pypi: HTSeq | Projects | Ecosyste.ms: Papers

10.1186/s12864-021-07367-x

The semi-dwarfing gene Rht-dp from dwarf polish wheat (Triticum polonicum L.) is the "Green Revolution” gene Rht-B1b
Cited by: 12
Author(s): Songyue Chai, Yao Qin, Xu Zhang, Xue Xiao, Xing Fan, Jian Zeng, Sha Li, Houyang Kang, Haiqin Zhang, Jun Li, Yong‐Hong Zhou, Yi Wang
Software Mentions: 3
Published: almost 6 years ago

10.1186/s12864-018-5333-2

Transcriptome profile in bursa of Fabricius reveals potential mode for stress-influenced immune function in chicken stress model
Cited by: 22
Author(s): Yanhua Zhang, Yanting Zhou, Guirong Sun, Kui Li, Zhuanjian Li, Aru Su, Xiaojun Liu, Guoxi Li, Ruirui Jiang, Ruili Han, Yadong Tian, Xiangtao Kang, Fengbin Yan
Software Mentions: 3
Published: almost 8 years ago

10.1186/s12864-019-6166-3

A comparative analysis of RNA sequencing methods with ribosome RNA depletion for degraded and low-input total RNA from formalin-fixed and paraffin-embedded samples
Cited by: 10
Author(s): Xiaojing Lin, Lihong Qiu, Xue Song, Junyan Hou, Weizhi Chen, Jun Zhao
Software Mentions: 3
Published: about 7 years ago

10.1186/1471-2164-14-578

RNA-Seq effectively monitors gene expression in Eutrema salsugineum plants growing in an extreme natural habitat and in controlled growth cabinet conditions
Cited by: 41
Author(s): Marc J. Champigny, Wilson W L Sung, Vasile Catana, Rupa Salwan, Peter S. Summers, Susan A. Dudley, Nicholas J. Provart, Robin K. Cameron, G. Brian Golding, Elizabeth A. Weretilnyk
Software Mentions: 3
Published: about 13 years ago

10.1186/s12864-015-2237-2

Simultaneous transcriptional profiling of Leishmania major and its murine macrophage host cell reveals insights into host-pathogen interactions
Cited by: 76
Author(s): Laura A. L. Dillon, Rahul Suresh, Kwame Okrah, Héctor Corrada Bravo, David M. Mosser, Najib M. El-Sayed
Software Mentions: 3
Published: almost 11 years ago

10.1186/s12864-015-1853-1

RNAseq analysis of Aspergillus fumigatus in blood reveals a just wait and see resting stage behavior
Cited by: 23
Author(s): Henriette Irmer, Sonia Tarazona, Christoph Sasse, Patrick Olbermann, Jürgen Loeffler, Sven Krappmann, Ana Conesa, Gerhard H. Braus
Software Mentions: 3
Published: about 11 years ago

10.1186/s12865-021-00418-8

Macrophage mediated recognition and clearance of Borrelia burgdorferi elicits MyD88-dependent and -independent phagosomal signals that contribute to phagocytosis and inflammation
Cited by: 9
Author(s): Sarah Benjamin, Kelly L. Hawley, Paola Vera-Licona, Carson J. La Vake, Jorge Cervantes, Yijun Ruan, Justin D. Radolf, Juan C. Salazar
Software Mentions: 3
Published: over 5 years ago

10.1186/s12920-018-0453-8

Identification of exon skipping events associated with Alzheimer’s disease in the human hippocampus
Cited by: 17
Author(s): Seonggyun Han, Jason E. Miller, Seyoun Byun, Dokyoon Kim, Shannon L. Risacher, Andrew J. Saykin, Younghee Lee, Kwangsik Nho
Software Mentions: 3
Published: almost 8 years ago

10.1186/s12920-020-00782-1

Improving lung cancer risk stratification leveraging whole transcriptome RNA sequencing and machine learning across multiple cohorts
Cited by: 11
Author(s): Yoonha Choi, Jianghan Qu, Esther Wu, Yangyang Hao, Jiarui Zhang, Jicai Ning, Xinwu Yang, Lori Lofaro, Daniel G. Pankratz, Joshua E. Babiarz, P. Sean Walsh, Ehab Billatos, Marc E. Lenburg, Giulia C. Kennedy, Jon McAuliffe, Jing Huang
Software Mentions: 3
Published: about 6 years ago

10.1186/s12866-020-1722-1

Integrative analysis of outer membrane vesicles proteomics and whole-cell transcriptome analysis of eravacycline induced Acinetobacter baumannii strains
Cited by: 19
Author(s): Dinesh Kumar Kesavan, Aparna Vasudevan, Liang Wu, Jianguo Chen, Zhaoliang Su, Shengjun Wang, Huaxi Xu
Software Mentions: 3
Published: over 6 years ago

10.1186/s12866-020-02020-1

Berberine alters gut microbial function through modulation of bile acids
Cited by: 10
Author(s): Patricia G. Wolf, Saravanan Devendran, Heidi L. Doden, Lindsey K. Ly, Tyler Moore, Hiroyuki Takei, Hiroshi Nittono, Tsuyoshi Murai, Takao Kurosawa, George E. Chlipala, Stefan J. Green, Genta Kakiyama, Purna C. Kashyap, Vance J. McCracken, H. Rex Gaskins, Patrick M. Gillevet, Jason M. Ridlon
Software Mentions: 3
Published: almost 6 years ago

10.1186/s12870-014-0348-6

chromoWIZ: a web tool to query and visualize chromosome-anchored genes from cereal and model genomes
Cited by: 7
Author(s): Thomas Nußbaumer, Karl G. Kugler, Wolfgang Schweiger, Kai Christian Bader, Heidrun Gundlach, Manuel Spannagl, Naser Poursarebani, Matthias Pfeifer, Klaus Mayer
Software Mentions: 3
Published: almost 12 years ago

10.1186/s12870-020-2309-6

A transcriptomic view of the ability of nascent hexaploid wheat to tolerate aneuploidy
Cited by: 6
Author(s): Deying Zeng, Jiantao Guan, Jiangtao Luo, Laibin Zhao, Yazhou Li, Wenshuai Chen, Lianquan Zhang, Shunzong Ning, Zhongwei Yuan, Aili Li, Youliang Zheng, Long Mao, Dengcai Liu, Ming Hao
Software Mentions: 3
Published: over 6 years ago

10.1186/s12870-019-1836-5

Genome-wide identification and classification of MIKC-type MADS-box genes in Streptophyte lineages and expression analyses to reveal their role in seed germination of orchid
Cited by: 15
Author(s): Chunmei He, Can Si, Jaime A. Teixeira da Silva, Mingzhi Li, Jun Duan
Software Mentions: 3
Published: over 7 years ago

10.1186/s12870-020-02673-0

Resistance analysis of cherry rootstock ‘CDR-1’ (Prunus mahaleb) to crown gall disease
Cited by: 5
Author(s): Chengcheng Liang, Tian Wang, Rendun Wu, Mei Zhao, Yong Zhao, Yuliang Cai
Software Mentions: 3
Published: almost 6 years ago

10.1186/s12870-016-0836-y

Vine nitrogen status and volatile thiols and their precursors from plot to transcriptome level
Cited by: 24
Author(s): Pierre Helwi, Sabine Guillaumie, Cécile Thibon, Céline Keime, Aude Habran, Ghislaine Hilbert, Éric Gomès, Philippe Darriet, Serge Delrot, Cornelis van Leeuwen
Software Mentions: 3
Published: over 10 years ago

10.1186/s12870-021-03041-2

Genome-wide association study and transcriptome analysis discover new genes for bacterial leaf blight resistance in rice (Oryza sativa L.)
Cited by: 10
Author(s): Xinyue Shu, Ai‐Jun Wang, Bo Jiang, Yuqi Jiang, Xiang Xiao, Xiaoqun Yi, Shuangcheng Li, Qi Deng, Yunlong Wang, Jun Zhu, Yueyang Liang, Huainian Liu, Ting Zou, Lingxia Wang, Ping Li, Aiping Zheng
Software Mentions: 3
Published: over 5 years ago

10.1186/s12870-017-1188-y

Physiological and transcriptomic responses in the seed coat of field-grown soybean (Glycine max L. Merr.) to abiotic stress
Cited by: 25
Author(s): Courtney P. Leisner, Craig R. Yendrek, Elizabeth A. Ainsworth
Software Mentions: 3
Published: almost 9 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 6 years ago

10.1186/s12870-019-1802-2

Transcript analyses reveal a comprehensive role of abscisic acid in modulating fruit ripening in Chinese jujube
Cited by: 8
Author(s): Zhang Zhong, C.K. Kang, Shuyi Zhang, Xingang Li
Software Mentions: 3
Published: over 7 years ago

10.1186/s12870-015-0468-7

Specific pools of endogenous peptides are present in gametophore, protonema, and protoplast cells of the moss Physcomitrella patens
Cited by: 37
Author(s): Igor Fesenko, Georgij Arapidi, Alexander Skripnikov, Dmitry Alexeev, Elena S. Kostryukova, Alexander I. Manolov, Ilya Altukhov, Regina Khazigaleeva, A. V. Seredina, Sergey I. Kovalchuk, Rustam H. Ziganshin, В. Г. Згода, Svetlana E. Novikova, Tatiana A. Semashko, D. K. Slizhikova, Vasilij V Ptushenko, A. Yu. Gorbachev, Vadim M. Govorun, В. Т. Иванов
Software Mentions: 3
Published: almost 12 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 9 years ago

10.1186/s12917-016-0881-7

RNA-Sequencing for profiling goat milk transcriptome in colostrum and mature milk
Cited by: 43
Author(s): Alessandra Crisà, Fabrizio Ferrè, Giovanni Chillemi, B. Moioli
Software Mentions: 3
Published: almost 10 years ago

10.1093/bioinformatics/btz433

CoCo: RNA-seq read assignment correction for nested genes and multimapped reads
Cited by: 27
Author(s): Gabrielle Deschamps-Francoeur, Vincent Boivin, Sherif Abou Elela, Michelle S. Scott
Software Mentions: 3
Published: over 7 years ago

10.1093/bioinformatics/btv488

Benchmark analysis of algorithms for determining and quantifying full-length mRNA splice forms from RNA-seq data
Cited by: 75
Author(s): Katharina E. Hayer, Angel Pizarro, Nicholas F. Lahens, John B. Hogenesch, Gregory R. Grant
Software Mentions: 3
Published: about 11 years ago

10.1242/bio.039917

Characterization and comparative analyses of transcriptomes of cloned and in vivo fertilized porcine pre-implantation embryos
Cited by: 7
Author(s): Xiaoyan He, Cheng Tan, Zicong Li, Chengfa Zhao, Junsong Shi, Rong Zhou, Xingwang Wang, Gelong Jiang, Guangyan Cai, Dewu Liu, Zhenfang Wu
Software Mentions: 3
Published: almost 8 years ago

10.1155/2020/1705387

Ammonia Exposure Induced Cilia Dysfunction of Nasal Mucosa in the Piglets
Cited by: 3
Author(s): Qiankun Wang, Mengyao Wang, Chun Liu, Liurong Huang, Yun Gao, Mei Yu, Zhao Song, Xiaoping Li
Software Mentions: 3
Published: over 6 years ago

10.1042/BSR20210495

RNA sequencing reveals potential interacting networks between the altered transcriptome and ncRNome in the skeletal muscle of diabetic mice
Cited by: 5
Author(s): Devesh Kesharwani, Amit Kumar, M. Damodara Poojary, Vinod Scaria, Malabika Datta
Software Mentions: 3
Published: over 5 years ago

10.1186/s13068-019-1466-z

Heterozygous diploid structure of Amorphotheca resinae ZN1 contributes efficient biodetoxification on solid pretreated corn stover
Cited by: 21
Author(s): Xia Yi, Qinghai Gao, Lei Zhang, Xia Wang, Yanqing He, Fengxian Hu, Jian Zhang, Gen Zou, Shihui Yang, Zhihua Zhou, Jie Bao
Software Mentions: 3
Published: over 7 years ago

10.1186/s13068-020-01810-z

Comparative transcriptome study of switchgrass (Panicum virgatum L.) homologous autopolyploid and its parental amphidiploid responding to consistent drought stress
Cited by: 17
Author(s): Peilin Chen, Jing Chen, Min Sun, Haidong Yan, Guangyan Feng, Bingchao Wu, Xinquan Zhang, Xiaoshan Wang, Linkai Huang
Software Mentions: 3
Published: about 6 years ago

10.1186/s13068-015-0208-0

A transcriptomic analysis of Neurospora crassa using five major crop residues and the novel role of the sporulation regulator rca-1 in lignocellulase production
Cited by: 22
Author(s): Bang Wang, Pengli Cai, Wenliang Sun, Jingen Li, Chaoguang Tian, Yanhe Ma
Software Mentions: 3
Published: over 11 years ago

10.1186/s13068-017-0705-4

Identification and characterization of the glucose dual-affinity transport system in Neurospora crassa: pleiotropic roles in nutrient transport, signaling, and carbon catabolite repression
Cited by: 49
Author(s): Bang Wang, Jingen Li, Jingfang Gao, Pengli Cai, Xiao Han, Chaoguang Tian
Software Mentions: 3
Published: almost 10 years ago

10.1186/s13068-015-0407-8

Enhanced degradation of softwood versus hardwood by the white-rot fungus Pycnoporus coccineus
Cited by: 65
Author(s): Marie Couturier, David Navarro, Didier Chevret, Bernard Henrissat, François Piumi, Francisco J. Ruíz-Dueñas, Ángel T. Martı́nez, Igor V. Grigoriev, Robert Riley, Anna Lipzen, Jean‐Guy Berrin, Emma R. Master, Marie‐Noëlle Rosso
Software Mentions: 3
Published: almost 11 years ago

10.1186/s13068-016-0534-x

Deep metagenome and metatranscriptome analyses of microbial communities affiliated with an industrial biogas fermenter, a cow rumen, and elephant feces reveal major differences in carbohydrate hydrolysis strategies
Cited by: 107
Author(s): Simon Güllert, Martin Fischer, Dmitrij Turaev, Britta Noebauer, Nele Ilmberger, Bernd Wemheuer, Malik Alawi, Thomas Rattei, Rolf Daniel, Ruth A. Schmitz, Adam Grundhoff, Wolfgang R. Streit
Software Mentions: 3
Published: over 10 years ago

10.1186/s13068-017-0944-4

Targeted metatranscriptomics of compost-derived consortia reveals a GH11 exerting an unusual exo-1,4-β-xylanase activity
Cited by: 29
Author(s): Bruno Luan Mello, Anna Alessi, Diego Mauricio Riaño‐Pachón, Eduardo R. deAzevedo, Francisco Eduardo Gontijo Guimarães, Melissa C. Espirito Santo, Simon J. McQueen‐Mason, Neil C. Bruce, Igor Polikarpov
Software Mentions: 3
Published: about 9 years ago

10.1186/s13068-020-01758-0

Comparative transcriptome analyses define genes and gene modules differing between two Populus genotypes with contrasting stem growth rates
Cited by: 14
Author(s): Xiao Han, Yi An, Yangyan Zhou, Chao Liu, Weilun Yin, Xinli Xia
Software Mentions: 3
Published: over 6 years ago

10.1186/s13068-020-01677-0

Hypoxia is regulating enzymatic wood decomposition and intracellular carbohydrate metabolism in filamentous white rot fungus
Cited by: 25
Author(s): Hans Kristian Mattila, Mari Mäkinen, Taina Lundell
Software Mentions: 3
Published: over 6 years ago

10.1038/s41416-021-01310-3

Checkpoint-blocker-induced autoimmunity is associated with favourable outcome in metastatic melanoma and distinct T-cell expression profiles
Cited by: 16
Author(s): Weiyu Ye, Anna Olsson‐Brown, Robert Watson, Vincent Cheung, Robert D. Morgan, Isar Nassiri, Rosalin Cooper, Taylor Ca, Umair Akbani, Oliver Brain, Rubeta Matin, Nicholas Coupe, Mark R. Middleton, Mark Coles, Joseph J. Sacco, Miranda Payne, Benjamin P. Fairfax
Software Mentions: 3
Published: over 5 years ago

10.1186/s13058-020-01362-y

Immuno-priming durvalumab with bevacizumab in HER2-negative advanced breast cancer: a pilot clinical trial
Cited by: 21
Author(s): Miguel Quintela‐Fandino, Esther Holgado, Luis Manso, Serafín Morales, Begoña Bermejo, Ramón Colomer, Juan V. Apala, Raquel Blanco, Manuel Muñoz, Eduardo Caleiras, Vega Iranzo, Mario Martínez, Orlando Domı́nguez, Javier Hornedo, Lucía González-Cortijo, Javier Cortés, Ariadna Gasol Cudós, Diego Malón, Antonio López-Alonso, Maria Carmen Moreno-Ortiz, Silvana Mourón, Santos Mañes
Software Mentions: 3
Published: almost 6 years ago

10.26508/lsa.201800082

Mitochondrial ubiquinone–mediated longevity is marked by reduced cytoplasmic mRNA translation
Cited by: 12
Author(s): Marte Molenaars, Georges E. Janssens, Toon Santermans, Marco Lezzerini, Rob Jelier, Alyson W. MacInnes, Riekelt H. Houtkooper
Software Mentions: 3
Published: about 8 years ago

10.26508/lsa.202000678

RNA exosome mutations in pontocerebellar hypoplasia alter ribosome biogenesis and p53 levels
Cited by: 16
Author(s): Juliane S. Müller, D T Burns, Helen Griffin, Graeme Raymond Wells, Romance A Zendah, Benjamin Munro, Claudia Schneider, Rita Horvath
Software Mentions: 3
Published: over 6 years ago

10.26508/lsa.202000645

Integrin α3β1 in hair bulge stem cells modulates CCN2 expression and promotes skin tumorigenesis
Cited by: 5
Author(s): Veronika Ramovs, Ana Krotenberg Garcia, Ji‐Ying Song, Iris de Rink, Maaike Kreft, Roel Goldschmeding, Arnoud Sonnenberg
Software Mentions: 3
Published: over 6 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 11 years ago

10.1007/s00335-016-9663-6

Genome characterization of the selected long- and short-sleep mouse lines
Cited by: 4
Author(s): Robin D. Dowell, Aaron Odell, Phillip A. Richmond, Daniel Malmer, Eitan Halper-Stromberg, Beth Bennett, Colin Larson, Sonia M. Leach, Richard A. Radcliffe
Software Mentions: 3
Published: about 10 years ago

10.1111/1751-7915.13863

Transcriptome analysis reveals the roles of nitrogen metabolism and sedoheptulose bisphosphatase pathway in methanol‐dependent growth of Corynebacterium glutamicum
Cited by: 4
Author(s): Liwen Fan, Yu Wang, Jin Qian, Ning Gao, Zhihui Zhang, Xiaomeng Ni, Letian Sun, Qianqian Yuan, Ping Zheng, Jibin Sun
Software Mentions: 3
Published: over 5 years ago

10.1186/s12934-015-0377-3

Genome-scale metabolic reconstructions and theoretical investigation of methane conversion in Methylomicrobium buryatense strain 5G(B1)
Cited by: 102
Author(s): Andrea De La Torre, Aisha Metivier, Frances Chu, Lieve M.L. Laurens, David A. C. Beck, Philip T. Pienkos, Mary E. Lidstrom, Marina G. Kalyuzhnaya
Software Mentions: 3
Published: almost 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 9 years ago

10.3390/microorganisms8071068

In vitro Edwardsiella piscicida CK108 Transcriptome Profiles with Subinhibitory Concentrations of Phenol and Formalin Reveal New Insights into Bacterial Pathogenesis Mechanisms
Cited by: 8
Author(s): Ju Bin Yoon, Sungmin Hwang, Se-Won Baek, Seung-Ki Lee, Woo Young Bang, Ki Hwan Moon
Software Mentions: 3
Published: over 6 years ago

10.3390/microorganisms8050707

Transcriptome Analysis of Gene Expression in Dermacoccus abyssi HZAU 226 under Lysozyme Stress
Cited by: 7
Author(s): Xinshuai Zhang, Yao Ruan, Wukang Liu, Qian Chen, Lihong Gu, Aizhen Guo
Software Mentions: 3
Published: over 6 years ago

10.3390/microorganisms9020382

Bacillus amyloliquefaciens TL Downregulates the Ileal Expression of Genes Involved in Immune Responses in Broiler Chickens to Improve Growth Performance
Cited by: 7
Author(s): Yuxuan Hong, Cheng Yang, Leluo Guan, Zutao Zhou, Xiaowen Li, Deshi Shi, Yufei Xiao
Software Mentions: 3
Published: over 5 years ago

10.3390/microorganisms9030656

Cranberry Proanthocyanidins and Dietary Oligosaccharides Synergistically Modulate Lactobacillus plantarum Physiology
Cited by: 7
Author(s): Ezgi Özcan, Michelle R Rozycki, David A. Sela
Software Mentions: 3
Published: over 5 years ago

10.1093/molbev/msab131

Diverse Molecular Mechanisms Contribute to Differential Expression of Human Duplicated Genes
Cited by: 9
Author(s): Colin J. Shew, Paulina Carmona-Mora, Daniela C. Soto, Mira Mastoras, Elizabeth S. Roberts, Joseph Rosas, Dhriti Jagannathan, Gulhan Kaya, Henriette O’Geen, Megan Y. Dennis
Software Mentions: 3
Published: over 5 years ago

10.1186/s12943-019-0977-3

MiR155 sensitized B-lymphoma cells to anti-PD-L1 antibody via PD-1/PD-L1-mediated lymphoma cell interaction with CD8+T cells
Cited by: 60
Author(s): Zhong Zheng, Rui Sun, Hongzheng Zhao, Di Fu, Hui Zhong, Xiang‐Qin Weng, Bin Qu, Yan Zhao, Li Wang, Wei‐Li Zhao
Software Mentions: 3
Published: over 7 years ago

10.1016/j.mcpro.2021.100092

The C-Mannosylome of Human Induced Pluripotent Stem Cells Implies a Role for ADAMTS16 C-Mannosylation in Eye Development
Cited by: 7
Author(s): Karsten Cirksena, Hermann J. Hütte, Aleksandra Shcherbakova, Thomas Thumberger, Roman Sakson, Stefan Weiß, Lars Riff Jensen, Alina Friedrich, Daniel Todt, Andreas W. Kuß, Thomas Ruppert, Joachim Wittbrodt, Hans Bakker, Falk F. R. Buettner
Software Mentions: 3
Published: almost 6 years ago

10.1016/j.molmet.2021.101231

Adhesion receptor ADGRG2/GPR64 is in the GI-tract selectively expressed in mature intestinal tuft cells
Cited by: 9
Author(s): Kaare V. Grunddal, Sarah Tonack, Kristoffer L. Egerod, Jonatan J Thompson, Natalia Petersen, Maja S. Engelstoft, Constance Vagne, Céline Keime, Gérard Gradwohl, Stefan Offermanns, Thue W. Schwartz
Software Mentions: 3
Published: about 5 years ago

10.1111/mmi.12345

The <scp>APSES</scp> transcription factor <scp>Efg</scp>1 is a global regulator that controls morphogenesis and biofilm formation in <scp>C</scp>andida parapsilosis
Cited by: 42
Author(s): Leona A. Connolly, Alessandro Riccombeni, Zsuzsana Grózer, Linda Holland, Denise B. Lynch, David R. Andes, Attila Gácser, Geraldine Butler
Software Mentions: 3
Published: about 13 years ago

10.1186/s13024-019-0335-3

Microglia affect α-synuclein cell-to-cell transfer in a mouse model of Parkinson’s disease
Cited by: 117
Author(s): Sonia George, Nolwen L. Rey, Trevor Tyson, Corinne R. Esquibel, Lindsay Meyerdirk, Emily Schulz, Steven Pierce, Amanda R. Burmeister, Zachary Madaj, Jennifer A. Steiner, Martha L. Escobar Galvis, Lena Brundin, Patrik Brundin
Software Mentions: 3
Published: about 7 years ago

10.1186/s13024-016-0133-0

Spinal cord injury induces astroglial conversion towards neuronal lineage
Cited by: 36
Author(s): Harun N. Noristani, Jean Charles Sabourin, Hassan Boukhaddaoui, Emilie Chan-Seng, Yannick Nicolas Gerber, Florence E. Perrin
Software Mentions: 3
Published: about 10 years ago

10.1002/1878-0261.12797

Optimized low‐dose combinatorial drug treatment boosts selectivity and efficacy of colorectal carcinoma treatment
Cited by: 19
Author(s): Marloes Zoetemelk, George M. Ramzy, Magdalena Rausch, Thibaud Koessler, Judy R. van Beijnum, Andrea Weiss, Valentin Mieville, Sander R. Piersma, Richard R. de Haas, Céline Delucinge-Vivier, Axel Andrès, Christian Toso, Alex A. Henneman, Simone Ragusa, Tatiana V. Petrova, Mylène Docquier, Thomas McKee, Connie R. Jiménez, Youssef Daali, Arjan W. Griffioen, Laura Rubbia‐Brandt, Pierre‐Yves Dietrich, Patrycja Nowak-Śliwińska
Software Mentions: 3
Published: about 6 years ago

10.1002/1878-0261.12525

Negative regulation of miR‐1275 by H3K27me3 is critical for glial induction of glioblastoma cells
Cited by: 12
Author(s): Jialuo Mai, Jiayu Gu, Ying Liu, Xincheng Liu, Ke Sai, Zhijie Chen, Wanjun Lu, Xiaozhi Yang, Jingyi Wang, Cui Guo, Shenghua Sun, Fan Xing, Longxiang Sheng, Bingzheng Lu, Zhu Zhu, Hongjiaqi Sun, Dongdong Xue, Yuan Lin, Jing Cai, Yaqian Tan, Chuntao Li, Wei Yin, Lin Cao, Ying Ouyang, Pengxin Qiu, Xingwen Su, Yan Gao, Jiankai Liang, Wenbo Zhu
Software Mentions: 3
Published: over 7 years ago

10.1111/mpp.12877

Show me your secret(ed) weapons: a multifaceted approach reveals a wide arsenal of type III‐secreted effectors in the cucurbit pathogenic bacterium Acidovorax citrulli and novel effectors in the Acidovorax genus
Cited by: 26
Author(s): Irene Jiménez‐Guerrero, Francisco Pérez‐Montaño, Gustavo Mateus da Silva, Naama Wagner, Dafna Shkedy, Mei Zhao, Lorena Pizarro, Maya Bar, R. R. Walcott, Guido Sessa, Tal Pupko, Saul Burdman
Software Mentions: 3
Published: about 7 years ago

10.1111/mpp.12429

Transcriptional reprogramming underpins enhanced plant growth promotion by the biocontrol fungus Trichoderma hamatum GD12 during antagonistic interactions with Sclerotinia sclerotiorum in soil
Cited by: 30
Author(s): Sophie Shaw, Kate Le Cocq, Konrad Paszkiewicz, Karen Moore, Rebecca Winsbury, Marta de Torres Zabala, David J. Studholme, Deborah Salmon, Christopher R. Thornton, Murray Grant
Software Mentions: 3
Published: over 10 years ago

10.15252/msb.20167461

Genetic circuit characterization and debugging using <scp>RNA</scp> ‐seq
Cited by: 74
Author(s): Thomas E. Gorochowski, Amin Espah Borujeni, Yong‐Jin Park, Alec A. K. Nielsen, Jing Zhang, Bryan S. Der, D. Benjamin Gordon, Christopher A. Voigt
Software Mentions: 3
Published: about 9 years ago

10.1186/s13567-018-0546-6

RNA-Seq based transcriptome of whole blood from immunocompetent pigs (Sus scrofa) experimentally infected with Mycoplasma suis strain Illinois
Cited by: 14
Author(s): Naíla Cannes do Nascimento, Ana M. S. Guimarães, Andrea Pires dos Santos, Yuefeng Chu, Lucas Miranda Marques, Joanne B. Messick
Software Mentions: 3
Published: over 8 years ago

10.1186/s13567-018-0545-7

Comparative liver transcriptome analysis in ducklings infected with duck hepatitis A virus 3 (DHAV-3) at 12 and 48 hours post-infection through RNA-seq
Cited by: 11
Author(s): Xuelian Zhang, Chen Cao, Yue Liu, Haihui Qi, Wenjing Zhang, Chunxue Hao, Haotian Chen, Qi Zhang, Wenlong Zhang, Mingchun Gao, Junwei Wang, Bo Ma
Software Mentions: 3
Published: over 8 years ago

10.1186/s12985-018-1044-1

Transcriptome analysis of Nicotiana benthamiana infected by Tobacco curly shoot virus
Cited by: 35
Author(s): Ke Li, Gentu Wu, Mingjun Li, Mingge Ma, Jie Du, Miao Sun, Xianchao Sun, Ling Qing
Software Mentions: 3
Published: about 8 years ago

10.1080/21505594.2020.1839231

A new regulator in the crossroads of oxidative stress resistance and virulence in Candida glabrata: The transcription factor CgTog1
Cited by: 5
Author(s): Pedro Pais, Susana Vagueiro, Dalila Mil‐Homens, Andreia I. Pimenta, Romeu Viana, Michiyo Okamoto, Hiroji Chibana, Arsénio M. Fialho, Miguel C. Teixeira
Software Mentions: 3
Published: about 6 years ago

10.3390/v11090793

Comparison of Transcriptome Differences in Soybean Response to Soybean Mosaic Virus under Normal Light and in the Shade
Cited by: 19
Author(s): Lei Zhang, Jing Shang, Wenming Wang, Junbo Du, Kai Li, Xiaoling Wu, Yu Liu, Chunyan Liu, Muhammad Ibrahim Khaskheli, Wenyu Yang
Software Mentions: 3
Published: about 7 years ago

10.3390/v13081603

Characterization of the SARS-CoV-2 Host Response in Primary Human Airway Epithelial Cells from Aged Individuals
Cited by: 9
Author(s): Subramaniyan Bharathiraja, Jason L. Larabee, Manish Bodas, Andrew R. Moore, Anthony W. G. Burgett, Dean A. Myers, Constantin Georgescu, Jonathan D. Wren, James F. Papin, Matthew S. Walters
Software Mentions: 3
Published: about 5 years ago

10.3390/v13091834

The MAPK/ERK Pathway and the Role of DUSP1 in JCPyV Infection of Primary Astrocytes
Cited by: 4
Author(s): Michael Wilczek, Francesca J. Armstrong, Remi P. Geohegan, Colleen L. Mayberry, Jeanne K. DuShane, Benjamin L. King, Melissa S. Maginnis
Software Mentions: 3
Published: about 5 years ago

10.1186/s13071-019-3650-1

Evaluation of dynamic developmental processes and the molecular basis of the high body fat percentage of different proglottid types of Moniezia expansa
Cited by: 8
Author(s): Yi Liu, Zhengrong Wang, Shuai Pang, Wenjuan Zhao, Lichao Kang, Yanyan Zhang, Hui Zhang, Jingquan Yang, Zhixin Wang, Pingping Lu, Mengfei Xu, Weiyi Wang, Xiaochen Bo, Zhenzhen Li
Software Mentions: 3
Published: over 7 years ago

10.1186/s13071-021-04915-y

Comparative analysis of the transcriptional responses of five Leishmania species to trivalent antimony
Cited by: 2
Author(s): Julián Medina, Lissa Cruz-Saavedra, Luz Helena Patiño, Marina Muñoz, Juan David Ramírez
Software Mentions: 3
Published: about 5 years ago

10.1186/s13071-017-2326-y

Differential gene expression in Anopheles stephensi following infection with drug-resistant Plasmodium yoelii
Cited by: 4
Author(s): Jingru Zhang, Jiacheng Huang, Feng Zhu, Jian Zhang
Software Mentions: 3
Published: about 9 years ago

10.7717/peerj.10671

RNA sequencing analysis of FGF2-responsive transcriptome in skin fibroblasts
Cited by: 4
Author(s): Bingcheng Wu, Xinjie Tang, Zhaoping Zhou, Hong-Lin Ke, Shao Tang, Ronghu Ke
Software Mentions: 3
Published: almost 6 years ago

10.7717/peerj.3631

RNA-seq reveals more consistent reference genes for gene expression studies in human non-melanoma skin cancers
Cited by: 34
Author(s): Van L.T. Hoang, Lisa Tom, Xiu-Cheng Quek, Jean-Marie Tan, Elizabeth Payne, Lynlee L. Lin, Sudipta Sinnya, Anthony P. Raphael, Duncan Lambie, Ian H. Frazer, Marcel E. Dinger, H. Peter Soyer, Tarl W. Prow
Software Mentions: 3
Published: about 9 years ago

10.7717/peerj.4466

Global analysis of A-to-I RNA editing reveals association with common disease variants
Cited by: 20
Author(s): Oscar Franzén, Raili Ermel, Katyayani Sukhavasi, Rajeev Jain, Anamika Jain, Christer Betsholtz, Chiara Giannarelli, Jason C. Kovacic, Arno Ruusalepp, Josefin Skogsberg, Ke Hao, Eric E. Schadt, Johan Björkegren
Software Mentions: 3
Published: over 8 years ago

10.7717/peerj.11919

The whole-genome and expression profile analysis of WRKY and RGAs in Dactylis glomerata showed that DG6C02319.1 and DgWRKYs may cooperate in the immunity against rust
Cited by: 4
Author(s): Juncai Ren, Jialing Hu, Ailing Zhang, Shuping Ren, Tingting Jing, Xiaoshan Wang, Min Sun, Linkai Huang, Bing Zeng
Software Mentions: 3
Published: about 5 years ago

10.14814/phy2.13019

Effect of energy restriction and physical exercise intervention on phenotypic flexibility as examined by transcriptomics analyses of mRNA from adipose tissue and whole body magnetic resonance imaging
Cited by: 19
Author(s): Sindre Lee, Frode Norheim, Torgrim M. Langleite, Hans Jørgen Noreng, Trygve H. Storås, Lydia A. Afman, Gary Frost, Jimmy D. Bell, E. Louise Thomas, Kristoffer Jensen Kolnes, Daniel S. Tangen, Hans Kristian Stadheim, Gregor D. Gilfillan, Hanne Løvdal Gulseth, Kåre I. Birkeland, Jørgen Jensen, Christian A. Drevon, Torgeir Holen
Software Mentions: 3
Published: about 10 years ago

10.1111/pbi.12910

Up‐regulation of Gh<scp>TT</scp>2‐3A in cotton fibres during secondary wall thickening results in brown fibres with improved quality
Cited by: 45
Author(s): Qian Yan, Yi Wang, Qian Li, Zhengsheng Zhang, Hui Ding, Yue Zhang, Housheng Liu, Ming Luo, Dexin Liu, Song Wu, Haifeng Liu, Dan Yao, Xufen Ouyang, Yaohua Li, Xin Li, Yan Pei, Yazhong Xiao
Software Mentions: 3
Published: over 8 years ago

10.1111/pbi.13637

ZmbHLH124 identified in maize recombinant inbred lines contributes to drought tolerance in crops
Cited by: 8
Author(s): Shaowei Wei, Xia R, Chengxuan Chen, Xiaoling Shang, Fengyong Ge, Huimin Wei, Huabang Chen, Yaorong Wu, Qi Xie
Software Mentions: 3
Published: over 5 years ago

10.1111/pbi.13499

The celery genome sequence reveals sequential paleo‐polyploidizations, karyotype evolution and resistance gene reduction in apiales
Cited by: 55
Author(s): Xiaoming Song, Pengchuan Sun, Jiaqing Yuan, Ke Gong, Nan Li, Fanbo Meng, Zhikang Zhang, Xinyu Li, Jingjing Hu, Jinpeng Wang, Qing Yang, Beibei Jiao, Fulei Nie, Tao Liu, Wei Chen, Shuyan Feng, Qiaoying Pei, Tong Yu, Xi Kang, Wei Zhao, Chunlin Cui, Ying Yu, Tong Wu, Lanxing Shan, Man Liu, Zhiji Qin, Hao Lin, Rajeev K. Varshney, Xiuqing Li, Andrew H. Paterson, Xiyin Wang
Software Mentions: 3
Published: almost 6 years ago

10.1111/pbi.13246

Genome‐wide expression quantitative trait locus analysis in a recombinant inbred line population for trait dissection in peanut
Cited by: 14
Author(s): Li Huang, Xia Liu, Manish K. Pandey, Xiaoping Ren, Haiwen Chen, Xiaomeng Xue, Nian Liu, Dongxin Huai, Yuning Chen, Xiaojing Zhou, Huaiyong Luo, Weigang Chen, Yong Lei, Kede Liu, Yingjie Xiao, Rajeev K. Varshney, Boshou Liao, Huifang Jiang
Software Mentions: 3
Published: about 7 years ago

10.1111/pbi.13007

A Ma10 gene encoding P‐type <scp>ATP</scp>ase is involved in fruit organic acid accumulation in apple
Cited by: 54
Author(s): Baiquan Ma, Liao Liao, Ting Fang, Qian Peng, Collins Ogutu, Hui Zhou, Fengwang Ma, Yuepeng Han
Software Mentions: 3
Published: about 8 years ago

10.1002/pld3.56

Waterlogging affects plant morphology and the expression of key genes in tef ( Eragrostis tef )
Cited by: 21
Author(s): Gina Cannarozzi, Annett Weichert, Mirjam Schnell, Celia Ruiz, Svenja Bossard, Regula Blösch, Sonia Plaza-Wüthrich, Solomon Chanyalew, Kebebew Assefa, Zerihun Tadele
Software Mentions: 3
Published: over 8 years ago

10.1002/pld3.326

slim shady is a novel allele of PHYTOCHROME B present in the T‐DNA line SALK_015201
Cited by: 5
Author(s): Linkan Dash, Robert E. McEwan, Christian Montes, Ludvin Mejia, Justin W. Walley, Brian P. Dilkes, Dior R. Kelley
Software Mentions: 3
Published: over 5 years ago

10.1002/pld3.92

Transcriptomic analysis of sweet potato under dehydration stress identifies candidate genes for drought tolerance
Cited by: 18
Author(s): Kin H. Lau, Mariana Herrera, Emily Crisovan, Shan Wu, Zhangjun Fei, Muhammad Awais Khan, C. Robin Buell, Dorcus C. Gemenet
Software Mentions: 3
Published: about 8 years ago

10.1002/pld3.154

Network‐based feature selection reveals substructures of gene modules responding to salt stress in rice
Cited by: 13
Author(s): Qian Du, Malachy T. Campbell, Huihui Yu, Kan Liu, Harkamal Walia, Chi Zhang, Chi Zhang
Software Mentions: 3
Published: over 7 years ago

10.1111/tpj.14417

Poplar carbohydrate‐active enzymes: whole‐genome annotation and functional analyses based on <scp>RNA</scp> expression data
Cited by: 29
Author(s): Vikash Kumar, Matthieu Hainaut, Nicolas Delhomme, Chanaka Mannapperuma, Peter Immerzeel, Nathaniel R. Street, Bernard Henrissat, Ewa J. Mellerowicz
Software Mentions: 3
Published: over 7 years ago

10.3390/plants10010103

Gene and Metabolite Integration Analysis through Transcriptome and Metabolome Brings New Insight into Heat Stress Tolerance in Potato (Solanum tuberosum L.)
Cited by: 10
Author(s): Bailin Liu, Lingshuang Kong, Yu Zhang, Yuncheng Liao
Software Mentions: 3
Published: almost 6 years ago

10.3390/plants8020047

Intrusive Growth of Phloem Fibers in Flax Stem: Integrated Analysis of miRNA and mRNA Expression Profiles
Cited by: 16
Author(s): Oleg Gorshkov, Tatyana Chernova, Natalia Mokshina, Natalia Gogoleva, Dmitry Suslov, А.А. Ткаченко, Т. А. Горшкова
Software Mentions: 3
Published: over 7 years ago

10.1371/journal.pbio.1002500

Allele-Specific Transcriptome and Methylome Analysis Reveals Stable Inheritance and Cis-Regulation of DNA Methylation in Nasonia
Cited by: 50
Author(s): Xiaozhu Wang, John H. Werren, Andrew G. Clark
Software Mentions: 3
Published: over 10 years ago

10.1371/journal.pbio.2005750

A systems genetics resource and analysis of sleep regulation in the mouse
Cited by: 50
Author(s): Shanaz Diessler, Jan M, Yann Emmenegger, Nicolas Guex, Benita Middleton, Debra J. Skene, Mark Ibberson, Frédéric Burdet, Lou Götz, Marco Pagni, Martial Sankar, Robin Liechti, Charlotte N. Hor, Ioannis Xénarios, Paul Franken
Software Mentions: 3
Published: over 8 years ago

10.1371/journal.pbio.3000369

Spectrin-based membrane skeleton supports ciliogenesis
Cited by: 20
Author(s): Ru Jia, Dongdong Li, Ming Li, Yunpeng Chai, Yufan Liu, Zhongyun Xie, Wenxin Shao, Chao Xie, Liuju Li, Xiaoshuai Huang, Liangyi Chen, Wei Li, Guangshuo Ou
Software Mentions: 3
Published: over 7 years ago

10.1371/journal.pcbi.1004400

Controlled Measurement and Comparative Analysis of Cellular Components in E. coli Reveals Broad Regulatory Changes in Response to Glucose Starvation
Cited by: 38
Author(s): John R. Houser, Craig S. Barnhart, Daniel R. Boutz, Sean M. Carroll, Aurko Dasgupta, Joshua K. Michener, Brittany D. Needham, Ophelia Papoulas, Viswanadham Sridhara, Dariya K. Sydykova, Christopher J. Marx, M. Stephen Trent, Jeffrey E. Barrick, Edward M. Marcotte, Claus O. Wilke
Software Mentions: 3
Published: about 11 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 8 years ago

10.1371/journal.pone.0225466

HeLa-CCL2 cell heterogeneity studied by single-cell DNA and RNA sequencing
Cited by: 15
Author(s): Waner Hu, Xin Zhang, Qiufang Guo, Jingwei Yang, Yuan Yang, Shicheng Wei, Xiao‐Dong Su
Software Mentions: 3
Published: almost 7 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 9 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 9 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 9 years ago

10.1371/journal.pone.0189476

Transcriptomic analysis of chicken Myozenin 3 regulation reveals its potential role in cell proliferation
Cited by: 12
Author(s): Maosen Ye, Fei Ye, Liutao He, Bin Luo, Feng Yang, Can Cui, Xiaoling Zhao, Huadong Yin, Diyan Li, Hengyong Xu, Yan Wang, Qing Zhu
Software Mentions: 3
Published: almost 9 years ago

Projects: pypi: HTSeq

Science Score: 65/100

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Papers Mentioning HTSeq 3,071