bioconductor: edgeR | Projects | Ecosyste.ms: Papers

10.1084/jem.20200137

PDGFA-associated protein 1 protects mature B lymphocytes from stress-induced cell death and promotes antibody gene diversification
Cited by: 6
Author(s): Verónica Delgado-Benito, Maria Berruezo-Llacuna, Robert Altwasser, Wiebke Winkler, Devakumar Sundaravinayagam, Sandhya Balasubramanian, Marieta Caganova, Robin Graf, Ali Rahjouei, Marie-Thérèse Henke, Madlen Driesner, Lisa Keller, Alessandro Prigione, Martin Janz, Altuna Akalin, Michela Di Virgilio
Software Mentions: 4
Published: about 6 years ago

10.1186/1471-2105-12-323

RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome
Cited by: 14,016
Author(s): Bo Li, Colin N. Dewey
Software Mentions: 4
Published: about 15 years ago

10.3390/ani11092705

Ruminal and Fecal Bacteriome of Dairy Calves Fed Different Levels and Sources of NDF
Cited by: 2
Author(s): Gercino Ferreira Virgínio Júnior, Ana Paula da Silva, Ariany Faria de Toledo, Milaine Poczynek, Amanda Moelemberg Cezar, Horácio Montenegro, Luiz Lehmann Coutinho, Carla Maris Machado Bittar
Software Mentions: 4
Published: almost 5 years ago

10.1534/g3.119.400757

Machine Learning Enables High-Throughput Phenotyping for Analyses of the Genetic Architecture of Bulliform Cell Patterning in Maize
Cited by: 9
Author(s): Pengfei Qiao, Lin Meng, Miguel Vasquez, Susanne Matschi, James Chamness, Matheus Baseggio, Laurie G. Smith, Mert R. Sabuncu, Michael A. Gore, Michael J. Scanlon
Software Mentions: 4
Published: over 6 years ago

10.3389/fgene.2014.00035

The analytical landscape of static and temporal dynamics in transcriptome data
Cited by: 26
Author(s): Sangwon Oh, Seongho Song, Nupur Dasgupta, Gregory A. Grabowski
Software Mentions: 4
Published: over 12 years ago

10.1186/s12896-015-0207-z

A Comparison of transgenic and wild type soybean seeds: analysis of transcriptome profiles using RNA-Seq
Cited by: 22
Author(s): Kevin Lambirth, Adam M. Whaley, Ivory C. Blakley, Jessica A. Schlueter, Kenneth L. Bost, Ann E. Loraine, Kenneth J. Piller
Software Mentions: 4
Published: almost 11 years ago

10.1186/s12859-019-2623-x

MNEMONIC: MetageNomic Experiment Mining to create an OTU Network of Inhabitant Correlations
Cited by: 2
Author(s): Aleksandra Perz, Cory B. Giles, Chase A. Brown, Hunter Porter, Xiavan Roopnarinesingh, Jonathan D. Wren
Software Mentions: 4
Published: over 7 years ago

10.3389/fonc.2020.556497

Landscape of N6-Methyladenosine Modification Patterns in Human Ameloblastoma
Cited by: 19
Author(s): Xing Niu, Jun Xu, Jinwen Liu, Lijie Chen, Xue Qin, Ming Zhong
Software Mentions: 4
Published: almost 6 years ago

10.1128/mSphereDirect.00120-18

Zika Virus Infection Preferentially Counterbalances Human Peripheral Monocyte and/or NK Cell Activity
Cited by: 26
Author(s): Fok‐Moon Lum, David Lee, Tze-Kwang Chua, Jeslin J. L. Tan, Cheryl Yi‐Pin Lee, Xuan Li, Yongxiang Fang, Bernett Lee, Wearn‐Xin Yee, Natasha Y. Rickett, Po Ying Chia, Vanessa Lim, Yee‐Sin Leo, David A. Matthews, Julian A. Hiscox, Lisa F. P. Ng
Software Mentions: 4
Published: over 8 years ago

10.1016/j.immuni.2021.05.016

A PGE2-MEF2A axis enables context-dependent control of inflammatory gene expression
Cited by: 22
Author(s): Francesco Cilenti, Giulia Barbiera, Nicoletta Caronni, Dario Iodice, Elisa Montaldo, Simona Barresi, Eleonora Lusito, Vincenzo Cuzzola, Francesco Maria Vittoria, Luca Mezzanzanica, Paolo Miotto, Pietro Di Lucia, Dejan Lazarevic, Daniela María Cirillo, Matteo Iannacone, Marco Genua, Renato Ostuni
Software Mentions: 4
Published: about 5 years ago

10.3390/ijms20143480

Discovering and Constructing ceRNA-miRNA-Target Gene Regulatory Networks during Anther Development in Maize
Cited by: 34
Author(s): Ziwen Li, Xianghai An, Taotao Zhu, Tingwei Yan, Wu Shu, Youhui Tian, Jinping Li, Xiangyuan Wan
Software Mentions: 4
Published: about 7 years ago

10.1097/MIB.0000000000001131

Azathioprine with Allopurinol
Cited by: 7
Author(s): Sally A. Coulthard, Phil Berry, Sarah McGarrity, Simon D. McLaughlin, Azhar Ansari, Christopher P.F. Redfern
Software Mentions: 4
Published: about 9 years ago

10.1111/jcmm.14779

Four transcription profile–based models identify novel prognostic signatures in oesophageal cancer
Cited by: 9
Author(s): Tongyan Liu, Panqi Fang, Chencheng Han, Zhongliang Ma, Weizhang Xu, Wenjia Xia, Jingwen Hu, Yongming Xu, Lin Xu, Rong Yin, Siwei Wang, Qin Zhang
Software Mentions: 4
Published: almost 7 years ago

10.1128/mBio.00588-21

An Infection-Tolerant Mammalian Reservoir for Several Zoonotic Agents Broadly Counters the Inflammatory Effects of Endotoxin
Cited by: 6
Author(s): Gabriela Balderrama-Gutierrez, Ana Milovic, Vanessa J. Cook, M. Nurul Islam, Youwen Zhang, Hippokratis Kiaris, John T. Belisle, A Mortazavi, Alan G. Barbour
Software Mentions: 4
Published: over 5 years ago

10.1128/mBio.00617-20

EspFu-Mediated Actin Assembly Enhances Enteropathogenic <i>Escherichia coli</i> Adherence and Activates Host Cell Inflammatory Signaling Pathways
Cited by: 12
Author(s): Fernando Henrique Martins, Ashwani Kumar, Cecília M. Abe, Enéas Carvalho, Milton Yutaka Nishiyama-Jr, Chao Xing, Vanessa Sperandio, Waldir P. Elias
Software Mentions: 4
Published: over 6 years ago

10.3390/ijms21061910

NR2F2 Orphan Nuclear Receptor is Involved in Estrogen Receptor Alpha-Mediated Transcriptional Regulation in Luminal A Breast Cancer Cells
Cited by: 8
Author(s): Edina Erdős, Bálint László Bálint
Software Mentions: 4
Published: over 6 years ago

10.3390/jcm10132973

Meteorin Is a Novel Therapeutic Target for Wet Age-Related Macular Degeneration
Cited by: 4
Author(s): Kimberley Delaunay, Alexandre Sellam, Virginie Dinet, Alexandre Moulin, Min Zhao, Emmanuelle Gélizé, Jérémie Canonica, Marie‐Christine Naud, Patricia Crisanti-Lassiaz, Francine Behar‐Cohen
Software Mentions: 4
Published: about 5 years ago

10.3390/ijms20225710

The Biological Effects of Complete Gasoline Engine Emissions Exposure in a 3D Human Airway Model (MucilAirTM) and in Human Bronchial Epithelial Cells (BEAS-2B)
Cited by: 13
Author(s): Pavel Rőssner, Tereza Červená, Michal Vojtíšek-Lom, Kristýna Vrbová, Antonín Ambrož, Zuzana Nováková, Fatima Elzeinová, Hasmik Margaryan, V. Beránek, Martin Pechout, David Macoun, Jǐŕı Kléma, Andrea Rössnerová, Miroslav Cigánek, Jan Topinka
Software Mentions: 4
Published: almost 7 years ago

10.1200/CCI.19.00118

Statistical Assessment of Depth Normalization for Small RNA Sequencing
Cited by: 7
Author(s): Li‐Xuan Qin, Jian Zou, Jiejun Shi, Ann Lee, Aleksandra Mihailović, Thalia A. Farazi, Thomas Tuschl, Samuel Singer
Software Mentions: 4
Published: almost 6 years ago

10.1111/jcmm.15271

Systematic prediction of key genes for ovarian cancer by co‐expression network analysis
Cited by: 12
Author(s): Mingyuan Wang, Jinjin Wang, Jinglan Liu, Lili Zhu, Heng Ma, Jian Zou, Wei Wu, Kangkai Wang
Software Mentions: 4
Published: over 6 years ago

10.1038/s41598-019-54935-z

Identification of potential chemosignals in the European water vole Arvicola terrestris
Cited by: 8
Author(s): Patricia Nagnan‐Le Meillour, Amandine Descamps, Chrystelle Le Danvic, Maurane Grandmougin, Jean‐Michel Saliou, Christophe Klopp, Marine Milhes, Coralie Bompard, Didier Chesneau, Kévin Poissenot, Matthieu Keller
Software Mentions: 4
Published: over 6 years ago

10.1038/s41598-019-55852-x

Multi-parameter immune profiling of peripheral blood mononuclear cells by multiplexed single-cell mass cytometry in patients with early multiple sclerosis
Cited by: 34
Author(s): Chotima Böttcher, Camila Fernández-Zapata, Stephan Schlickeiser, Désirée Kunkel, Axel Schulz, Henrik E. Mei, Carl Weidinger, René M. Gieß, Susanna Asseyer, Britta Siegmund, Friedemann Paul, Klemens Ruprecht, Josef Priller
Software Mentions: 4
Published: over 6 years ago

10.1128/mBio.02504-18

The Major RNA-Binding Protein ProQ Impacts Virulence Gene Expression in Salmonella enterica Serovar Typhimurium
Cited by: 73
Author(s): Alexander J. Westermann, Elisa Venturini, Mikael E. Sellin, Konrad U. Förstner, Wolf‐Dietrich Hardt, Jörg Vogel
Software Mentions: 4
Published: over 7 years ago

10.1111/jcmm.16133

Identification of Smad3‐related transcriptomes in type‐2 diabetic nephropathy by whole transcriptome RNA sequencing
Cited by: 3
Author(s): Qin Zhou, Hong-Hong Guo, Chaolun Yu, Xiao‐Ru Huang, Lijun Liang, Puhua Zhang, Jia-Kuo Yu, Jizhou Zhang, Ting‐Fung Chan, Rong Ma, Hui‐Yao Lan
Software Mentions: 4
Published: over 5 years ago

10.1038/s41398-019-0472-z

DLPFC transcriptome defines two molecular subtypes of schizophrenia
Cited by: 26
Author(s): Elijah F. W. Bowen, Jack L. Burgess, Richard Granger, Joel E. Kleinman, C. Harker Rhodes
Software Mentions: 4
Published: over 7 years ago

10.1038/s41398-017-0050-1

Gene expression associated with PTSD in World Trade Center responders: An RNA sequencing study
Cited by: 56
Author(s): Pei‐Fen Kuan, Monika A. Waszczuk, Roman Kotov, Sean Clouston, Xiaohua Yang, Prashant Singh, Sean T. Glenn, Eduardo Cortes Gomez, Jianmin Wang, Evelyn J. Bromet, Benjamin J. Luft
Software Mentions: 4
Published: over 8 years ago

10.1038/tp.2016.67

Candidate gene networks and blood biomarkers of methamphetamine-associated psychosis: an integrative RNA-sequencing report
Cited by: 26
Author(s): Michael S. Breen, Anne Uhlmann, Christiane M. Nday, Stephen J. Glatt, Mario Mitt, A. Metsalpu, Dan J. Stein, Nicola Illing
Software Mentions: 4
Published: over 10 years ago

10.1172/jci.insight.142980

Treating ICB-resistant glioma with anti-CD40 and mitotic spindle checkpoint controller BAL101553 (lisavanbulin)
Cited by: 5
Author(s): Vassilis Genoud, Felipe I Espinoza, Eliana Marinari, Viviane Rochemont, Pierre‐Yves Dietrich, Paul M.J. McSheehy, Felix Bachmann, Heidi A. Lane, Paul R Walker
Software Mentions: 4
Published: almost 5 years ago

10.7150/thno.55645

Deciphering the autophagy regulatory network via single-cell transcriptome analysis reveals a requirement for autophagy homeostasis in spermatogenesis
Cited by: 18
Author(s): Mei Wang, Yanwen Xu, Yuncong Zhang, Yuhan Chen, Gang Chang, Geng An, Xinyan Yang, Caihong Zheng, Jiexiang Zhao, Zhaoting Liu, Dazhuang Wang, Masahiro Kai, Rao S, Meng Dai, Dong Wang, Xiaoyang Zhao
Software Mentions: 4
Published: over 5 years ago

10.1038/s41598-020-58711-2

Nucleus accumbens pathways control cell-specific gene expression in the medial prefrontal cortex
Cited by: 5
Author(s): Takatoshi Hikida, Shuhei Yao, Tom Macpherson, Ayumi Fukakusa, Maki Morita, Haruhide Kimura, Keisuke Hirai, Tatsuya Ando, Hiroyoshi Toyoshiba, Akira Sawa
Software Mentions: 4
Published: over 6 years ago

10.3390/ijms20236040

Whole Genome Expression Analyses of miRNAs and mRNAs Suggest the Involvement of miR-320a and miR-155-3p and their Targeted Genes in Lithium Response in Bipolar Disorder
Cited by: 27
Author(s): Claudia Pisanu, Eleni Merkouri Papadima, Carla Melis, Donatella Congiu, Annalisa Loizedda, Nicola Orrù, Stefano Calza, Sandro Orrù, Carlo Carcassi, Giovanni Severino, Raffaella Ardau, Caterina Chillotti, Maria Del Zompo, Alessio Squassina
Software Mentions: 4
Published: over 6 years ago

10.3390/ijms21124470

Differences between Well-Differentiated Neuroendocrine Tumors and Ductal Adenocarcinomas of the Pancreas Assessed by Multi-Omics Profiling
Cited by: 8
Author(s): Teresa Starzyńska, Jakub Karczmarski, Agnieszka Paziewska, Maria Kulecka, Katarzyna Kuśnierz, Natalia Żeber‐Lubecka, Filip Ambrożkiewicz, Michał Mikula, Beata Kos‐Kudła, Jerzy Ostrowski
Software Mentions: 4
Published: about 6 years ago

10.3390/jcm8060849

MicroRNA Profile of HCV Spontaneous Clarified Individuals, Denotes Previous HCV Infection
Cited by: 10
Author(s): Óscar Brochado-Kith, Alicia Gómez Sanz, Luis Miguel Real, Javier Crespo, Pablo Ryan, Juan Macı́as, Joaquín Cabezas, Jesús Troya, Juan A Pineda, María Teresa Arias-Loste, Victorino Díez Viñas, María Ángeles Jiménez-Sousa, Luz María Medrano, Isabel Cuesta de la Plaza, Sara Monzón, Salvador Resino, Amanda Fernández‐Rodríguez
Software Mentions: 4
Published: about 7 years ago

10.1038/s41598-020-61633-8

MicroRNA hsa-mir-3923 serves as a diagnostic and prognostic biomarker for gastric carcinoma
Cited by: 11
Author(s): Xiaohui Yang, Ze Zhang, Lichao Zhang, Li Zhou
Software Mentions: 4
Published: over 6 years ago

10.3390/ijms19113687

Hierarchical Clustering of DNA k-mer Counts in RNAseq Fastq Files Identifies Sample Heterogeneities
Cited by: 5
Author(s): Wolfgang Kaisers, Holger Schwender, Heiner Schaal
Software Mentions: 4
Published: almost 8 years ago

10.3390/ijms20123101

Genome-Wide Analysis of ROS Antioxidant Genes in Resurrection Species Suggest an Involvement of Distinct ROS Detoxification Systems during Desiccation
Cited by: 29
Author(s): Saurabh Gupta, Yanni Dong, Paul P. Dijkwel, Bernd Mueller‐Roeber, Tsanko Gechev
Software Mentions: 4
Published: about 7 years ago

10.3390/ijms19010271

Integrated Analyses Reveal Overexpressed Notch1 Promoting Porcine Satellite Cells’ Proliferation through Regulating the Cell Cycle
Cited by: 21
Author(s): Yiren Jiao, Bo Huang, Yu Chen, Guang-liang Hong, Jian Xu, Chen Hu, Chong Wang
Software Mentions: 4
Published: over 8 years ago

10.3390/ijms19010031

Transcriptome Analysis of Tomato Leaf Spot Pathogen Fusarium proliferatum: De novo Assembly, Expression Profiling, and Identification of Candidate Effectors
Cited by: 15
Author(s): Meiling Gao, Siyu Yao, Yang Liu, Haining Yu, Pao Xu, Wenhui Sun, Zhongji Pu, Hongman Hou, Yongming Bao
Software Mentions: 4
Published: over 8 years ago

10.1074/jbc.RA120.015896

YAP contributes to DNA methylation remodeling upon mouse embryonic stem cell differentiation
Cited by: 21
Author(s): Fabiana Passaro, Ilaria De Martino, Federico Zambelli, Giorgia Di Benedetto, Matteo Barbato, Anna Maria D’Erchia, Caterina Manzari, Graziano Pesole, Margherita Mutarelli, Davide Cacchiarelli, Dario Antonini, Silvia Parisi, Tommaso Russo
Software Mentions: 4
Published: over 5 years ago

10.3390/ijms18030627

Evaluation and Adaptation of a Laboratory-Based cDNA Library Preparation Protocol for Retrospective Sequencing of Archived MicroRNAs from up to 35-Year-Old Clinical FFPE Specimens
Cited by: 14
Author(s): Olivier Loudig, Tao Wang, Kenny Ye, Juan Lin, Yihong Wang, Andrew Ramnauth, Christina Liu, Azadeh Stark, Dhananjay Chitale, Robert T. Greenlee, Deborah Multerer, Stacey Honda, Yihe G. Daida, Heather Spencer Feigelson, Andrew G. Glass, Fergus J. Couch, Thomas E. Rohan, Iddo Z. Ben‐Dov
Software Mentions: 4
Published: over 9 years ago

10.1038/s41598-019-49446-w

De novo transcriptome provides insights into the growth behaviour and resveratrol and trans-stilbenes biosynthesis in Dactylorhiza hatagirea - An endangered alpine terrestrial orchid of western Himalaya
Cited by: 19
Author(s): Nisha Dhiman, Nitesh Kumar Sharma, Pooja Thapa, Isha Sharma, Mohit Kumar Swarnkar, Amit Chawla, Ravi Shankar, Amita Bhattacharya
Software Mentions: 4
Published: almost 7 years ago

10.3390/ijms160921310

Gene Expression Variations of Red—White Skin Coloration in Common Carp (Cyprinus carpio)
Cited by: 19
Author(s): Xiaomin Li, Yijun Song, Gao Xiao, Bai-Han Zhu, Gui-Cai Xu, Mingyuan Sun, Jun Xiao, Shahid Mahboob, Khalid A. Al‐Ghanim, Xin Sun, Jiong-Tang Li
Software Mentions: 4
Published: almost 11 years ago

10.3390/insects11010004

Comparative Transcriptome Analysis of Thitarodes Armoricanus in Response to the Entomopathogenic Fungi Paecilomyces Hepiali and Ophiocordyceps Sinensis
Cited by: 7
Author(s): Zhongchen Rao, Li Cao, Hua Wu, Xuehong Qiu, Guiqing Liu, Richou Han
Software Mentions: 4
Published: over 6 years ago

10.3390/ijms20143583

Ureaplasma Species Modulate Cytokine and Chemokine Responses in Human Brain Microvascular Endothelial Cells
Cited by: 6
Author(s): Christine Silwedel, Christian P. Speer, Axel Haarmann, Markus Fehrholz, Heike Claus, Nicolas Schlegel, Kirsten Glaser
Software Mentions: 4
Published: about 7 years ago

10.7554/eLife.04235

Polycomb- and REST-associated histone deacetylases are independent pathways toward a mature neuronal phenotype
Cited by: 43
Author(s): James C. McGann, Jon A. Oyer, Saurabh Garg, Huilan Yao, Jun Li, Xin Feng, Lujian Liao, John R. Yates, Gail Mandel
Software Mentions: 4
Published: almost 12 years ago

10.7554/eLife.47013

An evolutionary recent IFN/IL-6/CEBP axis is linked to monocyte expansion and tuberculosis severity in humans
Cited by: 27
Author(s): Murilo Delgobo, Daniel A G B Mendes, Edgar Kozlova, Edroaldo Lummertz da Rocha, Gabriela F. Rodrigues-Luiz, Lucas Mascarin, Greicy Brisa Malaquias Dias, Daniel de Oliveira Patricio, Tim Dierckx, Maíra A. Bicca, G Bretton, Yonne Karoline Tenório de Menezes, Márick R Starick, Darcita Büerger Rovaris, Joanita Del Moral, Daniel Santos Mansur, Johan Van Weyenbergh, André Báfica
Software Mentions: 4
Published: almost 7 years ago

10.1038/s41598-019-49829-z

Adenovirus infection is associated with altered gut microbial communities in a non-human primate
Cited by: 27
Author(s): . Wasimuddin, Victor M. Corman, Jörg U. Ganzhorn, Jacques Rakotondranary, Yedidya R. Ratovonamana, Christian Drosten, Simone Sommer
Software Mentions: 4
Published: almost 7 years ago

10.3390/insects11050323

Transcriptome Analysis of the Oriental Fruit Fly Bactrocera dorsalis Early Embryos
Cited by: 2
Author(s): Wei Peng, Shu-Ning Yu, Alfred M. Handler, H. Zhang
Software Mentions: 4
Published: over 6 years ago

10.3390/ijms21124453

YBX1 Indirectly Targets Heterochromatin-Repressed Inflammatory Response-Related Apoptosis Genes through Regulating CBX5 mRNA
Cited by: 7
Author(s): Andreas Kloetgen, Sujitha Duggimpudi, Konstantin Schuschel, Kebria Hezaveh, Daniel Picard, Heiner Schaal, Marc Remke, Jan‐Henning Klusmann, Arndt Borkhardt, Alice C. McHardy, Jessica I. Hoell
Software Mentions: 4
Published: about 6 years ago

10.3390/ijms21218333

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

10.1093/hmg/ddab140

Human photoreceptor cells from different macular subregions have distinct transcriptional profiles
Cited by: 15
Author(s): Andrew P. Voigt, Nathaniel K. Mullin, S. Scott Whitmore, Adam P. DeLuca, Erin R Burnight, Xiuying Liu, Budd A. Tucker, Todd E. Scheetz, Edwin M Stone, Robert F. Mullins
Software Mentions: 4
Published: over 5 years ago

10.1038/s41598-019-47363-6

Whole transcriptome analysis reveals correlation of long noncoding RNA ZEB1-AS1 with invasive profile in melanoma
Cited by: 20
Author(s): Ádamo Davi Diógenes Siena, Jéssica Rodrigues Plaça, Luíza Ferreira de Araújo, Isabela Ichihara de Barros, Kamila Chagas Peronni, Greice Andreotti de Molfetta, Carlos Alberto Oliveira de Biagi, Enilza Maria Espreáfico, Josane F. Sousa, Wilson A. Silva
Software Mentions: 4
Published: about 7 years ago

10.1038/s41598-020-59934-z

Immunosuppressive effect and global dysregulation of blood transcriptome in response to psychosocial stress in vervet monkeys (Chlorocebus sabaeus)
Cited by: 2
Author(s): Anna J. Jasinska, Ivona Pandrea, Tianyu He, Cassandra Benjamin, Maurice Newton, Jen‐Chieh Lee, Nelson B. Freimer, Giovanni Coppola, J. David Jentsch
Software Mentions: 4
Published: over 6 years ago

10.7150/jca.44413

Comprehensive Analysis of the Tumor Microenvironment in Cutaneous Melanoma associated with Immune Infiltration
Cited by: 17
Author(s): Pan Wang, Xinyu Zhang, Nan Sun, Zhihong Zhao, Jie He
Software Mentions: 4
Published: over 6 years ago

10.1128/mSystems.00215-21

Time-Resolved Proteome Analysis of Listeria monocytogenes during Infection Reveals the Role of the AAA+ Chaperone ClpC for Host Cell Adaptation
Cited by: 5
Author(s): Marlène S Birk, Rina Ahmed-Begrich, Stefan Tran, Alexander K. W. Elsholz, Christian K. Frese, Emmanuelle Charpentier
Software Mentions: 4
Published: almost 5 years ago

10.1038/s41598-019-49915-2

RNAseq analysis reveals drought-responsive molecular pathways with candidate genes and putative molecular markers in root tissue of wheat
Cited by: 52
Author(s): Mir Asif Iquebal, Pradeep Sharma, Rahul Singh Jasrotia, Sarika Jaiswal, Amandeep Kaur, Monika Saroha, U. B. Angadi, Sonia Sheoran, Rajender Singh, Gyanendra Singh, Anil Rai, Ruchi Tiwari, Dinesh Kumar
Software Mentions: 4
Published: almost 7 years ago

10.1038/s41598-019-50573-7

Genome-wide association study and whole-genome sequencing identify a deletion in LRIT3 associated with canine congenital stationary night blindness
Cited by: 14
Author(s): Gautami Das, Doreen Becker, Vidhya Jagannathan, Orly Goldstein, Evelyn Santana, Kendall Carlin, Raghavi Sudharsan, Tosso Leeb, Yuji Nishizawa, Mineo Kondo, Gustavo D. Aguirre, Keiko Miyadera
Software Mentions: 4
Published: almost 7 years ago

10.1038/s41598-019-50271-4

Fractional Deletion of Compound Kushen Injection Indicates Cytokine Signaling Pathways are Critical for its Perturbation of the Cell Cycle
Cited by: 9
Author(s): Thazin Nwe Aung, Saeed Nourmohammadi, Zhibo Qu, Yuka Harata-Lee, Jingang Cui, Hao Shen, Andrea J. Yool, Tara L. Pukala, Hongling Du, R. Daniel Kortschak, Wenxin Wei, David L. Adelson
Software Mentions: 4
Published: almost 7 years ago

10.7150/jca.49557

Construction of novel mRNA-miRNA-lncRNA regulatory networks associated with prognosis of ovarian cancer
Cited by: 18
Author(s): Lingling Gao, Xiao Li, Xin Nie, Qin Guo, Qing Liu, Yue Qi, Juanjuan Liu, Bei Lin
Software Mentions: 4
Published: over 6 years ago

10.1128/mSystems.00596-19

Drug Repurposing of Bromodomain Inhibitors as Potential Novel Therapeutic Leads for Lymphatic Filariasis Guided by Multispecies Transcriptomics
Cited by: 7
Author(s): Matthew Chung, Laura Teigen, Silvia Libro, Robin E. Bromley, Dustin Olley, Nikhil Kumar, Lisa Sadzewicz, Luke J. Tallon, Anup Mahurkar, Jeremy M. Foster, Michelle L. Michalski, Julie C. Dunning Hotopp
Software Mentions: 4
Published: over 6 years ago

10.1128/mSystems.00284-18

Systems-Level Analysis of Oxygen Exposure in <i>Zymomonas mobilis</i> : Implications for Isoprenoid Production
Cited by: 22
Author(s): Julia Martien, Alexander S. Hebert, David Stevenson, Matthew Regner, Daven B. Khana, Joshua J. Coon, Daniel Amador‐Noguez
Software Mentions: 4
Published: over 7 years ago

10.1128/mSystems.00038-18

Holistic Assessment of Rumen Microbiome Dynamics through Quantitative Metatranscriptomics Reveals Multifunctional Redundancy during Key Steps of Anaerobic Feed Degradation
Cited by: 66
Author(s): Andrea Söllinger, Alexander Tøsdal Tveit, Morten Poulsen, Samantha Joan Noel, Mia M. Bengtsson, Jörg Bernhardt, Anne Louise Frydendahl Hellwing, Peter Lund, Katharina Riedel, Christa Schleper, Ole Højberg, Tim Urich
Software Mentions: 4
Published: almost 8 years ago

10.1186/2049-1891-3-8

Current status and future perspectives for sequencing livestock genomes
Cited by: 40
Author(s): Yongsheng Bai, Maureen A. Sartor, James D. Cavalcoli
Software Mentions: 4
Published: over 14 years ago

10.7150/jca.57260

Construction of a ceRNA Network and a Prognostic lncRNA Signature associated with Vascular Invasion in Hepatocellular Carcinoma based on Weighted Gene Co-Expression Network Analysis
Cited by: 10
Author(s): Haisu Tao, Li Jiang, Junjie Liu, Tong Yuan, Erlei Zhang, Huifang Liang, Zhiyong Huang
Software Mentions: 4
Published: over 5 years ago

10.3390/ijms21082800

Integration of ATAC-seq and RNA-seq Unravels Chromatin Accessibility during Sex Reversal in Orange-Spotted Grouper (Epinephelus coioides)
Cited by: 13
Author(s): Xi Wu, Yang Yang, Chaoyue Zhong, Yin Guo, Tengyu Wei, Shuisheng Li, Haoran Lin, Xiaochun Liu
Software Mentions: 4
Published: over 6 years ago

10.1038/s41598-019-52903-1

Sperm DNA Methylation Epimutation Biomarkers for Male Infertility and FSH Therapeutic Responsiveness
Cited by: 46
Author(s): S. Luján Marco, Ettore Caroppo, Craig S. Niederberger, Joan‐Carles Arce, Ingrid Sadler‐Riggleman, Daniel Beck, Eric Nilsson, Michael K. Skinner
Software Mentions: 4
Published: almost 7 years ago

10.1038/s41598-019-52841-y

Prospective validation in epithelial tumors of a gene expression predictor of liver metastasis derived from uveal melanoma
Cited by: 3
Author(s): Petros Tsantoulis, Mauro Delorenzi, Ivan Bièche, Sophie Vacher, Pascale Mariani, Nathalie Cassoux, Alexandre Houy, Marc‐Henri Stern, Sergio Román-Román, Pierre‐Yves Dietrich, Arnaud Roth, Wulfran Cacheux
Software Mentions: 4
Published: almost 7 years ago

10.1128/mSphere.00231-18

Kinome Expansion in the Fusarium oxysporum Species Complex Driven by Accessory Chromosomes
Cited by: 28
Author(s): Gregory A. DeIulio, Li Guo, Yong Zhang, Jonathan M. Goldberg, H. Corby Kistler, Lijun Ma
Software Mentions: 4
Published: about 8 years ago

10.1038/s41598-019-43862-8

CRISPR/Cas9-mediated ablation of elovl2 in Atlantic salmon (Salmo salar L.) inhibits elongation of polyunsaturated fatty acids and induces Srebp-1 and target genes
Cited by: 53
Author(s): Alex K. Datsomor, Nikola Zic, Keshuai Li, Rolf Erik Olsen, Yang Jin, Jon Olav Vik, Rolf B. Edvardsen, Fabian Grammes, Anna Wargelius, Per Winge
Software Mentions: 3
Published: over 7 years ago

10.1111/imm.13341

Modified recombinant human IgG1‐Fc is superior to natural intravenous immunoglobulin at inhibiting immune‐mediated demyelination
Cited by: 1
Author(s): Christine Baksmeier, Patricia A. Blundell, Julia Steckel, Verena Schultz, Quan Gu, Ana da Silva Filipe, Alain Kohl, Chris Linnington, Dongli Lu, Anne Dell, Stuart M. Haslam, Jiabin Wang, Dan Czajkowsky, Norbert Goebels, Richard J. Pleass
Software Mentions: 3
Published: over 5 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: over 6 years ago

10.3390/insects11110820

Transcriptomics-Based Approach Identifies Spinosad-Associated Targets in the Colorado Potato Beetle, Leptinotarsa decemlineata
Cited by: 10
Author(s): Pierre Bastarache, Gabriel Wajnberg, Pascal Dumas, Simi Chacko, Jacynthe Lacroix, Nicolas Crapoulet, Chandra E. Moffat, Pier Jr Morin
Software Mentions: 3
Published: almost 6 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 5 years ago

10.1172/jci.insight.147929

Adipocyte-like signature in ovarian cancer minimal residual disease identifies metabolic vulnerabilities of tumor initiating cells
Cited by: 2
Author(s): Mara Artibani, Kenta Masuda, Zhiyuan Hu, Pascal C. Rauher, Garry Mallett, Nina Wietek, Matteo Morotti, Kay Y. Chong, Mohammad KaramiNejadRanjbar, Christos E. Zois, Sunanda Dhar, Salma El-Sahhar, Leticia Campo, Sarah P. Blagden, Stephen Damato, Pubudu Pathiraja, Shibani Nicum, Fergus Gleeson, A Laios, Abdulkhaliq Alsaadi, Laura Santana González, Takeshi Motohara, Ashwag Albukhari, Zhen Lü, Robert C. Bast, Adrian L. Harris, Christer S. Ejsing, Robin W. Klemm, Christopher Yau, Tatjana Sauka‐Spengler, Ashfaq Ahmed
Software Mentions: 3
Published: over 5 years ago

10.1172/jci.insight.145607

A surgical method for continuous intraportal infusion of gut microbial metabolites in mice
Cited by: 5
Author(s): Danny Orabi, Lucas J Osborn, Kevin Fung, William Massey, Anthony Horak, Federico Aucejo, Ibrahim Choucair, Beckey DeLucia, Zeneng Wang, Jan Claesen, J. Mark Brown
Software Mentions: 3
Published: over 5 years ago

10.1172/jci.insight.149446

Combining multiomics and drug perturbation profiles to identify muscle-specific treatments for spinal muscular atrophy
Cited by: 5
Author(s): Katharina E. Meijboom, Viola Volpato, Jimena Monzón‐Sandoval, Joseph M. Hoolachan, Suzan M. Hammond, Frank Abendroth, Olivier G. de Jong, Gareth Hazell, Nina Ahlskog, Matthew J. Wood, Caleb Webber, Mélissa Bowerman
Software Mentions: 3
Published: about 5 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: about 9 years ago

10.1074/jbc.RA120.016009

Human genetic variants disrupt RGS14 nuclear shuttling and regulation of LTP in hippocampal neurons
Cited by: 9
Author(s): Katherine E. Squires, Kyle J. Gerber, Matthew Tillman, Daniel Lustberg, Carolina Montañez-Miranda, Mei Zhao, Suneela Ramineni, Christopher D. Scharer, Ramendra N. Saha, Shu Fang, Jeanne L. Schroeder, Eric A. Ortlund, David Weinshenker, Serena M. Dudek, John R. Hepler
Software Mentions: 3
Published: over 5 years ago

10.1074/jbc.RA120.014960

mTOR kinase inhibition disrupts neuregulin 1-ERBB3 autocrine signaling and sensitizes NF2-deficient meningioma cellular models to IGF1R inhibition
Cited by: 7
Author(s): Roberta L. Beauchamp, Serkan Erdin, Luke Witt, Justin T. Jordan, Scott R. Plotkin, James F. Gusella, Vijaya Ramesh
Software Mentions: 3
Published: over 5 years ago

10.7150/jca.31675

Comprehensive investigation of the clinical significance and molecular mechanisms of plasmacytoma variant translocation 1 in sarcoma using genome-wide RNA sequencing data
Cited by: 9
Author(s): Jianwei Liu, Rong Li, Xiwen Liao, Bang-li Hu, Jia Yu
Software Mentions: 3
Published: over 7 years ago

10.7150/jca.35801

Identification of a six-lncRNA signature based on a competing endogenous RNA network for predicting the risk of tumour recurrence in bladder cancer patients
Cited by: 8
Author(s): Danfeng Zhao, Qiang Peng, Lu Wang, Cong Li, Yulin Lv, Yong Liu, Zhichao Wang, Ruizhe Fang, Jiaqi Wang, Zhongqing Liu, Wanhai Xu
Software Mentions: 3
Published: over 6 years ago

10.7150/jca.34723

Signatures of circulating microRNA in four sarcoma subtypes
Cited by: 11
Author(s): Hanna Koseła-Paterczyk, Agnieszka Paziewska, Maria Kulecka, Aneta Bałabas, Anna Kluska, Michalina Dąbrowska, Magdalena Piątkowska, Natalia Żeber‐Lubecka, Filip Ambrożkiewicz, Jakub Karczmarski, Michał Mikula, Piotr Rutkowski, Jerzy Ostrowski
Software Mentions: 3
Published: over 6 years ago

10.7150/jca.38796

A Combined four-mRNA Signature Associated with Lymphatic Metastasis for Prognosis of Colorectal Cancer
Cited by: 7
Author(s): Xueping Li, Zhang Qiang, Liang Zhao, Longyang Jiang, Aoshuang Qi, Wei Qian, Xinyue Song, Wei Lin, Liwen Zhang, Yimeng Zhao, Xuemei Lv, Lin Zhao
Software Mentions: 3
Published: over 6 years ago

10.7150/jca.49138

LINC00184 involved in the regulatory network of ANGPT2 via ceRNA mediated miR-145 inhibition in gastric cancer
Cited by: 13
Author(s): Haiyan Piao, Shuai Guo, Haoyi Jin, Yue Wang, Jun Zhang
Software Mentions: 3
Published: over 5 years ago

10.7150/jca.50472

High Expression of RhoBTB3 Predicts Favorable Chemothrapy Outcomes in non-M3 Acute Myeloid Leukemia
Cited by: 3
Author(s): Shuanghui Yang, Wei Liu, Jie Peng, Yajing Xu, Yanfeng Liu, Yan Li, Minyuan Peng, Zhao Ouyang, Cong Chen, Enyi Liu
Software Mentions: 3
Published: over 5 years ago

10.7150/jca.59348

Long non-coding RNA RP4-694A7.2 Promotes Hepatocellular Carcinoma Cell Proliferation and Metastasis through the Regulation of PSAT1
Cited by: 5
Author(s): Yaoxin Fan, Lin Wang, Yang Ding, Qiuju Sheng, Chong Zhang, Yanwei Li, Chao Han, Bao-Liang Lu, Xiao-guang Dou
Software Mentions: 3
Published: over 5 years ago

10.1111/jcmm.15183

PTBP1 modulates osteosarcoma chemoresistance to cisplatin by regulating the expression of the copper transporter SLC31A1
Cited by: 33
Author(s): Cheng Cheng, Qiuyue Ding, Zhicai Zhang, Shangyu Wang, Botao Zhong, Xin Huang
Software Mentions: 3
Published: over 6 years ago

10.1111/jcmm.15193

To construct a ceRNA regulatory network as prognostic biomarkers for bladder cancer
Cited by: 45
Author(s): Jiazhi Jiang, Yaqiong Bi, Xiaoping Li, Donghu Yu, Xin Yan, Jie Yao, Tongzu Liu, Li Sheng
Software Mentions: 3
Published: over 6 years ago

10.1111/jcmm.15687

Development of a prognostic gene signature based on an immunogenomic infiltration analysis of osteosarcoma
Cited by: 14
Author(s): Yan Yu, Hongliang Zhang, Tingting Ren, Yi Huang, Xin Liang, Wei Wang, Jianfang Niu, Yu Han, Wei Guo
Software Mentions: 3
Published: about 6 years ago

10.1111/jcmm.15980

A novel autophagy‐related lncRNA prognostic risk model for breast cancer
Cited by: 74
Author(s): Xiaoying Li, Feng Jin, Yang Li
Software Mentions: 3
Published: almost 6 years ago

10.1111/jcmm.16596

Interplay between SARS‐CoV‐2 and human long non‐coding RNAs
Cited by: 32
Author(s): Maryam Moazzam-Jazi, Hossein Lanjanian, Samaneh Maleknia, Mehdi Hedayati, Maryam S. Daneshpour
Software Mentions: 3
Published: over 5 years ago

10.1002/jcp.29046

Identification of methylation‐driven genes related to prognosis in clear‐cell renal cell carcinoma
Cited by: 11
Author(s): Jia Wang, Qiujing Zhang, Qingqing Zhu, Chengxiang Li, Xueli Nan, Fuxia Wang, Lihua Fang, Jie Liu, Chao Xie, Shuai Fu, Bao-Liang Song
Software Mentions: 3
Published: about 7 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: over 8 years ago

10.3390/jcm8111928

B4GALT1 Is a New Candidate to Maintain the Stemness of Lung Cancer Stem Cells
Cited by: 12
Author(s): Claudia De Vitis, Giacomo Corleone, Valentina Salvati, Francesca Ascenzi, Matteo Pallocca, Francesca De Nicola, Maurizio Fanciulli, Simona Di Martino, Sara Bruschini, Christian Napoli, Alberto Rícci, Massimiliano Bassi, Federico Venuta, Erino Angelo Rendina, Gennaro Ciliberto, Rita Mancini
Software Mentions: 3
Published: almost 7 years ago

10.1093/ecco-jcc/jjaa021

A Pilot Integrative Analysis of Colonic Gene Expression, Gut Microbiota, and Immune Infiltration in Primary Sclerosing Cholangitis-Inflammatory Bowel Disease: Association of Disease With Bile Acid Pathways
Cited by: 75
Author(s): Mohammed Nabil Quraishi, Animesh Acharjee, Andrew D Beggs, Richard D. Horniblow, Chris Tselepis, Georgios V. Gkoutos, Subrata Ghosh, Amanda E. Rossiter, Nicholas J. Loman, Willem van Schaik, David R. Withers, Julian R.F. Walters, Gideon Hirschfield, Tariq Iqbal
Software Mentions: 3
Published: over 6 years ago

10.1155/2020/3980742

The Construction and Analysis of the Aberrant lncRNA-miRNA-mRNA Network in Adipose Tissue from Type 2 Diabetes Individuals with Obesity
Cited by: 21
Author(s): Wei Hu, Yuanlin Ding, Shu Wang, Lin Xu, Haibing Yu
Software Mentions: 3
Published: over 6 years ago

10.1038/s41598-019-43935-8

GREIN: An Interactive Web Platform for Re-analyzing GEO RNA-seq Data
Cited by: 105
Author(s): Naim Al Mahi, Mehdi Fazel Najafabadi, Marcin Pilarczyk, Michal Kouril, Mario Medvedovic
Software Mentions: 3
Published: over 7 years ago

10.1038/s41598-019-44944-3

Detection of novel biomarkers for early detection of Non-Muscle-Invasive Bladder Cancer using Competing Endogenous RNA network analysis
Cited by: 35
Author(s): Morteza Kouhsar, Sadegh Azimzadeh Jamalkandi, Ali Moeini, Ali Masoudi‐Nejad
Software Mentions: 3
Published: about 7 years ago

10.1038/s41598-019-44924-7

Whole-blood transcriptomic signatures induced during immunization by chloroquine prophylaxis and Plasmodium falciparum sporozoites
Cited by: 23
Author(s): Tuan M. Tran, Else M. Bijker, Mariëlle C. Haks, Tom H. M. Ottenhoff, Leo G. Visser, Remko Schats, Pratap Venepally, Hernán Lorenzi, Peter D. Crompton, Robert W. Sauerwein
Software Mentions: 3
Published: about 7 years ago

10.1038/s41598-019-44600-w

Genome-wide identification and characterization of long non-coding RNAs expressed during sheep fetal and postnatal hair follicle development
Cited by: 27
Author(s): Ablat Sulayman, Kechuan Tian, Xixia Huang, Yuezhen Tian, Xinming Xu, Xuefeng Fu, Bi Zhao, Weiwei Wu, Dan Wang, Aynur Yasin, Hanikezi Tulafu
Software Mentions: 3
Published: about 7 years ago

Projects: bioconductor: edgeR

Science Score: 100/100

Bonuses:

Papers Mentioning edgeR 6,568