software Mentions: 2
Published: about 5 years ago

10.3389/fendo.2018.00034

Regulatory Architecture of the LβT2 Gonadotrope Cell Underlying the Response to Gonadotropin-Releasing Hormone
Cited by: 14
Author(s): Frederique Ruf-Zamojski, Miguel Fribourg, Yongchao Ge, Venugopalan D. Nair, Hanna Pinças, Elena Zaslavsky, German Nudelman, Stephanie Tuminello, Hideo Watanabe, Judith L Turgeon, Stuart C. Sealfon
Software Mentions: 2
Published: over 8 years ago

10.1038/tp.2017.80

Maternal immune activation results in complex microglial transcriptome signature in the adult offspring that is reversed by minocycline treatment
Cited by: 157
Author(s): Daniele Mattei, Andranik Ivanov, Carmelo Ferrai, Philipp Jordan, Dilansu Güneykaya, Alice Buonfiglioli, W. Schaafsma, Piotr Przanowski, Winnie Deuther‐Conrad, Peter Brust, Swen Hesse, Marianne Patt, Osama Sabri, Tobias L. Roß, Bart J. L. Eggen, Erik Boddeke, Bożena Kamińska, Dieter Beule, Ana Pombo, Helmut Kettenmann, Susanne Wolf
Software Mentions: 2
Published: about 9 years ago

10.1038/s42003-019-0657-2

Transcriptional programming and T cell receptor repertoires distinguish human lung and lymph node memory T cells
Cited by: 14
Author(s): Nathan Schoettler, Cara L. Hrusch, Kelly M. Blaine, Anne I. Sperling, Carole Ober
Software Mentions: 2
Published: over 6 years ago

10.1038/tp.2017.202

The BET/BRD inhibitor JQ1 improves brain plasticity in WT and APP mice
Cited by: 52
Author(s): Eva Benito, Binu Ramachandran, Henning Schroeder, G. Schmídt, Hendrik Urbanke, Susanne Burkhardt, Vincenzo Capece, Camin Dean, André Fischer
Software Mentions: 2
Published: almost 9 years ago

10.7554/eLife.52504

Derivation of trophoblast stem cells from naïve human pluripotent stem cells
Cited by: 177
Author(s): Chen Dong, Mariana Beltcheva, Paul Gontarz, Bo Zhang, Pooja Popli, Laura A. Fischer, Shafqat Ali Khan, Kyoung Mi Park, Eun‐Ja Yoon, Xiaoyun Xing, Ramakrishna Kommagani, Ting Wang, Lilianna Solnica‐Krezel, Thorold W. Theunissen
Software Mentions: 2
Published: over 6 years ago

10.1038/s41398-018-0137-3

THC exposure of human iPSC neurons impacts genes associated with neuropsychiatric disorders
Cited by: 30
Author(s): Boris Guennewig, Mainá Bitar, Ifeanyi Obiorah, James B. Hanks, Elizabeth O’Brien, Dominik C. Kaczorowski, Yasmin L. Hurd, Panos Roussos, Kristen J. Brennand, Guy Barry
Software Mentions: 2
Published: about 8 years ago

10.1038/s41398-018-0319-z

Integrative system biology analyses of CRISPR-edited iPSC-derived neurons and human brains reveal deficiencies of presynaptic signaling in FTLD and PSP
Cited by: 43
Author(s): Shan Jiang, Natalie Wen, Zeran Li, Umber Dube, Jorge L. Del-Águila, John Budde, Rita Martinez, Simon Hsu, María Victoria Fernández, Nigel J. Cairns, Oscar Harari, Carlos Cruchaga, Celeste M. Karch
Software Mentions: 2
Published: over 7 years ago

10.3389/fendo.2021.671724

Attenuated Induction of the Unfolded Protein Response in Adult Human Primary Astrocytes in Response to Recurrent Low Glucose
Cited by: 3
Author(s): Paul G. Weightman Potter, Sam Washer, Aaron R. Jeffries, Janet E. Holley, N. J. Gutowski, Emma Dempster, Craig Beall
Software Mentions: 2
Published: about 5 years ago

10.1038/s41398-019-0517-3

Comparative characterization of human induced pluripotent stem cells (hiPSC) derived from patients with schizophrenia and autism
Cited by: 37
Author(s): Lena Marie Grunwald, Ricarda Stock, Kathrina Haag, Sandra Buckenmaier, Mark Eberle, Dirk Wildgruber, Helena Storchak, Martin Kriebel, Stephanie Weißgraeber, Lisha Mathew, Yasmin Singh, Maarten Loos, Ka Wan Li, Udo Kraushaar, Andreas J. Fallgatter, Hansjürgen Volkmer
Software Mentions: 2
Published: almost 7 years ago

10.18632/aging.202658

Insights into epithelial cell senescence from transcriptome and secretome analysis of human oral keratinocytes
Cited by: 10
Author(s): Rachael E Schwartz, Maxim N. Shokhirev, Leonardo R. Andrade, J. Silvio Gutkind, Ramiro Iglesias-Bartolomé, Gerald S. Shadel
Software Mentions: 2
Published: over 5 years ago

10.3390/genes8080206

Viral Infection Identifies Micropeptides Differentially Regulated in smORF-Containing lncRNAs
Cited by: 40
Author(s): Brandon S. Razooky, Benedikt Obermayer, Joshua Biggs O'May, Alexander Tarakhovsky
Software Mentions: 2
Published: almost 9 years ago

10.1038/s41413-020-0086-3

Osteoclasts are not a source of SLIT3
Cited by: 18
Author(s): Na Li, Kenzo Inoue, Jun Sun, Yingzhen Niu, Sarfaraz Lalani, Alisha R. Yallowitz, Xu Yang, Chao Zhang, Rong Shen, Baohong Zhao, Ren Xu, Matthew B. Greenblatt
Software Mentions: 2
Published: over 6 years ago

10.1038/s41398-020-0854-2

Long non-coding RNA Neat1 regulates adaptive behavioural response to stress in mice
Cited by: 33
Author(s): Michail S. Kukharsky, Natalia Ninkina, Haiyan An, Vsevolod Telezhkin, Wenbin Wei, Camille Rabesahala de Meritens, Johnathan Cooper‐Knock, Shinichi Nakagawa, Tetsuro Hirose, Vladimir L. Buchman, Tatyana A. Shelkovnikova
Software Mentions: 2
Published: about 6 years ago

10.1186/s12859-016-1238-8

A haplotype-based normalization technique for the analysis and detection of allele specific expression
Cited by: 8
Author(s): Alan Hodgkinson, Jean Grenier, Elias Gbeha, Philip Awadalla
Software Mentions: 2
Published: almost 10 years ago

10.1038/s41398-020-01050-7

Translational study of the whole transcriptome in rats and genetic polymorphisms in humans identifies LRP1B and VPS13A as key genes involved in tolerance to cocaine-induced motor disturbances
Cited by: 4
Author(s): Florence Vorspan, Romain Icick, Nawel Mekdad, Cindie Courtin, Vanessa Bloch, Frank Bellivier, Jean‐Louis Laplanche, Nathalie Prince, Dmitry Pishalin, Cyril Firmo, Corinne Blugeon, Bruno Mégarbane, Cynthia Marie-Claire, Nadia Benturquia
Software Mentions: 2
Published: over 5 years ago

10.1038/s41398-020-01163-z

Alcohol use disorder causes global changes in splicing in the human brain
Cited by: 21
Author(s): Derek Van Booven, Mengying Li, Jianhua Rao, Ilya O. Blokhin, R. Dayne Mayfield, Estelle Barbier, Markus Heilig, Claes Wahlestedt
Software Mentions: 2
Published: over 5 years ago

10.1186/s12859-019-3182-x

VARUS: sampling complementary RNA reads from the sequence read archive
Cited by: 10
Author(s): Mario Stanke, Willy Bruhn, Felix Becker, Katharina J. Hoff
Software Mentions: 2
Published: over 6 years ago

10.7554/eLife.33292

Nonsense mRNA suppression via nonstop decay
Cited by: 42
Author(s): Joshua A. Arribere, Andrew Fire
Software Mentions: 2
Published: over 8 years ago

10.1038/s41398-021-01443-2

A diet high in sugar and fat influences neurotransmitter metabolism and then affects brain function by altering the gut microbiota
Cited by: 35
Author(s): Yuna Guo, Xiangxiang Zhu, Miao Zhang, Longkai Qi, Xiaocui Tang, Dongdong Wang, Mei Zhang, Yizhen Xie, Hongye Li, Xuefei Yang, Diling Chen
Software Mentions: 2
Published: about 5 years ago

10.1186/s40478-021-01239-x

Microglial transcriptome analysis in the rNLS8 mouse model of TDP-43 proteinopathy reveals discrete expression profiles associated with neurodegenerative progression and recovery
Cited by: 20
Author(s): Mandana Hunter, Krista Spiller, Myrna A. Dominique, Hong Xu, Francis W. Hunter, Terry Fang, Rebecca G. Canter, Christopher J. Roberts, Richard M. Ransohoff, John Q. Trojanowski, Virginia M.‐Y. Lee
Software Mentions: 2
Published: almost 5 years ago

10.1038/s41398-021-01506-4

No evidence for differential gene expression in major depressive disorder PBMCs, but robust evidence of elevated biological ageing
Cited by: 13
Author(s): John Cole, Alison McColl, Robin Shaw, Mary Ellen Lynall, Philip J. Cowen, P. de Boer, Wayne C. Drevets, Neil A. Harrison, Carmine Pariante, Linda Pointon, Carl S. Goodyear, Edward T. Bullmore, Jonathan Cavanagh
Software Mentions: 2
Published: almost 5 years ago

10.1038/s41413-019-0070-y

Osteocyte dysfunction promotes osteoarthritis through MMP13-dependent suppression of subchondral bone homeostasis
Cited by: 60
Author(s): Courtney M. Mazur, Jonathon J. Woo, Cristal S. Yee, Aaron J. Fields, Claire Acevedo, Karsyn N. Bailey, Serra Kaya, Tristan W. Fowler, Jeffrey C. Lotz, Alexis Dang, Alfred C. Kuo, Thomas P. Vail, Tamara Alliston
Software Mentions: 2
Published: over 6 years ago

10.1186/1745-6215-12-S1-A84

Self-help therapy and recovery in psychosis: methodological considerations and service user involvement in a partially randomised preference trial
Cited by: 2
Author(s): Samantha Hartley, Gillian Haddock
Software Mentions: 2
Published: over 14 years ago

10.3390/genes9030123

Delimiting Coalescence Genes (C-Genes) in Phylogenomic Data Sets
Cited by: 29
Author(s): Mark S. Springer, John Gatesy
Software Mentions: 2
Published: over 8 years ago

10.3390/genes9030142

Integration of lncRNA and mRNA Transcriptome Analyses Reveals Genes and Pathways Potentially Involved in Calf Intestinal Growth and Development during the Early Weeks of Life
Cited by: 22
Author(s): Eveline M. Ibeagha‐Awemu, Duy Ngoc, Pier-Luc Dudemaine, Bridget E. Fomenky, Nathalie Bissonnette
Software Mentions: 2
Published: over 8 years ago

10.3389/fendo.2020.00238

Urinary Sediment Transcriptomic and Longitudinal Data to Investigate Renal Function Decline in Type 1 Diabetes
Cited by: 5
Author(s): Maria Beatriz Monteiro, Tatiana Souza Pelaes, Daniele Pereira Santos‐Bezerra, Karina Thieme, Antônio M. Lerário, Sueli Mieko Oba-Shinjo, Ubiratan Fabres Machado, Marisa Passarelli, Suely Kazue Nagahashi Marie, Maria Lúcia Corrêa-Giannella
Software Mentions: 2
Published: over 6 years ago

10.3389/fendo.2020.558344

Transcriptome Sequencing Analysis of Peripheral Blood of Type 2 Diabetes Mellitus Patients With Thirst and Fatigue
Cited by: 6
Author(s): Bohan Lv, Xueli Bao, Ping Li, Juan Lian, Yanxiang Wu, Tian An, Jing Zhang, Xiuyan Yang, Tingye Wang, Jiajian Zhu, Yuanyuan Hu, Guiyan Jiang, Gao S
Software Mentions: 2
Published: over 5 years ago

10.1186/s13063-016-1676-7

StereoTactic radiotherapy for wet Age-Related macular degeneration (STAR): study protocol for a randomised controlled clinical trial
Cited by: 13
Author(s): James E. Neffendorf, R. M. Desai, Yanzhong Wang, Joanna Kelly, Caroline Murphy, Barnaby C Reeves, Usha Chakravarthy, Sarah Wordsworth, Christopher Alan Lewis, Janet L. Peacock, Shahir Uddin, Joe M. O’Sullivan, Timothy L. Jackson
Software Mentions: 2
Published: over 9 years ago

10.3389/fgene.2020.562937

Transcriptomic Analysis Reveals Important Roles of Lignin and Flavonoid Biosynthetic Pathways in Rice Thermotolerance During Reproductive Stage
Cited by: 19
Author(s): Zhenzhen Cai, Fengyu He, Xin Feng, Tom Liang, Hongwei Wang, Shuangcheng Ding, Xiaohai Tian
Software Mentions: 2
Published: almost 6 years ago

10.3390/genes10010054

Genomes of Three Closely Related Caribbean Amazons Provide Insight for Species History and Conservation
Cited by: 8
Author(s): Sofia M. Kolchanova, Sergei Kliver, Aleksei S. Komissarov, Pavel Dobrinin, Gaik Tamazian, Kirill Grigorev, Walter Wolfsberger, Audrey J. Majeske, Jafet Vélez-Valentín, Ricardo Valentín de la Rosa, Joanne R Paul-Murphy, David Sánchez-Migallón Guzmán, Michael H. Court, Juan L. Rodríguez-Flores, Juan Carlos Martínez‐Cruzado, Tarás K. Oleksyk
Software Mentions: 2
Published: over 7 years ago

10.1186/s13063-019-3469-2

The HOSENG trial – Effect of the provision of oral self-testing for absent and refusing individuals during a door-to-door HIV-testing campaign on testing coverage: protocol of a cluster-randomized clinical trial in rural Lesotho
Cited by: 6
Author(s): Alain Amstutz, Thabo Ishmael Lejone, Lefu Khesa, Josephine Muhairwe, Bienvenu Lengo Nsakala, Katleho Tlali, Moniek Bresser, Fiona Vanobberghen, Mathebe Kopo, Mpho Kao, Thomas Klimkait, Manuel Battegay, Niklaus Daniel Labhardt, Tracy R. Glass
Software Mentions: 2
Published: almost 7 years ago

10.7717/peerj.11691

In silico-driven analysis of the <i>Glossina morsitans morsitans</i> antennae transcriptome in response to repellent or attractant compounds
Cited by: 2
Author(s): Consolata Gakii, Billiah K. Bwana, Grace Mugambi, Esther Mukoya, Paul O. Mireji, Richard Rimiru
Software Mentions: 2
Published: about 5 years ago

10.3390/ani11092558

Novel Facets of the Liver Transcriptome Are Associated with the Susceptibility and Resistance to Lipid-Related Metabolic Disorders in Periparturient Holstein Cows
Cited by: 2
Author(s): Ryan S. Pralle, Wenli Li, Brianna Murphy, H.T. Holdorf, H.M. White
Software Mentions: 2
Published: almost 5 years ago

10.3390/genes10030196

Cohesin-Mediated Genome Architecture Does Not Define DNA Replication Timing Domains
Cited by: 17
Author(s): Phoebe Oldach, Conrad A. Nieduszynski
Software Mentions: 2
Published: over 7 years ago

10.1016/j.tube.2017.08.004

Host blood RNA signatures predict the outcome of tuberculosis treatment
Cited by: 126
Author(s): Ethan Thompson, Ying Du, Stephanus T. Malherbe, Steven G. Smith, Jackie Braun, Joe Valvo, Katharina Ronacher, Gerard Tromp, David L. Tabb, David Alland, Shubhada Shenai, Laura E. Via, James Warwick, Alan Aderem, Thomas J. Scriba, Jill Winter, Gerhard Walzl, Daniel E. Zak, Nelita du Plessis, André G. Loxton, Novel N. Chegou, Myungsun Lee
Software Mentions: 2
Published: over 8 years ago

10.4274/tjh.galenos.2019.2019.0312

Expression Profile Screening and Bioinformatics Analysis of Circrna, Lncrna and Mrna in Acute Myeloid Leukemia Drug-Resistance Cells
Cited by: 8
Author(s): Meiling Li, Fuxue Meng, Quanyi Lu
Software Mentions: 2
Published: over 6 years ago

10.3390/genes10060406

Transcriptome Changes of Skeletal Muscle RNA-Seq Speculates the Mechanism of Postprandial Hyperglycemia in Diabetic Goto-Kakizaki Rats During the Early Stage of T2D
Cited by: 7
Author(s): Wenlu Zhang, Yuhuan Meng, Shuang Fu, Xingsong Li, Zixi Chen, Lizhen Huang, Hongli Du
Software Mentions: 2
Published: about 7 years ago

10.1186/s12859-021-04263-9

Computational comparison of common event-based differential splicing tools: practical considerations for laboratory researchers
Cited by: 10
Author(s): Ittai B. Muller, Stijn Meijers, Peter Kampstra, Steven van Dijk, Michel van Elswijk, Marry Lin, Anna Wojtuszkiewicz, Gerrit Jansen, Robert de Jonge, Jacqueline Cloos
Software Mentions: 2
Published: about 5 years ago

10.7554/eLife.40806

Ovaries absent links dLsd1 to HP1a for local H3K4 demethylation required for heterochromatic gene silencing
Cited by: 24
Author(s): Yang Fu, Zhenghui Quan, Huanwei Huang, Minghui He, Xicheng Liu, Tao Cai, Rongwen Xi
Software Mentions: 2
Published: over 7 years ago

10.1101/2021.07.02.450920

Betacoronavirus-specific alternate splicing
Cited by: 1
Author(s): Guy Karlebach, Aronow Bj, Baylin Sj, Daniel Butler, Jonathan Foox, Shawn Levy, Cem Meydan, Christopher Mozsary, Saravia-Butler Am, Taylor Dm, Eve Syrkin Wurtele, Cheryl L. Mason, Afshin Beheshti, Robinson Pn
Software Mentions: 2
Published: about 5 years ago

10.1128/mBio.00207-16

A Two-Component Regulatory System Impacts Extracellular Membrane-Derived Vesicle Production in Group A Streptococcus
Cited by: 118
Author(s): Ulrike Resch, James A. Tsatsaronis, Anaïs Le Rhun, Gerald Stübiger, Manfred Rohde, Sergo Kasvandik, Susanne Holzmeister, Philip Tinnefeld, Sun Nyunt Wai, Emmanuelle Charpentier
Software Mentions: 2
Published: over 9 years ago

10.3389/fbioe.2020.01021

GeTallele: A Method for Analysis of DNA and RNA Allele Frequency Distributions
Cited by: 2
Author(s): Piotr Słowiński, Muzi Li, Paula Restrepo, Nawaf Alomran, Liam F. Spurr, C. Ryan Miller, Krasimira Tsaneva-Atanasova, Anélia Horvath
Software Mentions: 2
Published: almost 6 years ago

10.1128/mBio.00845-17

Ebola Virus Binding to Tim-1 on T Lymphocytes Induces a Cytokine Storm
Cited by: 81
Author(s): Patrick Younan, Mathieu Iampietro, Andrew Nishida, Palaniappan Ramanathan, Rodrigo I. Santos, Mukta Dutta, Ndongala Michel Lubaki, Richard A. Koup, Michael G. Katze, Alexander Bukreyev
Software Mentions: 2
Published: over 8 years ago

10.18632/aging.102922

RNA sequencing analysis of monocrotaline-induced PAH reveals dysregulated chemokine and neuroactive ligand receptor pathways
Cited by: 17
Author(s): Genfa Xiao, Tingjun Wang, Wenxin Zhuang, Chaoyi Ye, Luo Lu, Huajun Wang, Guili Lian, Liangdi Xie
Software Mentions: 2
Published: over 6 years ago

10.1186/s40478-019-0709-3

RETRACTED ARTICLE: Unique RNA signature of different lesion types in the brain white matter in progressive multiple sclerosis
Cited by: 7
Author(s): Maria L. Elkjaer, Tobias Frisch, Richard Reynolds, Tim Kacprowski, Mark Burton, Torben A. Kruse, Mads Thomassen, Jan Baumbach, Zsolt Illés
Software Mentions: 2
Published: about 7 years ago

10.3390/ijms22179218

Sodium Iodate-Induced Degeneration Results in Local Complement Changes and Inflammatory Processes in Murine Retina
Cited by: 19
Author(s): Anne Enzbrenner, Rahel Zulliger, Josef Biber, Ana Maria Quintela Pousa, Nicole Schäfer, Corinne Stucki, Nicolas Giroud, Marco Berrera, Elöd Körtvely, Roland Schmucki, Laura Badi, Antje Grosche, Diana Pauly, Volker Enzmann
Software Mentions: 2
Published: almost 5 years ago

10.1038/s42003-021-01901-z

Inside-out chicken enteroids with leukocyte component as a model to study host–pathogen interactions
Cited by: 38
Author(s): Tessa Nash, Katrina M. Morris, Neil A. Mabbott, Lonneke Vervelde
Software Mentions: 2
Published: over 5 years ago

10.7554/eLife.26116

The conserved RNA helicase YTHDC2 regulates the transition from proliferation to differentiation in the germline
Cited by: 151
Author(s): Alexis S. Bailey, Pedro J. Batista, Rebecca Gold, Y. Grace Chen, Dirk G. de Rooij, Howard Y. Chang, Margaret T. Fuller
Software Mentions: 2
Published: over 8 years ago

10.3389/fgene.2019.01175

Conjoint Analysis of SMRT- and Illumina-Based RNA-Sequencing Data of Fenneropenaeus chinensis Provides Insight Into Sex-Biased Expression Genes Involved in Sexual Dimorphism
Cited by: 5
Author(s): Qiong Wang, HE Ya, Jian Li
Software Mentions: 2
Published: over 6 years ago

10.1128/mBio.00937-19

Endogenous Retrovirus-Derived Long Noncoding RNA Enhances Innate Immune Responses via Derepressing RELA Expression
Cited by: 34
Author(s): Bin Zhou, Fei Qi, Fang–Jing Wu, Hongbo Nie, Yifan Song, Lu Shao, Jingxuan Han, Zhiyong Wu, Hexige Saiyin, Gang Wei, Penghua Wang, Ting Ni, Feng Qian
Software Mentions: 2
Published: almost 7 years ago

10.1186/s12859-017-1890-7

Identification and characterization of conserved lncRNAs in human and rat brain
Cited by: 20
Author(s): Dan Li, Mary Qu Yang
Software Mentions: 2
Published: over 8 years ago

10.1007/s00401-020-02171-5

Patient-derived orthotopic xenografts of pediatric brain tumors: a St. Jude resource
Cited by: 38
Author(s): Kyle Smith, Ke Xu, Kimberly Mercer, Frederick A. Boop, Paul Klimo, Michael DeCupyere, José Grenet, Sarah Robinson, Paige S. Dunphy, Suzanne J. Baker, David W. Ellison, Thomas E. Merchant, Santhosh A Upadayaya, Amar Gajjar, Gang Wu, Brent A. Orr, Giles Robinson, Paul A. Northcott, Martine F. Roussel
Software Mentions: 2
Published: about 6 years ago

10.3390/genes11010103

The velvet Regulator VosA Governs Survival and Secondary Metabolism of Sexual Spores in Aspergillus nidulans
Cited by: 13
Author(s): Min-Ju Kim, Mi-Kyung Lee, Huy Quang Pham, Myeong Ju Gu, Bohan Zhu, Sung-Hun Son, Dongyup Hahn, Jae‐Ho Shin, Jae‐Hyuk Yu, Hee-Soo Park, Kap-Hoon Han
Software Mentions: 2
Published: over 6 years ago

10.18632/aging.101592

Sirtuin 3 attenuates amyloid-β induced neuronal hypometabolism
Cited by: 18
Author(s): Jun Yin, Shiping Li, Megan Nielsen, Tanner Carcione, Winnie S. Liang, Jiong Shi
Software Mentions: 2
Published: over 7 years ago

10.1186/s12859-021-03991-2

lncEvo: automated identification and conservation study of long noncoding RNAs
Cited by: 8
Author(s): Oleksii Bryzghalov, Izabela Makałowska, Michał Wojciech Szcześniak
Software Mentions: 2
Published: over 5 years ago

10.1186/s12859-019-2996-x

Magic-BLAST, an accurate RNA-seq aligner for long and short reads
Cited by: 178
Author(s): Grzegorz M. Boratyn, Jean Thierry‐Mieg, Danielle Thierry-Mieg, Ben Busby, Thomas Madden
Software Mentions: 2
Published: almost 7 years ago

10.1186/s12859-015-0849-9

The diagnostic application of RNA sequencing in patients with thyroid cancer: an analysis of 851 variants and 133 fusions in 524 genes
Cited by: 31
Author(s): Moraima Pagan, Richard T. Kloos, Chu-Fang Lin, Kevin Travers, Hajime Matsuzaki, Edward Tom, Su Yeon Kim, Michael Y. Wong, Andrew C. Stewart, Jing Huang, P. Sean Walsh, R. J. Monroe, Giulia C. Kennedy
Software Mentions: 2
Published: over 10 years ago

10.3389/fgene.2021.709937

SAP30 Gene Is a Probable Regulator of Muscle Hypertrophy in Chickens
Cited by: 1
Author(s): Bruna Petry, Gabriel Costa Monteiro Moreira, Aline Gonçalves Lio Copola, Marcela Maria de Souza, Fernanda Cristina da Veiga, Érika Cristina Jorge, J. de O. Peixoto, Mônica Corrêa Ledur, James E. Koltes, Luiz Lehmann Coutinho
Software Mentions: 2
Published: almost 5 years ago

10.1128/mBio.00719-20

Sterol-Response Pathways Mediate Alkaline Survival in Diverse Fungi
Cited by: 20
Author(s): Hannah E. Brown, Calla L. Telzrow, Joseph W. Saelens, Larissa Fernandes, J. Andrew Alspaugh
Software Mentions: 2
Published: about 6 years ago

10.3390/genes11020117

Inguinal Ring RNA Sequencing Reveals Downregulation of Muscular Genes Related to Scrotal Hernia in Pigs
Cited by: 6
Author(s): Gabriela Romano, A. M. G. Ibelli, William Raphael Lorenzetti, Tomás Weber, J. de O. Peixoto, Maurício Egídio Cantão, M. A. Z. Morés, N. Morés, Victor Breno Pedrosa, Luiz Lehmann Coutinho, Mônica Corrêa Ledur
Software Mentions: 2
Published: over 6 years ago

10.18632/aging.103236

Long noncoding RNA LINC00963 induces NOP2 expression by sponging tumor suppressor miR-542-3p to promote metastasis in prostate cancer
Cited by: 23
Author(s): Sun Feng, Ke Wu, Zhixian Yao, Xingyu Mu, Zhong Zheng, Menghao Sun, Yong Wang, Zhihong Liu, Yi-yong Zhu
Software Mentions: 2
Published: about 6 years ago

10.3389/fcvm.2021.662870

Acetazolamide Improves Right Ventricular Function and Metabolic Gene Dysregulation in Experimental Pulmonary Arterial Hypertension
Cited by: 4
Author(s): Fotios Spyropoulos, Zoe Michael, Benjamin Finander, Sally H. Vitali, Kosmas Kosmas, Panagiotis Zymaris, Brian T. Kalish, Stella Kourembanas, Helen Christou
Software Mentions: 2
Published: about 5 years ago

10.1128/mBio.02027-20

Survey of Early-Diverging Lineages of Fungi Reveals Abundant and Diverse Mycoviruses
Cited by: 32
Author(s): Jillian M. Myers, Anne E. Bonds, Rebecca A. Clemons, Natasha Thapa, D. Rabern Simmons, Derreck Carter-House, Jericho Ortañez, P. Liu, Alejandro Miralles-Durán, Alessandro Desirò, Joyce E. Longcore, Gregory Bonito, Jason E. Stajich, J. W. Spatafora, Ying Chang, Luis M. Corrochano, Andrii P. Gryganskyi, Igor V. Grigoriev, Timothy Y. James
Software Mentions: 2
Published: over 5 years ago

10.1128/mBio.02623-20

DDX56 Binds to Chikungunya Virus RNA To Control Infection
Cited by: 12
Author(s): Frances Taschuk, Iulia Tapescu, Ryan H. Moy, Sara Cherry
Software Mentions: 2
Published: over 5 years ago

10.1128/mBio.03044-20

A Noncanonical DNA Damage Checkpoint Response in a Major Fungal Pathogen
Cited by: 10
Author(s): Erika Shor, Rocio Garcia-Rubio, Lucius DeGregorio, David S. Perlin
Software Mentions: 2
Published: over 5 years ago

10.1186/s12859-018-2129-y

ASTRAL-III: polynomial time species tree reconstruction from partially resolved gene trees
Cited by: 1,247
Author(s): Chao Zhang, Maryam Rabiee, Erfan Sayyari, Siavash Mirarab
Software Mentions: 2
Published: about 8 years ago

10.1038/s41408-020-00362-7

FBXO11 is a candidate tumor suppressor in the leukemic transformation of myelodysplastic syndrome
Cited by: 11
Author(s): Michael Schieber, Christian Marinaccio, Lyndsey Bolanos, Wendy D. Haffey, Kenneth D. Greis, Daniel T. Starczynowski, John D. Crispino
Software Mentions: 2
Published: almost 6 years ago

10.3390/genes11040353

Genome-Wide Identification, Classification, and Expression Profiling Reveals R2R3-MYB Transcription Factors Related to Monoterpenoid Biosynthesis in Osmanthus fragrans
Cited by: 18
Author(s): Haiyan Li, Yuanzheng Yue, Wenjie Ding, Gongwei Chen, Ling Li, Yuli Li, Tingting Shi, Xia Yang
Software Mentions: 2
Published: over 6 years ago

10.1038/s41408-019-0194-8

CBFβ-MYH11 interferes with megakaryocyte differentiation via modulating a gene program that includes GATA2 and KLF1
Cited by: 7
Author(s): Guoqiang Yi, Amit Mandoli, Laura Jussen, Esther Tijchon, Maaike G.J.M. van Bergen, Gaëlle Cordonnier, Marten Hansen, Bowon Kim, Luan N. Nguyen, Pascal W.T.C. Jansen, Michiel Vermeulen, Bert van der Reijden, Emile van den Akker, Jonathan Bond, Joost H.A. Martens
Software Mentions: 2
Published: over 7 years ago

10.1186/s12859-016-0881-4

PTESFinder: a computational method to identify post-transcriptional exon shuffling (PTES) events
Cited by: 40
Author(s): Osagie Izuogu, Abd A. Alhasan, Hani M. Al-Afghani, Mauro Santibanez‐Koref, David J. Elliott, Michael S. Jackson
Software Mentions: 2
Published: over 10 years ago

10.5713/ajas.18.0533

Comparison of characteristics of long noncoding RNA in Hanwoo according to sex
Cited by: 0
Author(s): Jae-Ho Choi, Kyeong Hye Won, Seung‐Woo Son, Donghyun Shin, Jae-Don Oh
Software Mentions: 2
Published: about 6 years ago

10.3390/genes11050549

Single-Cell RNA Sequencing of Hematopoietic Stem and Progenitor Cells Treated with Gemcitabine and Carboplatin
Cited by: 2
Author(s): Niclas Björn, Ingrid Jakobsen Falk, Kourosh Lotfi, Henrik Gréen
Software Mentions: 2
Published: about 6 years ago

10.7554/eLife.53159

FoxO suppresses endoplasmic reticulum stress to inhibit growth of Tsc1-deficient tissues under nutrient restriction
Cited by: 4
Author(s): Avantika Gupta, Hugo Stocker
Software Mentions: 2
Published: about 6 years ago

10.1186/s13075-021-02477-z

Periostin loss-of-function protects mice from post-traumatic and age-related osteoarthritis
Cited by: 18
Author(s): Mukundan Attur, Xin Duan, Lei Cai, Tianzhen Han, Weili Zhang, Eric Tycksen, Jonathan Samuels, Robert H. Brophy, Steven B. Abramson, Muhammad Farooq
Software Mentions: 2
Published: over 5 years ago

10.1186/s12888-020-2467-y

Reliability and validity of the Japanese version of the INSPIRE measure of staff support for personal recovery in community mental health service users in Japan
Cited by: 5
Author(s): Risa Kotake, Akiko Kanehara, Yuki Miyamoto, Yousuke Kumakura, Utako Sawada, Ayumi Takano, Rie Chiba, Makoto Ogawa, Shinsuke Kondō, Kiyoto Kasai, Norito Kawakami
Software Mentions: 2
Published: over 6 years ago

10.1186/s13068-020-01825-6

Evolutionary engineering of E. coli MG1655 for tolerance against isoprenol
Cited by: 12
Author(s): Heiko Babel, Jens O. Krömer
Software Mentions: 2
Published: over 5 years ago

10.1128/mSphere.00219-19

Robust Transcriptional Response to Heat Shock Impacting Diverse Cellular Processes despite Lack of Heat Shock Factor in Microsporidia
Cited by: 6
Author(s): Nora K. McNamara-Bordewick, Mia McKinstry, Jonathan W. Snow
Software Mentions: 2
Published: about 7 years ago

10.3390/genes11070784

Differential Alternative Splicing Genes and Isoform Regulation Networks of Rapeseed (Brassica napus L.) Infected with Sclerotinia sclerotiorum
Cited by: 9
Author(s): Jinqi Ma, Wen Xu, Fei Xu, Lin Ai, Wei Sun, Huanhuan Jiang, Kun Lu, Jiana Li, Lijuan Wei
Software Mentions: 2
Published: about 6 years ago

10.1128/mSphere.00248-19

High-Throughput Sequence Analysis of Peripheral T-Cell Lymphomas Indicates Subtype-Specific Viral Gene Expression Patterns and Immune Cell Microenvironments
Cited by: 12
Author(s): Hani Nakhoul, Zhen Lin, Xia Wang, Claire Roberts, Yan Dong, Erik K. Flemington
Software Mentions: 2
Published: almost 7 years ago

10.1128/mSphere.00545-19

Rapid Bladder Interleukin-10 Synthesis in Response to Uropathogenic Escherichia coli Is Part of a Defense Strategy Triggered by the Major Bacterial Flagellar Filament FliC and Contingent on TLR5
Cited by: 19
Author(s): Dev Raj Acharya, Matthew J. Sullivan, Benjamin L. Duell, Kelvin G. K. Goh, Lahiru Katupitiya, Dean Gosling, Michelle N. Chamoun, Asha Kakkanat, Debasish Chattopadhyay, Michael R. Crowley, David K. Crossman, Mark A. Schembri, Glen C. Ulett
Software Mentions: 2
Published: over 6 years ago

10.1186/s12951-018-0439-x

Tri-mannose grafting of chitosan nanocarriers remodels the macrophage response to bacterial infection
Cited by: 15
Author(s): Juan Manuel Coya, Laura De Matteis, Alexandre Giraud-Gatineau, Anne Biton, Inés Serrano‐Sevilla, Anne Danckært, Marie‐Agnès Dillies, Brigitte Gicquel, Jesús M. de la Fuente, Ludovic Tailleux
Software Mentions: 2
Published: over 7 years ago

10.1152/ajpheart.00036.2021

Racial and socioeconomic disparity associates with differences in cardiac DNA methylation among men with end-stage heart failure
Cited by: 14
Author(s): Mark E Pepin, Chae-Myeong Ha, Luke Potter, Sayan Bakshi, Joseph Barchue, Ayman Asaad, Steven M. Pogwizd, Salpy V. Pamboukian, Bertha Hidalgo, Selwyn M. Vickers, Adam R. Wende
Software Mentions: 2
Published: about 5 years ago

10.3390/ijms22137164

Transcriptional Modulation of the Hippo Signaling Pathway by Drugs Used to Treat Bipolar Disorder and Schizophrenia
Cited by: 9
Author(s): Bruna Panizzutti, Chiara C. Bortolasci, Briana Spolding, Srisaiyini Kidnapillai, Timothy Connor, Mark F. Richardson, Trang T. T. Truong, Zoe Liu, Gerwyn Morris, Laura J. Gray, Jee Hyun Kim, Olivia Dean, Michael Berk, Ken Walder
Software Mentions: 2
Published: about 5 years ago

10.1128/mSphere.00105-21

Cellular Management of Zinc in Group B Streptococcus Supports Bacterial Resistance against Metal Intoxication and Promotes Disseminated Infection
Cited by: 16
Author(s): Matthew J. Sullivan, Kelvin G. K. Goh, Glen C. Ulett
Software Mentions: 2
Published: about 5 years ago

10.3389/fgene.2021.628041

Effects of Monochromatic Lighting During Incubation and Vaccination on the Splenic Transcriptome Profiles of Chicken
Cited by: 3
Author(s): Mohamed M. Ibrahim, Jill R. Nelson, Gregory S. Archer, Giridhar Athrey
Software Mentions: 2
Published: about 5 years ago