Ecosyste.ms: Papers

10.1186/s12863-017-0569-4

Identification and integrated analysis of differentially expressed lncRNAs and circRNAs reveal the potential ceRNA networks during PDLSC osteogenic differentiation
Cited by: 124
Author(s): Xiuge Gu, Mengying Li, Yongfeng Jin, Dongxu Liu, Fulan Wei
Software Mentions: 3
Published: almost 7 years ago

10.1186/1471-2164-14-49

Genome reannotation of the lizard Anolis carolinensis based on 14 adult and embryonic deep transcriptomes
Cited by: 54
Author(s): Walter L. Eckalbar, Elizabeth Hutchins, Glenn J. Markov, April N. Allen, Jason J. Corneveaux, Kerstin Lindblad‐Toh, Federica Di Palma, Jessica Alföldi, Matthew J. Huentelman, Kenro Kusumi
Software Mentions: 3
Published: almost 12 years ago

10.1371/journal.ppat.1008035

Phytoplasma SAP11 effector destabilization of TCP transcription factors differentially impact development and defence of Arabidopsis versus maize
Cited by: 35
Author(s): Pascal Pecher, Gabriele Moro, Maria Cristina Canale, Sylvain Capdevielle, Archana Archana, Allyson M. MacLean, Akiko Sugio, Chih-Horng Kuo, João Roberto Spotti Lopes, Saskia A. Hogenhout
Software Mentions: 3
Published: about 5 years ago

10.1371/journal.pone.0173094

Transgenic expression of fungal accessory hemicellulases in Arabidopsis thaliana triggers transcriptional patterns related to biotic stress and defense response
Cited by: 6
Author(s): Alex Yi‐Lin Tsai, Kin Chan, Chi-Yip Ho, Thomas Canam, Resmi Capron, Emma R. Master, Katharina Bräutigam
Software Mentions: 3
Published: over 7 years ago

10.1371/journal.pone.0201854

Genome-wide analysis of DNA polymorphisms, the methylome and transcriptome revealed that multiple factors are associated with low pollen fertility in autotetraploid rice
Cited by: 21
Author(s): Xiang Li, Hang Yu, Yamin Jiao, Muhammad Qasim Shahid, Jinwen Wu, Xiangdong Liu
Software Mentions: 3
Published: over 6 years ago

10.1186/s12864-018-4925-1

Characterization of kinase gene expression and splicing profile in prostate cancer with RNA-Seq data
Cited by: 5
Author(s): Huijuan Feng, Tingting Li, Xuegong Zhang
Software Mentions: 3
Published: over 6 years ago

10.1038/srep28075

Cellular responses to HSV-1 infection are linked to specific types of alterations in the host transcriptome
Cited by: 52
Author(s): Benxia Hu, Li X, Yongxia Huo, Yafen Yu, Qiuping Zhang, Guijun Chen, Yaping Zhang, Nigel W. Fraser, Dong‐Dong Wu, Jumin Zhou
Software Mentions: 3
Published: over 8 years ago

10.1371/journal.pone.0079874

Phenotypic and Transcriptional Fidelity of Patient-Derived Colon Cancer Xenografts in Immune-Deficient Mice
Cited by: 31
Author(s): Jeffrey Chou, Matthew Fitzgibbon, Christie-Lynn Mortales, Andrea M. H. Towlerton, Melissa P. Upton, Raymond S. Yeung, Martin W. McIntosh, Edus H. Warren
Software Mentions: 3
Published: about 11 years ago

10.1371/journal.ppat.1003341

Differences in Gastric Carcinoma Microenvironment Stratify According to EBV Infection Intensity: Implications for Possible Immune Adjuvant Therapy
Cited by: 132
Author(s): Michael J. Strong, Guiyin Xu, Joseph Coco, Carl Baribault, Dass S. Vinay, Michelle Lacey, Amy L. Strong, Teresa A. Lehman, Michael Seddon, Zhen Lin, Monica Concha, Melody Baddoo, MaryBeth Ferris, Kenneth F. Swan, Deborah E. Sullivan, Matthew E. Burow, Christopher M. Taylor, Erik K. Flemington
Software Mentions: 3
Published: over 11 years ago

10.1371/journal.ppat.1004156

Dynamics of HIV Latency and Reactivation in a Primary CD4+ T Cell Model
Cited by: 71
Author(s): Pejman Mohammadi, Julia di Iulio, Miguel Muñoz, Raquel Martínez, István Bartha, Matthias Cavassini, Christian W. Thorball, Jacques Fellay, Niko Beerenwinkel, Angela Ciuffi, Amalio Telenti
Software Mentions: 3
Published: over 10 years ago

10.1093/jxb/erx219

Transcriptomic and metabolomics responses to elevated cell wall invertase activity during tomato fruit set
Cited by: 36
Author(s): Lei Ru, Sonia Osorio, Lu Wang, Alisdair R. Fernie, John W. Patrick, Yong‐Ling Ruan
Software Mentions: 3
Published: over 7 years ago

10.1186/s12863-014-0158-8

Identification of gene co-expression clusters in liver tissues from multiple porcine populations with high and low backfat androstenone phenotype
Cited by: 6
Author(s): Sudeep Sahadevan, Ernst Tholen, Christine Große‐Brinkhaus, K. Schellander, Dawit Tesfaye, Martin Hofmann‐Apitius, Mehmet Ulaş Çınar, Asep Gunawan, Michael Hölker, Christiane Neuhoff
Software Mentions: 3
Published: over 9 years ago

10.1093/jxb/ery062

Thermopriming triggers splicing memory in Arabidopsis
Cited by: 91
Author(s): Lexiang Yu, Natalia Serrano, Ge Gao, Mohamed A. M. Atia, Morad M. Mokhtar, Yong Woo, Jérémie Bazin, Alaguraj Veluchamy, Moussa Benhamed, Martín Crespi, Chris Gehring, Anireddy S. N. Reddy, Magdy M. Mahfouz
Software Mentions: 3
Published: over 6 years ago

10.1093/jxb/erx010

Gene expression atlas of pigeonpea and its application to gain insights into genes associated with pollen fertility implicated in seed formation
Cited by: 48
Author(s): Lekha T. Pazhamala, Shilp Purohit, Rachit K. Saxena, Vanika Garg, L. Krishnamurthy, Jérôme Verdier, Rajeev K. Varshney
Software Mentions: 3
Published: over 7 years ago

10.1093/jxb/ery142

Arabidopsis HEAT SHOCK TRANSCRIPTION FACTORA1b regulates multiple developmental genes under benign and stress conditions
Cited by: 46
Author(s): Waleed S. Albihlal, Irabonosi Obomighie, Thomas Blein, Ramona Persad, Igor Chernukhin, Martín Crespi, Ulrike Bechtold, Phil Mullineaux
Software Mentions: 3
Published: over 6 years ago

10.1371/journal.ppat.1004809

Transgenic Expression of the Dicotyledonous Pattern Recognition Receptor EFR in Rice Leads to Ligand-Dependent Activation of Defense Responses
Cited by: 94
Author(s): Benjamin Schwessinger, Ofir Bahar, Nicholas Thomas, Nicholas Holton, Vladimir Nekrasov, Deling Ruan, Patrick E. Canlas, Arsalan Daudi, Young-Mo Kim, Vasanth Singan, Rita C. Kuo, Mansi Chovatia, Christopher Daum, Joshua L. Heazlewood, Cyril Zipfel, Pamela C. Ronald
Software Mentions: 3
Published: over 9 years ago

10.1093/jxb/erv553

Comparative cell-specific transcriptomics reveals differentiation of C₄photosynthesis pathways in switchgrass and other C₄lineages
Cited by: 45
Author(s): Xiaolan Rao, Nan Lu, Guifen Li, Jin Nakashima, Yuhong Tang, Richard A. Dixon
Software Mentions: 3
Published: almost 9 years ago

10.1186/1471-2164-15-S3-S1

Characterization of a genetic mouse model of lung cancer: a promise to identify Non-Small Cell Lung Cancer therapeutic targets and biomarkers
Cited by: 19
Author(s): Federica Riccardo, Maddalena Arigoni, Genny Buson, Elisa Zago, Manuela Iezzi, Dario Livio Longo, Matteo Carrara, Alessandra Fiore, Simona Nuzzo, Silvio Bicciato, Patrizia Nanni, Lorena Landuzzi, Federica Cavallo, Raffaele Calogero, Elena Quaglino
Software Mentions: 3
Published: over 10 years ago

10.1186/s12864-017-4019-5

SAIC: an iterative clustering approach for analysis of single cell RNA-seq data
Cited by: 29
Author(s): Lu Yang, Jiancheng Liu, Qiang Lü, Arthur D. Riggs, Xiwei Wu
Software Mentions: 3
Published: about 7 years ago

10.1371/journal.pone.0115717

Melanocytes in the Skin – Comparative Whole Transcriptome Analysis of Main Skin Cell Types
Cited by: 42
Author(s): Paula Reemann, Ene Reimann, Sten Ilmjärv, Orm Porosaar, Helgi Silm, Viljar Jaks, Eero Vasar, Külli Kingo, Sulev Kõks
Software Mentions: 3
Published: almost 10 years ago

10.1371/journal.pone.0148039

Reduced CYFIP1 in Human Neural Progenitors Results in Dysregulation of Schizophrenia and Epilepsy Gene Networks
Cited by: 27
Author(s): Rebecca A. Nebel, Dejian Zhao, Erika Pedrosa, Jill Kirschen, Herbert M. Lachman, Deyou Zheng, Brett S. Abrahams
Software Mentions: 3
Published: almost 9 years ago

10.1371/journal.pone.0233394

Gene expression regulation by the Chromodomain helicase DNA-binding protein 9 (CHD9) chromatin remodeler is dispensable for murine development
Cited by: 11
Author(s): Andrej Alendar, Jan-Paul Lambooij, Rajith Bhaskaran, Cesare Lancini, Ji‐Ying Song, H. van Vugt, Michiel Snoek, Anton Berns
Software Mentions: 3
Published: over 4 years ago

10.1093/jxb/erw021

Copy number variation of a gene cluster encoding endopolygalacturonase mediates flesh texture and stone adhesion in peach
Cited by: 62
Author(s): Chao Gu, Lu Wang, Wei Wang, Hui Zhou, Baiquan Ma, Hongyu Zheng, Ting Fang, Collins Ogutu, Sornkanok Vimolmangkang, Yuepeng Han
Software Mentions: 3
Published: almost 9 years ago

10.1371/journal.ppat.1005166

Global Analysis of Mouse Polyomavirus Infection Reveals Dynamic Regulation of Viral and Host Gene Expression and Promiscuous Viral RNA Editing
Cited by: 12
Author(s): Seth B. Garren, Yuvabharath Kondaveeti, Michael O. Duff, Gordon G. Carmichael
Software Mentions: 3
Published: about 9 years ago

10.1172/JCI83408

The chromatin remodeling factor CHD7 controls cerebellar development by regulating reelin expression
Cited by: 55
Author(s): Danielle Whittaker, Kimberley L. H. Riegman, Sahrunizam Kasah, Conor Mohan, Tian Yu, Blanca Pijuan-Sala, Husam Hebaishi, Angela Caruso, Ana C. Marques, Caterina Michetti, María Eugenia Sanz Smachetti, Apar Shah, Mara Sabbioni, Omer Kulhanci, Wee Wei Tee, Danny Reinberg, María Luisa Scattoni, Holger A. Volk, Imelda M. McGonnell, Fiona C. Wardle, Cathy Fernandes, M. Albert Basson
Software Mentions: 3
Published: almost 8 years ago

10.1186/s12864-016-2720-4

Genome-wide analysis of the transcriptional response to porcine reproductive and respiratory syndrome virus infection at the maternal/fetal interface and in the fetus
Cited by: 27
Author(s): Jamie M. Wilkinson, Hua Bao, Andrea Ladinig, Linjun Hong, Paul Stothard, Joan K. Lunney, Graham Plastow, John C. S. Harding
Software Mentions: 3
Published: over 8 years ago

10.5334/jcr.213

Genes Relevant to Tissue Response to Cancer Therapy Display Diurnal Variation in mRNA Expression in Human Oral Mucosa
Cited by: 3
Author(s): Fangyi Gu, Eduardo Cortes Gomez, Jianhong Chen, Matthew F. Buas, Nicolas F. Schlecht, Karen Hulme, Shweta Vishwas Kulkarni, Prashant Singh, Richard J. O’Connor, Christine B. Ambrosone, Anurag Singh, Jianmin Wang
Software Mentions: 3
Published: over 3 years ago

10.1172/JCI97007

Hypothalamic loss of Snord116 recapitulates the hyperphagia of Prader-Willi syndrome
Cited by: 73
Author(s): Joseph Polex-Wolf, Brian Lam, Rachel Larder, John Tadross, Debra Rimmington, Fàtima Bosch, Verónica Jiménez Cenzano, Eduard Ayuso, Marcella Kl, Kara Rainbow, Anthony P. Coll, Stephen O’Rahilly, Giles S.H. Yeo
Software Mentions: 3
Published: almost 7 years ago

10.1016/j.ajhg.2016.07.001

Adiposity-Dependent Regulatory Effects on Multi-tissue Transcriptomes
Cited by: 24
Author(s): Craig A. Glastonbury, Ana Viñuela, Alfonso Buil, Gisli H. Halldorsson, Guðmar Þorleifsson, Hannes Helgason, Unnur Þorsteinsdóttir, Kāri Stefánsson, Emmanouil T. Dermitzakis, Tim D. Spector, Kerrin S. Small
Software Mentions: 3
Published: about 8 years ago

10.1186/s12864-016-3384-9

Placental transcriptome co-expression analysis reveals conserved regulatory programs across gestation
Cited by: 25
Author(s): Sam Buckberry, Tina Bianco‐Miotto, Stephen J. Bent, Vicki L. Clifton, Cheryl Shoubridge, Kartik Shankar, Claire T. Roberts
Software Mentions: 3
Published: almost 8 years ago

10.1371/journal.pone.0079118

Discovering Transcription and Splicing Networks in Myelodysplastic Syndromes
Cited by: 11
Author(s): Hongyan Wang, Jianguo Wen, Chung‐Che Chang, Xiaobo Zhou
Software Mentions: 3
Published: about 11 years ago

10.1186/s12862-015-0316-2

Evidence that natural selection maintains genetic variation for sleep in Drosophila melanogaster
Cited by: 31
Author(s): Nicolas Svetec, Li Zhao, Perot Saelao, Joanna C. Chiu, David J. Begun
Software Mentions: 3
Published: over 9 years ago

10.1186/s12864-020-07086-9

In vitro resynthesis of lichenization reveals the genetic background of symbiosis-specific fungal-algal interaction in Usnea hakonensis
Cited by: 26
Author(s): Mieko Kono, Yoshiaki Kon, Yoshihito Ohmura, Yoko Satta, Yohey Terai
Software Mentions: 3
Published: about 4 years ago

10.1186/s12929-021-00718-6

HCV eradication with IFN-based therapy does not completely restore gene expression in PBMCs from HIV/HCV-coinfected patients
Cited by: 4
Author(s): Óscar Brochado, Isidoro Martı́nez, Juan Berenguer, Luz María Medrano, Juan González-García, María Ángeles Jiménez-Sousa, Ana Carrero, Víctor Hontañón, Jordi Navarro, Josep M. Guardiola, Amanda Fernández‐Rodríguez, Salvador Resino
Software Mentions: 3
Published: over 3 years ago

10.1186/s12864-015-1494-4

De novo transcriptome assembly of the wild relative of tea tree (Camellia taliensis) and comparative analysis with tea transcriptome identified putative genes associated with tea quality and stress response
Cited by: 41
Author(s): Hai-Bin Zhang, Enhua Xia, Hui Huang, Jianjun Jiang, Benying Liu, Li‐Zhi Gao
Software Mentions: 3
Published: over 9 years ago

10.1186/s12929-020-00642-1

Long-term expansion of directly reprogrammed keratinocyte-like cells and in vitro reconstitution of human skin
Cited by: 2
Author(s): Jie Zheng, Wonjin Yun, Junghyun Park, Phil Jun Kang, Gilju Lee, Gwonhwa Song, In Yong Kim, Seungkwon You
Software Mentions: 3
Published: over 4 years ago

10.1371/journal.pone.0156723

Genome-Wide Analysis of Long Noncoding RNAs and Their Responses to Drought Stress in Cotton (Gossypium hirsutum L.)
Cited by: 76
Author(s): Xuke Lu, Xiugui Chen, Mingchun Mu, Junjuan Wang, Xiaoge Wang, Delong Wang, Zujun Yin, Weili Fan, Shuai Wang, Lixue Guo, Wuwei Ye
Software Mentions: 3
Published: over 8 years ago

10.1074/jbc.M116.751644

Bromodomain and extraterminal inhibitors block the Epstein-Barr virus lytic cycle at two distinct steps
Cited by: 25
Author(s): Kristin M. Keck, S. Moquin, Amanda He, Samantha G. Fernandez, Jessica J. Somberg, Stephanie M. Liu, Delsy M. Martinez, JJ L. Miranda
Software Mentions: 3
Published: over 7 years ago

10.1186/s12864-016-3170-8

Numerous genetic loci identified for drought tolerance in the maize nested association mapping populations
Cited by: 52
Author(s): Chunhui Li, Bo Sun, Yongxiang Li, Cheng Liu, Xun Wu, Dengfeng Zhang, Yunsu Shi, Yi Song, Edward S. Buckler, Zhiwu Zhang, Tianyu Wang, Yu Liu
Software Mentions: 3
Published: about 8 years ago

10.1172/jci.insight.146364

Deficient adaptation to centrosome duplication defects in neural progenitors causes microcephaly and subcortical heterotopias
Cited by: 11
Author(s): José González‐Martínez, Andrzej Cwetsch, Diego Martínez-Alonso, Luis R. López-Sainz, Jorge Almagro, Anna Melati, Jesus Omar Gomez, Manuel Pérez‐Martínez, Diego Megı́as, Jasminka Boskovic, Javier Gilabert-Juan, Osvaldo Graña‐Castro, Alessandra Pierani, Axel Behrens, Sagrario Ortega, Marcos Malumbres
Software Mentions: 3
Published: over 3 years ago

10.1186/s12864-017-3663-0

Transcriptome analysis of the two unrelated fungal β-lactam producers Acremonium chrysogenum and Penicillium chrysogenum: Velvet-regulated genes are major targets during conventional strain improvement programs
Cited by: 22
Author(s): Dominik Terfehr, Tim A. Dahlmann, Ulrich Kück
Software Mentions: 3
Published: over 7 years ago

10.1172/jci.insight.141690

Aging imparts cell-autonomous dysfunction to regulatory T cells during recovery from influenza pneumonia
Cited by: 20
Author(s): Luisa Morales‐Nebreda, Kathryn A. Helmin, Manuel A. Torres Acosta, Nikolay S. Markov, Jennifer Yuan Shih Hu, Anthony M. Joudi, Raul Piseaux‐Aillon, Hiam Abdala‐Valencia, Yuliya Politanska, Benjamin D. Singer
Software Mentions: 3
Published: over 3 years ago

10.3390/insects11090634

Diversity and Regulation of S-Adenosylmethionine Dependent Methyltransferases in the Anhydrobiotic Midge
Cited by: 4
Author(s): Ruslan Deviatiiarov, R. T. Ayupov, Alexander Laikov, Elena Shagimardanova, Takahiro Kikawada, Oleg Gusev
Software Mentions: 3
Published: about 4 years ago

10.1172/jci.insight.133393

Histone deacetylases 1 and 2 restrain CD4+ cytotoxic T lymphocyte differentiation
Cited by: 20
Author(s): Teresa Preglej, Patricia Hamminger, Maik Luu, Tanja Bulat, Liisa Andersen, Lisa Göschl, Valentina Stolz, Ramona Rica, Lisa Sandner, Darina Waltenberger, Roland Tschismarov, Thomas Faux, Thorina Boenke, Asta Laiho, Laura L. Elo, Shoji Sakaguchi, Günter Steiner, Thomas Decker, Barbara Bohle, Alexander Visekruna, Christoph Bock, Birgit Strobl, Christian Seiser, Nicole Boucheron, Wilfried Ellmeier
Software Mentions: 3
Published: over 4 years ago

10.1007/s13361-016-1544-4

Prognostic Metabolite Biomarkers for Soft Tissue Sarcomas Discovered by Mass Spectrometry Imaging
Cited by: 37
Author(s): Sha Lou, Benjamin Balluff, Arjen H.G. Cleven, Judith V.M.G. Bovée, Liam A. McDonnell
Software Mentions: 3
Published: about 8 years ago

10.1371/journal.pone.0094270

Improved Annotation of 3′ Untranslated Regions and Complex Loci by Combination of Strand-Specific Direct RNA Sequencing, RNA-Seq and ESTs
Cited by: 27
Author(s): Nicholas J. Schurch, Christian Callebaut, Alexander Sherstnev, Junfang Song, Céline Duc, Kate G. Storey, Whi McLean, Sara J. Brown, Gordon G. Simpson, Geoffrey J. Barton
Software Mentions: 3
Published: over 10 years ago

10.1093/insilicoplants/diaa005

Within- and cross-species predictions of plant specialized metabolism genes using transfer learning
Cited by: 7
Author(s): Bethany M. Moore, Peipei Wang, Pengxiang Fan, Aaron Lee, Bryan J. Leong, Yann‐Ru Lou, Craig A. Schenck, Koh‐ichi Sugimoto, Melissa D. Lehti-Shiu, Cornelius S. Barry, Shin-Han Shiu
Software Mentions: 3
Published: almost 5 years ago

10.1371/journal.pone.0192362

Transporter genes identified in landraces associated with high zinc in polished rice through panicle transcriptome for biofortification
Cited by: 21
Author(s): C. N. Neeraja, Kalyani S. Kulkarni, P. Madhu Babu, D. N. Rao, K. Surekha, V. Ravindra Babu
Software Mentions: 3
Published: almost 7 years ago

10.1371/journal.pone.0078868

Inferring Polymorphism-Induced Regulatory Gene Networks Active in Human Lymphocyte Cell Lines by Weighted Linear Mixed Model Analysis of Multiple RNA-Seq Datasets
Cited by: 4
Author(s): Wensheng Zhang, Andrea Edwards, Erik K. Flemington, Kun Zhang
Software Mentions: 3
Published: about 11 years ago

10.1371/journal.pone.0180842

RNA sequencing to determine the contribution of kinase receptor transactivation to G protein coupled receptor signalling in vascular smooth muscle cells
Cited by: 15
Author(s): Danielle Kamato, Venkata Vijayanand Bhaskarala, Nitin Mantri, Tae Gyu Oh, Dora Ling, Reearna Janke, Wenhua Zheng, Peter J. Little, Narin Osman
Software Mentions: 3
Published: over 7 years ago

10.1371/journal.pone.0128041

Transcriptome Profiling of the Potato (Solanum tuberosum L.) Plant under Drought Stress and Water-Stimulus Conditions
Cited by: 85
Author(s): Lei Gong, Hongxia Zhang, Xiaoyan Gan, Li Zhang, Yuchao Chen, Fengjie Nie, Lei Shi, Miao Li, Zhiqian Guo, Guohui Zhang, Song Yao
Software Mentions: 3
Published: over 9 years ago

10.1186/s13040-021-00237-y

DASSI: differential architecture search for splice identification from DNA sequences
Cited by: 2
Author(s): Shabir Moosa, Abbes Amira, Sabri Boughorbel
Software Mentions: 3
Published: almost 4 years ago

10.1371/journal.pone.0177814

ANK1 is up-regulated in laser captured microglia in Alzheimer’s brain; the importance of addressing cellular heterogeneity
Cited by: 35
Author(s): Diego Mastroeni, Shobana Sekar, Jennifer Nolz, Elaine Delvaux, Katie Lunnon, Jonathan Mill, Winnie S. Liang, Paul D. Coleman
Software Mentions: 3
Published: over 7 years ago

10.1371/journal.pone.0245749

Effects of Chinese wolfberry and Astragalus extract on the antioxidant capacity of Tibetan pig liver
Cited by: 6
Author(s): Zhuang Hao, Zhen Li, Jinjin Huo, Jiandong Li, Peng Yin
Software Mentions: 3
Published: almost 4 years ago

10.1016/j.immuni.2017.11.024

Cellular Differentiation of Human Monocytes Is Regulated by Time-Dependent Interleukin-4 Signaling and the Transcriptional Regulator NCOR2
Cited by: 118
Author(s): Jil Sander, Susanne V. Schmidt, Branko Cirovic, Naomi McGovern, Olympia Papantonopoulou, A. Hardt, Anna C. Aschenbrenner, Christoph Kreer, Thomas Quast, Alexander M. Xu, Lisa Schmidleithner, Heidi Theis, Lan Do Thi Huong, Hermi Sumatoh, Mario A. Lauterbach, Jonas Schulte-Schrepping, Patrick Günther, Jia Xue, Kevin Baßler, Thomas Ulas, Kathrin Klee, Natalie Katzmarski, Stefanie Herresthal, Wolfgang Krebs, Bianca Martin, Eicke Latz, Kristian Händler, Michael Kraut, Waldemar Kolanus, Marc Beyer, Christine S. Falk, Bettina Wiegmann, Sven Burgdorf, Nicholas A. Melosh, Evan W. Newell, Florent Ginhoux, Andreas Schlitzer, Joachim L. Schultze
Software Mentions: 3
Published: almost 7 years ago

10.3390/jcm8081253

Multi-Omics Characterization of the Spontaneous Mesenchymal–Epithelial Transition in the PMC42 Breast Cancer Cell Lines
Cited by: 22
Author(s): Sugandha Bhatia, James Monkman, Tony Blick, Pascal H.G. Duijf, Shivashankar H. Nagaraj, Erik W. Thompson
Software Mentions: 3
Published: over 5 years ago

10.1038/srep28995

Characterization and target genes of nine human PRD-like homeobox domain genes expressed exclusively in early embryos
Cited by: 30
Author(s): Elo Madissoon, Eeva-Mari Jouhilahti, Liselotte Vesterlund, Virpi Töhönen, Kaarel Krjutškov, Sophie Petropoulos, Elisabet Einarsdottir, Sten Linnarsson, Fredrik Lanner, Robert Månsson, Outi Hovatta, Thomas R. Bürglin, Shintaro Katayama, Juha Kere
Software Mentions: 3
Published: over 8 years ago

10.1038/s41438-020-0328-y

A chromosome-scale reference genome of Aquilegia oxysepala var. kansuensis
Cited by: 18
Author(s): Jinghe Xie, Haifeng Zhao, Kunpeng Li, Rui Zhang, Yanling Jiang, Meimei Wang, Xijie Guo, Ben Yu, Hongzhi Kong, Yuannian Jiao, Guiyun Xu
Software Mentions: 3
Published: over 4 years ago

10.1186/1746-6148-10-146

Effect of photoperiod on the feline adipose transcriptome as assessed by RNA sequencing
Cited by: 5
Author(s): Akira Mori, Kelly Kappen, A. C. Dilger, Kelly S. Swanson
Software Mentions: 3
Published: over 10 years ago

10.1186/s12885-019-6338-1

Comparing biological information contained in mRNA and non-coding RNAs for classification of lung cancer patients
Cited by: 14
Author(s): Johannes Smolander, Alexey Stupnikov, Galina Glazko, Matthias Dehmer, Frank Emmert‐Streib
Software Mentions: 3
Published: almost 5 years ago

10.1371/journal.pone.0162402

Comprehensive Transcriptome Analyses of the Fructose-Fed Syrian Golden Hamster Liver Provides Novel Insights into Lipid Metabolism
Cited by: 8
Author(s): Ziyang Li, Chaoliang Xiong, Suo Mo, Haiying Tian, Mengqian Yu, Tingting Mao, Qian Chen, Huai‐Rong Luo, Quan-Zhen Li, Jianxin Lü, Yi Zhao, Wei Li
Software Mentions: 3
Published: about 8 years ago

10.1186/s12885-017-3252-2

Genome-wide DNA methylation measurements in prostate tissues uncovers novel prostate cancer diagnostic biomarkers and transcription factor binding patterns
Cited by: 47
Author(s): Marie K. Kirby, Ryne C. Ramaker, Brian S. Roberts, Brittany N. Lasseigne, David S. Gunther, Todd C. Burwell, Nicholas S. Davis, Zulfiqar Gulzar, Devin Absher, Sara J. Cooper, James D. Brooks, R Myers
Software Mentions: 3
Published: over 7 years ago

10.1038/hortres.2017.5

Differential gene expression analysis of ‘Chili’ (Pyrus bretschneideri) fruit pericarp with two types of bagging treatments
Cited by: 22
Author(s): Yuling Wang, Xinfu Zhang, Ran Wang, Ying-Xin Bai, Chenglian Liu, Yuan Yang, Yingjie Yang, Shaolan Yang
Software Mentions: 3
Published: over 7 years ago

10.1186/s12918-016-0366-0

Integrative transcriptome network analysis of iPSC-derived neurons from schizophrenia and schizoaffective disorder patients with 22q11.2 deletion
Cited by: 87
Author(s): Mingyan Lin, Erika Pedrosa, Anastasia Hrabovsky, Jian Chen, Benjamin R. Puliafito, Stephanie R. Gilbert, Deyou Zheng, Herbert M. Lachman
Software Mentions: 3
Published: about 8 years ago

10.1038/s41438-021-00597-w

Transcriptional profiling reveals multiple defense responses in downy mildew-resistant transgenic grapevine expressing a TIR-NBS-LRR gene located at the MrRUN1/MrRPV1 locus
Cited by: 3
Author(s): Junjie Qu, Ian B. Dry, Lulu Liu, Zhanbao Guo, Ling Yin
Software Mentions: 3
Published: over 3 years ago

10.1038/s41438-020-0238-z

MdMYB8 is associated with flavonol biosynthesis via the activation of the MdFLS promoter in the fruits of Malus crabapple
Cited by: 32
Author(s): Hua Li, Li Yu, Jiaxuan Yu, Ting Wu, Jie Zhang, Ji Tian
Software Mentions: 3
Published: almost 5 years ago

10.1038/s41438-020-00452-4

Induced defense response in red mango fruit against Colletotrichum gloeosporioides
Cited by: 22
Author(s): Sudheeran Pradeep Kumar, Noa Sela, Mira Carmeli-Weissberg, Rinat Ovadia, Sayantan Panda, Oleg Feygenberg, Dalia Maurer, Michal Oren-Shamir, Asaph Aharoni, Noam Alkan
Software Mentions: 3
Published: almost 4 years ago

10.1371/journal.pone.0174236

Enhancement of Arabidopsis growth characteristics using genome interrogation with artificial transcription factors
Cited by: 7
Author(s): Niels van Tol, Martijn Rolloos, Johan E. Pinas, Christiaan V. Henkel, Dieuwertje Augustijn, Paul J. J. Hooykaas, Bert J. van der Zaal
Software Mentions: 3
Published: over 7 years ago

10.1038/s41438-020-00414-w

The de novo genome assembly of Tapiscia sinensis and the transcriptomic and developmental bases of androdioecy
Cited by: 3
Author(s): Peng Zhao, Guiliang Xin, Feng Yan, Huan Wang, Xiaolong Ren, Keith Woeste, Wenzhe Liu
Software Mentions: 3
Published: almost 4 years ago

10.1038/s41438-019-0164-0

Draft genome sequence of cauliflower (Brassica oleracea L. var. botrytis) provides new insights into the C genome in Brassica species
Cited by: 46
Author(s): Sun DeLing, Chunguo Wang, Xiaoli Zhang, Wenlin Zhang, Hanmin Jiang, Xingwei Yao, Li‐Li Liu, Wen Zhang, Guobao Niu, Xiaozheng Shan
Software Mentions: 3
Published: over 5 years ago

10.1186/s12864-019-5497-4

PLAIDOH: a novel method for functional prediction of long non-coding RNAs identifies cancer-specific LncRNA activities
Cited by: 28
Author(s): Sarah C. Pyfrom, Hong Luo, Jacqueline E. Payton
Software Mentions: 3
Published: almost 6 years ago

10.1186/s12885-019-6179-y

BC200 overexpression contributes to luminal and triple negative breast cancer pathogenesis
Cited by: 14
Author(s): Maria Barton, Julia Santucci-Pereira, Olivia G. Vaccaro, Theresa D. Nguyen, Yanhong Su, José Russo
Software Mentions: 3
Published: about 5 years ago

10.1093/gigascience/giaa132

Chromosomal genome of <i>Triplophysa bleekeri</i> provides insights into its evolution and environmental adaptation
Cited by: 18
Author(s): Dengyue Yuan, Xuehui Chen, Haoran Gu, Ming Zou, Yu Zeng, Jian Fang, Wenjing Tao, Xiangyan Dai, Shijun Xiao, Zhijian Wang
Software Mentions: 3
Published: about 4 years ago

10.1371/journal.pntd.0005461

Modulation of the immune response by Fonsecaea pedrosoi morphotypes in the course of experimental chromoblastomycosis and their role on inflammatory response chronicity
Cited by: 26
Author(s): Isaque Medeiros Siqueira, Raffael Júnio Araújo de Castro, Luiza Chaves de Miranda Leonhardt, Márcio Sousa Jerônimo, A.J.M. Soares, Tainá Raiol, Christiane Nishibe, Nalvo F. Almeida, Aldo Henrique Tavares, Christian Hoffmann, Anamélia Lorenzetti Bocca
Software Mentions: 3
Published: over 7 years ago

10.1186/s12864-015-1670-6

NanoCAGE-XL and CapFilter: an approach to genome wide identification of high confidence transcription start sites
Cited by: 31
Author(s): Jason S. Cumbie, Maria G. Ivanchenko, Molly Megraw
Software Mentions: 3
Published: over 9 years ago

10.1007/s00418-020-01887-5

Pcdh18a regulates endocytosis of E-cadherin during axial mesoderm development in zebrafish
Cited by: 6
Author(s): Bernadett Bösze, Yuzo Ono, Benjamin Mattes, Claude Sinner, Victor Gourain, Thomas Thumberger, Sham Tlili, Joachim Wittbrodt, Timothy E. Saunders, Uwe Strähle, Alexander Schug, Steffen Scholpp
Software Mentions: 3
Published: over 4 years ago

10.1371/journal.pntd.0007589

The cell fate regulator NUPR1 is induced by Mycobacterium leprae via type I interferon in human leprosy
Cited by: 5
Author(s): Priscila Ribeiro Andrade, Manali Mehta, Jing Lü, Rosane M. B. Teles, Dennis Montoya, Phillip Scumpia, Euzenir Nunes Sarno, Marîa Teresa Ochoa, Feiyang Ma, Matteo Pellegrini, Robert L. Modlin
Software Mentions: 3
Published: over 5 years ago

10.1371/journal.pntd.0007152

Host and parasite responses in human diffuse cutaneous leishmaniasis caused by L. amazonensis
Cited by: 52
Author(s): Stephen M Christensen, Ashton T. Belew, Najib M. El-Sayed, Wagner Luiz Tafuri, Fernando Tobias Sílveira, David M. Mosser
Software Mentions: 3
Published: over 5 years ago

10.1093/gigascience/giaa006

Chromosomal-level assembly of Juglans sigillata genome using Nanopore, BioNano, and Hi-C analysis
Cited by: 28
Author(s): Delu Ning, Wu Tao, Xiao Liang-jun, Ting Ma, Wen‐Liang Fang, Dong Run-quan, Fuliang Cao
Software Mentions: 3
Published: almost 5 years ago

10.1186/s13059-015-0596-2

Bridger: a new framework for de novo transcriptome assembly using RNA-seq data
Cited by: 246
Author(s): Zheng Chang, Guojun Li, Juntao Liu, Yu Zhang, Cody Ashby, De Li Liu, Carole L. Cramer, Xiuzhen Huang
Software Mentions: 3
Published: almost 10 years ago

10.1371/journal.pgen.1006108

Transposable Elements versus the Fungal Genome: Impact on Whole-Genome Architecture and Transcriptional Profiles
Cited by: 148
Author(s): Raúl Castanera, Leticia López-Varas, Alessandra Borgognone, Kurt LaButti, Alla Lapidus, Jeremy Schmutz, Jane Grimwood, Gúmer Pérez, Antonio G. Pisabarro, Igor V. Grigoriev, Jason E. Stajich, Lucı́a Ramı́rez
Software Mentions: 3
Published: over 8 years ago

10.1371/journal.pntd.0007764

Identification of a systemic interferon-γ inducible antimicrobial gene signature in leprosy patients undergoing reversal reaction
Cited by: 20
Author(s): Rosane M. B. Teles, Jing Lü, Maria Tió-Coma, Isabela M. B. Goulart, Sayera Banu, Deanna A. Hagge, Kidist Bobosha, Tom H. M. Ottenhoff, Matteo Pellegrini, Annemieke Geluk, Robert L. Modlin
Software Mentions: 3
Published: about 5 years ago

10.1093/gigascience/giaa114

Pacific Biosciences assembly with Hi-C mapping generates an improved, chromosome-level goose genome
Cited by: 14
Author(s): Yan Li, Guangliang Gao, Yu Lin, Silu Hu, Yi Luo, Guosong Wang, Long Jin, Qigui Wang, Jiwen Wang, Qianzi Tang, Mingzhou Li
Software Mentions: 3
Published: about 4 years ago

10.1038/s41438-020-00449-z

A chromosome-level reference genome of non-heading Chinese cabbage [Brassica campestris (syn. Brassica rapa) ssp. chinensis]
Cited by: 41
Author(s): Ying Li, Gao-Feng Liu, Liming Ma, Tongkun Liu, Changwei Zhang, Dong Xiao, Hongkun Zheng, Fei Chen, Xilin Hou
Software Mentions: 3
Published: almost 4 years ago

10.1186/s12885-021-08276-8

Differential gene expression identifies a transcriptional regulatory network involving ER-alpha and PITX1 in invasive epithelial ovarian cancer
Cited by: 6
Author(s): Yichao Li, Sushila Jaiswal, Rupleen Kaur, Dana Alsaadi, Xiaoyu Liang, Frank A. Drews, Julie A. DeLoia, Thomas C. Krivak, Hanna M. Petrykowska, Valer Gotea, Lonnie R. Welch, Laura Elnitski
Software Mentions: 3
Published: over 3 years ago

10.1186/s13059-014-0540-x

Elucidating variations in the nucleotide sequence of Ebola virus associated with increasing pathogenicity
Cited by: 33
Author(s): Stuart Dowall, David A. Matthews, Isabel García-Dorival, Irene Taylor, John Kenny, Christiane Hertz‐Fowler, Neil Hall, Kara Corbin-Lickfett, Cyril Empig, Kyle Schlunegger, John N. Barr, Miles W. Carroll, Roger Hewson, Julian A. Hiscox
Software Mentions: 3
Published: about 10 years ago

10.1186/s12864-018-4679-9

Transcriptional profiling of human bronchial epithelial cell BEAS-2B exposed to diesel and biomass ultrafine particles
Cited by: 39
Author(s): Andrea Grilli, Rossella Bengalli, Eleonora Longhin, Laura Capasso, Maria Carla Proverbio, Mattia Forcato, Silvio Bicciato, Maurizio Gualtieri, Cristina Battaglia, Marina Camatini
Software Mentions: 3
Published: over 6 years ago

10.1186/s13059-014-0551-7

Transcriptome-wide modulation of splicing by the exon junction complex
Cited by: 75
Author(s): Zhen Wang, Valentine Murigneux, Hervé Le Hir
Software Mentions: 3
Published: almost 10 years ago

10.1186/s13059-014-0558-0

Identification of novel fusion genes in lung cancer using breakpoint assembly of transcriptome sequencing data
Cited by: 40
Author(s): Lynnette Fernández-Cuesta, Ruping Sun, Roopika Menon, Julie George, Susanne Lorenz, Leonardo A. Meza‐Zepeda, Martin Peifer, Dennis Plenker, Johannes M. Heuckmann, Frauke Leenders, Thomas Zander, Ilona Dahmen, Mirjam Koker, Jakob Schöttle, Roland T. Ullrich, Janine Altmüller, Christian Becker, Peter Nürnberg, Henrik Seidel, Diana Böhm, Friederike Göke, Sascha Ansén, Prudence A. Russell, Gavin Wright, Zoe Wainer, Benjamin Solomon, Iver Petersen, Joachim H. Clement, Jörg Sänger, O.T. Brustugun, Åslaug Helland, Steinar Solberg, Marius Lund‐Iversen, Reinhard Buettner, Jürgen Wolf, Élisabeth Brambilla, Martin Vingron, Sven Perner, Stefan A. Haas, Roman K. Thomas
Software Mentions: 3
Published: almost 10 years ago

10.1186/s13059-014-0411-5

Non-exhaustive DNA methylation-mediated transposon silencing in the black truffle genome, a complex fungal genome with massive repeat element content
Cited by: 54
Author(s): Barbara Montanini, Pao‐Yang Chen, Marco Morselli, Artur Jaroszewicz, David López, Francis Martin, Simone Ottonello, Matteo Pellegrini
Software Mentions: 3
Published: over 10 years ago

10.1186/gb-2014-15-6-r77

Transcriptome and methylome profiling reveals relics of genome dominance in the mesopolyploid Brassica oleracea
Cited by: 388
Author(s): Isobel A. P. Parkin, ChuShin Koh, Haibao Tang, Stephen J. Robinson, Sateesh Kagale, Wayne E. Clarke, Chris Town, John Nixon, Vivek Krishnakumar, Shelby L. Bidwell, France Denœud, Harry Belcram, Matthew G. Links, Jérémy Just, Carling Clarke, Tricia Bender, Terry Huebert, Annaliese S. Mason, J. Chris Pires, Guy C. Barker, Jonathan D. Moore, Paul Walley, Sahana Manoli, Jacqueline Batley, David Edwards, Matthew N. Nelson, Xiyin Wang, Andrew H. Paterson, Graham J. King, Ian Bancroft, Boulos Chalhoub, Andrew Sharpe
Software Mentions: 3
Published: almost 11 years ago

10.1186/s13059-014-0468-1

The genome sequence of the Antarctic bullhead notothen reveals evolutionary adaptations to a cold environment
Cited by: 81
Author(s): Seung Chul Shin, Do Hwan Ahn, Su Jin Kim, Chul Woo Pyo, Yongrok Choi, Mi-Kyeong Kim, Jung-Eun Lee, Jong Eun Lee, H. William Detrich, John H. Postlethwait, David Edwards, Sung Gu Lee, Hyun Park
Software Mentions: 3
Published: about 10 years ago

10.1371/journal.pcbi.1003517

Long Non-Coding RNA and Alternative Splicing Modulations in Parkinson's Leukocytes Identified by RNA Sequencing
Cited by: 145
Author(s): Lilach Soreq, Alessandro Guffanti, Nathan Salomonis, Alon Simchovitz, Zvi Israel, Hagai Bergman, Hermona Soreq
Software Mentions: 3
Published: over 10 years ago

10.1155/2016/3791214

A Support Vector Machine Classification of Thyroid Bioptic Specimens Using MALDI-MSI Data
Cited by: 17
Author(s): Manuel Galli, Italo Zoppis, Gabriele De Sio, Clizia Chinello, Fabio Pagni, Fulvio Magni, Giancarlo Mauri
Software Mentions: 3
Published: over 8 years ago

10.1186/s13059-014-0414-2

Discovery of novel transcripts and gametophytic functions via RNA-seq analysis of maize gametophytic transcriptomes
Cited by: 67
Author(s): Antony M. Chettoor, Scott A. Givan, Rex A. Cole, Clayton T Coker, Erica Unger-Wallace, Zuzana Vejlupkova, Erik Vollbrecht, John E. Fowler, Evans Mulenga
Software Mentions: 3
Published: over 10 years ago

10.1186/s12870-021-02825-w

Transcriptional and proteomic insights into phytotoxic activity of interspecific potato hybrids with low glycoalkaloid contents
Cited by: 5
Author(s): Katarzyna Szajko, Jarosław Ciekot, Iwona Wasilewicz‐Flis, Waldemar Marczewski, Dorota Sołtys‐Kalina
Software Mentions: 3
Published: almost 4 years ago

10.1186/s12864-018-4856-x

Genome-wide expression profiling of leaves and roots of watermelon in response to low nitrogen
Cited by: 25
Author(s): Muhammad Azher Nawaz, Chen Chen, Fareeha Shireen, Zhuhua Zheng, Hamza Sohail, Muhammad Afzal, Muhammad Amjad Ali, Zhilong Bie, Yuan Huang
Software Mentions: 3
Published: over 6 years ago

10.1186/s12885-015-1955-9

The genomic and transcriptomic landscape of anaplastic thyroid cancer: implications for therapy
Cited by: 51
Author(s): Katayoon Kasaian, Sam M. Wiseman, Blair Walker, Jacqueline E. Schein, Yongjun Zhao, Martin Hirst, Richard A. Moore, Andrew J. Mungall, Marco A. Marra, Steven J.M. Jones
Software Mentions: 3
Published: almost 9 years ago

10.1186/s12870-021-03129-9

Tomato transcriptomic response to Tuta absoluta infestation
Cited by: 11
Author(s): Daniela D’Esposito, Daniele Manzo, Alessandro Ricciardi, Antonio P. Garonna, Antonino De Natale, Luigi Frusciante, Francesco Pennacchio, Maria Raffaella Ercolano
Software Mentions: 3
Published: over 3 years ago

10.1186/gb-2013-14-3-r30

CRAC: an integrated approach to the analysis of RNA-seq reads
Cited by: 70
Author(s): Philippe Naveilhan, Mikaël Salson, Thérèse Commes, Éric Rivals
Software Mentions: 3
Published: almost 12 years ago