cran: STAR | Projects | Ecosyste.ms: Papers

10.1016/j.molcel.2019.03.010

A Secreted RNA Binding Protein Forms RNA-Stabilizing Granules in the Honeybee Royal Jelly
Cited by: 35
Author(s): Eyal Maori, Isabela Cunha Navarro, Humberto Boncristiani, David J. Seilly, Konrad L. M. Rudolph, Alexandra Sapetschnig, Chi-Chuan Lin, John E. Ladbury, Jay D. Evans, Jonathan L. Heeney, Eric A. Miska
Software Mentions: 4
Published: over 7 years ago

10.3390/genes10090719

WGCNA Analysis of Salt-Responsive Core Transcriptome Identifies Novel Hub Genes in Rice
Cited by: 50
Author(s): Mei-Ling Zhu, Hongjun Xie, Xiangjin Wei, Komivi Dossa, Yaying Yu, Suozhen Hui, Guohua Tang, Xiaoshan Zeng, Ye Yu, Jianlong Wang
Software Mentions: 4
Published: about 7 years ago

10.3390/genes11060709

Extensive Involvement of Alternative Polyadenylation in Single-Nucleus Neurons
Cited by: 3
Author(s): Ying Wang, Weixing Feng, Siwen Xu, Bo He
Software Mentions: 4
Published: over 6 years ago

10.3390/genes11060651

Transcription Analysis of the Chemerin Impact on Gene Expression Profile in the Luteal Cells of Gilts
Cited by: 7
Author(s): Karol G Makowczenko, J Jastrzebski, Karol Szeszko, Nina Smolińska, Łukasz Paukszto, Marta Kieżun, Edyta Rytelewska, Barbara Kamińska, Tadeusz Kamiński
Software Mentions: 4
Published: over 6 years ago

10.1371/journal.pone.0256148

RNA-sequencing of AVPV and ARH reveals vastly different temporal and transcriptomic responses to estradiol in the female rat hypothalamus
Cited by: 5
Author(s): Margaret A. Mohr, Angela Wong, Gauthaman Sukumar, Clifton L. Dalgard, Weizhe Hong, Tao Wu, Ye Wu, Paul E. Micevych
Software Mentions: 4
Published: about 5 years ago

10.1038/s41598-021-97909-w

Joint changes in RNA, RNA polymerase II, and promoter activity through the cell cycle identify non-coding RNAs involved in proliferation
Cited by: 7
Author(s): Siv Anita Hegre, Helle Samdal, Antonin Klima, Endre Bakken Stovner, Kristin G. Nørsett, Nina Beate Liabakk, Lene Christin Olsen, Konika Chawla, Per Arne, Pål Sætrom
Software Mentions: 4
Published: about 5 years ago

10.1371/journal.pone.0115740

Allele Workbench: Transcriptome Pipeline and Interactive Graphics for Allele-Specific Expression
Cited by: 10
Author(s): Carol Soderlund, William M. Nelson, Stephen A. Goff
Software Mentions: 4
Published: almost 12 years ago

10.18632/oncotarget.12180

The transcriptional signature of human ovarian carcinoma macrophages is associated with extracellular matrix reorganization
Cited by: 72
Author(s): Florian Finkernagel, Silke Reinartz, Sonja Lieber, Till Adhikary, Annika Wortmann, Nathalie Hoffmann, Tim Bieringer, Andrea Nist, Thorsten Stiewe, Julia M. Jansen, Uwe Wagner, Sabine Müller‐Brüsselbach, Rolf Müller
Software Mentions: 4
Published: about 10 years ago

10.3390/genes12020255

Transcriptome Response of Liver and Muscle in Heat-Stressed Laying Hens
Cited by: 6
Author(s): Yan Wang, Xiaoyun Jia, John Hsieh, Melissa S. Monson, J. Zhang, Dingming Shu, Qinghua Nie, Michael E. Persia, Max F. Rothschild, Susan J. Lamont
Software Mentions: 4
Published: over 5 years ago

10.3390/genes12030424

The Effects of Artificially Dosed Adult Rumen Contents on Abomasum Transcriptome and Associated Microbial Community Structure in Calves
Cited by: 2
Author(s): Gaowa Naren, Wenli Li, Brianna Murphy, Madison S. Cox
Software Mentions: 4
Published: over 5 years ago

10.1038/s41598-021-97306-3

Differentially expressed genes in the femur cartilage transcriptome clarify the understanding of femoral head separation in chickens
Cited by: 3
Author(s): Ludmila Mudri Hul, A. M. G. Ibelli, Igor Ricardo Savoldi, Débora Ester Petry Marcelino, Lana Teixeira Fernandes, J. O. Peixoto, Maurício Egídio Cantão, R. H. Higa, P. F. Giachetto, Luiz Lehmann Coutinho, Mônica Corrêa Ledur
Software Mentions: 4
Published: about 5 years ago

10.1016/j.molcel.2018.09.023

Phosphorylation of Histone H4T80 Triggers DNA Damage Checkpoint Recovery
Cited by: 20
Author(s): Gonzalo Millán-Zambrano, Helena Santos‐Rosa, Fabio Puddu, Samuel Robson, Stephen Jackson, Tony Kouzarides
Software Mentions: 4
Published: almost 8 years ago

10.3390/genes12060917

Sex-Differences in Traumatic Brain Injury in the Absence of Tau in Drosophila
Cited by: 4
Author(s): Ekta Shah, Katherine Gurdziel, Douglas M. Ruden
Software Mentions: 4
Published: over 5 years ago

10.3390/genes12070952

Identification of Key Metabolic Pathways and Biomarkers Underlying Flowering Time of Guar (Cyamopsis tetragonoloba (L.) Taub.) via Integrated Transcriptome-Metabolome Analysis
Cited by: 4
Author(s): Elizaveta Grigoreva, А.А. Ткаченко, Serafima Arkhimandritova, Aleksandar Beatovic, Pavel Ulianich, В. А. Волков, Dmitry Karzhaev, Cécile Ben, Laurent Gentzbittel, Elena Potokina
Software Mentions: 4
Published: over 5 years ago

10.1093/gigascience/giz012

Haplotype-phased genome and evolution of phytonutrient pathways of tetraploid blueberry
Cited by: 138
Author(s): Marivi Colle, Courtney P. Leisner, Ching Man Wai, Shujun Ou, Kevin A. Bird, Jie Wang, Jennifer H. Wisecaver, Alan E. Yocca, Elizabeth I. Alger, Haibao Tang, Zhiyong Xiong, Pete Callow, Gil Ben-Zvi, Avital Brodt, Kobi Baruch, Thomas Swale, Lily Shiue, Guo Qing Song, Kevin L. Childs, Anthony L. Schilmiller, Nicholi Vorsa, C. Robin Buell, Robert VanBuren, Ning Jiang, Patrick P. Edger
Software Mentions: 4
Published: over 7 years ago

10.1038/s41598-021-96055-7

Assessment of reference genes at six different developmental stages of Schistosoma mansoni for quantitative RT-PCR
Cited by: 6
Author(s): Gilbert O. Silveira, Murilo Sena Amaral, Helena S. Coelho, Lucas F. Maciel, Adriana S. A. Pereira, Giovanna G. O. Olberg, Patrícia A. Miyasato, Eliana Nakano, Sérgio Verjovski-Almeida
Software Mentions: 4
Published: about 5 years ago

10.1093/gigascience/giz052

Accumulating computational resource usage of genomic data analysis workflow to optimize cloud computing instance selection
Cited by: 8
Author(s): Toshio Ohta, Tomoya Tanjo, Osamu Ogasawara
Software Mentions: 4
Published: over 7 years ago

10.1074/mcp.RA118.001141

Proteome Analysis of Human Neutrophil Granulocytes From Patients With Monogenic Disease Using Data-independent Acquisition
Cited by: 45
Author(s): Piotr Grabowski, Sebastian Hesse, Sebastian Hollizeck, Meino Rohlfs, Uta Behrends, Roya Sherkat, Hannah Tamary, Ekrem Ünal, Raz Somech, Türkan Patıroğlu, Stefan Canzar, Jutte van der Werff ten Bosch, Christoph Klein, Juri Rappsilber
Software Mentions: 4
Published: over 7 years ago

10.1093/gigascience/giaa111

IDseq—An open source cloud-based pipeline and analysis service for metagenomic pathogen detection and monitoring
Cited by: 134
Author(s): Katrina Kalantar, Tiago Rodrigues De Carvalho, Charles F. A. de Bourcy, Boris Dimitrov, Greg Dingle, Rebecca Egger, Julie Han, Olivia B. Holmes, Yun Fang Juan, Ryan J. King, Andrey Kislyuk, Michael Lin, Maria Mariano, Todd Morse, Lucia V. Reynoso, David Rissato Cruz, Jonathan Sheu, Jennifer Tang, James Wang, Mark A. Zhang, Emily Zhong, Vida Ahyong, Sreyngim Lay, Sophana Chea, Jennifer A. Bohl, Jessica E. Manning, Cristina M. Tato, Joseph L. DeRisi
Software Mentions: 4
Published: about 6 years ago

10.1007/s00401-021-02347-7

Targeting cancer stem cells in medulloblastoma by inhibiting AMBRA1 dual function in autophagy and STAT3 signalling
Cited by: 17
Author(s): Francesca Nazio, Agnese Pò, Luana Abballe, Claudio Ballabio, Francesca Diomedi Camassei, Matteo Bordi, Antonio Camera, Simona Caruso, Ignazio Caruana, Marco Pezzullo, Caterina Ferraina, Giacomo Milletti, Matteo Gianesello, Sofia Reddel, Luca Compagnucci, Donatella Ceglie, Sara Marinelli, Silvia Campello, Elena Papaleo, Evelina Miele, Antonella Cacchione, Andrea Carai, Maria Vinci, Enrico Velardi, Biagio De Angelis, Luca Tiberi, Concetta Quintarelli, Angela Mastronuzzi, Elisabetta Ferretti, Franco Locatelli, Francesco Cecconi
Software Mentions: 4
Published: about 5 years ago

10.1371/journal.pgen.1003075

A Unified Method for Detecting Secondary Trait Associations with Rare Variants: Application to Sequence Data
Cited by: 6
Author(s): Dajiang Liu, Suzanne M. Leal
Software Mentions: 4
Published: almost 14 years ago

10.1186/s12711-016-0257-2

Fine mapping of a QTL on bovine chromosome 6 using imputed full sequence data suggests a key role for the group-specific component (GC) gene in clinical mastitis and milk production
Cited by: 31
Author(s): Harald Olsen, Tim Martin Knutsen, Anna Lewandowska-Sabat, Harald Grove, Torfinn Nome, Mathias Tiedemann Svendsen, Mariann Árnyasi, Marte Sodeland, Kristil Kindem Sundsaasen, Sandra Rinne Dahl, B. Heringstad, Hanne Hellerud Hansen, I. Olsaker, Matthew Kent, Sigbjørn Lien
Software Mentions: 4
Published: almost 10 years ago

10.3390/ijms21186946

Proteomic and Transcriptomic Patterns during Lipid Remodeling in Nannochloropsis gaditana
Cited by: 13
Author(s): Chris J. Hulatt, Irina Smolina, Adam Dowle, Martina Kopp, Ghana Kalerammana Vasanth, Galice Hoarau, René H. Wijffels, Viswanath Kiron
Software Mentions: 4
Published: about 6 years ago

10.1186/s12868-021-00622-7

Construction of competitive endogenous RNA network reveals regulatory role of long non-coding RNAs in intracranial aneurysm
Cited by: 7
Author(s): Yutong Pan, Jianing Lu, Biao Yang, Cameron Lenahan, Jianmin Zhang, Anwen Shao
Software Mentions: 4
Published: over 5 years ago

10.1002/gepi.22346

Fine‐mapping and QTL tissue‐sharing information improves the reliability of causal gene identification
Cited by: 25
Author(s): Alvaro N. Barbeira, Owen Melia, Yanyu Liang, Rodrigo Bonazzola, Gao Wang, Heather E. Wheeler, François Aguet, Kristin Ardlie, Xiaoquan Wen, Hae Kyung Im
Software Mentions: 4
Published: about 6 years ago

10.1371/journal.ppat.1009665

Single-cell RNA-seq landscape midbrain cell responses to red spotted grouper nervous necrosis virus infection
Cited by: 17
Author(s): Qing Wang, Cheng Yuan Peng, Min Yang, Fengqi Huang, Xuzhuo Duan, Shaowen Wang, Huitao Cheng, Huirong Yang, Haifeng Zhao, Qiwei Qin
Software Mentions: 4
Published: over 5 years ago

10.1002/gcc.22799

Insertional oncogenesis by HPV70 revealed by multiple genomic analyses in a clinically HPV‐negative cervical cancer
Cited by: 2
Author(s): A.R. Van Arsdale, Nicole E. Patterson, Elaine C. Maggi, Lorenzo Agoni, Koenraad Van Doorslaer, Bryan Harmon, Nicole S. Nevadunsky, D.Y.S. Kuo, Mark H. Einstein, Jack Lenz, Cristina Montagna
Software Mentions: 4
Published: about 7 years ago

10.1186/s12870-020-02706-8

Molecular insights into the compatible and incompatible interactions between sugar beet and the beet cyst nematode
Cited by: 19
Author(s): Razieh Ghaemi, Ebrahim Pourjam, Naser Safaie, Bruno Verstraeten, S B Mahmoudi, Rahim Mehrabi, Tim De Meyer, Tina Kyndt
Software Mentions: 4
Published: almost 6 years ago

10.1038/celldisc.2017.13

Genome-wide profiling of DNA 5-hydroxymethylcytosine during rat Sertoli cell maturation
Cited by: 7
Author(s): Miriam Landfors, Jostein Johansen, Jan Magnus Aronsen, Cathrine Broberg Vågbø, Louis C. Doré, Chuan He, Ivar Sjaastad, Pål Sætrom, Péter Fedorcsák, John Arne Dahl, Håvard Aanes, Markus Fußer, Arne Klungland
Software Mentions: 4
Published: over 9 years ago

10.18632/genesandcancer.188

Transcriptomic analysis functionally maps the intrinsically disordered domain of EWS/FLI and reveals novel transcriptional dependencies for oncogenesis
Cited by: 15
Author(s): Emily R. Theisen, Kyle R. Miller, Iftekhar A. Showpnil, Cenny Taslim, Kathleen I. Pishas, Stephen L. Lessnick
Software Mentions: 4
Published: over 7 years ago

10.3390/genes12091337

The Tomato ddm1b Mutant Shows Decreased Sensitivity to Heat Stress Accompanied by Transcriptional Alterations
Cited by: 4
Author(s): Prashant Kumar Singh, Golan Miller, Adi Faigenboim, Michal Lieberman‐Lazarovich
Software Mentions: 4
Published: about 5 years ago

10.1371/journal.pgen.1008358

Multi-omics analysis identifies mitochondrial pathways associated with anxiety-related behavior
Cited by: 34
Author(s): R. Zuzanna Misiewicz, Stella Iurato, Natalia Kulesskaya, Laura Salminen, Luís Filipe Rodrigues, Giuseppina Maccarrone, Jade Martins, Darina Czamara, Mikaela Laine, Ewa Sokołowska, Kalevi Trontti, Christiane Rewerts, Božidar Novak, Naama Volk, Dong Ik Park, Eija Jokitalo, Lars Paulín, Petri Auvinen, Vootele Võikar, Alon Chen, Angelika Erhardt, Christoph W. Turck, Iiris Hovatta
Software Mentions: 4
Published: about 7 years ago

10.3390/genes12081258

Systematic Identification of circRNAs in Alzheimer’s Disease
Cited by: 9
Author(s): Kyle R. Cochran, Kirtana Veeraraghavan, Gautam Kundu, Krystyna Mazan-Mamczarz, Christopher Coletta, Madhav Thambisetty, Myriam Gorospe, Supriyo De
Software Mentions: 4
Published: about 5 years ago

10.1186/s12870-019-2202-3

Root system traits impact early fire blight susceptibility in apple (Malus × domestica)
Cited by: 11
Author(s): Jugpreet Singh, Jack Fabrizio, Elsa Desnoues, Julliany Pereira Silva, Wolfgang Busch, Awais Khan
Software Mentions: 4
Published: almost 7 years ago

10.1186/s12864-018-4632-y

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

10.15252/embr.201846557

Tamoxifen mechanically reprograms the tumor microenvironment via <scp>HIF</scp> ‐1A and reduces cancer cell survival
Cited by: 55
Author(s): Ernesto Cortés, Dariusz Lachowski, Benjamin Robinson, Müge Sarper, Jaakko Teppo, Stephen D. Thorpe, Tyler J Lieberthal, Kenji Iwamoto, David A. Lee, Mariko Okada‐Hatakeyama, Markku Varjosalo, Armando E. del Río Hernández
Software Mentions: 4
Published: almost 8 years ago

10.3389/fnsyn.2021.660718

Dichotomic Hippocampal Transcriptome After Glutamatergic vs. GABAergic Deletion of the Cannabinoid CB1 Receptor
Cited by: 0
Author(s): Diego Pascual Cuadrado, Anna Wierczeiko, Charlotte Hewel, Susanne Gerber, Beat Lutz
Software Mentions: 4
Published: over 5 years ago

10.1186/s12864-021-07491-8

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

10.1084/jem.20201729

Yolk sac, but not hematopoietic stem cell–derived progenitors, sustain erythropoiesis throughout murine embryonic life
Cited by: 40
Author(s): Francisca Soares-da-Silva, Laina Freyer, Ramy Elsaid, Odile Burlen-Defranoux, Lorea Iturri, Odile Sismeiro, Perpétua Pinto-do-Ó, Elisa Gomez Perdiguero, Ana Cumano
Software Mentions: 4
Published: over 5 years ago

10.1186/s12870-014-0276-5

Populus tremula (European aspen) shows no evidence of sexual dimorphism
Cited by: 46
Author(s): Kathryn M. Robinson, Nicolas Delhomme, Niklas Mähler, Bastian Schiffthaler, Jenny Önskog, Benedicte Riber Albrectsen, Pär K. Ingvarsson, Torgeir R. Hvidsten, Stefan Jansson, Nathaniel R. Street
Software Mentions: 4
Published: almost 12 years ago

10.15252/embr.201948882

Mitochondrial protein biogenesis in the synapse is supported by local translation
Cited by: 56
Author(s): Bożena Kuźniewska, Dominik Cysewski, Michał Wasilewski, Paulina Sakowska, Jacek Miłek, Tomasz M. Kuliński, M. Winiarski, Paweł Kozielewicz, Ewelina Knapska, Michał Dadlez, Agnieszka Chacińska, Andrzej Dziembowski, Magdalena Dziembowska
Software Mentions: 4
Published: over 6 years ago

10.1186/s12870-020-02334-2

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

10.1038/srep20759

Comparative transcriptome analysis of peripheral blood mononuclear cells in hepatitis B-related acute-on-chronic liver failure
Cited by: 10
Author(s): Qian Zhou, Wenchao Ding, Liangliang Jiang, Jiaojiao Xin, Tianzhou Wu, Dongyan Shi, Jing Jiang, Cao H, Lanjuan Li, Jun Li
Software Mentions: 4
Published: over 10 years ago

10.1186/s12870-017-0996-4

Stress-responsive pathways and small RNA changes distinguish variable developmental phenotypes caused by MSH1 loss
Cited by: 24
Author(s): Mon Ray Shao, Sunil Kumar Kenchanmane Raju, John D. Laurie, Robersy Sánchez, Sally A. Mackenzie
Software Mentions: 4
Published: over 9 years ago

10.1371/journal.pbio.3000187

Single-cell RNA sequencing reveals regulatory mechanism for trophoblast cell-fate divergence in human peri-implantation conceptuses
Cited by: 49
Author(s): Bo Lv, Qin An, Qiao Zeng, Xunyi Zhang, Ping Lü, Yanqiu Wang, Xianmin Zhu, Yao Ji, Guoping Fan, Zhigang Xue
Software Mentions: 4
Published: about 7 years ago

10.1038/srep29122

The transcriptomes of novel marmoset monkey embryonic stem cell lines reflect distinct genomic features
Cited by: 16
Author(s): Katharina Debowski, Charis Drummer, Jana Lentes, Maren Cors, Ralf Dressel, Thomas Lingner, Gabriela Salinas-Riester, Sigrid Fuchs, Erika Sasaki, Rüdiger Behr
Software Mentions: 4
Published: over 10 years ago

10.1186/s12864-020-07141-5

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

10.1038/srep38820

Acfs: accurate circRNA identification and quantification from RNA-Seq data
Cited by: 67
Author(s): Xintian You, Tim Conrad
Software Mentions: 4
Published: almost 10 years ago

10.3390/ijms21218333

Transcriptional Effects of Psychoactive Drugs on Genes Involved in Neurogenesis
Cited by: 7
Author(s): Chiara C. Bortolasci, Briana Spolding, Srisaiyini Kidnapillai, Timothy Connor, Trang T. T. Truong, Zoe Liu, Bruna Panizzutti, Mark F. Richardson, Laura J. Gray, Michael Berk, Olivia Dean, Ken Walder
Software Mentions: 4
Published: almost 6 years ago

10.1371/journal.pgen.1008007

Genetic association and transcriptome integration identify contributing genes and tissues at cystic fibrosis modifier loci
Cited by: 57
Author(s): Jiafen Gong, Fan Wang, Bowei Xiao, Naim Panjwani, Lin Fan, Katherine Keenan, Julie Avolio, Mohsen Esmaeili, Lin Zhang, Gengming He, David Soave, Scott Mastromatteo, Zeynep Baskurt, Sangook Kim, Wanda K. O’Neal, Deepika Polineni, Scott M. Blackman, Harriet Corvol, Garry R. Cutting, Mitchell L. Drumm, Michael R. Knowles, Johanna M. Rommens, Lei Sun, Lisa J. Strug
Software Mentions: 4
Published: over 7 years ago

10.1186/s12870-019-1968-7

Reconstruction of the full-length transcriptome atlas using PacBio Iso-Seq provides insight into the alternative splicing in Gossypium australe
Cited by: 40
Author(s): Shouli Feng, Min Xu, Fujie Liu, Changjiang Cui, Baoliang Zhou
Software Mentions: 4
Published: about 7 years ago

10.3389/fpls.2020.588846

Genome-Wide Identification of Populus Malectin/Malectin-Like Domain-Containing Proteins and Expression Analyses Reveal Novel Candidates for Signaling and Regulation of Wood Development
Cited by: 8
Author(s): Vikash Kumar, Evgeniy N. Donev, Félix Barbut, Sunita Kushwah, Chanaka Mannapperuma, János Urbancsok, Ewa J. Mellerowicz
Software Mentions: 4
Published: almost 6 years ago

10.1186/s12870-018-1602-0

Dual RNA-seq analysis provides new insights into interactions between Norway spruce and necrotrophic pathogen Heterobasidion annosum s.l.
Cited by: 31
Author(s): Andriy Kovalchuk, Zhen Zeng, Rajendra P. Ghimire, Minna Kivimäenpää, Tommaso Raffaello, Mengxia Liu, Mukrimin Mukrimin, Risto Kasanen, Hui Sun, Riitta Julkunen‐Tiitto, Jarmo K. Holopainen, Fred O. Asiegbu
Software Mentions: 4
Published: almost 8 years ago

10.1186/s12870-016-0926-x

Identification of nuclear genes controlling chlorophyll synthesis in barley by RNA-seq
Cited by: 9
Author(s): Nikolay A. Shmakov, Gennady V. Vasiliev, Natalya V. Shatskaya, А. В. Дорошков, Е. И. Гордеева, D. A. Afonnikov, Е. К. Хлесткина
Software Mentions: 4
Published: almost 10 years ago

10.3389/fpls.2021.649634

Cotranscriptional and Posttranscriptional Features of the Transcriptome in Soybean Shoot Apex and Leaf
Cited by: 5
Author(s): Jiafu Zhu, Han Zhao, Fanjiang Kong, Baohui Liu, Min Liu, Zhicheng Dong
Software Mentions: 4
Published: over 5 years ago

10.3389/fpls.2018.01222

Generalist and Specialist Mite Herbivores Induce Similar Defense Responses in Maize and Barley but Differ in Susceptibility to Benzoxazinoids
Cited by: 35
Author(s): Huyen Bui, Robert Greenhalgh, Alice Ruckert, Gunbharpur S. Gill, Sarah Lee, Ricardo A. Ramirez, Richard M. Clark
Software Mentions: 4
Published: about 8 years ago

10.3389/fpls.2021.666310

Aux/IAA and ARF Gene Families in Salix suchowensis: Identification, Evolution, and Dynamic Transcriptome Profiling During the Plant Growth Process
Cited by: 9
Author(s): Suyun Wei, Yingnan Chen, Jing Hou, Yonghua Yang, Tongming Yin
Software Mentions: 4
Published: over 5 years ago

10.3389/fpls.2018.00049

Non-parent of Origin Expression of Numerous Effector Genes Indicates a Role of Gene Regulation in Host Adaption of the Hybrid Triticale Powdery Mildew Pathogen
Cited by: 28
Author(s): Coraline R. Praz, Fabrizio Menardo, Mark D. Robinson, Marion Müller, Thomas Wicker, Salim Bourras, Beat Keller
Software Mentions: 4
Published: over 8 years ago

10.3390/ijms21228640

Whole Transcriptome Analysis of Myeloid Dendritic Cells Reveals Distinct Genetic Regulation in Patients with Allergies
Cited by: 5
Author(s): Kijeong Lee, Mi Ryung Han, Ji Yeon, Byoung Jae Kim, Tae Hoon Kim
Software Mentions: 4
Published: almost 6 years ago

10.1038/s41598-017-02391-y

Whole blood transcriptome analysis reveals potential competition in metabolic pathways between negative energy balance and response to inflammatory challenge
Cited by: 13
Author(s): Juliette Bouvier-Muller, Charlotte Allain, Guillaume Tabouret, Francis Enjalbert, David Portes, Céline Noirot, Rachel Rupp, Gilles Foucras
Software Mentions: 4
Published: over 9 years ago

10.1016/j.chom.2018.06.005

Mother-to-Infant Microbial Transmission from Different Body Sites Shapes the Developing Infant Gut Microbiome
Cited by: 714
Author(s): Pamela Ferretti, Edoardo Pasolli, Adrian Tett, Francesco Asnicar, Valentina Gorfer, Sabina Fedi, Federica Armanini, Duy Tin Truong, Serena Manara, Moreno Zolfo, Francesco Beghini, Roberto Bertorelli, Veronica De Sanctis, Ilaria Bariletti, Rosarita Canto, Rosanna Clementi, Marina Cologna, Tiziana Crifò, Giuseppina Cusumano, Stefania Gottardi, Claudia Innamorati, Caterina Masè, Daniela Postai, Daniela Savoi, Sabrina Duranti, Gabriele Andrea Lugli, Leonardo Mancabelli, Francesca Turroni, Chiara Ferrario, Christian Milani, Marta Mangifesta, Rosaria Anzalone, Alice Viappiani, Moran Yassour, Hera Vlamakis, Ramnik J. Xavier, María Carmen Collado, Omry Koren, Saverio Tateo, Massimo Soffiati, Anna Pedrotti, Marco Ventura, Curtis Huttenhower, Peer Bork, Nicola Segata
Software Mentions: 4
Published: over 8 years ago

10.3389/fpls.2019.01249

Finding New Cell Wall Regulatory Genes in Populus trichocarpa Using Multiple Lines of Evidence
Cited by: 9
Author(s): Anna Furches, David Kainer, Deborah Weighill, Annabel Large, Piet Jones, Angelica M. Walker, Jonathon Romero, João Gabriel Felipe Machado Gazolla, Wayne Joubert, Manesh Shah, Jared Streich, Priya Ranjan, Jeremy Schmutz, Avinash Sreedasyam, David Macaya‐Sanz, Nan Zhao, Madhavi Z. Martin, Xiaolan Rao, Richard A. Dixon, Stephen P. DiFazio, Timothy J. Tschaplinski, Jay Chen, Gerald A. Tuskan, Daniel Jacobson
Software Mentions: 4
Published: about 7 years ago

10.1038/s41598-017-03390-9

Aberrant plasticity of peripheral sensory axons in a painful neuropathy
Cited by: 30
Author(s): Takashi Hirai, Yatendra Mulpuri, Yanbing Cheng, Zheng Xia, Wei Li, Supanigar Ruangsri, Igor Spigelman, Ichiro Nishimura
Software Mentions: 4
Published: over 9 years ago

10.1186/s12864-015-1704-0

A semi-supervised approach uncovers thousands of intragenic enhancers differentially activated in human cells
Cited by: 6
Author(s): Juan González-Vallinas, Amadís Pagès, Babita Singh, Eduardo Eyras
Software Mentions: 4
Published: about 11 years ago

10.1371/journal.pgen.1007216

The INO80 chromatin remodeler sustains metabolic stability by promoting TOR signaling and regulating histone acetylation
Cited by: 20
Author(s): Sean L. Beckwith, Erich Schwartz, Pablo E. García-Nieto, D. A. King, Graeme J. Gowans, Ka Man Wong, Tessa L. Eckley, Alexander P. Paraschuk, Egan Peltan, Laura R. Lee, Wei Yao, Ashby J. Morrison
Software Mentions: 4
Published: over 8 years ago

10.1186/s12864-019-6384-8

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

10.1186/s12864-017-4002-1

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

10.1186/s12864-020-07334-y

scReQTL: an approach to correlate SNVs to gene expression from individual scRNA-seq datasets
Cited by: 9
Author(s): Hongyu Liu, N M Prashant, Liam F. Spurr, Pavlos Bousounis, Nawaf Alomran, Helen Ibeawuchi, Justin Sein, Piotr Słowiński, Krasimira Tsaneva-Atanasova, Anélia Horvath
Software Mentions: 4
Published: almost 6 years ago

10.3389/fpls.2018.01209

Nuclear Speckle RNA Binding Proteins Remodel Alternative Splicing and the Non-coding Arabidopsis Transcriptome to Regulate a Cross-Talk Between Auxin and Immune Responses
Cited by: 39
Author(s): Jérémie Bazin, Natali Romero, Richard Rigo, Céline Charon, Thomas Blein, Federico Ariel, Martín Crespi
Software Mentions: 4
Published: about 8 years ago

10.1038/s41598-017-07100-3

Bmal1 regulates inflammatory responses in macrophages by modulating enhancer RNA transcription
Cited by: 59
Author(s): Yumiko Oishi, Shinichiro Hayashi, Takayuki Isagawa, Motohiko Oshima, Atsushi Iwama, Shigeki Shimba, Hitoshi Okamura, Ichiro Manabe
Software Mentions: 4
Published: about 9 years ago

10.7554/eLife.46418

Self-sperm induce resistance to the detrimental effects of sexual encounters with males in hermaphroditic nematodes
Cited by: 20
Author(s): Lauren N. Booth, Travis J. Maures, Robin Yeo, Cindy Tantilert, Anne Brunet
Software Mentions: 4
Published: over 7 years ago

10.1038/s41598-017-07757-w

Use antibiotics in cell culture with caution: genome-wide identification of antibiotic-induced changes in gene expression and regulation
Cited by: 63
Author(s): Ann H. Ryu, Walter L. Eckalbar, Anat Kreimer, Nir Yosef, Nadav Ahituv
Software Mentions: 4
Published: about 9 years ago

10.7554/eLife.10607

PHF13 is a molecular reader and transcriptional co-regulator of H3K4me2/3
Cited by: 20
Author(s): Ho‐Ryun Chung, Chao Xu, Alisa Fuchs, Andreas Mund, Martin Lange, Hannah Staege, Tobias Schubert, Chuanbing Bian, Ilona Dunkel, Anton Eberharter, Catherine Regnard, Henrike Klinker, David Meierhofer, Luca Cozzuto, Andreas Winterpacht, Luciano Di Croce, Jinrong Min, Hans Will, Sarah Kinkley
Software Mentions: 4
Published: over 10 years ago

10.1136/jitc-2020-001610

Neoadjuvant chemoradiation alters biomarkers of anticancer immunotherapy responses in locally advanced rectal cancer
Cited by: 17
Author(s): Incheol Seo, Hye Won Lee, Sang Jun Byun, Jee Young Park, Hyeonji Min, Sung Hwan Lee, Ju-Seog Lee, Shin Kim, Sung Uk Bae
Software Mentions: 4
Published: over 5 years ago

10.3389/fpls.2020.587185

Comprehensive Identification and Expression Profiling of Circular RNAs During Nodule Development in Phaseolus vulgaris
Cited by: 9
Author(s): Zhihua Wu, Wen Huang, Erdai Qin, Shuo Liu, Huan Liu, Aleel K. Grennan, Hong Liu, Rui Qin
Software Mentions: 4
Published: almost 6 years ago

10.7554/eLife.55775

Homeostatic plasticity fails at the intersection of autism-gene mutations and a novel class of common genetic modifiers
Cited by: 13
Author(s): Özgür Genç, Joon Yong An, Richard D. Fetter, Yelena Kulik, Giulia Zunino, Stephan J. Sanders, Graeme W. Davis
Software Mentions: 4
Published: over 6 years ago

10.1038/s41598-017-13462-5

Spatial detection of fetal marker genes expressed at low level in adult human heart tissue
Cited by: 54
Author(s): Michaela Asp, Fredrik Salmén, Patrik L. Ståhl, Sanja Vicković, Ulrika Felldin, Marie Löfling, José Fernández Navarro, Jonas Maaskola, Maria Eriksson, Bengt Persson, Matthias Corbascio, Hans Persson, Cecilia Linde, Joakim Lundeberg
Software Mentions: 4
Published: about 9 years ago

10.1016/j.celrep.2015.12.082

Single-Cell RNA-Sequencing Reveals a Continuous Spectrum of Differentiation in Hematopoietic Cells
Cited by: 157
Author(s): Iain C. Macaulay, Valentine Svensson, Charlotte Labalette, Lauren Ferreira, Fiona Hamey, Thierry Voet, Sarah A. Teichmann, Ana Cvejic
Software Mentions: 4
Published: over 10 years ago

10.3390/metabo11050329

Iron-Bound Lipocalin-2 Protects Renal Cell Carcinoma from Ferroptosis
Cited by: 19
Author(s): Julia K. Meier, Matthias Schnetz, Susanne Beck, Tobias Schmid, Monica Dominguez, Sanela Kalinovic, Andreas Daiber, Bernhard Brüne, Michaela Jung
Software Mentions: 4
Published: over 5 years ago

10.3390/ijms21239211

Transcriptomic Leaf Profiling Reveals Differential Responses of the Two Most Traded Coffee Species to Elevated [CO2]
Cited by: 10
Author(s): Isabel Marques, Isabel Fernandes, Pedro Henrique Chorão David, Octávio S. Paulo, Luís F. Goulão, Ana S. Fortunato, Fernando C. Lidon, Fábio M. DaMatta, José C. Ramalho, Ana I. Ribeiro‐Barros
Software Mentions: 4
Published: almost 6 years ago

10.3389/fpls.2020.00180

Distinctive Gene Expression Patterns Define Endodormancy to Ecodormancy Transition in Apricot and Peach
Cited by: 32
Author(s): Jiali Yu, Anna O. Conrad, Véronique Decroocq, Tetyana Zhebentyayeva, Daniel E. Williams, Dennis Bennett, Guillaume Roch, Jean Marc Audergon, Christopher Dardick, Zongrang Liu, Albert G. Abbott, Margaret Staton
Software Mentions: 4
Published: over 6 years ago

10.3390/metabo10120513

Single-Cell Transcriptional Profiling of Mouse Islets Following Short-Term Obesogenic Dietary Intervention
Cited by: 12
Author(s): Annie R. Piñeros, Hongyu Gao, Wenting Wu, Yunlong Liu, Sarah A. Tersey, Raghavendra G. Mirmira
Software Mentions: 4
Published: almost 6 years ago

10.1002/btm2.10232

Targeting thymidine phosphorylase as a potential therapy for bone loss associated with periprosthetic osteolysis
Cited by: 11
Author(s): Gen Matsumae, Tomohiro Shimizu, Yuan Tian, Daisuke Takahashi, Taku Ebata, Hend Alhasan, Shunichi Yokota, Ken Kadoya, Mohamad Alaa Terkawi, Norimasa Iwasaki
Software Mentions: 4
Published: over 5 years ago

10.3389/fpls.2021.612382

High-Resolution Transcriptome Atlas and Improved Genome Assembly of Common Buckwheat, Fagopyrum esculentum
Cited by: 15
Author(s): Aleksey A. Penin, Artem S. Kasianov, Anna V. Klepikova, Ilya Kirov, Evgeny S. Gerasimov, А Н Фесенко, Maria D. Logacheva
Software Mentions: 4
Published: over 5 years ago

10.3390/metabo11010029

Gut Microbiota Dysbiosis Is Associated with Elevated Bile Acids in Parkinson’s Disease
Cited by: 68
Author(s): Peipei Li, Bryan A. Killinger, Elizabeth Ensink, Ian Beddows, Ali Yılmaz, Noah Lubben, Jared Lamp, Meghan Schilthuis, Irving E. Vega, Randy Woltjer, J. Andrew Pospisilik, Patrik Brundin, Lena Brundin, Stewart F. Graham, Viviane Labrie
Software Mentions: 4
Published: almost 6 years ago

10.1186/s12864-019-5793-z

Identification of genes underlying phenotypic plasticity of wing size via insulin signaling pathway by network-based analysis in Sogatella furcifera
Cited by: 7
Author(s): Xinlei Gao, Yating Fu, Olugbenga Emmanuel Ajayi, Dongyang Guo, Liqin Zhang, Qingfa Wu
Software Mentions: 4
Published: over 7 years ago

10.1186/s12864-017-3566-0

Exploratory bioinformatics investigation reveals importance of “junk” DNA in early embryo development
Cited by: 51
Author(s): Steven Ge
Software Mentions: 4
Published: over 9 years ago

10.3390/metabo11070414

Analysis of Host Jejunum Transcriptome and Associated Microbial Community Structure Variation in Young Calves with Feed-Induced Acidosis
Cited by: 3
Author(s): Gaowa Naren, Wenli Li, S.L. Gelsinger, Brianna Murphy, Shengli Li
Software Mentions: 4
Published: over 5 years ago

10.3389/fphys.2021.616055

Phenotypic Changes in T Cell and Macrophage Subtypes in Perivascular Adipose Tissues Precede High-Fat Diet-Induced Hypertension
Cited by: 6
Author(s): Ramya Kumar, Yongliang Yang, Andres Contreras, Hannah Garver, Sudin Bhattacharya, Gregory D. Fink, Cheryl E. Rockwell, Stephanie W. Watts
Software Mentions: 4
Published: over 5 years ago

10.1186/s12864-017-4011-0

A comparison of Illumina and Ion Torrent sequencing platforms in the context of differential gene expression
Cited by: 54
Author(s): Nicholas F. Lahens, Emanuela Ricciotti, Olga Smirnova, Erik Toorens, Young Ho Kim, Giacomo Baruzzo, Katharina E. Hayer, Tapan Ganguly, Jonathan Schug, Gregory R. Grant
Software Mentions: 4
Published: about 9 years ago

10.1084/jem.20201290

Neuronal metabotropic glutamate receptor 8 protects against neurodegeneration in CNS inflammation
Cited by: 16
Author(s): Marcel S Woo, Friederike Ufer, Nicola Rothammer, Giovanni Di Liberto, Lars Binkle, Undine Haferkamp, Jana K. Sonner, Jan Broder Engler, Sönke Hornig, Simone Bauer, Ingrid Wagner, Kristóf Égervári, Jacob Raber, Robert M. Duvoisin, Ole Pleß, Doron Merkler, Manuel A. Friese
Software Mentions: 4
Published: over 5 years ago

10.3389/fphys.2020.01019

Genome-Wide Network of lncRNA–mRNA During Ovine Oocyte Development From Germinal Vesicle to Metaphase II in vitro
Cited by: 15
Author(s): Jun-Jie Wang, Menghan Niu, Teng Zhang, Wei Shen, Cao H
Software Mentions: 4
Published: about 6 years ago

10.1093/bioinformatics/btab178

PRISM: recovering cell-type-specific expression profiles from individual composite RNA-seq samples
Cited by: 13
Author(s): Antti Häkkinen, Kaiyang Zhang, Amjad Alkodsi, Noora Andersson, Erdoğan Pekcan Erkan, Jun Dai, Katja Kaipio, Tarja Lamminen, Naziha Mansuri, Kaisa Huhtinen, Anna Vähärautio, Olli Carpén, Johanna Hynninen, Sakari Hietanen, Rainer Lehtonen, Sampsa Hautaniemi
Software Mentions: 4
Published: over 5 years ago

10.1186/s12864-017-4359-1

A next generation sequencing based approach to identify extracellular vesicle mediated mRNA transfers between cells
Cited by: 19
Author(s): Jialiang Yang, Jacob Hagen, Kalyani V. P. Guntur, Kimaada Allette, Sarah Schuyler, Jyoti Ranjan, Francesca Petralia, Stéphane Gesta, Robert Sebra, Milind Mahajan, Bin Zhang, Jun Zhu, Sander M. Houten, Andrew Kasarskis, Vivek K. Vishnudas, Viatcheslav R. Akmaev, Rangaprasad Sarangarajan, Niven R. Narain, Eric E. Schadt, Carmen Argmann, Zhidong Tu
Software Mentions: 4
Published: almost 9 years ago

10.3389/fphys.2021.707116

Transcriptional Time Course After Rotator Cuff Tear
Cited by: 3
Author(s): Laura S Vasquez-Bolanos, Michael C. Gibbons, Severin Ruoss, Isabella T. Wu, Mario Vargas-Vila, Sydnee A Hyman, Mary C. Esparza, Donald C. Fithian, Joseph R. Lane, Anshuman Singh, Chanond A. Nasamran, Kathleen M. Fisch, Samuel R. Ward
Software Mentions: 4
Published: about 5 years ago

10.3390/cells10051008

Transcriptome Analysis of Hypoxic Lymphatic Endothelial Cells Indicates Their Potential to Contribute to Extracellular Matrix Rearrangement
Cited by: 18
Author(s): Jürgen Becker, Sonja Schwoch, Christina Zelent, Maren Sitte, Gabriela Salinas, Jörg Wilting
Software Mentions: 4
Published: over 5 years ago

10.1186/s12864-021-07615-0

Identification of the conserved long non-coding RNAs in myogenesis
Cited by: 0
Author(s): Anupam Bhattacharya, Simang Champramary, Tanya Tripathi, Debajit Thakur, Ilya Ioshikhes, Satyendra Kumar Singh, Soumyadeep Nandi
Software Mentions: 4
Published: over 5 years ago

10.1038/s41598-017-15822-7

Functional annotation of structural ncRNAs within enhancer RNAs in the human genome: implications for human disease
Cited by: 23
Author(s): Chao Ren, Feng Liu, Zhangyi Ouyang, Gaole An, Chenghui Zhao, Jun Shuai, Shuhong Cai, Xiaochen Bo, Wenjie Shu
Software Mentions: 4
Published: almost 9 years ago

10.3390/ijms21249560

Identification of Novel Potential Genes Involved in Cancer by Integrated Comparative Analyses
Cited by: 2
Author(s): Francesco Monticolo, Emanuela Palomba, Maria Luisa Chiusano
Software Mentions: 4
Published: almost 6 years ago

10.1038/s41598-017-19072-5

Integrative approach using liver and duodenum RNA-Seq data identifies candidate genes and pathways associated with feed efficiency in pigs
Cited by: 45
Author(s): Yuliaxis Ramayo-Caldas, María Ballester, Juan Pablo Sánchez, Olga González‐Rodríguez, Manuel Revilla, Henry Reyer, Klaus Wimmers, D. Torrallardona, Raquel Quintanilla
Software Mentions: 4
Published: almost 9 years ago

Projects: cran: STAR

Science Score: 100/100

Bonuses:

Papers Mentioning STAR 5,759