Ecosyste.ms: Papers

10.1371/journal.pone.0120020

Assessing Associations between the AURKA-HMMR-TPX2-TUBG1 Functional Module and Breast Cancer Risk in BRCA1/2 Mutation Carriers
Cited by: 34
Author(s): Ignacio Blanco, Karoline Kuchenbaecker, Daniel Cuadras, Xianshu Wang, Daniel Barrowdale, Gorka Ruíz de Garibay, Pablo Librado, Alejandro Sánchez-Gracia, Julio Rozas, Núria Bonifaci, Lesley McGuffog, V. Shane Pankratz, Abul B.M.M.K. Islam, Francesca Mateo, Antoni Berenguer, Audrey Petit, Isabel Catalá, Joan Brunet, Lídia Feliubadaló, Eva Tornero, Javier Benı́tez, Ana Osorio, Teresa Ramón, Cajal Teresa, Heli Nevanlinna, Kristiina Aittomäki, Banu K. Arun, Amanda E. Toland, Beth Y. Karlan, Christine Walsh, Jenny Lester, Mark H. Greene, L. Phuong, Robert L. Nussbaum, Irene L. Andrulis, Susan M. Domchek, Katherine L. Nathanson, Timothy R. Rebbeck, Rósa B. Barkardóttir, Anna Jakubowska, Jan Lubiński, Katarzyna Durda, Katarzyna Jaworska–Bieniek, Kathleen Claes, Tom Van Maerken, Orland Dı́ez, Thomas V.O. Hansen, Lars Jønson, Anne–Marie Gerdes, Bent Ejlertsen, Miguel de la Hoya, Trinidad Caldés, Alison M. Dunning, Clare Oliver, Elena Fineberg, Margaret Cook, Susan Peock, Emma McCann, Alex Murray, Chris Jacobs, Gabriella Pichert, Fiona Lalloo, Carol Chu, Huw Dorkins, Joan Paterson, Kai Ren Ong, Manuel R. Teixeira, Thais Bonfim Teixeira, Frans B.L. Hogervorst, Annemarie H. van der Hout, Caroline Seynaeve, Rob B. van der Luijt, Marjolijn J. L. Ligtenberg, Peter Devilee, Juul T. Wijnen, Matti A. Rookus, Hanne Meijers-Heijboer, Marinus J. Blok, Ans M.W. van den Ouweland, Cora M. Aalfs, Gustavo C. Rodriguez, Kelly‐Anne Phillips, Marion Piedmonte, Stacy Nerenstone, Victoria Bae‐Jump, David M. O’Malley, Elena Ratner, Rita K. Schmutzler, Barbara Wappenschmidt, Kerstin Rhiem, Christoph Engel, Alfons Meindl, Nina Ditsch, Norbert Arnold, Hansjoerg Plendl, Dieter Niederacher, Christian Sutter, Shan Wang-Gohrke, Doris Steinemann, Sabine Preisler-Adams, Karin Kast, Raymonda Varon-Mateeva, Andrea Gehrig, Anders Bojesen, Inge Søkilde Pedersen, Lone Sunde, Uffe Birk Jensen, Mads Thomassen, Torben A. Kruse, Lenka Foretová, Paolo Peterlongo, Loris Bernard, Bernard Peissel, Giulietta Scuvera, Siranoush Manoukian, Paolo Radice, Laura Ottini, Marco Montagna, Simona Agata, Christine M. Maugard, Jacques Simard, Penny Soucy, Andreas Berger, A. Fink-Retter, Christian F. Singer, Christine Rappaport, Daphne Geschwantler-Kaulich, Muy Kheng Tea, Georg Pfeiler, Esther M. John, Alexander Miron, Susan L. Neuhausen, Mary Beth Terry, Wendy K. Chung, Mary B. Daly, David E. Goldgar, Ramūnas Janavičius, Cecilia M. Dorfling, Elizabeth J. van Rensburg, Florentia Fostira, Irene Konstantopoulou, Judy E. Garber, Andrew K. Godwin, Edith Olàh, Steven A. Narod, Gad Rennert, Shani Shimon Paluch, Yael Laitman, Eitan Friedman, Annelie Liljegren, Johanna Rantala, Marie Stenmark-Askmalm, Niklas Loman, Evgeny N. Imyanitov, Ute Hamann, Amanda B. Spurdle, Sue Healey, Jeffrey N. Weitzel, Josef Herzog, David A. Margileth, Chiara Gorrini, Manel Esteller, Antonio Gómez, Sergi Sayols, Enrique Vidal, Holger Heyn, Dominique Stoppa‐Lyonnet, Mélanie Léone, Laure Barjhoux, Marion Fassy-Colcombet, Antoine de Pauw, Christine Lasset, Sandra Fert Ferrer, Laurent Castéra, Pascaline Berthet, François Cornélis, Yves Jean Bignon, Francesca Damiola, Sylvie Mazoyer, Olga M. Sinilnikova, Christopher A. Maxwell, Joseph Vijai, Mark E. Robson, Noah D. Kauff, Marina Corines, Danylko Villano, Julie M. Cunningham, Adam F. Lee, Noralane M. Lindor, Conxi Lázaro, Douglas F. Easton, Kenneth Offit, Georgia Chenevix-Trench, Fergus J. Couch, Antonis C. Antoniou, Miguel Ángel Pujana
Software Mentions: 3
Published: over 9 years ago

10.1186/s12864-018-5175-y

RNA-seq of muscle from pigs divergent in feed efficiency and product quality identifies differences in immune response, growth, and macronutrient and connective tissue metabolism
Cited by: 39
Author(s): Justyna Horodyska, Klaus Wimmers, Henry Reyer, Nares Trakooljul, Anne Maria Mullen, Peadar G. Lawlor, Ruth M. Hamill
Software Mentions: 3
Published: about 6 years ago

10.1016/j.celrep.2018.07.058

Oral Cavity Squamous Cell Carcinoma Xenografts Retain Complex Genotypes and Intertumor Molecular Heterogeneity
Cited by: 25
Author(s): Katie M. Campbell, Tianxiang Lin, Paul Zolkind, Erica K. Barnell, Zachary L. Skidmore, Ashley E. Winkler, Jonathan H. Law, Elaine R. Mardis, Lukas D. Wartman, Douglas R. Adkins, Rebecca D. Chernock, Malachi Griffith, Ravindra Uppaluri
Software Mentions: 3
Published: over 6 years ago

10.1038/sdata.2014.21

Transcriptomic profiling of rat liver samples in a comprehensive study design by RNA-Seq
Cited by: 24
Author(s): Binsheng Gong, Charles Wang, Zhenqiang Su, Huasheng Hong, Jean Thierry‐Mieg, Danielle Thierry-Mieg, Leming Shi, Scott S. Auerbach, Weida Tong, Joshua Xu
Software Mentions: 3
Published: about 10 years ago

10.1038/sdata.2016.19

Genome-scale DNA methylome and transcriptome profiling of human neutrophils
Cited by: 17
Author(s): Aniruddha Chatterjee, Peter A. Stockwell, Euan J. Rodger, Ian M. Morison
Software Mentions: 3
Published: over 8 years ago

10.1126/sciadv.abe5357

S100A8/S100A9 cytokine acts as a transcriptional coactivator during breast cellular transformation
Cited by: 24
Author(s): Ruisheng Song, Kevin Struhl
Software Mentions: 3
Published: almost 4 years ago

10.1186/1471-2164-15-1134

Discovery of osmotic sensitive transcription factors in fish intestine via a transcriptomic approach
Cited by: 35
Author(s): Marty Kwok‐Shing Wong, Haruka Ozaki, Yutaka Suzuki, Wataru Iwasaki, Yoshiyuki Takei
Software Mentions: 3
Published: almost 11 years ago

10.1371/journal.pone.0181761

The integrated analysis of RNA-seq and microRNA-seq depicts miRNA-mRNA networks involved in Japanese flounder (Paralichthys olivaceus) albinism
Cited by: 12
Author(s): Na Wang, Ruoqing Wang, Renkai Wang, Yongsheng Tian, Changwei Shao, Xiaodong Jia, Songlin Chen
Software Mentions: 3
Published: over 7 years ago

10.3390/antiox9090884

The Transcriptomic Response of the Murine Thyroid Gland to Iodide Overload and the Role of the Nrf2 Antioxidant System
Cited by: 7
Author(s): Dionysios V. Chartoumpekis, Panos G. Ziros, Ilias Georgakopoulos-Soares, Alexander Smith, Ana C. Marques, Mark Ibberson, Peter Kopp, Ioannis Habeos, Ioannis P. Trougakos, Nicholas K.H. Khoo, Gerasimos P. Sykiotis
Software Mentions: 3
Published: about 4 years ago

10.1186/1471-2164-15-337

Transcriptome differences between two sister desert poplar species under salt stress
Cited by: 36
Author(s): Jian Zhang, Jiexiong Feng, Jing Lü, Yongzhi Yang, Xu Zhang, Dongshi Wan, Jianquan Liu
Software Mentions: 3
Published: over 10 years ago

10.1038/sdata.2017.118

A gene expression atlas of adult Schistosoma mansoni and their gonads
Cited by: 44
Author(s): Zhigang Lu, Florian Sessler, Nancy Holroyd, Steffen Hahnel, Thomas Quack, Matthew Berriman, Christoph G. Grevelding
Software Mentions: 3
Published: over 7 years ago

10.1038/s41597-019-0291-3

A de novo genome assembly of the dwarfing pear rootstock Zhongai 1
Cited by: 23
Author(s): C. Ou, Fei Wang, Jiahong Wang, Li Song, Yanjie Zhang, Ming Fang, Li Ma, Yanan Zhao, Shuling Jiang
Software Mentions: 3
Published: almost 5 years ago

10.1016/j.celrep.2020.108154

Protein Stability Buffers the Cost of Translation Attenuation following eIF2α Phosphorylation
Cited by: 15
Author(s): Kim Schneider, Geoffrey M. Nelson, J. P. Watson, Jörg Morf, Maximillian M. Dalglish, Laura M. Luh, Annika Weber, Anne Bertolotti
Software Mentions: 3
Published: about 4 years ago

10.1186/s12864-018-4825-4

Liver transcriptome analysis reveals extensive transcriptional plasticity during acclimation to low salinity in Cynoglossus semilaevis
Cited by: 40
Author(s): Yufeng Si, Haishen Wen, Yun Li, Feng He, Jifang Li, Siping Li, Huiwen He
Software Mentions: 3
Published: over 6 years ago

10.7554/eLife.31250

eIF1A residues implicated in cancer stabilize translation preinitiation complexes and favor suboptimal initiation sites in yeast
Cited by: 34
Author(s): Pilar Martín-Marcos, Fujun Zhou, Charm Karunasiri, Fan Zhang, Jinsheng Dong, Jagpreet S. Nanda, Shardul D. Kulkarni, Neelam Dabas Sen, Mercedes Tamame, Michael Zeschnigk, Jon R. Lorsch, Alan G. Hinnebusch
Software Mentions: 3
Published: almost 7 years ago

10.1186/1471-2164-15-955

Comparative transcriptomics reveals striking similarities between the bovine and feline isolates of Tritrichomonas foetus: consequences for in silico drug-target identification
Cited by: 34
Author(s): Victoria Morin-Adeline, Rodrigo Lomas, Denis O’Meally, Colin M. Stack, Ana Conesa, Jan Šlapeta
Software Mentions: 3
Published: about 10 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

10.1186/s12915-020-00897-y

Long-term experimental evolution reveals purifying selection on piRNA-mediated control of transposable element expression
Cited by: 7
Author(s): Ulfar Bergthorsson, Caroline J. Sheeba, Anke Konrad, Tony Bélicard, Toni Beltran, Vaishali Katju, Peter Sarkies
Software Mentions: 3
Published: about 4 years ago

10.1186/s12977-018-0417-2

CLIP-related methodologies and their application to retrovirology
Cited by: 10
Author(s): Paul D. Bieniasz, Sebla B. Kutluay
Software Mentions: 3
Published: over 6 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

10.1186/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

10.1007/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

10.1186/1471-2164-15-406

Differential gene expression between functionally specialized polyps of the colonial hydrozoan Hydractinia symbiolongicarpus (Phylum Cnidaria)
Cited by: 43
Author(s): Steven M. Sanders, Mariya Shcheglovitova, Paulyn Cartwright
Software Mentions: 3
Published: almost 11 years ago

10.1371/journal.pone.0199021

Transcriptomic response to GABA-producing Lactobacillus plantarum CGMCC 1.2437T induced by L-MSG
Cited by: 28
Author(s): Kejin Zhuang, Yujun Jiang, Xiaohan Feng, Li Li, Fangfang Dang, Wei Zhang, Chaoxin Man
Software Mentions: 3
Published: over 6 years ago

10.1371/journal.pone.0158621

Comparative Digital Gene Expression Analysis of the Arabidopsis Response to Volatiles Emitted by Bacillus amyloliquefaciens
Cited by: 26
Author(s): Haiting Hao, Xia Zhao, Qianhan Shang, Yun Wang, Zhihong Guo, Yubao Zhang, Ruo–Yu Wang
Software Mentions: 3
Published: over 8 years ago

10.1186/s12864-020-06788-4

Identification of genetic loci associated with higher resistance to pancreas disease (PD) in Atlantic salmon (Salmo salar L.)
Cited by: 15
Author(s): Borghild Hillestad, Shokouh Makvandi‐Nejad, Aleksei Krasnov, Hooman K. Moghadam
Software Mentions: 3
Published: over 4 years ago

10.1186/s12917-017-1279-x

RNA sequencing reveals candidate genes and polymorphisms related to sperm DNA integrity in testis tissue from boars
Cited by: 14
Author(s): Maren van Son, Nina Hårdnes Tremoen, Ann Helen Gaustad, Frøydis Deinboll Myromslien, Dag Inge Våge, Else‐Berit Stenseth, Teklu T Zeremichael, Eli Grindflek
Software Mentions: 3
Published: almost 7 years ago

10.1186/1471-2164-15-499

Identification of large intergenic non-coding RNAs in bovine muscle using next-generation transcriptomic sequencing
Cited by: 105
Author(s): Coline Billerey, Mekki Boussaha, Diane Esquerré, Emmanuelle Rebours, Anis Djari, Cédric Meersseman, Christophe Klopp, Daniel Gautheret, Dominique Rocha
Software Mentions: 3
Published: over 10 years ago

10.1371/journal.pone.0111407

Whole Transcriptome Profiling of Maize during Early Somatic Embryogenesis Reveals Altered Expression of Stress Factors and Embryogenesis-Related Genes
Cited by: 82
Author(s): Stella Salvo, Candice N. Hirsch, C. Robin Buell, Shawn M. Kaeppler, Heidi F. Kaeppler
Software Mentions: 3
Published: about 10 years ago

10.1186/1471-2164-15-570

Comparing reference-based RNA-Seq mapping methods for non-human primate data
Cited by: 33
Author(s): Ashlee M. Benjamin, Marshall Nichols, Thomas W. Burke, Geoffrey S. Ginsburg, Joseph E. Lucas
Software Mentions: 3
Published: almost 11 years ago

10.1186/s12935-021-02170-w

RNA sequencing analysis reveals the competing endogenous RNAs interplay in resected hepatocellular carcinoma patients who received interferon-alpha therapy
Cited by: 5
Author(s): Yibin Wu, Longrong Wang, Xiaoshuang Wang, Yiming Zhao, Anrong Mao, Ning Zhang, Jiamin Zhou, Qi Pan, Weiping Zhu
Software Mentions: 3
Published: about 3 years ago

10.1371/journal.pone.0155378

CTCF and CohesinSA-1 Mark Active Promoters and Boundaries of Repressive Chromatin Domains in Primary Human Erythroid Cells
Cited by: 7
Author(s): Laurie A. Steiner, Vincent P. Schulz, Yelena Makismova, Kimberly Lezon-Geyda, Patrick G. Gallagher
Software Mentions: 3
Published: over 8 years ago

10.1371/journal.pone.0187966

RNA-seq reveals transcriptome changes in goats following myostatin gene knockout
Cited by: 24
Author(s): Lamei Wang, Bei Cai, Shiwei Zhou, Haijing Zhu, Qu Liu, Xiaolong Wang
Software Mentions: 3
Published: almost 7 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/s12284-021-00515-7

A Genome Doubling Event Reshapes Rice Morphology and Products by Modulating Chromatin Signatures and Gene Expression Profiling
Cited by: 5
Author(s): Chao Zhou, Xiaoyun Liu, Xinglei Li, Hanlin Zhou, Sijia Wang, Yanfei Zhu, Yonghong Zhang, Sanhe Li, Aiqing You, Lei Zhou, Zhengquan He
Software Mentions: 3
Published: over 3 years ago

10.1038/srep08957

Systematic identification and characterization of long intergenic non-coding RNAs in fetal porcine skeletal muscle development
Cited by: 84
Author(s): Weimin Zhao, Yulian Mu, Lei Ma, Chen Wang, Zhonglin Tang, Shulin Yang, Rong Zhou, Xiaoju Hu, Menghua Li, Kui Li
Software Mentions: 3
Published: over 9 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

10.1371/journal.pone.0206055

Transcriptome profiling of transgenic potato plants provides insights into variability caused by plant transformation
Cited by: 9
Author(s): Dae Kwan Ko, Satya Swathi Nadakuduti, David S. Douches, C. Robin Buell
Software Mentions: 3
Published: about 6 years ago

10.7554/eLife.43352

Identification of EOMES-expressing spermatogonial stem cells and their regulation by PLZF
Cited by: 39
Author(s): Manju Sharma, Anuj Srivastava, Heather Fairfield, David E. Bergstrom, William F. Flynn, Robert E. Braun
Software Mentions: 3
Published: over 5 years ago

10.1128/AAC.00554-20

Candida glabrata Transcription Factor Rpn4 Mediates Fluconazole Resistance through Regulation of Ergosterol Biosynthesis and Plasma Membrane Permeability
Cited by: 18
Author(s): Pedro Pais, Raquel Califórnia, Mónica Galocha, Romeu Viana, Mihaela Ola, Mafalda Cavalheiro, Azusa Takahashi‐Nakaguchi, Hiroji Chibana, Geraldine Butler, Miguel C. Teixeira
Software Mentions: 3
Published: over 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

10.1016/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

10.1186/s12864-016-3009-3

Genome-wide identification and characterization of long non-coding RNAs in developmental skeletal muscle of fetal goat
Cited by: 79
Author(s): Siyuan Zhan, Yao Dong, Wei Zhao, Jiazhong Guo, Tao Zhong, Linjie Wang, Li Li, Hongping Zhang
Software Mentions: 3
Published: over 8 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

10.1186/s12859-016-1111-9

multiDE: a dimension reduced model based statistical method for differential expression analysis using RNA-sequencing data with multiple treatment conditions
Cited by: 5
Author(s): Guangliang Kang, Lijun Du, Hong Zhang
Software Mentions: 3
Published: over 8 years ago

10.1186/s12864-017-3592-y

A reference gene set for sex pheromone biosynthesis and degradation genes from the diamondback moth, Plutella xylostella, based on genome and transcriptome digital gene expression analyses
Cited by: 46
Author(s): Peng He, Yun‐Fei Zhang, Duan‐Yang Hong, Jun Wang, Xingliang Wang, Ling-Hua Zuo, Xianfu Tang, Weiming Xu, Ming He
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

10.1038/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

10.1038/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

10.1038/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

10.26508/lsa.202000659

Dynamic changes in RNA–protein interactions and RNA secondary structure in mammalian erythropoiesis
Cited by: 2
Author(s): Mengge Shan, Xinjun Ji, Kevin A. Janssen, Ian M. Silverman, Jesse Humenik, Ben Garcia, Stephen A. Liebhaber, Brian D. Gregory
Software Mentions: 3
Published: over 3 years ago

10.1186/1471-2164-14-818

Exploration of the gene fusion landscape of glioblastoma using transcriptome sequencing and copy number data
Cited by: 67
Author(s): Nameeta Shah, Michael Lankerovich, Hwahyung Lee, Jae-Geun Yoon, Brett Schroeder, Greg Foltz
Software Mentions: 3
Published: almost 12 years ago

10.1371/journal.pone.0184115

Transcriptome analysis of the pectoral muscles of local chickens and commercial broilers using Ribo-Zero ribonucleic acid sequencing
Cited by: 12
Author(s): Yanhua Zhang, Donghua Li, Ruili Han, Yanbin Wang, Guoxi Li, Xiaojun Liu, Yadong Tian, Xiangtao Kang, Zhuanjian Li
Software Mentions: 3
Published: about 7 years ago

10.1186/s40478-019-0712-8

Inhibition of mitochondrial respiration prevents BRAF-mutant melanoma brain metastasis
Cited by: 30
Author(s): Terje Sundstrøm, Lars Prestegarden, Francisco Azuaje, Synnøve Nymark Aasen, Gro Vatne Røsland, Jobin K. Varughese, Marzieh Bahador, Simon Bernatz, Yannick Braun, Patrick N. Harter, Kai Ove Skaftnesmo, Elizabeth S. Ingham, Lisa M. Mahakian, Sarah Tam, Clifford G. Tepper, Kjell Petersen, Katherine W. Ferrara, Karl Johan Tronstad, Morten Lund‐Johansen, Rudi Beschorner, Rolf Bjerkvig, Frits Thorsen
Software Mentions: 3
Published: over 5 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

10.1371/journal.pone.0136653

RNA-Seq Analysis of Differential Splice Junction Usage and Intron Retentions by DEXSeq
Cited by: 42
Author(s): Yafang Li, Xiayu Rao, William Mattox, Christopher I. Amos, Bin Liu
Software Mentions: 3
Published: about 9 years ago

10.1186/s12864-019-5894-8

Integrated analysis of long non-coding RNA and mRNA expression in different colored skin of koi carp
Cited by: 35
Author(s): Ming Luo, Lanmei Wang, Hao Yin, Wenbin Zhu, Jianjun Fu, Zaijie Dong
Software Mentions: 3
Published: over 5 years ago

10.1186/s12936-015-1081-9

UTR introns, antisense RNA and differentially spliced transcripts between Plasmodium yoelii subspecies
Cited by: 13
Author(s): Jian Li, Baowei Cai, Yanwei Qi, Wenting Zhao, Jianwen Liu, Rui-Xue Xu, Qiuxiang Pang, Zhi‐Yong Tao, Liu Hong, Shengfa Liu, Maarten Leerkes, Mariam Quiñones, Xin-zhuan Su
Software Mentions: 3
Published: almost 9 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

10.1038/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

10.1007/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.pone.0194036

Allele-specific DNA methylation of disease susceptibility genes in Japanese patients with inflammatory bowel disease
Cited by: 11
Author(s): Hirofumi Chiba, Yoichi Kakuta, Yoshitaka Kinouchi, Yosuke Kawai, Kazuhiro Watanabe, Munenori Nagao, Takeo Naito, Motoyuki Onodera, Rintaro Moroi, Masatake Kuroha, Yoshitake Kanazawa, Tsutomu Kimura, Hisashi Shiga, Katsuya Endo, Kenichi Negoro, Masao Nagasaki, Michiaki Unno, Tooru Shimosegawa
Software Mentions: 3
Published: over 6 years ago

10.1186/s12859-020-03831-9

Tissue-associated microbial detection in cancer using human sequencing data
Cited by: 6
Author(s): Rebecca M. Rodriguez, Vedbar S. Khadka, Mark Menor, Brenda Y. Hernandez, Youping Deng
Software Mentions: 3
Published: almost 4 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

10.1038/s42003-018-0089-4

De novo genome assembly of Oryza granulata reveals rapid genome expansion and adaptive evolution
Cited by: 19
Author(s): Zhigang Wu, Dongming Fang, Rui Yang, Fei Gao, Xingyu An, Xiaoxuan Zhuo, Yafei Li, Chuandeng Yi, Tao Zhang, Chengzhi Liang, Peng Cui, Zhukuan Cheng, Qiong Luo
Software Mentions: 3
Published: over 6 years ago

10.1038/s42003-020-01143-5

Host-parasite tissue adhesion by a secreted type of β-1,4-glucanase in the parasitic plant Phtheirospermum japonicum
Cited by: 26
Author(s): Ken-ichi Kurotani, Takanori Wakatake, Yasunori Ichihashi, Koji Okayasu, Yu Sawai, Satoshi Ogawa, Songkui Cui, Takamasa Suzuki, Ken Shirasu, Michitaka Notaguchi
Software Mentions: 3
Published: over 4 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

10.1371/journal.pone.0070053

Full Transcriptome Analysis of Early Dorsoventral Patterning in Zebrafish
Cited by: 11
Author(s): Erika Fodor, Áron Zsigmond, Balázs Horváth, J. Molnár, István Nagy, Gábor Tóth, Stephen W. Wilson, Máté Varga
Software Mentions: 3
Published: over 11 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.pone.0133751

Smooth Muscle Cell Genome Browser: Enabling the Identification of Novel Serum Response Factor Target Genes
Cited by: 43
Author(s): Moon Young Lee, Chanjae Park, Robyn M. Berent, Paul J. Park, Robert Fuchs, Syn Hannah, Chin Albert, Jared Townsend, Craig C. Benson, Doug Redelman, Tong Shen, Sang-Youel Park, Joseph M. Miano, Kenton M. Sanders, Seungil Ro
Software Mentions: 3
Published: over 9 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

10.1371/journal.pone.0251732

Phlpp1 is induced by estrogen in osteoclasts and its loss in Ctsk-expressing cells does not protect against ovariectomy-induced bone loss
Cited by: 2
Author(s): Marcelline K. Hanson, Ismael Y. Karkache, David H. H. Molstad, Andrew Norton, Kim C. Mansky, Elizabeth W. Bradley
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

10.18632/aging.101536

A Drosophila model of cigarette smoke induced COPD identifies Nrf2 signaling as an expedient target for intervention
Cited by: 21
Author(s): R. Prange, Marcus Thiedmann, Anita Bhandari, Neha Mishra, Anupam Sinha, Robert Häsler, Philip Rosenstiel, Karin Uliczka, Christina Wagner, Ali Önder Yildirim, Christine Fink, Thomas Roeder
Software Mentions: 3
Published: about 6 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/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/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/s12864-021-07971-x

Unveiling the transcriptomic complexity of Miscanthus sinensis using a combination of PacBio long read- and Illumina short read sequencing platforms
Cited by: 2
Author(s): Yongli Wang, Xia Li, Congsheng Wang, Lu Gao, Yanfang Wu, Xingnan Ni, Jianzhong Sun, Jianxiong Jiang
Software Mentions: 3
Published: about 3 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.0147147

Systematic Identification and Characterization of Long Non-Coding RNAs in the Silkworm, Bombyx mori
Cited by: 94
Author(s): Yuqian Wu, Tingcai Cheng, Chun Li, Duolian Liu, Quan Zhang, Rodney Long, Ping Zhao, Qingyou Xia
Software Mentions: 3
Published: almost 9 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

10.1038/s41598-018-35231-8

Sendai Virus Infection Induces Expression of Novel RNAs in Human Cells
Cited by: 5
Author(s): Roli Mandhana, Curt M. Horvath
Software Mentions: 3
Published: about 6 years ago

10.1186/s12864-020-06827-0

Transcriptome analysis reveals a molecular understanding of nicotinamide and butyrate sodium on meat quality of broilers under high stocking density
Cited by: 10
Author(s): Yuqin Wu, Youli Wang, Dafei Yin, Tahir Mahmood, Jianmin Yuan
Software Mentions: 3
Published: over 4 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

10.1371/journal.pone.0081925

Gene Expression, Single Nucleotide Variant and Fusion Transcript Discovery in Archival Material from Breast Tumors
Cited by: 51
Author(s): Nadine Norton, Zhifu Sun, Yan W. Asmann, Daniel J. Serie, Brian M. Necela, Aditya Bhagwate, Jin Jen, Bruce W. Eckloff, Krishna R. Kalari, Kevin J. Thompson, Jennifer M. Carr, Jennifer M. Kachergus, Xochiquetzal J. Geiger, Edith A. Perez, E. Aubrey Thompson
Software Mentions: 3
Published: about 11 years ago

10.1099/mic.0.000550

Whole genome transcriptomics reveals global effects including up-regulation of Francisella pathogenicity island gene expression during active stringent response in the highly virulent Francisella tularensis subsp. tularensis SCHU S4
Cited by: 11
Author(s): Amber L. Murch, Paul Skipp, Peter L. Roach, Petra C. F. Oyston
Software Mentions: 3
Published: about 7 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

10.1186/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/s40168-017-0341-z

Associations among dietary non-fiber carbohydrate, ruminal microbiota and epithelium G-protein-coupled receptor, and histone deacetylase regulations in goats
Cited by: 39
Author(s): Hong Shen, Zhongyan Lu, Zhihui Xu, Zhan Chen, Zongzhuan Shen
Software Mentions: 3
Published: about 7 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/s12864-018-5156-1

A fast detection of fusion genes from paired-end RNA-seq data
Cited by: 19
Author(s): Trung Nghia Vu, Wenjiang Deng, Quang Thinh Trac, Stefano Calza, Woochang Hwang, Yudi Pawitan
Software Mentions: 3
Published: about 6 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

10.1371/journal.pone.0074256

Gene Regulatory Networks Elucidating Huanglongbing Disease Mechanisms
Cited by: 90
Author(s): Federico Martinelli, Russell L. Reagan, Sandra L. Uratsu, My L. Phu, Ute Albrecht, Wenwei Zhao, Cristina E. Davis, Kim D. Bowman, Abhaya M. Dandekar
Software Mentions: 3
Published: about 11 years ago

10.1186/s12864-018-4739-1

Whole genome and transcriptome analysis reveal adaptive strategies and pathogenesis of Calonectria pseudoreteaudii to Eucalyptus
Cited by: 14
Author(s): Xiaozhen Ye, Zhenhui Zhong, Hongyi Liu, Lian‐Yu Lin, Mengmeng Guo, Wenhui Guo, Zonghua Wang, Qinghua Zhang, Li Feng, Guodong Lu, Feiping Zhang, Quanzhu Chen
Software Mentions: 3
Published: over 6 years ago

10.1371/journal.pone.0207715

Distinct genes and pathways associated with transcriptome differences in early cardiac development between fast- and slow-growing broilers
Cited by: 9
Author(s): J. Zhang, Carl J. Schmidt, Susan J. Lamont
Software Mentions: 3
Published: almost 6 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/s12864-015-1390-y

Transcript profiling of Populus tomentosa genes in normal, tension, and opposite wood by RNA-seq
Cited by: 41
Author(s): Jinhui Chen, Beibei Chen, Deqiang Zhang
Software Mentions: 3
Published: over 9 years ago

10.1186/1471-2164-15-35

Bidirectional promoters are the major source of gene activation-associated non-coding RNAs in mammals
Cited by: 91
Author(s): Masahiro Uesaka, Osamu Nishimura, Yasuhiro Go, Kinichi Nakashima, Kiyokazu Agata, Takuya Imamura
Software Mentions: 3
Published: almost 11 years ago