cran: STAR | Projects | Ecosyste.ms: Papers

10.1093/molbev/msaa082

The Drosophila Y Chromosome Affects Heterochromatin Integrity Genome-Wide
Cited by: 42
Author(s): Emily J. Brown, Alison H. Nguyen, Doris Bachtrog
Software Mentions: 2
Published: over 6 years ago

Identification of TIA1 mRNA targets during human neuronal development
Cited by: 6
Author(s): Loryn Byres, Marat Mufteev, Kyoko E. Yuki, Wei Wei, Alina Piekna, Michael D. Wilson, Deivid C. Rodrigues, James Ellis
Software Mentions: 2
Published: almost 5 years ago

10.1186/s13041-019-0479-7

The leukodystrophy mutation Polr3b R103H causes homozygote mouse embryonic lethality and impairs RNA polymerase III biogenesis
Cited by: 23
Author(s): Karine Choquet, Maxime Pinard, Sharon Yang, Robyn D. Moir, Christian Poitras, Marie Josée Dicaire, Nicolas Sgarioto, Roxanne Larivière, Claudia L. Kleinman, Ian M. Willis, Marie Soleil Gauthier, Benoit Coulombe, Bernard Brais
Software Mentions: 2
Published: about 7 years ago

10.1186/s13041-018-0376-5

RNAseq analysis of hippocampal microglia after kainic acid-induced seizures
Cited by: 35
Author(s): Dale B. Bosco, Jiaying Zheng, Zhiyan Xu, Jinrong Peng, Ukpong B. Eyo, Ke Tang, Cheng Yan, Jun Huang, Lijie Feng, Guoying Wu, Jason R. Richardson, Hui Wang, Long Wu
Software Mentions: 2
Published: about 8 years ago

10.1186/s12943-019-1105-0

LncRNA LINRIS stabilizes IGF2BP2 and promotes the aerobic glycolysis in colorectal cancer
Cited by: 285
Author(s): Yun Wang, Jia Liu, Qi Wu, Ying Jin, De Shen Wang, Yan Xing Chen, Jia Liu, Xiao-Jing Luo, Meng Qi, Heng Ying Pu, Ying Nan Wang, Pei Hu, Zexian Liu, Zhao Lei Zeng, Qi Zhao, Rong Deng, Xiao Feng Zhu, Huai-Qiang Ju, Rui‐Hua Xu
Software Mentions: 2
Published: over 6 years ago

10.1186/s12943-021-01366-y

Novel induction of CD40 expression by tumor cells with RAS/RAF/PI3K pathway inhibition augments response to checkpoint blockade
Cited by: 18
Author(s): Chi Yan, Nabil Saleh, Jinming Yang, Caroline A. Nebhan, Anna E. Vilgelm, E. Premkumar Reddy, Joseph T. Roland, Douglas B. Johnson, Sheau-Chiann Chen, Rebecca L. Shattuck-Brandt, Gregory D. Ayers, Ann Richmond
Software Mentions: 2
Published: about 5 years ago

10.1186/s12943-018-0932-8

RNA-Seq profiling of circular RNAs in human colorectal Cancer liver metastasis and the potential biomarkers
Cited by: 130
Author(s): Hanchen Xu, Chunyan Wang, Haiyan Song, Yangxian Xu, Guang Ji
Software Mentions: 2
Published: over 7 years ago

10.1016/j.molcel.2020.10.005

Activation of Clustered IFNγ Target Genes Drives Cohesin-Controlled Transcriptional Memory
Cited by: 27
Author(s): Wojciech Siwek, Sahar S. H. Tehrani, João F. Mata, Lars Jansen
Software Mentions: 2
Published: over 5 years ago

10.1016/j.molcel.2019.07.037

Elongation Factor TFIIS Prevents Transcription Stress and R-Loop Accumulation to Maintain Genome Stability
Cited by: 71
Author(s): Diana Zatreanu, Zhong Chao Han, Richard Mitter, Emanuela Tumini, Hannah Williams, Lea H. Gregersen, A. Barbara Dirac-Svejstrup, Stefania Roma, Aengus Stewart, Andrés Aguilera, Jesper Q. Svejstrup
Software Mentions: 2
Published: almost 7 years ago

10.1016/j.molcel.2021.02.021

Structural basis for conformational equilibrium of the catalytic spliceosome
Cited by: 21
Author(s): Max E. Wilkinson, Sebastian M. Fica, Wojciech P. Galej, Kiyoshi Nagai
Software Mentions: 2
Published: over 5 years ago

10.1016/j.mce.2021.111220

AKR1C2 and AKR1C3 expression in adipose tissue: Association with body fat distribution and regulatory variants
Cited by: 9
Author(s): Giada Ostinelli, Jinchu Vijay, Marie‐Claude Vohl, Elin Grundberg, André Tchernof
Software Mentions: 2
Published: about 5 years ago

10.3390/molecules26102836

The RNA-Binding Protein HuD Regulates Alternative Splicing and Alternative Polyadenylation in the Mouse Neocortex
Cited by: 9
Author(s): Rebecca M Sena, Jeffery L. Twiss, Amy S. Gardiner, Michela Dell’Orco, David N. Linsenbardt, Nora I. Perrone‐Bizzozero
Software Mentions: 2
Published: about 5 years ago

10.1016/j.ymgmr.2019.100531

Effectiveness of integrated interpretation of exome and corresponding transcriptome data for detecting splicing variants of genes associated with autosomal recessive disorders
Cited by: 9
Author(s): Mamiko Yamada, Hisato Suzuki, Yuichi Shiraishi, Kenjiro Kosaki
Software Mentions: 2
Published: over 6 years ago

10.1186/s10020-021-00370-8

MicroRNA regulation of the proliferation and apoptosis of Leydig cells in diabetes
Cited by: 11
Author(s): Li Hu, Shaochai Wei, Yuqi Wu, Shulin Li, Ping Zhu, Xiangwei Wang
Software Mentions: 2
Published: almost 5 years ago

10.1186/s10020-021-00362-8

An mRNA assay system demonstrates proteasomal-specific degradation contributes to cardiomyopathic phospholamban null mutation
Cited by: 1
Author(s): Eduarde Rohner, Nevin Witman, Jesper Sohlmér, Erwin De Genst, William E. Louch, Makoto Sahara, Kenneth R. Chien
Software Mentions: 2
Published: almost 5 years ago

10.1016/j.molmet.2020.101094

Ozone-induced fetal growth restriction in rats is associated with sexually dimorphic placental and fetal metabolic adaptation
Cited by: 9
Author(s): Colette N. Miller, Janice A. Dye, Andres R. Henriquez, Erica Stewart, Katelyn S. Lavrich, Gleta Carswell, Hongzu Ren, Danielle L. Freeborn, Samantha J. Snow, Mette C. Schladweiler, Judy H. Richards, Prasada Rao S. Kodavanti, Anna Fisher, Brian N. Chorley, Urmila P. Kodavanti
Software Mentions: 2
Published: over 5 years ago

10.1016/j.molmet.2019.11.004

The core clock gene, Bmal1, and its downstream target, the SNARE regulatory protein secretagogin, are necessary for circadian secretion of glucagon-like peptide-1
Cited by: 32
Author(s): Andrew D. Biancolin, Alexandre Martchenko, Emilia Mitova, Patrick Gurges, Everan Michalchyshyn, J. P. Chalmers, Alessandro Doria, Josyf C. Mychaleckyj, Alice E. Adriaenssens, Frank Reimann, Fiona M. Gribble, Manuel Gil‐Lozano, Brian Cox, Patricia L. Brubaker
Software Mentions: 2
Published: over 6 years ago

10.1016/j.molmet.2020.101026

STAT5 is required for lipid breakdown and beta-adrenergic responsiveness of brown adipose tissue
Cited by: 15
Author(s): Doris Kaltenecker, Katrin Spirk, Frank Ruge, Florian Grebien, Marco Herling, Anne Rupprecht, Lukas Kenner, Elena E. Pohl, Kristina M. Mueller, Richard Moriggl
Software Mentions: 2
Published: almost 6 years ago

10.1007/s12035-018-1368-2

Bezafibrate Upregulates Mitochondrial Biogenesis and Influence Neural Differentiation of Human-Induced Pluripotent Stem Cells
Cited by: 23
Author(s): Justyna Augustyniak, Jacek Lenart, Paweł Gaj, Monika Kolanowska, Krystian Jażdżewski, Piotr P. Stępień, Leonora Bużańska
Software Mentions: 2
Published: over 7 years ago

10.1186/s13024-017-0210-z

Prevention of C5aR1 signaling delays microglial inflammatory polarization, favors clearance pathways and suppresses cognitive loss
Cited by: 58
Author(s): Michael Hernandez, Shan Jiang, Tracy Cole, Shu Hui Chu, María Isabel Fonseca, Melody J. Fang, Lindsay A. Hohsfield, M.D. Martínez del Valle Torres, Kim N. Green, Rick A. Wetsel, A Mortazavi, Andrea J. Tenner
Software Mentions: 2
Published: almost 9 years ago

10.1186/s13024-020-00387-3

BIN1 protein isoforms are differentially expressed in astrocytes, neurons, and microglia: neuronal and astrocyte BIN1 are implicated in tau pathology
Cited by: 24
Author(s): Mariko Taga, Vladislav Petyuk, Charles C. White, Graham Marsh, Yiyi Ma, Hans‐Ulrich Klein, Sarah M. Connor, Alexandra Kroshilina, Christina J. Yung, Anthony Khairallah, Marta Olah, Julie A. Schneider, Kyle W. Karhohs, Anne E. Carpenter, Richard M. Ransohoff, David A. Bennett, Andrea Crotti, Elizabeth M. Bradshaw, Philip L. De Jager
Software Mentions: 2
Published: almost 6 years ago

10.1186/s13024-019-0319-3

TREM2 brain transcript-specific studies in AD and TREM2 mutation carriers
Cited by: 56
Author(s): Jorge L. Del‐Aguila, Bruno A. Benitez, Zeran Li, Umber Dube, Kathie A. Mihindukulasuriya, John Budde, Fabiana H.G. Farias, María Victoria Fernández, Laura Ibáñez, Shan Jiang, Richard J. Perrin, Nigel J. Cairns, John C. Morris, Oscar Harari, Carlos Cruchaga
Software Mentions: 2
Published: about 7 years ago

10.1002/mnfr.201900999

Anthocyanin‐Biofortified Colored Wheat Prevents High Fat Diet–Induced Alterations in Mice: Nutrigenomics Studies
Cited by: 29
Author(s): Saloni Sharma, Pragyanshu Khare, Ashish Kumar, Venkatesh Chunduri, Aman Kumar, Payal Kapoor, Priyanka Mangal, Kanthi Kiran Kondepudi, Mahendra Bishnoi, Monika Garg
Software Mentions: 2
Published: about 6 years ago

10.1002/1878-0261.12649

Prolyl 4‐hydroxylase subunit alpha 1 (P4HA1) is a biomarker of poor prognosis in primary melanomas, and its depletion inhibits melanoma cell invasion and disrupts tumor blood vessel walls
Cited by: 11
Author(s): Johanna Eriksson, Vadim Le Joncour, Tiina Jahkola, Susanna Juteau, Pirjo Laakkonen, Olli Saksela, Erkki Hölttä
Software Mentions: 2
Published: over 6 years ago

10.1038/s41380-019-0563-5

Discovery of autism/intellectual disability somatic mutations in Alzheimer's brains: mutated ADNP cytoskeletal impairments and repair as a case study
Cited by: 55
Author(s): Yanina Ivashko-Pachima, Adva Hadar, Iris Grigg, Vlasta Korenková, Oxana Kapitansky, Gidon Karmon, Michael Gershovits, CL Sayas, R. Frank Kooy, Johannes Attems, David Genevieve, Illana Gozes
Software Mentions: 2
Published: over 6 years ago

10.1038/s41380-020-00994-y

Serotonin receptor 4 in the hippocampus modulates mood and anxiety
Cited by: 29
Author(s): Remzi Karayol, Lucian Medrihan, Jennifer L. Warner-Schmidt, Benjamin W. Fait, Meghana N. Rao, E Hölzner, Paul Greengard, Nathaniel Heintz, Eric F. Schmidt
Software Mentions: 2
Published: over 5 years ago

10.15252/msb.20209864

Precise transcriptional control of cellular quiescence by BRAVO/WOX5 complex in <i>Arabidopsis</i> roots
Cited by: 8
Author(s): Isabel Betegón‐Putze, Josep Mercadal, Nadja Bosch, Ainoa Planas-Riverola, María Mar Marquès-Bueno, Josep Vilarrasa-Blasi, David Frigola, Rebecca C. Burkart, Consuelo Martı́nez, Ana Conesa, Rosangela Sozzani, Yvonne Stahl, Salomé Prat, Marta Ibañes, Ana I. Caño‐Delgado
Software Mentions: 2
Published: about 5 years ago

10.15252/msb.20188266

Single‐cell <scp>mRNA</scp> profiling reveals the hierarchical response of mi <scp>RNA</scp> targets to mi <scp>RNA</scp> induction
Cited by: 20
Author(s): Andrzej J. Rzepiela, Souvik Ghosh, Jérémie Breda, Arnau Viña-Vilaseca, Afzal Pasha Syed, Andreas J. Gruber, Katja Eschbach, Christian Beisel, Erik van Nimwegen, Mihaela Zavolan
Software Mentions: 2
Published: almost 8 years ago

10.1038/s41385-019-0231-8

NK cell recruitment limits tissue damage during an enteric helminth infection
Cited by: 20
Author(s): Maria E. Gentile, Yue Li, Amicha Robertson, Kathleen Shah, Ghislaine Fontés, Eva Kaufmann, Barbara Polese, Nargis Khan, Marc Parisien, Hans Markus Münter, Judith N. Mandl, Luda Diatchenko, Maziar Divangahi, Irah L. King
Software Mentions: 2
Published: over 6 years ago

10.3390/plants10020304

Preferential Ribosome Loading on the Stress-Upregulated mRNA Pool Shapes the Selective Translation under Stress Conditions
Cited by: 5
Author(s): Yan Chen, Min Liu, Zhicheng Dong
Software Mentions: 2
Published: over 5 years ago

10.3390/plants9060674

Regulatory Potential of bHLH-Type Transcription Factors on the Road to Rubber Biosynthesis in Hevea brasiliensis
Cited by: 3
Author(s): Tomoko Yamaguchi, Y. Kurihara, Yuko Makita, Emiko Okubo-Kurihara, Ami Kageyama, Emi Osada, Setsuko Shimada, Hiroko Tsuchida, Hiroaki Shimada, Minami Matsui
Software Mentions: 2
Published: about 6 years ago

10.3390/plants9111548

RNA-Seq Time Series of Vitis vinifera Bud Development Reveals Correlation of Expression Patterns with the Local Temperature Profile
Cited by: 6
Author(s): Boas Pucker, Anna Schwandner, Sarah Becker, Ludger Hausmann, Prisca Viehöver, Reinhard Töpfer, Bernd Weißhaar, Daniela Holtgräwe
Software Mentions: 2
Published: over 5 years ago

10.1371/journal.pbio.1002435

How Many Parameters Does It Take to Describe Disease Tolerance?
Cited by: 72
Author(s): Alan K. Louie, Kyung Han Song, Alejandra Guzmán Hotson, Ann T. Tate, David Schneider
Software Mentions: 2
Published: about 10 years ago

10.1371/journal.pbio.3000582

Back-spliced RNA from retrotransposon binds to centromere and regulates centromeric chromatin loops in maize
Cited by: 57
Author(s): Yalin Liu, Handong Su, Jing Zhang, Yang Liu, Chao Feng, Fangpu Han
Software Mentions: 2
Published: over 6 years ago

10.1371/journal.pbio.1002379

Phylogenomics Reveals Three Sources of Adaptive Variation during a Rapid Radiation
Cited by: 335
Author(s): James B. Pease, David C. Haak, Matthew W. Hahn, Leonie C. Moyle
Software Mentions: 2
Published: over 10 years ago

10.1371/journal.pbio.3000498

Dissecting the dynamics of signaling events in the BMP, WNT, and NODAL cascade during self-organized fate patterning in human gastruloids
Cited by: 116
Author(s): Sapna Chhabra, Lizhong Liu, Ryan Goh, Xiangyu Kong, Aryeh Warmflash
Software Mentions: 2
Published: over 6 years ago

10.1371/journal.pbio.3000324

DPPA2/4 and SUMO E3 ligase PIAS4 opposingly regulate zygotic transcriptional program
Cited by: 71
Author(s): Yao-Long Yan, Chao Zhang, Jun Hao, Xuelian Wang, Ming Jia, Mi Li, Jie Na, Xinli Hu, Yangming Wang
Software Mentions: 2
Published: about 7 years ago

10.1371/journal.pbio.2005903

Lso2 is a conserved ribosome-bound protein required for translational recovery in yeast
Cited by: 27
Author(s): Yinuo J. Wang, Pavanapuresan P. Vaidyanathan, María F. Rojas-Durán, Namrata D. Udeshi, Kristen M. Bartoli, Steven A. Carr, Wendy V. Gilbert
Software Mentions: 2
Published: almost 8 years ago

10.1371/journal.pbio.3000087

Inhibition of Notch signaling rescues cardiovascular development in Kabuki Syndrome
Cited by: 19
Author(s): María de los Ángeles Serrano, Bradley L. Demarest, Tarlynn Tone-Pah-Hote, Martin Tristani‐Firouzi, H. Joseph Yost
Software Mentions: 2
Published: almost 7 years ago

10.1371/journal.pbio.3001385

The induction of preterm labor in rhesus macaques is determined by the strength of immune response to intrauterine infection
Cited by: 11
Author(s): Monica Cappelletti, Pietro Presicce, Feiyang Ma, Paranthaman Senthamaraikannan, Lisa Miller, Matteo Pellegrini, Myung Shin Sim, Alan H. Jobe, Senad Divanovic, Sing Sing Way, Claire Chougnet, Suhas G. Kallapur
Software Mentions: 2
Published: almost 5 years ago

10.1371/journal.pbio.3000245

Simple nutrients bypass the requirement for HLH-30 in coupling lysosomal nutrient sensing to survival
Cited by: 15
Author(s): John T. Murphy, Haiyan Liu, Xiucui Ma, Alexander Shaver, Brian M. Egan, Clara Oh, Alexander Boyko, Travis Mazer, Samuel Ang, Rohan Khopkar, Ali Javaheri, Sandeep Kumar, Xuntian Jiang, Daniel S. Ory, Kartik Mani, Scot J. Matkovich, Kerry Kornfeld, Abhinav Diwan
Software Mentions: 2
Published: about 7 years ago

10.1371/journal.pcbi.1008173

Capturing cell type-specific chromatin compartment patterns by applying topic modeling to single-cell Hi-C data
Cited by: 53
Author(s): Hyeon Jin Kim, Galip Gürkan Yardımcı, Giancarlo Bonora, Vijay Ramani, Jie Liu, Ruolan Qiu, Choli Lee, Jennifer Hesson, Carol B. Ware, Jay Shendure, Zhijun Duan
Software Mentions: 2
Published: almost 6 years ago

10.1371/journal.pcbi.1007278

Cooperative adaptation to therapy (CAT) confers resistance in heterogeneous non-small cell lung cancer
Cited by: 22
Author(s): Morgan Craig, Kamran Kaveh, Alec N. Woosley, Andrew S. Brown, David Goldman, Elliot O. Eton, Ravindra Mehta, Andrew Dhawan, Kazuya Arai, Mahbuba Rahman, Sidi Chen, Martin A. Nowak, Aaron Goldman
Software Mentions: 2
Published: almost 7 years ago

10.1371/journal.pcbi.1005766

C-reactive protein upregulates the whole blood expression of CD59 - an integrative analysis
Cited by: 41
Author(s): Kaido Lepik, Tarmo Annilo, Viktorija Kukuškina, Kai Kisand, Zoltán Kutalik, Pärt Peterson, Hedi Peterson
Software Mentions: 2
Published: almost 9 years ago

10.1371/journal.pcbi.1007925

Detecting differential alternative splicing events in scRNA-seq with or without Unique Molecular Identifiers
Cited by: 19
Author(s): Yu Hu, Kai Wang, Mingyao Li
Software Mentions: 2
Published: about 6 years ago

10.1371/journal.pgen.1006635

Retrotransposon activation contributes to neurodegeneration in a Drosophila TDP-43 model of ALS
Cited by: 146
Author(s): Lisa Krug, Nabanita Chatterjee, Rebeca Borges-Monroy, Stephen Hearn, Wen‐Wei Liao, Kathleen M. Morrill, Lisa Prazak, Nikolay V. Rozhkov, Delphine Theodorou, Molly Gale Hammell, Josh Dubnau
Software Mentions: 2
Published: over 9 years ago

10.1371/journal.pgen.1007932

Lysine 27 of replication-independent histone H3.3 is required for Polycomb target gene silencing but not for gene activation
Cited by: 34
Author(s): Mary Leatham-Jensen, Christopher M. Uyehara, Brian D. Strahl, A. Gregory Matera, Robert J. Duronio, Daniel J. McKay
Software Mentions: 2
Published: over 7 years ago

10.1371/journal.pgen.1008916

Trappc9 deficiency causes parent-of-origin dependent microcephaly and obesity
Cited by: 17
Author(s): Zhengzheng S. Liang, Irène Cimino, Binnaz Yalcin, Narayanan Raghupathy, Valerie E. Vancollie, Ximena Ibarra-Soria, Helen V. Firth, Debra Rimmington, I. Sadaf Farooqi, Christopher J. Lelliott, Steven C. Munger, Stephen O’Rahilly, Anne C. Ferguson‐Smith, Anthony P. Coll, Darren W. Logan
Software Mentions: 2
Published: almost 6 years ago

10.1371/journal.pgen.1009642

Repeated evolution of circadian clock dysregulation in cavefish populations
Cited by: 22
Author(s): Katya L. Mack, James B. Jaggard, Jenna Persons, Emma Y. Roback, Courtney N. Passow, Bethany A. Stanhope, Estephany Ferrufino, Dai Tsuchiya, Sarah E. Smith, Brian D. Slaughter, Johanna E. Kowalko, Nicolas Rohner, Alex C. Keene, Suzanne E. McGaugh
Software Mentions: 2
Published: about 5 years ago

10.1371/journal.pgen.1009284

A rare coding mutation in the MAST2 gene causes venous thrombosis in a French family with unexplained thrombophilia: The Breizh MAST2 Arg89Gln variant
Cited by: 4
Author(s): Pierre‐Emmanuel Morange, Franck Peiretti, Lénaïck Gourhant, Carole Proust, Omar Soukarieh, Anne-Sophie Pulcrano-Nicolas, Ganapathi-Varma Saripella, Luca Stefanucci, Romaric Lacroix, Manal Ibrahim‐Kosta, Catherine A. Lemarié, Mattia Frontini, Marie‐Christine Alessi, David‐Alexandre Trégouët, Francis Couturaud
Software Mentions: 2
Published: over 5 years ago

10.1371/journal.pgen.1008650

GLP-1 Notch—LAG-1 CSL control of the germline stem cell fate is mediated by transcriptional targets lst-1 and sygl-1
Cited by: 31
Author(s): Jian Chen, Ariz Mohammad, Nanette J. Pazdernik, Huiyan Huang, Elizabeth Bowman, Eric Tycksen, Tim Schedl
Software Mentions: 2
Published: over 6 years ago

10.1371/journal.pgen.1007665

Hrg1 promotes heme-iron recycling during hemolysis in the zebrafish kidney
Cited by: 18
Author(s): Jianbing Zhang, Ian G. Chambers, Sijung Yun, John D. Phillips, Michael Krause, Iqbal Hamza
Software Mentions: 2
Published: almost 8 years ago

10.1371/journal.pgen.1008272

Effector gene reshuffling involves dispensable mini-chromosomes in the wheat blast fungus
Cited by: 91
Author(s): Zhao Peng, Ely Oliveira-Garcia, Guifang Lin, Ying Hu, Matthew J. Dalby, Pierre Migeon, Haibao Tang, Mark L. Farman, David E. Cook, Frank F. White, Barbara Valent, Sanzhen Liu
Software Mentions: 2
Published: almost 7 years ago

10.1371/journal.pgen.1008091

Expression estimation and eQTL mapping for HLA genes with a personalized pipeline
Cited by: 57
Author(s): Vitor R. C. Aguiar, Jônatas César, Olivier Delaneau, Emmanouil T. Dermitzakis, Diogo Meyer
Software Mentions: 2
Published: about 7 years ago

10.1371/journal.pgen.1007842

RNA-on-X 1 and 2 in Drosophila melanogaster fulfill separate functions in dosage compensation
Cited by: 20
Author(s): Maria Kim, Marie-Line Faucillion, Jonas Larsson
Software Mentions: 2
Published: over 7 years ago

10.1371/journal.pgen.1008581

Makorin 1 controls embryonic patterning by alleviating Bruno1-mediated repression of oskar translation
Cited by: 11
Author(s): Annabelle Dold, Hong Han, Niankun Liu, Andrea Hildebrandt, Mirko Brüggemann, Cornelia Rücklé, Heike Hänel, Anke Busch, Petra Beli, Kathi Zarnack, Julian König, Jean‐Yves Roignant, Paul Lasko
Software Mentions: 2
Published: over 6 years ago

10.1371/journal.pgen.1006552

SBDS-Deficient Cells Have an Altered Homeostatic Equilibrium due to Translational Inefficiency Which Explains their Reduced Fitness and Provides a Logical Framework for Intervention
Cited by: 31
Author(s): Piera Calamita, Annarita Miluzio, Andrew F. Russo, Elisa Pesce, Sara Ricciardi, Farhat L. Khanim, Cristina Cheroni, Roberta Alfieri, Marilena Mancino, Chiara Gorrini, Grazisa Rossetti, Ilaria Peluso, Massimiliano Pagani, Diego L. Medina, Johanna M. Rommens, Stefano Biffo
Software Mentions: 2
Published: over 9 years ago

10.1371/journal.pgen.1008676

Germ cell-intrinsic effects of sex chromosomes on early oocyte differentiation in mice
Cited by: 17
Author(s): Norio Hamada, Nobuhiko Hamazaki, So Shimamoto, Orie Hikabe, Go Nagamatsu, Yuki Takada, Kiyoko Kato, Kozaburo Hayashi
Software Mentions: 2
Published: over 6 years ago

10.1371/journal.pone.0225186

Mineral absorption is an enriched pathway in a brain region of restless legs syndrome patients with reduced MEIS1 expression
Cited by: 9
Author(s): Faezeh Sarayloo, Alexandre Dionne‐Laporte, Hélène Catoire, Daniel Rochefort, Gabrielle Houle, Jay P. Ross, Fulya Akçimen, Rachel De Barros Oliveira, Gustavo Turecki, Patrick A. Dion, Guy A. Rouleau
Software Mentions: 2
Published: over 6 years ago

10.1371/journal.pone.0211128

Tolerance and dose-response assessment of subchronic dietary ethoxyquin exposure in Atlantic salmon (Salmo salar L.)
Cited by: 6
Author(s): A. Bernhard, Josef Daniel Rasinger, Mónica B. Betancor, M. J. Caballero, Marc H.G. Berntssen, Anne Katrine Lundebye, Robin Ørnsrud
Software Mentions: 2
Published: over 7 years ago

10.1371/journal.pone.0218133

Sex differences in sympathetic gene expression and cardiac neurochemistry in Wistar Kyoto rats
Cited by: 6
Author(s): Richard Bayles, Joanne Tran, Antoinette Olivas, William R. Woodward, Suzanne S. Fei, Lina Gao, Beth A. Habecker
Software Mentions: 2
Published: about 7 years ago

10.1371/journal.pone.0239804

Nuclear response to divergent mitochondrial DNA genotypes modulates the interferon immune response
Cited by: 0
Author(s): M Isabel G Lopez Sanchez, Mark Ziemann, Annabell Bachem, Rahul Makam, Jonathan G Crowston, Carl A. Pinkert, Matthew McKenzie, Sammy Bedoui, Ian A. Trounce
Software Mentions: 2
Published: almost 6 years ago

10.1371/journal.pone.0167698

PeTMbase: A Database of Plant Endogenous Target Mimics (eTMs)
Cited by: 52
Author(s): Gökhan Karakülah, Kuaybe Yücebilgili Kurtoğlu, Turgay Ünver
Software Mentions: 2
Published: over 9 years ago

10.1371/journal.pone.0202305

Bioinformatic characterisation of the effector repertoire of the strawberry pathogen Phytophthora cactorum
Cited by: 30
Author(s): Andrew D. Armitage, Erik Lysøe, Charlotte F. Nellist, Laura Lewis, Liliana Cano, Richard J. Harrison, May Bente Brurberg
Software Mentions: 2
Published: almost 8 years ago

10.1371/journal.pone.0176768

Induction of endogenous retroelements as a potential mechanism for mouse-specific drug-induced carcinogenicity
Cited by: 3
Author(s): Timothy Coskran, Zhijie Jiang, James E. Klaunig, Dixie L. Mager, Leslie Obert, Andrew W. Robertson, Nicholas F. Tsinoremas, Zemin Wang, Mark Gosink
Software Mentions: 2
Published: about 9 years ago

10.1371/journal.pone.0244407

A science impact framework to measure impact beyond journal metrics
Cited by: 7
Author(s): Mary D. Ari, John K. Iskander, John Jairo Araujo, Christine Casey, John J. Kools, Bin Chen, Robert Swain, Miriam Kelly, Tanja Popović
Software Mentions: 2
Published: over 5 years ago

10.1371/journal.pone.0171435

A novel RNA sequencing data analysis method for cell line authentication
Cited by: 24
Author(s): Erik Fasterius, Cinzia Raso, Susan Kennedy, Nora Rauch, Per Lundin, Walter Kölch, Mathias Uhlén, Cristina Al‐Khalili Szigyarto
Software Mentions: 2
Published: over 9 years ago

10.1371/journal.pone.0223980

Dysregulation of macrophage development and phenotype in diabetic human macrophages can be rescued by Hoxa3 protein transduction
Cited by: 17
Author(s): Salma Saleh Alrdahe, Hadeel Al Sadoun, Tanja Torbica, Edward A. McKenzie, Frank L. Bowling, Andrew J.M. Boulton, Kimberly A. Mace
Software Mentions: 2
Published: over 6 years ago

10.1371/journal.pone.0209694

Macrophages attenuate the transcription of CYP1A1 in breast tumor cells and enhance their proliferation
Cited by: 6
Author(s): Sofia Winslow, Anica Scholz, Peter Rappl, Thilo F. Brauß, Claudia Mertens, Michaela Jung, Andreas Weigert, Bernhard Brüne, Tobias Schmid
Software Mentions: 2
Published: over 7 years ago

10.1371/journal.pone.0175367

Nicotinic alpha 7 receptor expression and modulation of the lung epithelial response to lipopolysaccharide
Cited by: 26
Author(s): Lorise C. Gahring, Elizabeth J. Myers, Diane M. Dunn, Robert B. Weiss, Scott W. Rogers
Software Mentions: 2
Published: over 9 years ago

10.1371/journal.pone.0146114

Influence of Familial Renal Glycosuria Due to Mutations in the SLC5A2 Gene on Changes in Glucose Tolerance over Time
Cited by: 23
Author(s): Emilia Ottosson-Laakso, Tiinamaija Tuomi, Björn Forsén, Monika Gullström, Per‐Henrik Groop, Leif Groop, Petter Vikman
Software Mentions: 2
Published: over 10 years ago

10.1371/journal.pone.0201822

RNA variant identification discrepancy among splice-aware alignment algorithms
Cited by: 7
Author(s): Ji Hyung Hong, Yoon Ho Ko, Keunsoo Kang
Software Mentions: 2
Published: almost 8 years ago

10.1371/journal.pone.0108095

High-Resolution Transcriptome Analysis with Long-Read RNA Sequencing
Cited by: 42
Author(s): Hyunghoon Cho, Joe R. Davis, Xin Li, Kevin S. Smith, Alexis Battle, Stephen B. Montgomery
Software Mentions: 2
Published: almost 12 years ago

10.1371/journal.pone.0191033

Epigenome comparisons reveal linkage between gene expression and postnatal remodeling of chromatin domain topology
Cited by: 0
Author(s): Bruce H. Howard, Tazuko H. Hirai, Valya R. Russanova
Software Mentions: 2
Published: over 8 years ago

10.1371/journal.pone.0204967

Loss of murine Paneth cell function alters the immature intestinal microbiome and mimics changes seen in neonatal necrotizing enterocolitis
Cited by: 48
Author(s): Shiloh R. Lueschow, Jessica E. Stumphy, Huiyu Gong, Stacy L. Kern, Timothy G. Elgin, Mark A. Underwood, Karen M. Kalanetra, David A. Mills, Melissa H. Wong, David K. Meyerholz, Misty Good, Steven J. McElroy
Software Mentions: 2
Published: almost 8 years ago

10.1371/journal.pone.0190086

MiR-34a regulates the invasive capacity of canine osteosarcoma cell lines
Cited by: 25
Author(s): Carmen López, Peter Y. Yu, Xiaoli Zhang, Ayse Selen Yilmaz, Cheryl A. London, Joelle M. Fenger
Software Mentions: 2
Published: over 8 years ago

10.1371/journal.pone.0227522

Expression and function of voltage gated proton channels (Hv1) in MDA-MB-231 cells
Cited by: 12
Author(s): Dan J. Bare, Vladimir V. Cherny, Thomas E. DeCoursey, Abde M. Abukhdeir, Deri Morgan
Software Mentions: 2
Published: about 6 years ago

10.1371/journal.pone.0177708

The Agassiz’s desert tortoise genome provides a resource for the conservation of a threatened species
Cited by: 31
Author(s): Marc Tollis, Dale F. DeNardo, John A. Cornelius, Greer A. Dolby, Taylor Edwards, Brian T. Henen, Alice E. Karl, Robert W. Murphy
Software Mentions: 2
Published: about 9 years ago

10.1371/journal.pone.0233789

Sevoflurane depletes macrophages from the melanoma microenvironment
Cited by: 7
Author(s): Isabella Sztwiertnia, Judith Schenz, Katharina Bomans, Dominik Schaack, Johanna Ohnesorge, Sandra Tamulyte, Markus Weigand, Florian Uhle
Software Mentions: 2
Published: about 6 years ago

10.1371/journal.pone.0197123

Anti-angiogenic VEGFAxxxb transcripts are not expressed in the medio-basal hypothalamus of the seasonal sheep
Cited by: 10
Author(s): Didier Lomet, Benoît Piégu, Shona H. Wood, Hugues Dardente
Software Mentions: 2
Published: about 8 years ago

10.1371/journal.pone.0206379

De novo transcriptome based on next-generation sequencing reveals candidate genes with sex-specific expression in Arapaima gigas (Schinz, 1822), an ancient Amazonian freshwater fish
Cited by: 12
Author(s): Luciana Watanabe, Fátima Gomes, João L.S.G. Vianez, Márcio Roberto Teixeira Nunes, Jedson Ferreira Cardoso, Clayton Pereira da Silva de Lima, Horácio Schneider, Iracilda Sampaio
Software Mentions: 2
Published: over 7 years ago

10.1371/journal.pone.0100883

A GPBAR1 (TGR5) Small Molecule Agonist Shows Specific Inhibitory Effects on Myeloid Cell Activation In Vitro and Reduces Experimental Autoimmune Encephalitis (EAE) In Vivo
Cited by: 51
Author(s): Nuruddeen D. Lewis, Lori Patnaude, Josephine Pelletier, Donald Souza, Susan Lukas, Jim King, Jonathan D. Hill, Dimitria E. Stefanopoulos, Kelli R. Ryan, Sudha Desai, Donna Skow, Stefan G. Kauschke, Andre Broermann, Daniel Kuzmich, Christian Harcken, Eugene R. Hickey, Louise K. Modis
Software Mentions: 2
Published: about 12 years ago

10.1371/journal.pone.0182568

Genome-wide identification of autosomal genes with allelic imbalance of chromatin state
Cited by: 7
Author(s): Andrej J. Savol, Peggy I. Wang, Yongho Jeon, David Colognori, E. Yildirim, Stefan F. Pinter, Bernhard Payer, Jeannie T. Lee, Ruslan I. Sadreyev
Software Mentions: 2
Published: almost 9 years ago

10.1371/journal.pone.0136764

Impact of Genomics Platform and Statistical Filtering on Transcriptional Benchmark Doses (BMD) and Multiple Approaches for Selection of Chemical Point of Departure (PoD)
Cited by: 43
Author(s): Anna Francina Webster, Nikolai L. Chepelev, Rémi Gagné, Byron Kuo, Leslie Recio, Andrew Williams, Carole L. Yauk
Software Mentions: 2
Published: almost 11 years ago

10.1371/journal.pone.0176675

Optimized approach for Ion Proton RNA sequencing reveals details of RNA splicing and editing features of the transcriptome
Cited by: 13
Author(s): Roger B. Brown, Nathaniel J. Madrid, Hideaki Suzuki, Scott A. Ness
Software Mentions: 2
Published: about 9 years ago

10.1371/journal.pone.0220101

Enhanced efficacy of sitravatinib in metastatic models of antiangiogenic therapy resistance
Cited by: 20
Author(s): Melissa Dolan, Michalis Mastri, Amanda Tracz, James G. Christensen, Gurkamal S. Chatta, John M.L. Ebos
Software Mentions: 2
Published: almost 7 years ago

10.1371/journal.pone.0054848

A Phylogeny of Birds Based on Over 1,500 Loci Collected by Target Enrichment and High-Throughput Sequencing
Cited by: 290
Author(s): John E. McCormack, Michael Harvey, Brant C. Faircloth, Nicholas G. Crawford, Travis C. Glenn, Robb T. Brumfield
Software Mentions: 2
Published: over 13 years ago

10.1371/journal.pone.0210404

Screening human cell lines for viral infections applying RNA-Seq data analysis
Cited by: 13
Author(s): Cord C. Uphoff, Claudia Pommerenke, Sabine A. Denkmann, Hans G. Drexler
Software Mentions: 2
Published: over 7 years ago

10.1371/journal.pone.0229170

CD20 is dispensable for B-cell receptor signaling but is required for proper actin polymerization, adhesion and migration of malignant B cells
Cited by: 13
Author(s): Veronika Kozlová, Aneta Ledererová, Adriana Ladungová, Helena Peschelová, Pavlína Janovská, Aleksander Ślusarczyk, J Domagała, Pavel Kopcil, Viera Vakulová, Jan Oppelt, Vı́tězslav Bryja, Michael Doubek, Jiřı́ Mayer, Šárka Pospı́šilová, Michal Šmída
Software Mentions: 2
Published: over 6 years ago

10.1371/journal.pone.0195893

A20 regulates canonical wnt-signaling through an interaction with RIPK4
Cited by: 8
Author(s): Brooke N. Nakamura, Alison Glazier, Michael G. Kattah, Bao Duong, Yulin Jia, Daniel Campo, Ling Shao
Software Mentions: 2
Published: about 8 years ago

10.1371/journal.pone.0224835

Metformin strongly affects transcriptome of peripheral blood cells in healthy individuals
Cited by: 19
Author(s): Monta Ustinova, Ivars Silamiķelis, Ineta Kalniņa, Laura Ansone, Vita Rovīte, Ilze Elbere, Ilze Radoviča-Spalviņa, Dāvids Fridmanis, Ekaterina Aladyeva, Ilze Konrāde, Valdis Pīrāgs, Jānis Kloviņš
Software Mentions: 2
Published: over 6 years ago

10.1371/journal.pone.0194485

Expression profiling of disease progression in canine model of Duchenne muscular dystrophy
Cited by: 16
Author(s): Candice Brinkmeyer-Langford, Candice P. Chu, Cynthia Balog-Alvarez, Xue Yu, James J. Cai, Mary B. Nabity, Joe N. Kornegay
Software Mentions: 2
Published: over 8 years ago

10.1371/journal.pone.0171221

PI3Kδ inhibitor idelalisib in combination with BTK inhibitor ONO/GS-4059 in diffuse large B cell lymphoma with acquired resistance to PI3Kδ and BTK inhibitors
Cited by: 43
Author(s): Anella Yahiaoui, Sarah Meadows, Rick Sorensen, Zhi-Hua Cui, Kathleen Keegan, Robert Brockett, Guang Chen, Christophe Quéva, Li Li, Stacey Tannheimer
Software Mentions: 2
Published: over 9 years ago

10.1371/journal.pone.0174575

Halvade-RNA: Parallel variant calling from transcriptomic data using MapReduce
Cited by: 15
Author(s): Dries Decap, Joke Reumers, Charlotte Herzeel, Pascal Costanza, Jan Fostier
Software Mentions: 2
Published: over 9 years ago

10.1371/journal.pone.0249658

Koala cathelicidin PhciCath5 has antimicrobial activity, including against Chlamydia pecorum
Cited by: 5
Author(s): Emma Peel, Yuanyuan Cheng, Julianne T. Djordjevic, Denis O’Meally, Mark S. Thomas, Michael Kuhn, Tania C. Sorrell, Wilhelmina M. Huston, Katherine Belov
Software Mentions: 2
Published: about 5 years ago

10.1371/journal.pone.0255085

Identification of conserved transcriptome features between humans and Drosophila in the aging brain utilizing machine learning on combined data from the NIH Sequence Read Archive
Cited by: 0
Author(s): J. L. Webb, Simon M. Moe, Andrew Bolstad, Elizabeth McNeill
Software Mentions: 2
Published: almost 5 years ago

10.1371/journal.pone.0246615

Deciphering the transcriptomic regulation of heat stress responses in Nothofagus pumilio
Cited by: 4
Author(s): Maximiliano Estravis-Barcalá, Katrin Heer, Paula Marchelli, Birgit Ziegenhagen, María Verónica Arana, Nicolás Bellora
Software Mentions: 2
Published: over 5 years ago

10.3390/cancers13051067

Dive into Single, Seek Out Multiple: Probing Cancer Metastases via Single-Cell Sequencing and Imaging Techniques
Cited by: 3
Author(s): Shang Su, Xiaohong Li
Software Mentions: 2
Published: over 5 years ago

10.3390/cancers12061603

A Novel JAK1 Mutant Breast Implant-Associated Anaplastic Large Cell Lymphoma Patient-Derived Xenograft Fostering Pre-Clinical Discoveries
Cited by: 11
Author(s): Danilo Fiore, Luca Vincenzo Cappelli, Paul Zumbo, Jude M. Phillip, Zhaoqi Liu, Shuhua Cheng, Liron Yoffe, Paola Ghione, Federica Maggio, Ahmet Doğan, Inna Khodos, Elisa de Stanchina, Joseph Casano, Clarisse Kayembe, Wayne Tam, Doron Betel, Robin Foà, Leandro Cerchietti, Raúl Rabadán, Steven M. Horwitz, David M. Weinstock, Giorgio Inghirami
Software Mentions: 2
Published: about 6 years ago

10.3390/cancers11020208

ORAI1 and ORAI3 in Breast Cancer Molecular Subtypes and the Identification of ORAI3 as a Hypoxia Sensitive Gene and a Regulator of Hypoxia Responses
Cited by: 42
Author(s): Iman Azimi, Michael J. G. Milevskiy, Silke B. Chalmers, Kunsala T. D. S. Yapa, Mélanie Robitaille, Christopher Henry, Gregory J. Baillie, Erik W. Thompson, Sarah J. Roberts‐Thomson, Gregory R. Monteith
Software Mentions: 2
Published: over 7 years ago

Projects: cran: STAR

Science Score: 100/100

Bonuses:

Papers Mentioning STAR 5,759