bioconductor: edgeR | Projects | Ecosyste.ms: Papers

10.1186/s12864-015-2114-z

Molecular tools for studying the major malaria vector Anopheles funestus: improving the utility of the genome using a comparative poly(A) and Ribo-Zero RNAseq analysis
Cited by: 9
Author(s): Gareth D. Weedall, Helen Irving, Margaret Hughes, Charles S. Wondji
Software Mentions: 4
Published: almost 11 years ago

10.3389/fonc.2021.614497

Molecular and Clinical Characterization of CCT2 Expression and Prognosis via Large-Scale Transcriptome Profile of Breast Cancer
Cited by: 6
Author(s): Qiang Liu, Yihang Qi, Xiangyi Kong, Xiangyu Wang, Wenxiang Zhang, Jie Zhai, Yazhe Yang, Yi Fang, Jing Wang
Software Mentions: 4
Published: over 5 years ago

10.7554/eLife.55911

Histone deacetylase knockouts modify transcription, CAG instability and nuclear pathology in Huntington disease mice
Cited by: 4
Author(s): Marina Kovalenko, Serkan Erdin, Marissa A Andrew, Jason St. Claire, Melissa Shaughnessey, Leroy Hubert, João Luís Neto, Alexei Stortchevoi, Daniel M. Fass, Ricardo Mouro Pinto, Stephen J. Haggarty, John H. Wilson, Michael E. Talkowski, Vanessa C. Wheeler
Software Mentions: 4
Published: about 6 years ago

10.3390/microorganisms9010149

Hallmarks of Basidiomycete Soft- and White-Rot in Wood-Decay -Omics Data of Two Armillaria Species
Cited by: 21
Author(s): Niranjan P. Sahu, Zsolt Merényi, Balázs Bálint, Brigitta Kiss, György Sipos, Rebecca A. Owens, László G. Nagy
Software Mentions: 4
Published: almost 6 years ago

10.3390/microorganisms7010017

Socioeconomic Status and the Gut Microbiome: A TwinsUK Cohort Study
Cited by: 84
Author(s): Ruth C E Bowyer, Matthew A. Jackson, Caroline I. Le Roy, Mary Ní Lochlainn, Timothy D. Spector, Jennifer Beam Dowd, Claire J. Steves
Software Mentions: 4
Published: almost 8 years ago

10.1186/s13229-021-00432-y

Neuroanatomy and behavior in mice with a haploinsufficiency of AT-rich interactive domain 1B (ARID1B) throughout development
Cited by: 17
Author(s): Jacob Ellegood, Stela P. Petkova, Adrienne Kinman, Lily R. Qiu, Anna Adhikari, A. Ayanna Wade, Darren Fernandes, Zsuzsa Lindenmaier, Amie Creighton, Lauryl M. J. Nutter, Alexander Nord, Jill L. Silverman, Jason P. Lerch
Software Mentions: 4
Published: over 5 years ago

10.1093/molbev/msaa172

Gene Loss Predictably Drives Evolutionary Adaptation
Cited by: 49
Author(s): Jana Helsen, Karin Voordeckers, Laura Vanderwaeren, Toon Santermans, Maria Tsontaki, Kevin J. Verstrepen, Rob Jelier
Software Mentions: 4
Published: over 6 years ago

10.1093/molbev/msab197

Functional Characterization of the Cnidarian Antiviral Immune Response Reveals Ancestral Complexity
Cited by: 13
Author(s): Magda Lewandowska, Ton Sharoni, Yael Admoni, Reuven Aharoni, Yehu Moran
Software Mentions: 4
Published: over 5 years ago

10.1093/molbev/msv016

The Avian Transcriptome Response to Malaria Infection
Cited by: 71
Author(s): Elin Videvall, Charlie K. Cornwallis, Vaidas Palinauskas, Gediminas Valkiūnas, Olof Hellgren
Software Mentions: 4
Published: almost 12 years ago

10.1002/emmm.201201974

Alteration of the micro <scp>RNA</scp> network during the progression of Alzheimer's disease
Cited by: 393
Author(s): Pierre Lau, Koen Bossers, Rekin’s Janky, Evgenia Salta, Carlo Sala Frigerio, Shahar Barbash, Roy Rothman, Annerieke Sierksma, Amantha Thathiah, David Greenberg, Aikaterini S. Papadopoulou, Tilmann Achsel, Torik Ayoubi, Hermona Soreq, Joost Verhaagen, Dick F. Swaab, Stein Aerts, Bart De Strooper
Software Mentions: 4
Published: about 13 years ago

10.1371/journal.pone.0181192

Analysis of aquaporins from the euryhaline barnacle Balanus improvisus reveals differential expression in response to changes in salinity
Cited by: 23
Author(s): Ulrika Lind, Michael Järvå, Magnus Alm Rosenblad, Piero Pingitore, Emil Karlsson, Anna-Lisa Wrange, Emelie Kamdal, Kristina Sundell, Carl André, Per R. Jonsson, Jonathan N. Havenhand, Leif A. Eriksson, Kristina Hedfalk, Anders Blomberg
Software Mentions: 4
Published: over 9 years ago

10.3390/ijms22157939

Comparative Transcriptome Analysis of Human Adipose-Derived Stem Cells Undergoing Osteogenesis in 2D and 3D Culture Conditions
Cited by: 5
Author(s): Byung Chul Kim, Kyu Hwan Kwack, Jeewan Chun, Jae Hyung Lee
Software Mentions: 4
Published: over 5 years ago

10.1371/journal.pone.0231125

Analysis of circulating-microRNA expression in lactating Holstein cows under summer heat stress
Cited by: 14
Author(s): Jihwan Lee, Mi Kyung Lee, Jun-Kyu Son, Hyeonju Lim, Euntae Kim, Dong-Hyun Kim, Seungmin Ha, Tai-Young Hur, Seung Hwan Lee, Inchul Choi
Software Mentions: 4
Published: about 6 years ago

10.7554/eLife.36828

Hypoxia-inducible factor cell non-autonomously regulates C. elegans stress responses and behavior via a nuclear receptor
Cited by: 12
Author(s): Corinne L Pender, H. Robert Horvitz
Software Mentions: 4
Published: over 8 years ago

10.1371/journal.pone.0227882

Comparison of the myometrial transcriptome from singleton and twin pregnancies by RNA-Seq
Cited by: 5
Author(s): Sarah Arrowsmith, Yongxiang Fang, Andrew Sharp
Software Mentions: 4
Published: almost 7 years ago

10.1016/j.dib.2018.11.034

Differential gene expression analysis and SNP/InDel marker discovery in resistant wild Asparagus kiusianus and susceptible A. officinalis in response to Phomopsis asparagi infection
Cited by: 4
Author(s): Mostafa Abdelrahman, Mai Mitoma, Takao Ikeuchi, Motoyuki Mori, Kyoko Murakami, Yukio Ozaki, Masaru Matsumoto, Atsuko Uragami, Akira Kanno
Software Mentions: 4
Published: almost 8 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: over 6 years ago

10.1371/journal.pone.0186794

A deep transcriptomic resource for the copepod crustacean Labidocera madurae: A potential indicator species for assessing near shore ecosystem health
Cited by: 16
Author(s): Vittoria Roncalli, Andrew E. Christie, Stephanie A. Sommer, Matthew Cieslak, Daniel K. Hartline, Petra H. Lenz
Software Mentions: 4
Published: about 9 years ago

10.1186/s12864-016-2403-1

RNA sequencing-based analysis of the spleen transcriptome following infectious bronchitis virus infection of chickens selected for different mannose-binding lectin serum concentrations
Cited by: 20
Author(s): Edin Hamzić, Rikke Brødsgaard Kjærup, Núria Mach, Guilietta Minozzi, Francesco Strozzi, V. Gualdi, J. L. Williams, Jun Chen, Eva Wattrang, Bart Buitenhuis, Helle R. Juul‐Madsen, Tina Sørensen Dalgaard
Software Mentions: 4
Published: almost 11 years ago

10.1371/journal.pone.0150094

Development of the Intestinal RNA Virus Community of Healthy Broiler Chickens
Cited by: 8
Author(s): Jigna Shah, Prerak Desai, Ying Zhang, Sarah K. Scharber, Joshua A. Baller, Zheng Xing, Carol J. Cardona
Software Mentions: 4
Published: over 10 years ago

10.1371/journal.pone.0192383

Adaptability of the Saccharomyces cerevisiae yeasts to wine fermentation conditions relies on their strong ability to consume nitrogen
Cited by: 40
Author(s): Claire Brice, Francisco A. Cubillos, Sylvie Dequin, Carole Camarasa, Claudio Martı́nez
Software Mentions: 4
Published: over 8 years ago

10.1093/database/baw168

KTCNlncDB—a first platform to investigate lncRNAs expressed in human keratoconus and non-keratoconus corneas
Cited by: 13
Author(s): Michał Wojciech Szcześniak, Michał Kabza, Justyna A. Karolak, Małgorzata Rydzanicz, Dorota Nowak, Barbara Ginter-Matuszewska, Piotr Polakowski, Rafał Płoski, Jacek P. Szaflik, Marzena Gajęcka
Software Mentions: 4
Published: almost 10 years ago

10.7554/eLife.41641

IFNγ induces epigenetic programming of human T-bethi B cells and promotes TLR7/8 and IL-21 induced differentiation
Cited by: 104
Author(s): Esther Zumaquero, Sara L Stone, Christopher D. Scharer, Scott A. Jenks, Anoma Nellore, Betty Mousseau, Antonio Rosal-Vela, Davide Botta, John E. Bradley, Wojciech Wojciechowski, Travis Ptacek, Maria I. Danila, Jeffrey C. Edberg, S. Louis Bridges, Robert P. Kimberly, W. Winn Chatham, Trenton R. Schoeb, Alexander F. Rosenberg, Jeremy M. Boss, Igñacio Sanz, Frances E. Lund
Software Mentions: 4
Published: over 7 years ago

10.1186/1755-8794-7-32

Conserved recurrent gene mutations correlate with pathway deregulation and clinical outcomes of lung adenocarcinoma in never-smokers
Cited by: 45
Author(s): Zhifu Sun, Liang Wang, Bruce W. Eckloff, Bo Deng, Yi Wang, Jason A. Wampfler, Jiseon Jang, Eric D. Wieben, Jin Jen, Ming You, Ping Yang
Software Mentions: 4
Published: over 12 years ago

10.1371/journal.pone.0252452

Comprehensive analysis of lncRNA biomarkers in kidney renal clear cell carcinoma by lncRNA-mediated ceRNA network
Cited by: 4
Author(s): Ke Gong, Ting Xie, Yiliao Luo, Hui Guo, Jinlan Chen, Zhiping Tan, Yifeng Yang, Li Xie
Software Mentions: 4
Published: over 5 years ago

10.7554/eLife.24414

Host-selected mutations converging on a global regulator drive an adaptive leap towards symbiosis in bacteria
Cited by: 38
Author(s): M. Sabrina Pankey, Randi L Foxall, Ian M Ster, Lauren A Perry, Brian G. Schuster, Rachel A Donner, Matthew Coyle, Vaughn S. Cooper, Cheryl A. Whistler
Software Mentions: 4
Published: over 9 years ago

10.1186/s12866-020-01979-1

Habitat disturbance influences the skin microbiome of a rediscovered neotropical-montane frog
Cited by: 14
Author(s): Randall R. Jiménez, Gilbert Alvarado, José Luís Sandoval, Simone Sommer
Software Mentions: 4
Published: about 6 years ago

10.1371/journal.pone.0251121

Melanocytes determine angiogenesis gene expression across human tissues
Cited by: 3
Author(s): Shirly Freilikhman, Marianna Halasi, Alal Eran, Irit Adini
Software Mentions: 4
Published: over 5 years ago

10.1371/journal.pone.0235763

Comparative transcriptome analysis uncovers different heat stress responses in heat-resistant and heat-sensitive jujube cultivars
Cited by: 17
Author(s): Juan Jin, Lei Yang, Dingyu Fan, Xuxin Liu, Qing Hao
Software Mentions: 4
Published: about 6 years ago

10.7554/eLife.55775

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

10.1371/journal.pone.0115842

Identifying Glioblastoma Gene Networks Based on Hypergeometric Test Analysis
Cited by: 14
Author(s): Vasileios Stathias, Chiara Pastori, Tess Z. Griffin, Ricardo J. Komotar, Jennifer Clarke, Ming Zhang, Nagi G. Ayad
Software Mentions: 4
Published: almost 12 years ago

10.1371/journal.pone.0109262

De Novo Assembly of the Common Bean Transcriptome Using Short Reads for the Discovery of Drought-Responsive Genes
Cited by: 48
Author(s): Jing Wu, Lanfen Wang, Long Li, Shumin Wang
Software Mentions: 4
Published: about 12 years ago

10.1371/journal.pone.0089445

RNA CoMPASS: A Dual Approach for Pathogen and Host Transcriptome Analysis of RNA-Seq Datasets
Cited by: 38
Author(s): Guiyin Xu, Michael J. Strong, Michelle Lacey, Carl Baribault, Erik K. Flemington, Christopher M. Taylor
Software Mentions: 4
Published: over 12 years ago

10.15252/embj.2019103932

<scp>RNF</scp> 43 truncations trap <scp>CK</scp> 1 to drive niche‐independent self‐renewal in cancer
Cited by: 24
Author(s): Maureen Spit, Nicola Fenderico, Ingrid Jordens, Tomasz Radaszkiewicz, Rik G.H. Lindeboom, Jeroen M. Bugter, Alba Cristobal, Lars Ootes, Max van Osch, Eline Janssen, Kim E. Boonekamp, Kateřina Hanáková, David Potěšil, Zbyněk Zdráhal, Sylvia F. Boj, Jan Paul Medema, Vı́tězslav Bryja, Bon‐Kyoung Koo, Michiel Vermeulen, Madelon M. Maurice
Software Mentions: 4
Published: about 6 years ago

10.1371/journal.pone.0253741

Transcriptome and proteome of the corm, leaf and flower of Hypoxis hemerocallidea (African potato)
Cited by: 0
Author(s): Mihai-Silviu Tomescu, Selisha A. Sooklal, Thuto Ntsowe, Previn Naicker, Barbara Darnhofer, Robert H. Archer, Stoyan Stoychev, Dirk Swanevelder, Ruth Birner‐Grünberger, Karl Rumbold
Software Mentions: 4
Published: over 5 years ago

10.7554/eLife.64204

Single-PanIN-seq unveils that ARID1A deficiency promotes pancreatic tumorigenesis by attenuating KRAS-induced senescence
Cited by: 5
Author(s): Shou Liu, Wenjian Cao, Yichi Niu, Jiayi Luo, Yanhua Zhao, Zheng Hu, Chenghang Zong
Software Mentions: 4
Published: over 5 years ago

10.1371/journal.pone.0244593

Comparative RNA-Seq analysis unfolds a complex regulatory network imparting yellow mosaic disease resistance in mungbean [Vigna radiata (L.) R. Wilczek]
Cited by: 24
Author(s): Uttarayan Dasgupta, Gyan P. Mishra, Harsh Kumar Dikshit, Dwijesh Chandra Mishra, Tejas C. Bosamia, Anirban Roy, Jyotika Bhati, Priti, Muraleedhar S. Aski, Ranjeet Kumar, Amit Kumar Singh, Atul Kumar, S. K. Sinha, Sundeep Chaurasia, Shelly Praveen, Ramakrishnan M. Nair
Software Mentions: 4
Published: almost 6 years ago

10.1371/journal.pone.0213535

Possible cross-feeding pathway of facultative methylotroph Methyloceanibacter caenitepidi Gela4 on methanotroph Methylocaldum marinum S8
Cited by: 22
Author(s): Mio Takeuchi, Haruka Ozaki, Satoshi Hiraoka, Yoichi Kamagata, Susumu Sakata, Hideyoshi Yoshioka, Wataru Iwasaki
Software Mentions: 4
Published: over 7 years ago

10.7554/eLife.67740

Bacterial–fungal interactions in the neonatal gut influence asthma outcomes later in life
Cited by: 16
Author(s): Rozlyn C.T. Boutin, Charisse Petersen, Sarah E. Woodward, Antonio Serapio-Palacios, Tahereh Bozorgmehr, Rachelle Loo, Alina Chalanuchpong, Mihai Cirstea, Bernard C. Lo, Kelsey E. Huus, Weronika Barcik, Meghan B. Azad, Allan B. Becker, Piush J. Mandhane, Theo J. Moraes, Malcolm R. Sears, Padmaja Subbarao, Kelly M. McNagny, Stuart E. Turvey, B. Brett Finlay
Software Mentions: 4
Published: over 5 years ago

10.1371/journal.pone.0228722

Iron metabolic pathways in the processes of sponge plasticity
Cited by: 8
Author(s): Alexander D. Finoshin, Kim I. Adameyko, Kirill V. Mikhailov, О. И. Кравчук, Anton Georgiev, Н. Г. Горностаев, Igor A. Kosevich, Victor S. Mikhailov, Guzel Gazizova, Elena Shagimardanova, Oleg Gusev, Yu. V. Lyupina
Software Mentions: 4
Published: over 6 years ago

10.1371/journal.pone.0057886

Integrative Genome-Wide Gene Expression Profiling of Clear Cell Renal Cell Carcinoma in Czech Republic and in the United States
Cited by: 94
Author(s): Magdalena B. Wozniak, Florence Le Calvez-Kelm, Behnoush Abedi-Ardekani, Graham Byrnes, G. Durand, Christine Carreira, Jocelyne Michelon, Vladimír Janout, Ivana Holcátová, Lenka Foretová, A. Brisuda, Fabienne Lesueur, James McKay, Paul Brennan, Ghislaine Scélo
Software Mentions: 4
Published: over 13 years ago

10.1371/journal.pone.0246367

Multi-omic modelling of inflammatory bowel disease with regularized canonical correlation analysis
Cited by: 6
Author(s): Lluís Revilla, Aida Mayorgas, A M Corraliza, Maria Carme Masamunt, Amira Metwaly, Dirk Haller, Eva Tristán, Anna Carrasco, María Esteve, Julián Panés, Elena Ricart, Juan José Lozano, Azucena Salas
Software Mentions: 4
Published: over 5 years ago

10.18632/oncotarget.8239

Integrated epigenomic analyses of enhancer as well as promoter regions in gastric cancer
Cited by: 13
Author(s): Su‐Jin Baek, Mirang Kim, Donghyuck Bae, Jeong‐Hwan Kim, Hee‐Jin Kim, Myoung‐Eun Han, Sae‐Ock Oh, Yong‐Sung Kim, Seon‐Young Kim
Software Mentions: 4
Published: over 10 years ago

10.1371/journal.pone.0198191

Early responses to dehydration in contrasting wild Arachis species
Cited by: 21
Author(s): C. C. Vinson, Ana Paula Zotta Mota, Thais Nicolini Oliveira, Larissa Arrais Guimarães, Soraya C. M. Leal‐Bertioli, Thomas Christopher Rhys Williams, Alexandre Lima Nepomuceno, Mario Alfredo Passos Saraiva, Ana Cláudia Guerra Araújo, P. M. Guimarães, Ana Cristina Miranda Brasileiro
Software Mentions: 4
Published: over 8 years ago

10.1186/s12864-016-2952-3

Global transcriptional analysis suggests Lasiodiplodia theobromae pathogenicity factors involved in modulation of grapevine defensive response
Cited by: 46
Author(s): Marcos Paolinelli, José Manuel Villalobos-Escobedo, Philippe E. Rolshausen, Alfredo Herrera-Estrella, Clara E. Galindo-Sánchez, José Fabricio López-Hernández, Rufina Hernández-Martínez
Software Mentions: 4
Published: about 10 years ago

10.7554/eLife.45310

A cis-carotene derived apocarotenoid regulates etioplast and chloroplast development
Cited by: 45
Author(s): Christopher I. Cazzonelli, Xin Hou, Yağiz Alagöz, John Rivers, Namraj Dhami, Jiwon Lee, Shashikanth Marri, Barry J. Pogson
Software Mentions: 4
Published: almost 7 years ago

10.1186/1471-2164-15-133

Virus-independent and common transcriptome responses of leafhopper vectors feeding on maize infected with semi-persistently and persistent propagatively transmitted viruses
Cited by: 33
Author(s): Bryan J. Cassone, Saranga Wijeratne, Andrew P. Michel, Lucy R. Stewart, Yuting Chen, Pearlly S. Yan, Margaret G. Redinbaugh
Software Mentions: 4
Published: over 12 years ago

10.1093/database/baw052

ToxDB: pathway-level interpretation of drug-treatment data
Cited by: 18
Author(s): Christopher Hardt, Moritz Emanuel Beber, Axel Rasche, Atanas Kamburov, Dennie G. A. J. Hebels, Jos Kleinjans, Ralf Herwig
Software Mentions: 4
Published: almost 11 years ago

10.1371/journal.pone.0211491

A five-gene signature predicts overall survival of patients with papillary renal cell carcinoma
Cited by: 29
Author(s): Zhe Gao, Dong Zhang, Yi Duan, Lei Yan, Yi‐Ming Fan, Zhiqing Fang, Zhaoxu Liu
Software Mentions: 4
Published: over 7 years ago

10.7554/eLife.53127

Translational control of one-carbon metabolism underpins ribosomal protein phenotypes in cell division and longevity
Cited by: 23
Author(s): Nairita Maitra, Chi He, Heidi M. Blank, Mitsuhiro Tsuchiya, Birgit Schilling, Matt Kaeberlein, Rodolfo Aramayo, Brian K. Kennedy, Michael Polymenis
Software Mentions: 4
Published: over 6 years ago

10.3390/cancers12092543

CeRNA Network Analysis Representing Characteristics of Different Tumor Environments Based on 1p/19q Codeletion in Oligodendrogliomas
Cited by: 4
Author(s): Ju Won Ahn, Young Joon Park, Su Jung Kang, So Jung Hwang, Kyung Gi Cho, Jaejoon Lim, KyuBum Kwack
Software Mentions: 4
Published: about 6 years ago

10.3390/ijms22105066

The AraC-Type Transcriptional Regulator GliR (PA3027) Activates Genes of Glycerolipid Metabolism in Pseudomonas aeruginosa
Cited by: 10
Author(s): Karolina Kotecka, Adam Kawałek, Kamil Kobyłecki, Aneta Agnieszka Bartosik
Software Mentions: 4
Published: over 5 years ago

10.3390/cancers12102918

Time-Resolved Profiling Reveals ATF3 as a Novel Mediator of Endocrine Resistance in Breast Cancer
Cited by: 8
Author(s): Simone Borgoni, Emre Sofyalı, Maryam Soleimani, Heike Wilhelm, Karin Müller‐Decker, Rainer Will, Ashish Noronha, Lukas Beumers, Pernette J. Verschure, Yosef Yarden, Luca Magnani, Antoine H. C. van Kampen, Perry D. Moerland, Stefan Wiemann
Software Mentions: 4
Published: about 6 years ago

10.3390/cancers12051143

Differential B-Cell Receptor Signaling Requirement for Adhesion of Mantle Cell Lymphoma Cells to Stromal Cells
Cited by: 8
Author(s): Laia Sadeghi, Gustav Arvidsson, Magali Merrien, Agata M. Wasik, André Görgens, C. I. Edvard Smith, Birgitta Sander, Anthony P. H. Wright
Software Mentions: 4
Published: over 6 years ago

10.3390/cancers12123789

Neural Networks Recapitulation by Cancer Cells Promotes Disease Progression: A Novel Role of p73 Isoforms in Cancer-Neuronal Crosstalk
Cited by: 16
Author(s): Stella Logotheti, Stephan Marquardt, Christin Richter, Renée Sophie Hain, Nico Murr, Işıl Takan, Athanasia Pavlopoulou, Brigitte M. Pützer
Software Mentions: 4
Published: almost 6 years ago

10.3390/cancers13061421

Efficacy of Targeted Radionuclide Therapy Using [131I]ICF01012 in 3D Pigmented BRAF- and NRAS-Mutant Melanoma Models and In Vivo NRAS-Mutant Melanoma
Cited by: 5
Author(s): Hussein Akil, Mercédès Quintana, J. Raymond, Tommy Billoux, Valentin Benboubker, Sophie Besse, Philippe Auzeloux, Véronique Delmas, Valérie Petit, Lionel Larue, M. D’Incan, Françoise Degoul, Jacques Rouanet
Software Mentions: 4
Published: over 5 years ago

10.1016/j.devcel.2021.07.018

Reprogrammed lipid metabolism protects inner nuclear membrane against unsaturated fat
Cited by: 28
Author(s): Anete Romanauska, Alwin Köhler
Software Mentions: 4
Published: about 5 years ago

10.3390/cancers13030559

Type 2 Innate Lymphoid Cells Protect against Colorectal Cancer Progression and Predict Improved Patient Survival
Cited by: 29
Author(s): Qiutong Huang, Nicolas Jacquelot, Adele Preaudet, Soroor Hediyeh-Zadeh, Fernando Souza-Fonseca-Guimarães, Andrew N. J. McKenzie, Philip M. Hansbro, Melissa J. Davis, Lisa A. Mielke, Tracy L. Putoczki, Gabrielle T. Belz
Software Mentions: 4
Published: almost 6 years ago

10.1016/j.ebiom.2019.11.046

Prioritization of novel ADPKD drug candidates from disease-stage specific gene expression profiles
Cited by: 15
Author(s): Tareq B. Malas, Wouter N. Leonhard, Hester Bange, Zoraide Granchi, Kristina Hettne, Gerard J. P. van Westen, Leo Price, Peter A C ‘t Hoen, Dorien J.M. Peters
Software Mentions: 4
Published: almost 7 years ago

10.3390/cancers12082210

Human FBXL8 Is a Novel E3 Ligase Which Promotes BRCA Metastasis by Stimulating Pro-Tumorigenic Cytokines and Inhibiting Tumor Suppressors
Cited by: 10
Author(s): Shu Chun Chang, Wei‐Hsiu Hsu, Emily Chia Yu Su, Chin Sheng Hung, Jeak Ling Ding
Software Mentions: 4
Published: about 6 years ago

10.3390/cancers13174250

Transcriptional Reprogramming and Constitutive PD-L1 Expression in Melanoma Are Associated with Dedifferentiation and Activation of Interferon and Tumour Necrosis Factor Signalling Pathways
Cited by: 10
Author(s): Antonio Ahn, Euan J. Rodger, Jyoti Motwani, Grégory Gimenez, Peter A. Stockwell, Matthew Parry, Peter Hersey, Aniruddha Chatterjee, Michael R. Eccles
Software Mentions: 4
Published: about 5 years ago

10.1186/s12870-021-02997-5

Low nitrogen availability inhibits the phosphorus starvation response in maize (Zea mays ssp. mays L.)
Cited by: 10
Author(s): J. Vladimir Torres-Rodríguez, M. Nancy Salazar-Vidal, Ricardo A. Chávez Montes, Julio A. Massange‐Sánchez, C. Stewart Gillmor, Ruairidh J. H. Sawers
Software Mentions: 4
Published: over 5 years ago

10.1186/s12864-017-3809-0

Gene dispersion is the key determinant of the read count bias in differential expression analysis of RNA-seq data
Cited by: 20
Author(s): Susan A. Yoon, Dougu Nam
Software Mentions: 4
Published: over 9 years ago

10.3390/cancers12123786

Stroma Transcriptomic and Proteomic Profile of Prostate Cancer Metastasis Xenograft Models Reveals Prognostic Value of Stroma Signatures
Cited by: 9
Author(s): Sofia Karkampouna, Maria Rosaria De Filippo, Charlotte K.Y. Ng, Irena Klima, Eugenio Zoni, Martin Spahn, Frank Stein, Per Haberkant, George N. Thalmann, Marianna Kruithof-de Julio
Software Mentions: 4
Published: almost 6 years ago

10.3390/cancers13030548

Identification of RCC Subtype-Specific microRNAs–Meta-Analysis of High-Throughput RCC Tumor microRNA Expression Data
Cited by: 11
Author(s): Arkadiusz Kajdasz, Weronika Majer, Katarzyna Kluzek, Jacek Sobkowiak, Tomasz Milecki, Natalia Derebecka, Zbigniew Kwias, Hans A.R. Bluyssen, Joanna Wesoły
Software Mentions: 4
Published: almost 6 years ago

10.3390/cancers12051325

Tumor Cell Associated Hyaluronan-CD44 Signaling Promotes Pro-Tumor Inflammation in Breast Cancer
Cited by: 18
Author(s): Patrice M Witschen, Thomas S. Chaffee, Nicholas J. Brady, Danielle N. Huggins, Todd P. Knutson, Rebecca S. LaRue, Sarah A. Munro, Lyubov Tiegs, James B. McCarthy, Andrew C. Nelson, Kathryn L. Schwertfeger
Software Mentions: 4
Published: over 6 years ago

10.1186/s12870-020-02757-x

Differential gene expression reveals mechanisms related to habitat divergence between hybridizing orchids from the Neotropical coastal plains
Cited by: 5
Author(s): Bárbara Simões Santos Leal, Marcelo Mendes Brandão, Clarisse Palma‐Silva, Fábio Pinheiro
Software Mentions: 4
Published: almost 6 years ago

10.1016/j.isci.2021.102751

The effects of aging on molecular modulators of human embryo implantation
Cited by: 6
Author(s): Panagiotis Ntostis, Grace Swanson, Georgia Kokkali, David Iles, John Huntriss, Agni Pantou, Maria Tzetis, Konstantinos Pantos, Helen M. Picton, Stephen A. Krawetz, D. H. Miller
Software Mentions: 4
Published: over 5 years ago

10.3390/ijms22073674

Can miRNA Indicate Risk of Illness after Continuous Exposure to M. tuberculosis?
Cited by: 3
Author(s): Cleonardo Augusto Silva, André M. Ribeiro-dos-Santos, Wanderson Gonçalves e Gonçalves, Pablo Diego do Carmo Pinto, Rafael Pompeu Pantoja, Tatiana Vinasco-Sandoval, André M. Ribeiro-dos-Santos, Mara H. Hutz, Amanda Ferreira Vidal, Gilderlanio Santana de Araújo, Sidney Emanuel Batista dos Santos
Software Mentions: 4
Published: over 5 years ago

10.3390/cancers13163954

Prognostication of Primary Tumor Location in Early-Stage Nodal Diffuse Large B-Cell Lymphoma: An Analysis of the SEER Database
Cited by: 2
Author(s): Yi Xia, Silan Huang, Yu Wang, Dexin Lei, Yanlou Wang, Hang Yang, Yan Gao, Panpan Li
Software Mentions: 4
Published: about 5 years ago

10.7554/eLife.65979

Unbiased identification of novel transcription factors in striatal compartmentation and striosome maturation
Cited by: 8
Author(s): Maria-Daniela Cirnaru, Sicheng Song, Kizito-Tshitoko Tshilenge, Chuhyon Corwin, Justyna Mleczko, Carlos Galicia Aguirre, Houda Benlhabib, Jaroslav Bendl, Pasha Apontes, John F. Fullard, Jordi Creus-Muncunill, Azadeh Reyahi, Ali Moussavi Nik, Peter Carlsson, Panos Roussos, Sean D. Mooney, Lisa M. Ellerby, Michelle E. Ehrlich
Software Mentions: 4
Published: about 5 years ago

10.3390/cancers12092397

Combined Targeting of Estrogen Receptor Alpha and Exportin 1 in Metastatic Breast Cancers
Cited by: 9
Author(s): Eylem Kulkoyluoglu-Cotul, Qianying Zuo, Ashlie Santaliz-Casiano, Ozan Berk Imir, Ayca Nazli Mogol, Elif Tunç, Kevin Duong, Jenna Kathryn Lee, Rithva Ramesh, Elijah Odukoya, Mrinali P. Kesavadas, Monika Ziogaite, Brandi Patrice Smith, Chengjian Mao, David J. Shapiro, Ben Ho Park, Benita S. Katzenellenbogen, Drew Daly, Evelyn Aranda, John D. O’Neill, Christopher J. Walker, Yosef Landesman, Zeynep Madak-Erdoğan
Software Mentions: 4
Published: about 6 years ago

10.1016/j.cell.2013.03.012

Exit from Pluripotency Is Gated by Intracellular Redistribution of the bHLH Transcription Factor Tfe3
Cited by: 288
Author(s): Joerg Betschinger, Jennifer Nichols, Sabine Dietmann, Philip Corrin, Patrick J. Paddison, Austin Smith
Software Mentions: 4
Published: over 13 years ago

10.1016/j.cell.2018.11.041

The Implication of Early Chromatin Changes in X Chromosome Inactivation
Cited by: 188
Author(s): J. Ż̷ylicz, Aurélie Bousard, Kristina Žumer, François Dossin, Eusra Mohammad, Simão Teixeira da Rocha, Björn Schwalb, Laurène Syx, Florent Dingli, Damarys Loew, Patrick Cramer, Edith Heard
Software Mentions: 4
Published: almost 8 years ago

10.3390/ijms22063125

A Transcriptomic Approach to Understanding the Combined Impacts of Supra-Optimal Temperatures and CO2 Revealed Different Responses in the Polyploid Coffea arabica and Its Diploid Progenitor C. canephora
Cited by: 12
Author(s): Isabel Marques, Isabel Fernandes, Octávio S. Paulo, Fernando C. Lidon, Fábio M. DaMatta, José C. Ramalho, Ana I. Ribeiro‐Barros
Software Mentions: 4
Published: over 5 years ago

10.7554/eLife.63556

Deficient spermiogenesis in mice lacking Rlim
Cited by: 7
Author(s): Feng Wang, María Gracia Gervasi, Ana Bošković, Fengyun Sun, Vera D. Rinaldi, Jun Yu, Mary C. Wallingford, Darya A Tourzani, Jesse Mager, Lihua Julie Zhu, Oliver J. Rando, Pablo E. Visconti, Lara Strittmatter, Ingolf Bach
Software Mentions: 4
Published: over 5 years ago

10.1186/2045-3701-2-26

Statistical methods for identifying differentially expressed genes in RNA-Seq experiments
Cited by: 43
Author(s): Zhide Fang, Jeffrey A. Martin, Zhong Wang
Software Mentions: 4
Published: almost 15 years ago

10.1242/dmm.042713

Leptin and fractalkine: Novel subcutaneous cytokines in burn injury
Cited by: 4
Author(s): Dominic Friston, Sini Junttila, Júlia Borges Paes Lemes, Helen Laycock, Jose Vicente Torres-Pérez, Elizabeth J. Want, Attila Gyenesei, I. Nagy
Software Mentions: 4
Published: almost 7 years ago

10.3390/ijms22052481

Differential Morpho-Physiological and Transcriptomic Responses to Heat Stress in Two Blueberry Species
Cited by: 5
Author(s): Jodi B Callwood, Kalpalatha Melmaiee, Krishnanand P. Kulkarni, Amaranatha R. Vennapusa, Diarra Aicha, Michael J. Moore, Nicholi Vorsa, Purushothaman Natarajan, Umesh K. Reddy, Sathya Elavarthi
Software Mentions: 4
Published: over 5 years ago

10.1038/s41419-021-03727-3

Interrogation of gender disparity uncovers androgen receptor as the transcriptional activator for oncogenic miR-125b in gastric cancer
Cited by: 14
Author(s): Ben Liu, Meng Zhou, Xiangchun Li, Xining Zhang, Qinghua Wang, Luyang Liu, Meng Yang, Da Yang, Yan Guo, Qiang Zhang, Hong Zheng, Qiong Wang, Lian Li, Xinlei Chu, Wei Wang, Haixin Li, Fengju Song, Yuan Pan, Wei Zhang, Kexin Chen
Software Mentions: 4
Published: over 5 years ago

10.1038/s41419-018-1141-5

Plau and Tgfbr3 are YAP-regulated genes that promote keratinocyte proliferation
Cited by: 18
Author(s): Susan M. Corley, Veronica Mendoza-Reinoso, Nichole Giles, Emma Suwanun Singer, John E.A. Common, Marc R. Wilkins, Annemiek Beverdam
Software Mentions: 4
Published: about 8 years ago

10.7554/eLife.21221

Pharmacological targeting of the transcription factor SOX18 delays breast cancer in mice
Cited by: 45
Author(s): Jeroen Overman, Frank Fontaine, Mehdi Moustaqil, Deepak Mittal, Emma Sierecki, Natalia Sacilotto, Johannes Zuegg, Avril A. B. Robertson, Kelly A. Holmes, Angela A. Salim, Sreeman K. Mamidyala, Mark S. Butler, Ashley Robinson, Emmanuelle Lesieur, Wayne A. Johnston, Kirill Alexandrov, Brian L. Black, Benjamin M. Hogan, Sarah De Val, Robert J. Capon, Jason S. Carroll, Timothy L. Bailey, Peter Koopman, Ralf Jauch, Mark J. Smyth, Matthew A. Cooper, Yann Gambin, Mathias François
Software Mentions: 4
Published: almost 10 years ago

10.7554/eLife.29750

cAMP signaling regulates DNA hydroxymethylation by augmenting the intracellular labile ferrous iron pool
Cited by: 29
Author(s): Vladimir Camarena, David W. Sant, Tyler C. Huff, Sushmita Mustafi, Ryan K Muir, Allegra T. Aron, Christopher J. Chang, Adam R. Renslo, Paula V. Monje, Gaofeng Wang
Software Mentions: 4
Published: almost 9 years ago

10.1038/s41419-021-04144-2

LncRNA PCBP1-AS1-mediated AR/AR-V7 deubiquitination enhances prostate cancer enzalutamide resistance
Cited by: 19
Author(s): Boya Zhang, Mingpeng Zhang, Chunyi Shen, Guancong Liu, Fan Zhang, Jingyu Hou, Weitao Yao
Software Mentions: 4
Published: about 5 years ago

10.7554/eLife.55102

The S-phase-induced lncRNA SUNO1 promotes cell proliferation by controlling YAP1/Hippo signaling pathway
Cited by: 17
Author(s): Qinyu Hao, Xinying Zong, Qinyu Sun, Yo Chuen Lin, You Shang, Seyedsasan Hashemikhabir, Rosaline Y.C. Hsu, Mohammad Kamran, Ritu Chaudhary, Vidisha Tripathi, Deepak Kumar Singh, Arindam Chakraborty, Xiao Ling Li, Yoonjung Kim, Arturo V. Orjalo, Maria Polycarpou‐Schwarz, Branden S. Moriarity, Lisa M. Miller Jenkins, Hans Johansson, Yuelin J. Zhu, Sven Diederichs, Anindya Bagchi, Tae Hoon Kim, Sarath Chandra Janga, Ashish Lal, Supriya G. Prasanth, Kannanganattu V. Prasanth
Software Mentions: 4
Published: about 6 years ago

10.1186/s12870-018-1293-6

Integrative genomics approaches validate PpYUC11-like as candidate gene for the stony hard trait in peach (P. persica L. Batsch)
Cited by: 20
Author(s): Marco Cirilli, D. Giovannini, Angelo Ciacciulli, Remo Chiozzotto, Stefano Gattolin, Laura Rossini, A. Liverani, D. Bassi
Software Mentions: 4
Published: over 8 years ago

10.7554/eLife.21052

Embryonic origin of adult stem cells required for tissue homeostasis and regeneration
Cited by: 66
Author(s): Erin L. Davies, Kai Y. Lei, Christopher Seidel, Amanda E Kroesen, Sean A. McKinney, Longhua Guo, Sofia Robb, E. J. Ross, Kirsten Gotting, Alejandro Sánchez Alvarado
Software Mentions: 4
Published: almost 10 years ago

10.3390/ijms21249560

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

10.3389/fonc.2020.613333

Construction of Bone Metastasis-Specific Regulation Network Based on Prognostic Stemness-Related Signatures in Breast Invasive Carcinoma
Cited by: 2
Author(s): Runzhi Huang, Zhenyu Li, Jiayao Zhang, Zhiwei Zeng, Jiaqi Zhang, Mingxiao Li, Siqao Wang, Shuyuan Xian, Yuna Xue, Xi Chen, Jie Li, Wing Yan Elizabeth Cheng, Bin Wang, Penghui Yan, Daoke Yang, Zongqiang Huang
Software Mentions: 4
Published: almost 6 years ago

10.1038/s42003-019-0406-6

P38 inhibition reverses TGFβ1 and TNFα-induced contraction in a model of proliferative vitreoretinopathy
Cited by: 27
Author(s): Lauren Schiff, Nathan C. Boles, Marie Fernandes, Bar Nachmani, Ronald C. Gentile, Timothy A. Blenkinsop
Software Mentions: 4
Published: over 7 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

10.1038/s42003-020-01469-0

DNA methylation patterns identify subgroups of pancreatic neuroendocrine tumors with clinical association
Cited by: 27
Author(s): Vanessa Lakis, Rita T. Lawlor, Felicity Newell, Ann‐Marie Patch, Andrea Mafficini, Anguraj Sadanandam, Lambros T. Koufariotis, Rebecca L. Johnston, Conrad Leonard, Scott Wood, Borislav Rusev, Vincenzo Corbo, Claudio Luchini, Sara Cingarlini, Luca Landoni, Roberto Salvia, Michèle Milella, David K. Chang, Peter J. Bailey, Nigel B. Jamieson, Fraser Duthie, Marie‐Claude Gingras, Donna M. Muzny, David A. Wheeler, Richard A. Gibbs, Massimo Milione, Apgi, ARC-Net, Paolo Pederzoli, Jaswinder S. Samra, Anthony J. Gill, Amber Johns, John V. Pearson, Andrew V. Biankin, Sean M. Grimmond, Nicola Waddell, Kátia Nones, Aldo Scarpa
Software Mentions: 4
Published: almost 6 years ago

10.1038/s42003-021-02203-0

The chaperonin CCT8 controls proteostasis essential for T cell maturation, selection, and function
Cited by: 5
Author(s): Bergithe E. Oftedal, Stefano Maio, Adam E. Handel, White Mpj., Duncan Howie, Simon Davis, Nicolas Prevot, Ioanna A. Rota, Mary E. Deadman, Benedikt M. Kessler, Román Fischer, Nikolaus S. Trede, Erdinç Sezgin, Rick M. Maizels, G A Holländer
Software Mentions: 4
Published: over 5 years ago

10.1186/s12864-016-2973-y

Transcriptome analysis of seed dormancy after rinsing and chilling in ornamental peaches (Prunus persica (L.) Batsch)
Cited by: 15
Author(s): Kanjana Worarad, Tomohiro Suzuki, Kazuo Ishii, Toshinori Kozaki, Masayuki Iigo, Kenji Yamane
Software Mentions: 4
Published: about 10 years ago

10.1038/s42003-019-0391-9

Pharmacological systems analysis defines EIF4A3 functions in cell-cycle and RNA stress granule formation
Cited by: 25
Author(s): Alborz Mazloomian, Shinsuke Araki, Momoko Ohori, Amal M. El-Naggar, Damian Yap, Ali Bashashati, Shigetomi Nakao, Poul H. Sorensen, Atsushi Nakanishi, Sohrab P. Shah, Samuel Aparicio
Software Mentions: 4
Published: over 7 years ago

10.1186/s12870-015-0661-8

A bulk segregant transcriptome analysis reveals metabolic and cellular processes associated with Orange allelic variation and fruit β-carotene accumulation in melon fruit
Cited by: 51
Author(s): Noam Chayut, Hui Yuan, Shachar Ohali, Ayala Meir, Yelena Yeselson, Vitaly Portnoy, Yi Zheng, Zhangjun Fei, Efraim Lewinsohn, Nurit Katzir, Arthur A. Schaffer, Shimon Gepstein, Joseph Burger, L i Li, Yaakov Tadmor
Software Mentions: 4
Published: almost 11 years ago

10.3389/fonc.2021.546455

Identification of an Individualized Immune-Related Prognostic Risk Score in Lung Squamous Cell Cancer
Cited by: 9
Author(s): Yuan Zhuang, Sihan Li, Chang Liu, Guang Li
Software Mentions: 4
Published: over 5 years ago

10.1186/s12864-018-5184-x

Transcriptome analyses of reprogrammed feather / scale chimeric explants revealed co-expressed epithelial gene networks during organ specification
Cited by: 7
Author(s): Yung-Chih Lai, Ya-Chen Liang, Ting‐Xin Jiang, Randall B. Widelitz, Ping Wu, Cheng‐Ming Chuong
Software Mentions: 4
Published: about 8 years ago

10.3389/fcell.2020.00808

Integrated Microarray and RNAseq Transcriptomic Analysis of Retinal Pigment Epithelium/Choroid in Age-Related Macular Degeneration
Cited by: 10
Author(s): Dhanach Dhirachaikulpanich, Xin Li, Louise F. Porter, Luminita Paraoan
Software Mentions: 4
Published: about 6 years ago

10.3389/fcell.2021.591754

Scaffold-Mediated Developmental Effects on Human Induced Pluripotent Stem Cell-Derived Cardiomyocytes Are Preserved After External Support Removal
Cited by: 1
Author(s): Jun Li, Jong-Kook Lee, Keiko Miwa, Yuki Kuramoto, Kiyoshi Masuyama, Hideki Yasutake, Satoki Tomoyama, Hiroyuki Nakanishi, Yasushi Sakata
Software Mentions: 4
Published: over 5 years ago

Projects: bioconductor: edgeR

Science Score: 100/100

Bonuses:

Papers Mentioning edgeR 6,568