pypi: HTSeq | Projects | Ecosyste.ms: Papers

10.1038/s41598-020-70131-w

Transcriptomic profile of adverse neurodevelopmental outcomes after neonatal encephalopathy
Cited by: 6
Author(s): Paolo Montaldo, Aubrey J. Cunnington, Vânia Oliveira, Ravi Swamy, Prathik Bandya, Stuti Pant, Peter J Lally, Phoebe Ivain, Josephine Mendoza, Gaurav Atreja, Padmesh Vadakepat, Mythili Baburaj, Monica Sebastian, Indiramma Yasashwi, Chinnathambi Kamalarathnam, Rema Chandramohan, Mangalabharathi Sundaram, Kumutha Kumaraswami, Shobha Kumar, Naveen Benakappa, Swati Manerkar, Jayashree Mondhkar, Vinayagam Prakash, Mohammed Sajjid, Arasar Seeralar, Ismat Jahan, Sadeka Choudhury Moni, Mohammod Shahidullah, Radhika Sujatha, M Chandrasekaran, Siddarth Ramji, Seetha Shankaran, Myrsini Kaforou, Jethro Herberg, Sudhin Thayyil
Software Mentions: 5
Published: about 6 years ago

10.1371/journal.pone.0252685

Expanded transcriptomic view of strawberry fruit ripening through meta-analysis
Cited by: 0
Author(s): Gibum Yi, Hosub Shin, Kyeonglim Min, Eun Jin Lee
Software Mentions: 5
Published: over 5 years ago

10.1038/s41419-021-03644-5

Eradication of specific donor-dependent variations of mesenchymal stem cells in immunomodulation to enhance therapeutic values
Cited by: 19
Author(s): Chunxue Zhang, Liqiang Zhou, Zhen Wang, Wenxia Gao, Wei Chen, Huina Zhang, Bo Jing, Zhu Xu, Lei Chen, Changhong Zheng, Kaiyan Shi, Wu Li, Liming Cheng, Kunshan Zhang, Yi Sun
Software Mentions: 5
Published: over 5 years ago

10.7554/eLife.23645

Cooperation between a hierarchical set of recruitment sites targets the X chromosome for dosage compensation
Cited by: 27
Author(s): Sarah Elizabeth Albritton, Anna Lena Kranz, Lara Winterkorn, Lena Annika Street, Sevinç Ercan
Software Mentions: 5
Published: over 9 years ago

10.1186/s12864-021-07924-4

Transcriptomic analysis to elucidate the effects of high stocking density on grass carp (Ctenopharyngodon idella)
Cited by: 10
Author(s): Yan He, Hongyan Yu, Hongling Zhao, Hua Zhu, Qingjing Zhang, Anqi Wang, Yubang Shen, Xiaoyan Xu, Jiale Li
Software Mentions: 5
Published: about 5 years ago

10.1186/s12864-019-5974-9

Comparison of gene expression profile of the spinal cord of sprouting-capable neonatal and sprouting-incapable adult mice
Cited by: 9
Author(s): Hiroshi Tsujioka, Toshio Yamashita
Software Mentions: 5
Published: about 7 years ago

10.1038/s41598-017-09335-6

Integrative epigenomics, transcriptomics and proteomics of patient chondrocytes reveal genes and pathways involved in osteoarthritis
Cited by: 85
Author(s): Julia Steinberg, Graham R. S. Ritchie, Theodoros I. Roumeliotis, Raveen L Jayasuriya, Matthew Clark, Roger A. Brooks, Abbie L. A. Binch, Karan M. Shah, Rachael Coyle, Mercedes Pardo, Christine Le Maitre, Yolande F M Ramos, Rob G H H Nelissen, Ingrid Meulenbelt, Andrew W. McCaskie, Jyoti S. Choudhary, J. Mark Wilkinson, Eleftheria Zeggini
Software Mentions: 5
Published: about 9 years ago

10.1038/s41598-017-08094-8

CD24 induces changes to the surface receptors of B cell microvesicles with variable effects on their RNA and protein cargo
Cited by: 14
Author(s): D. Craig Ayre, Ian C. Chute, Andrew P. Joy, David A. Barnett, Andrew M. Hogan, Marc P. Grüll, Lourdes Peña‐Castillo, Andrew S. Lang, Stephen M. Lewis, Sherri L. Christian
Software Mentions: 5
Published: about 9 years ago

10.1002/1878-0261.12655

Transcriptome profiling of Ewing sarcomas – treatment resistance pathways and IGF‐dependency
Cited by: 6
Author(s): Yi Chen, Asle Charles Hesla, Yingbo Lin, Mehran Ghaderi, Mingzhi Liu, Yang Chen, Yifan Zhang, Panagiotis Tsagozis, Olle Larsson, Felix Haglund
Software Mentions: 5
Published: over 6 years ago

10.1371/journal.ppat.1009349

PD-1 is imprinted on cytomegalovirus-specific CD4+ T cells and attenuates Th1 cytokine production whilst maintaining cytotoxicity
Cited by: 15
Author(s): Helen Parry, Alexander C. Dowell, Jianmin Zuo, Kriti Verma, Francesca Kinsella, Jusnara Begum, Wayne Croft, Archana Sharma-Oates, Guy Pratt, Paul Moss
Software Mentions: 5
Published: over 5 years ago

10.1186/s12864-015-2246-1

High-throughput transcriptomics reveals common and strain-specific responses of human macrophages to infection with Mycobacterium abscessus Smooth and Rough variants
Cited by: 12
Author(s): Anna Aulicino, Adam M. Dinan, Aleksandra A. Miranda-CasoLuengo, John A. Browne, Kévin Rue-Albrecht, David E. MacHugh, Brendan J. Loftus
Software Mentions: 5
Published: almost 11 years ago

10.1371/journal.ppat.1006699

The yeast form of the fungus Candida albicans promotes persistence in the gut of gnotobiotic mice
Cited by: 70
Author(s): Lena Böhm, Sanda Torsin, Su Hlaing Tint, Marie Therese Eckstein, Tobias Ludwig, J. Christian Pérez
Software Mentions: 5
Published: almost 9 years ago

10.1371/journal.pone.0182507

A comprehensive simulation study on classification of RNA-Seq data
Cited by: 26
Author(s): Gökmen Zararsız, Dinçer Göksülük, Selçuk Korkmaz, Vahap Eldem, Gözde Ertürk Zararsız, İzzet Paruğ Duru, Ahmet Öztürk
Software Mentions: 5
Published: about 9 years ago

10.1186/s12864-018-4746-2

SWI/SNF regulates half of its targets without the need of ATP-driven nucleosome remodeling by Brahma
Cited by: 19
Author(s): Antonio Jordán-Pla, Simei Yu, Johan Waldholm, Thomas Källman, Ann‐Kristin Östlund Farrants, Neus Visa
Software Mentions: 5
Published: over 8 years ago

10.1371/journal.pone.0153932

Transcriptional Profiling of Ileocecal Valve of Holstein Dairy Cows Infected with Mycobacterium avium subsp. Paratuberculosis
Cited by: 24
Author(s): Randy J. Hempel, John P. Bannantine, Judith R. Stabel
Software Mentions: 5
Published: over 10 years ago

10.1186/s13024-018-0261-9

Transcriptional profiling and biomarker identification reveal tissue specific effects of expanded ataxin-3 in a spinocerebellar ataxia type 3 mouse model
Cited by: 37
Author(s): Lodewijk J.A. Toonen, Maurice Overzier, Melvin M. Evers, Leticia G. León, Sander A.J. van der Zeeuw, Hailiang Mei, Szymon M. Kiełbasa, Jelle J. Goeman, Kristina Hettne, Ólafur Þ. Magnússon, Marion Poirel, Alexandre Seyer, Peter A.C. ’t Hoen, Willeke M. C. van Roon‐Mom
Software Mentions: 5
Published: over 8 years ago

10.1186/s40478-019-0805-4

Profiling the unique protective properties of intracranial arterial endothelial cells
Cited by: 7
Author(s): Dorien Hermkens, Olga C.G. Stam, Nienke M. de Wit, Ruud D. Fontijn, Aldo Jongejan, Perry D. Moerland, Claire Mackaaij, Ingeborg S. E. Waas, M. J. A. P. Daemen, Helga E. de Vries
Software Mentions: 5
Published: almost 7 years ago

10.1371/journal.pone.0235218

Transcriptome profiling of longissimus lumborum in Holstein bulls and steers with different beef qualities
Cited by: 17
Author(s): Yan Li, Meimei Wang, Qiufeng Li, Yanxia Gao, Qian Li, Jianguo Li, Yong Cao
Software Mentions: 5
Published: over 6 years ago

10.1371/journal.ppat.1008444

Surfing motility is a complex adaptation dependent on the stringent stress response in Pseudomonas aeruginosa LESB58
Cited by: 16
Author(s): Daniel Pletzer, Evelyn Sun, Caleb Ritchie, Lauren Wilkinson, Leo T. Liu, Michael J. Trimble, Heidi Wolfmeier, Travis M. Blimkie, Robert E. W. Hancock
Software Mentions: 5
Published: over 6 years ago

10.1038/s41598-018-27078-w

Global miRNA expression profile reveals novel molecular players in aneurysmal subarachnoid haemorrhage
Cited by: 19
Author(s): Kátia de Paiva Lopes, Tatiana Vinasco-Sandoval, Ricardo Assunção Vialle, Fernando Mendes Paschoal, Vanessa Albuquerque Paschoal Aviz Bastos, Edson Bor‐Seng‐Shu, Manoel Jacobsen Teixeira, Elizabeth Sumi Yamada, Pablo Diego do Carmo Pinto, Amanda Ferreira Vidal, André M. Ribeiro-dos-Santos, Fabiano Cordeiro Moreira, Sidney Emanuel Batista dos Santos, Eric Homero Albuquerque Paschoal, Ândrea Ribeiro‐dos‐Santos
Software Mentions: 5
Published: over 8 years ago

10.1038/s41437-020-00398-2

Sex-specific responses to cold in a very cold-tolerant, northern Drosophila species
Cited by: 12
Author(s): Darren J. Parker, Tapio Envall, Michael G. Ritchie, Maaria Kankare
Software Mentions: 5
Published: over 5 years ago

10.1371/journal.pone.0101374

Assessment of the Impact of Using a Reference Transcriptome in Mapping Short RNA-Seq Reads
Cited by: 21
Author(s): Shanrong Zhao
Software Mentions: 5
Published: over 12 years ago

10.3390/ani11092606

Jejunal Transcriptomic Profiling for Differences in Feed Conversion Ratio in Slow-Growing Chickens
Cited by: 2
Author(s): Panpradub Sinpru, Cindy Riou, Shin Kubota, Chotima Poompramun, Wittawat Molee, Amonrat Molee
Software Mentions: 5
Published: about 5 years ago

10.1172/jci.insight.143469

Activation of skeletal muscle–resident glial cells upon nerve injury
Cited by: 17
Author(s): Daisy Proietti, Lorenzo Giordani, Marco De Bardi, Chiara D’Ercole, Biliana Lozanoska-Ochser, Susanna Amadio, Cinzia Volonté, Sara Marinelli, Antoine Muchir, Marina Bouchè, Giovanna Borsellino, Alessandra Sacco, Pier Lorenzo Puri, Luca Madaro
Software Mentions: 5
Published: over 5 years ago

10.1371/journal.pone.0088515

Extensive Expression Differences along Porcine Small Intestine Evidenced by Transcriptome Sequencing
Cited by: 29
Author(s): Núria Mach, Mustapha Berri, Diane Esquerré, Claire Chevaleyre, Gaëtan Lemonnier, Yvon Billon, Patricia Lepage, Isabelle P. Oswald, Joël Doré, Claire Rogel–Gaillard, Jordi Estellé
Software Mentions: 5
Published: over 12 years ago

10.1093/gigascience/giz145

Benchmark of long non-coding RNA quantification for RNA sequencing of cancer samples
Cited by: 31
Author(s): Hong Zheng, Kevin Brennan, Mikel Hernáez, Olivier Gevaert
Software Mentions: 5
Published: almost 7 years ago

10.1371/journal.pone.0139868

NGS-QCbox and Raspberry for Parallel, Automated and Rapid Quality Control Analysis of Large-Scale Next Generation Sequencing (Illumina) Data
Cited by: 31
Author(s): Mohan A. V. S. K. Katta, Aamir W. Khan, Dadakhalandar Doddamani, Mahendar Thudi, Rajeev K. Varshney
Software Mentions: 5
Published: almost 11 years ago

10.1093/gigascience/giaa112

A molecular map of lung neuroendocrine neoplasms
Cited by: 15
Author(s): Aurélie Gabriel, Emilie Mathian, Lise Mangiante, Catherine Voegele, Vincent Cahais, Akram Ghantous, James McKay, Nicolas Alcala, Lynnette Fernández-Cuesta, Matthieu Foll
Software Mentions: 5
Published: almost 6 years ago

10.1186/s13041-020-00603-7

Ocular hypertension suppresses homeostatic gene expression in optic nerve head microglia of DBA/2 J mice
Cited by: 28
Author(s): James R. Tribble, Jeffrey M. Harder, Pete A. Williams, Simon W. M. John
Software Mentions: 5
Published: over 6 years ago

10.1186/s12943-017-0653-4

Human germ/stem cell-specific gene TEX19 influences cancer cell proliferation and cancer prognosis
Cited by: 18
Author(s): Vicente Planells-Palop, Ali Hazazi, Julia Feichtinger, Jana Jezkova, Gerhard G. Thallinger, Naif Alsiwiehri, Mikhlid H. Almutairi, Lee Parry, Jane A. Wakeman, Ramsay J. McFarlane
Software Mentions: 5
Published: over 9 years ago

10.1007/s11357-021-00329-x

Are the 50’s, the transition decade, in choroid plexus aging?
Cited by: 5
Author(s): Ana Carolina Tahira, Fernanda Marques, Bianca Cristina Garcia Lisbôa, Arthur Sant’Anna Feltrin, André Rocha Barbosa, Kátia C. Oliveira, Carlos Alberto de Bragança Pereira, Renata Leite, Lea T. Grinberg, Cláudia Kimie Suemoto, Renata Eloah de Lucena Ferretti‐Rebustini, Carlos Augusto Pasqualucci, Wilson Jacob‐Filho, Helena Brentani, Joana Almeida Palha
Software Mentions: 5
Published: over 5 years ago

10.1371/journal.pone.0197162

A comparative study of RNA-Seq and microarray data analysis on the two examples of rectal-cancer patients and Burkitt Lymphoma cells
Cited by: 15
Author(s): Alexander Wolff, Michaela Bayerlová, Jochen Gaedcke, Dieter Kube, Tim Beißbarth
Software Mentions: 5
Published: over 8 years ago

10.1186/s13073-021-00938-3

The DNA methylation landscape of multiple myeloma shows extensive inter- and intrapatient heterogeneity that fuels transcriptomic variability
Cited by: 9
Author(s): Jennifer Derrien, Catherine Guérin‐Charbonnel, Victor Gaborit, Loı̈c Campion, Martine Devic, Elise Douillard, Nathalie Roi, Hervé Avet‐Loiseau, Olivier Decaux, Thierry Facon, Jan‐Philipp Mallm, Roland Eils, Nikhil C. Munshi, Philippe Moreau, Carl Herrmann, Florence Magrangeas, Stέphane Minvielle
Software Mentions: 5
Published: about 5 years ago

10.3390/ijms22115858

Calreticulin Deficiency Disturbs Ribosome Biogenesis and Results in Retardation in Embryonic Kidney Development
Cited by: 4
Author(s): Nazli Serin, Gry H. Dihazi, Asima Tayyeb, Christof Lenz, Gerhard A. Müller, Michael Zeisberg, Hassan Dihazi
Software Mentions: 5
Published: over 5 years ago

10.18632/aging.202582

Pan-cancer investigation reveals mechanistic insights of planar cell polarity gene Fuz in carcinogenesis
Cited by: 5
Author(s): Zhefan Stephen Chen, Xiao Lin, Ting-Fung Chan, Ho Yin Chan
Software Mentions: 5
Published: over 5 years ago

10.1016/j.gpb.2020.08.001

G9a/GLP-sensitivity of H3K9me2 Demarcates Two Types of Genomic Compartments
Cited by: 3
Author(s): Zixiang Yan, Luzhang Ji, Xiangru Huo, Qianfeng Wang, Yuwen Zhang, Bo Wen
Software Mentions: 5
Published: about 6 years ago

10.1093/gigascience/giy132

Comprehensive evaluation of RNA-seq analysis pipelines in diploid and polyploid species
Cited by: 21
Author(s): Miriam Payá‐Milans, James W. Olmstead, Gerardo H. Nunez, Timothy A. Rinehart, Margaret Staton
Software Mentions: 5
Published: almost 8 years ago

10.1093/jxb/eraa124

Transcriptomics in Erigeron canadensis reveals rapid photosynthetic and hormonal responses to auxin herbicide application
Cited by: 19
Author(s): Cara L. McCauley, Scott A. M. McAdam, Ketaki P. Bhide, Jyothi Thimmapuram, Jo Ann Banks, Bryan G. Young
Software Mentions: 5
Published: over 6 years ago

10.1186/s13073-020-00760-3

ASXL3 bridges BRD4 to BAP1 complex and governs enhancer activity in small cell lung cancer
Cited by: 32
Author(s): Aileen P. Szczepanski, Zibo Zhao, Victoria Sosnowski, Young Ah Goo, Elizabeth T. Bartom, Lu Wang
Software Mentions: 5
Published: about 6 years ago

10.1186/s12864-020-06911-5

Wild mice with different social network sizes vary in brain gene expression
Cited by: 2
Author(s): Patrícia C. Lopes, Barbara König
Software Mentions: 5
Published: about 6 years ago

10.1371/journal.pone.0232963

Identifying the key regulators that promote cell-cycle activity in the hearts of early neonatal pigs after myocardial injury
Cited by: 11
Author(s): Eric Zhang, Thanh Nguyen, Meng Zhao, Son Do Hai Dang, Jake Y. Chen, Weihua Bian, Gregory P. Walcott
Software Mentions: 5
Published: about 6 years ago

10.1186/s12915-021-01084-3

Long-term persistence of crAss-like phage crAss001 is associated with phase variation in Bacteroides intestinalis
Cited by: 31
Author(s): Andrey N. Shkoporov, Е. В. Хохлова, Niamh Stephens, Cara M. Hueston, Samuel Seymour, Andrew J. Hryckowian, Dimitri Scholz, R. Paul Ross, Colin Hill
Software Mentions: 5
Published: about 5 years ago

10.1186/s12915-018-0558-8

Clonal raider ant brain transcriptomics identifies candidate molecular mechanisms for reproductive division of labor
Cited by: 27
Author(s): Romain Libbrecht, Peter R. Oxley, Daniel J. C. Kronauer
Software Mentions: 5
Published: about 8 years ago

10.1186/s13073-016-0348-2

Epigenomic and metabolic responses of hypothalamic POMC neurons to gestational nicotine exposure in adult offspring
Cited by: 9
Author(s): José P. Silva, Guerline Lambert, Derek Van Booven, Claes Wahlestedt
Software Mentions: 5
Published: about 10 years ago

10.1186/s40168-021-01037-6

When your host shuts down: larval diapause impacts host-microbiome interactions in Nasonia vitripennis
Cited by: 15
Author(s): Jessica Dittmer, Robert M. Brucker
Software Mentions: 5
Published: over 5 years ago

10.1186/s13059-021-02397-w

A trans locus causes a ribosomopathy in hypertrophic hearts that affects mRNA translation in a protein length-dependent fashion
Cited by: 4
Author(s): Franziska Witte, Jorge Ruiz-Orera, Camilla Ciolli Mattioli, Susanne Blachut, Eleonora Adami, Jana Felicitas Schulz, Valentin Schneider-Lunitz, Oliver Hummel, Giannino Patone, Michael Mücke, Jan Šilhavý, Matthias Heinig, Leonardo Bottolo, Daniel Sanchı́s, Martin Vingron, Marina Chekulaeva, Michal Pravenec, Norbert Hübner, Sebastiaan van Heesch
Software Mentions: 5
Published: over 5 years ago

10.1186/s13059-020-02175-0

Multiomics profiling of primary lung cancers and distant metastases reveals immunosuppression as a common characteristic of tumor cells with metastatic plasticity
Cited by: 32
Author(s): Won‐Chul Lee, Alexandre Reuben, Xin Hu, Nicholas McGranahan, Runzhe Chen, Ali Jalali, Marcelo V. Negrão, Shawna M. Hubert, Chad Tang, Chia-Chin Wu, Anthony San Lucas, Whijae Roh, Kenichi Suda, Jihye Kim, Aik-Choon Tan, David H. Peng, Wei Lü, Ximing Tang, Chi-Wan Chow, Junya Fujimoto, Carmen Behrens, Neda Kalhor, Kazutaka Fukumura, Marcus Coyle, Rebecca Thornton, Curtis Gumbs, Jun Li, Chang-Jiun Wu, Latasha Little, Emily Roarty, Xingzhi Song, J. Jack Lee, Erik P. Sulman, Ganesh Rao, Stephen G. Swisher, Lixia Diao, Jing Wang, John V. Heymach, Jason T. Huse, Paul Scheet, Ignacio I. Wistuba, Don L. Gibbons, P. Andrew Futreal, Jianhua Zhang, Daniel R. Gomez, Jianjun Zhang
Software Mentions: 5
Published: almost 6 years ago

10.1186/s13059-021-02464-2

Systematic functional interrogation of human pseudogenes using CRISPRi
Cited by: 11
Author(s): Ming Sun, Yunfei Wang, Caishang Zheng, Yanjun Wei, Jiakai Hou, Peng Zhang, Wei He, Xiangdong Lv, Yao Ding, Han Liang, Chung-Chau Hon, Xi Chen, Xu Han, Yiwen Chen
Software Mentions: 5
Published: about 5 years ago

10.3390/biom11020291

Determination of Genotoxicity Attributed to Diesel Exhaust Particles in Normal Human Embryonic Lung Cell (WI-38) Line
Cited by: 4
Author(s): Joong Won Lee, Hee Jae Lee, Young Joo Lee, Yong Beom Lim, Woo Jong Sim, Ji Hye Jang, Hye Ryeon Heo, Hyunwoo Lim, Ji Won Jung, Jin Sik Kim
Software Mentions: 5
Published: over 5 years ago

10.3390/microorganisms9020347

Global Transcriptional Response of Methylorubrum extorquens to Formaldehyde Stress Expands the Role of EfgA and Is Distinct from Antibiotic Translational Inhibition
Cited by: 3
Author(s): Jannell V. Bazurto, Siavash Riazi, Simon D’Alton, Daniel E. Deatherage, Eric L. Bruger, Jeffrey E. Barrick, Christopher J. Marx
Software Mentions: 5
Published: over 5 years ago

10.3389/fimmu.2018.01286

seq-ImmuCC: Cell-Centric View of Tissue Transcriptome Measuring Cellular Compositions of Immune Microenvironment From Mouse RNA-Seq Data
Cited by: 61
Author(s): Ziyi Chen, Lijun Quan, Anfei Huang, Qiang Zhao, Yuan Yao, Xuye Yuan, Qin Shen, Jingzhe Shang, Yinyin Ben, F. Xiao-Feng Qin, Aiping Wu
Software Mentions: 5
Published: over 8 years ago

10.1093/hmg/ddab031

Sexual dimorphism in cancer: insights from transcriptional signatures in kidney tissue and renal cell carcinoma
Cited by: 10
Author(s): Ruhina Shirin Laskar, Peng Li, Szilvia Ecsedi, Behnoush Abedi‐Ardekani, G. Durand, Nivonirina Robinot, Jean-Noël Hubert, Vladimír Janout, Давид Заридзе, Anush Mukeria, Dana Mateș, Ivana Holcátová, Lenka Foretová, Beata Świątkowska, Zoran Džamić, Saša Milosavljević, Robert Olaso, Anne Boland, Jean‐François Deleuze, David C. Muller, James McKay, Paul Brennan, Florence Le Calvez-Kelm, Ghislaine Scélo, Estelle Chanudet
Software Mentions: 5
Published: over 5 years ago

10.1534/g3.119.400770

Experimental DNA Demethylation Associates with Changes in Growth and Gene Expression of Oak Tree Seedlings
Cited by: 10
Author(s): Luke Browne, Alayna Mead, Courtney Horn, Kevin W. Chang, Zeynep A Celikkol, Claudia L. Henriquez, Feiyang Ma, Eric Beraut, Rachel S. Meyer, Victoria L. Sork
Software Mentions: 5
Published: over 6 years ago

10.3389/fimmu.2020.01095

Peptidylarginine Deiminase 4 Promotes the Renal Infiltration of Neutrophils and Exacerbates the TLR7 Agonist-Induced Lupus Mice
Cited by: 14
Author(s): Norio Hanata, Hirofumi Shoda, Hiroaki Hatano, Yasuo Nagafuchi, Takashi Komai, Tomohisa Okamura, Akari Suzuki, I Ketut Gunarta, Katsuji Yoshioka, Kazuhiko Yamamoto, Keishi Fujio
Software Mentions: 5
Published: over 6 years ago

10.1534/g3.119.400044

HSB-1 Inhibition and HSF-1 Overexpression Trigger Overlapping Transcriptional Changes To Promote Longevity in Caenorhabditis elegans
Cited by: 20
Author(s): Surojit Sural, Tzu-Chiao Lu, Seung Ah Jung, Ao Lin Hsu
Software Mentions: 5
Published: over 7 years ago

10.3389/fimmu.2019.01863

Molecular Characterization of Human Lymph Node Stromal Cells During the Earliest Phases of Rheumatoid Arthritis
Cited by: 13
Author(s): Emmanuel Karouzakis, J Hähnlein, Cristoforo Grasso, Johanna F. Semmelink, Paul P. Tak, Daniëlle M. Gerlag, Caroline Ospelt, Lisa G. M. van Baarsen
Software Mentions: 5
Published: about 7 years ago

10.3389/fpls.2018.00037

Comparative Transcriptome Profiles of Near-Isogenic Hexaploid Wheat Lines Differing for Effective Alleles at the 2DL FHB Resistance QTL
Cited by: 37
Author(s): Chiara Biselli, Paolo Bagnaresi, Primetta Faccioli, Xinkun Hu, Margaret Balcerzak, M. Gabriela Mattera, Zehong Yan, Thérèse Ouellet, Luigi Cattivelli, Giampiero Valè
Software Mentions: 5
Published: over 8 years ago

10.1038/s42003-018-0037-3

The GTPase domain of gamma-tubulin is required for normal mitochondrial function and spatial organization
Cited by: 18
Author(s): Lisa Lindström, Tongbin Li, Darina Malycheva, Arun Kancharla, Helén Nilsson, Neelanjan Vishnu, Hindrik Mulder, Martin Johansson, Catalina Ana Rosselló, María Alvarado-Kristensson
Software Mentions: 5
Published: over 8 years ago

10.1038/s42003-020-01181-z

Transcriptomic and proteomic signatures of stemness and differentiation in the colon crypt
Cited by: 27
Author(s): Amber N. Habowski, Jessica L. Flesher, Jennifer Bates, Chia‐Feng Tsai, Kendall J. Martin, Rui Zhao, Anand K. Ganesan, Robert A. Edwards, Tujin Shi, H. Steven Wiley, Yongsheng Shi, Klemens J. Hertel, Marian L. Waterman
Software Mentions: 5
Published: about 6 years ago

10.3389/fphys.2019.00278

Weighted Gene Co-expression Network Analysis for RNA-Sequencing Data of the Varicose Veins Transcriptome
Cited by: 14
Author(s): Jianbin Zhang, Qiangqiang Nie, Chaozeng Si, Wang Cheng, Yang Chen, Weiliang Sun, Pei Lin, Jing Guo, Jie Kong, Yiyao Cui, Feng Wang, Xueqiang Fan, Zhidong Ye, Jianyan Wen, Peng Liu
Software Mentions: 5
Published: over 7 years ago

10.1038/s42003-021-02167-1

JAK inhibitors dampen activation of interferon-stimulated transcription of ACE2 isoforms in human airway epithelial cells
Cited by: 15
Author(s): Hye Kyung Lee, Olive Jung, Lothar Hennighausen
Software Mentions: 5
Published: over 5 years ago

10.3390/cells10081971

PopulusPtERF85 Balances Xylem Cell Expansion and Secondary Cell Wall Formation in Hybrid Aspen
Cited by: 8
Author(s): Carolin Seyfferth, Bernard A. Wessels, Jorma Vahala, Jaakko Kangasjärvi, Nicolas Delhomme, Torgeir R. Hvidsten, Hannele Tuominen, Judith Lundberg‐Felten
Software Mentions: 5
Published: about 5 years ago

10.1128/mBio.00575-18

Microbiota and Metatranscriptome Changes Accompanying the Onset of Gingivitis
Cited by: 76
Author(s): Emily M. Nowicki, Raghav Shroff, Jacqueline A. Singleton, Diane E. Renaud, Debra L. Wallace, Julie Drury, Jolene Zirnheld, Brock Colleti, Andrew D. Ellington, Richard J. Lamont, David A. Scott, Marvin Whiteley
Software Mentions: 5
Published: over 8 years ago

10.1101/2021.01.15.426908

Interferon-regulated genetic programs and JAK/STAT pathway activate the intronic promoter of the short ACE2 isoform in renal proximal tubules
Cited by: 2
Author(s): Jakub Jankowski, Hye Kyung Lee, Julia Wilflingseder, Lothar Hennighausen
Software Mentions: 5
Published: over 5 years ago

10.1016/j.cels.2018.06.011

Correcting the Mean-Variance Dependency for Differential Variability Testing Using Single-Cell RNA Sequencing Data
Cited by: 63
Author(s): Nils Eling, Alison F. Richard, Sylvia Richardson, John C. Marioni, Catalina A. Vallejos
Software Mentions: 5
Published: about 8 years ago

10.7150/thno.60031

Astrocytic YAP protects the optic nerve and retina in an experimental autoimmune encephalomyelitis model through TGF-β signaling
Cited by: 27
Author(s): Wei Qian, Xuemeng Miao, Jingjing Zhang, Ludan Xiang, Xiuchun Li, Xiaomei Bao, Siyu Du, Mianxian Wang, Shuangda Miao, Yiren Fan, Wei Wang, Xingxing Xu, Xiya Shen, Dongren Yang, Xiwu Wang, Yuanyuan Fang, Li‐Xin Hu, Xuyi Pan, Haoru Dong, Hui Wang, Ying Wang, Jia Li, Zhihui Huang
Software Mentions: 5
Published: almost 6 years ago

10.1016/j.devcel.2021.07.019

Genetically variant human pluripotent stem cells selectively eliminate wild-type counterparts through YAP-mediated cell competition
Cited by: 25
Author(s): Christopher J. Price, Dylan Stavish, Paul J. Gokhale, Ben A. Stevenson, Samantha Sargeant, Joanne Lacey, Tristan A. Rodríguez, Ivana Barbaric
Software Mentions: 5
Published: about 5 years ago

10.3390/cells8080919

The Combination of IFN β and TNF Induces an Antiviral and Immunoregulatory Program via Non-Canonical Pathways Involving STAT2 and IRF9
Cited by: 11
Author(s): Mélissa K. Mariani, Pouria Dasmeh, Audray Fortin, Élise Caron, Mario Kalamujic, Alexander N. Harrison, Diana Ioana Hotea, Dacquin M. Kasumba, Sandra Cervantes-Ortiz, Espérance Mukawera, Adrian W.R. Serohijos, Nathalie Grandvaux
Software Mentions: 5
Published: about 7 years ago

10.1186/s13148-020-00879-5

G9a regulates tumorigenicity and stemness through genome-wide DNA methylation reprogramming in non-small cell lung cancer
Cited by: 25
Author(s): Rajendra P. Pangeni, Lu Yang, Keqiang Zhang, Jinhui Wang, Wendong Li, Chao Guo, Xinwei Yun, Ting Sun, Jami Wang, Dan J. Raz
Software Mentions: 5
Published: over 6 years ago

10.1007/s00122-020-03759-x

Multi-omics-based prediction of hybrid performance in canola
Cited by: 19
Author(s): Dominic Knoch, Christian R. Werner, Rhonda C. Meyer, David Riewe, Amine Abbadi, Sophie Lücke, Rod J. Snowdon, Thomas Altmann
Software Mentions: 5
Published: over 5 years ago

10.1242/dev.146811

Epigenetic resetting of human pluripotency
Cited by: 210
Author(s): Ge Guo, Ferdinand von Meyenn, Maria Rostovskaya, James Clarke, Sabine Dietmann, Duncan Baker, Anna Sahakyan, Samuel A. Myers, Paul Bertone, Wolf Reik, Kathrin Plath, Austin Smith
Software Mentions: 5
Published: about 9 years ago

10.1242/dev.131664

Tissue- and stage-specific Wnt target gene expression is controlled subsequent to β‑catenin recruitment
Cited by: 99
Author(s): Yukio Nakamura, Eduardo Rodrigues Alves, Gert Jan C. Veenstra, Stefan Hoppler
Software Mentions: 5
Published: almost 11 years ago

10.1038/s41598-017-03489-z

Comparative genomics and transcriptomics of Escherichia coli isolates carrying virulence factors of both enteropathogenic and enterotoxigenic E. coli
Cited by: 38
Author(s): Tracy H. Hazen, Jane Michalski, Qingwei Luo, Amol C. Shetty, Sean C. Daugherty, James M. Fleckenstein, David A. Rasko
Software Mentions: 5
Published: over 9 years ago

10.1038/srep46156

Integrated host and viral transcriptome analyses reveal pathology and inflammatory response mechanisms to ALV-J injection in SPF chickens
Cited by: 18
Author(s): Xi Lan, Yan Wang, Kai Tian, Fei Ye, Huadong Yin, Xiaoling Zhao, Hengyong Xu, Yong Huang, Haibo Li, John Hsieh, Susan J. Lamont, Qing Zhu
Software Mentions: 5
Published: over 9 years ago

10.1084/jem.20171738

A broad atlas of somatic hypermutation allows prediction of activation-induced deaminase targets
Cited by: 75
Author(s): Ángel F. Álvarez-Prado, Pablo Pérez-Durán, Arantxa Pérez-García, Alberto Benguría, Carlos Torroja, Virginia G. de Yébenes, Almudena R. Ramiro
Software Mentions: 5
Published: over 8 years ago

10.15252/embj.2020105479

Repression of Irs2 by let‐7 mi <scp>RNA</scp> s is essential for homeostasis of the telencephalic neuroepithelium
Cited by: 9
Author(s): Virgínia Fernández, Maria Ángeles Martínez-Martinez, Anna Prieto-Colomina, Adrián Cárdenas, Rafael Soler, Martina Dori, Ugo Tomasello, Yuki Nomura, José P. López‐Atalaya, Federico Calegari, Vı́ctor Borrell
Software Mentions: 5
Published: about 6 years ago

10.15252/emmm.202013328

Peripheral blood transcriptome profiling enables monitoring disease progression in dystrophic mice and patients
Cited by: 11
Author(s): Mirko Signorelli, Mitra Ebrahimpoor, Olga Veth, Kristina Hettne, Nisha Verwey, R. García-Rodríguez, Christa L Tanganyika-deWinter, Luz Berenice López-Hernández, Rosa Escobar Cedillo, Benjamín Gómez-D́iaz, Ólafur Þ. Magnússon, Hailiang Mei, Roula Tsonaka, Annemieke Aartsma‐Rus, Pietro Spitali
Software Mentions: 5
Published: over 5 years ago

10.1038/srep33813

Contrasting diets reveal metabolic plasticity in the tree-killing beetle, Anoplophora glabripennis (Cerambycidae: Lamiinae)
Cited by: 20
Author(s): Charles J. Mason, Erin D. Scully, Scott M. Geib, Kelli Hoover
Software Mentions: 5
Published: about 10 years ago

10.1038/srep25948

Integrated metabolomic and transcriptome analyses reveal finishing forage affects metabolic pathways related to beef quality and animal welfare
Cited by: 58
Author(s): José A. Carrillo, Yanghua He, Yaokun Li, Jianan Liu, R.A. Erdman, Tad S. Sonstegard, Jiuzhou Song
Software Mentions: 5
Published: over 10 years ago

10.3389/fgene.2020.567812

Integrated Transcriptome and Histone Modification Analysis Reveals NDV Infection Under Heat Stress Affects Bursa Development and Proliferation in Susceptible Chicken Line
Cited by: 13
Author(s): Ganrea Chanthavixay, Colin Kern, Ying Wang, Perot Saelao, Susan J. Lamont, Rodrigo A. Gallardo, Gonzalo Rincón, Huaijun Zhou
Software Mentions: 5
Published: about 6 years ago

10.3389/fgene.2018.00026

Transcriptomic and Proteomic Profiling Revealed High Proportions of Odorant Binding and Antimicrobial Defense Proteins in Olfactory Tissues of the House Mouse
Cited by: 26
Author(s): Barbora Kuntová, Romana Stopková, Pavel Stopka
Software Mentions: 5
Published: over 8 years ago

10.1038/sdata.2018.290

Transcriptome profiling of a beach-adapted wild legume for dissecting novel mechanisms of salinity tolerance
Cited by: 5
Author(s): Hengyou Zhang, Christine Zuelsdorf, Darin S. Penneys, Shoujin Fan, Janice Kofsky, Bao‐Hua Song
Software Mentions: 5
Published: almost 8 years ago

10.3389/fgene.2018.00441

Gene Co-expression Analysis Indicates Potential Pathways and Regulators of Beef Tenderness in Nellore Cattle
Cited by: 30
Author(s): Tassia M. Goncalves, Luciana Correia de Almeida Regitano, James E. Koltes, Aline Silva Mello Cesar, Sónia Cristina da Silva Andrade, Gérson Barreto Mourão, G. Gasparin, Gabriel Costa Monteiro Moreira, Eric R. Fritz-Waters, James M. Reecy
Software Mentions: 5
Published: about 8 years ago

10.1038/sdata.2016.51

Comprehensive RNA-Seq profiling to evaluate lactating sheep mammary gland transcriptome
Cited by: 40
Author(s): Aroa Suárez-Vega, Beatriz Gutiérrez-Gil, Christophe Klopp, Gwenola Tosser‐Klopp, J. J. Arranz
Software Mentions: 5
Published: over 10 years ago

10.1126/sciadv.abd7819

High-resolution 3D imaging uncovers organ-specific vascular control of tissue aging
Cited by: 54
Author(s): Junyu Chen, Unnikrishnan Sivan, Sin Lih Tan, Luciana Lippo, Jessica De Angelis, Rossella Labella, Amit Singh, Alexandros Chatzis, Stanley Cheuk, Mino Medhghalchi, Jesús Gil, Georg A. Holländer, Brian D. Marsden, R. J. P. Williams, Saravana K. Ramasamy, Anjali P. Kusumbe
Software Mentions: 5
Published: over 5 years ago

10.3389/fgene.2021.663091

Identification of a Potentially Functional circRNA-miRNA-mRNA Regulatory Network in Melanocytes for Investigating Pathogenesis of Vitiligo
Cited by: 4
Author(s): Lili Li, Zhi Xie, Xiliang Qian, Tai Wang, Minmin Jiang, Jinglin Qin, Chen Wang, Rongqun Wu, Canling Song
Software Mentions: 5
Published: over 5 years ago

10.3389/fgene.2016.00080

Recursive Indirect-Paths Modularity (RIP-M) for Detecting Community Structure in RNA-Seq Co-expression Networks
Cited by: 12
Author(s): Bahareh Rahmani, Michael T. Zimmermann, Diane E. Grill, Richard B. Kennedy, Ann L. Oberg, Bill C. White, Gregory A. Poland, Brett A. McKinney
Software Mentions: 5
Published: over 10 years ago

10.1038/s42003-020-01398-y

Genomic retargeting of p53 and CTCF is associated with transcriptional changes during oncogenic HRas-induced transformation
Cited by: 2
Author(s): Michal Schwartz, Avital Sarusi Portugez, Bracha Zukerman Attia, Miriam Tannenbaum, Leslie E. Cohen, Olga Loza, Emily Chase, Yousef Turman, Tommy Kaplan, Zaidoun Salah, Ofir Hakim
Software Mentions: 5
Published: almost 6 years ago

10.3389/fgene.2019.00277

Genome-Wide Identification of Histone Modifications Involved in Placental Development in Pigs
Cited by: 19
Author(s): Kun Han, Ruimin Ren, Jianhua Cao, Shuhong Zhao, Mei Yu
Software Mentions: 5
Published: over 7 years ago

10.21203/rs.3.rs-119695/v1

Activation of Interferon-Stimulated Transcriptomes and ACE2 Isoforms in Human Airway Epithelium Is Curbed by Janus Kinase Inhibitors
Cited by: 5
Author(s): Hye Kyung Lee, Olive Jung, Lothar Hennighausen
Software Mentions: 5
Published: almost 6 years ago

10.1098/rsos.200792

Tissue-specific developmental regulation and isoform usage underlie the role ofdoublesexin sex differentiation and mimicry inPapilioswallowtails
Cited by: 13
Author(s): Riddhi Deshmukh, Dhanashree Lakhe, Krushnamegh Kunte
Software Mentions: 5
Published: about 6 years ago

10.3389/fgene.2017.00168

A Pipeline for High-Throughput Concentration Response Modeling of Gene Expression for Toxicogenomics
Cited by: 44
Author(s): John S. House, Fabian A. Grimm, Dereje D. Jima, Yifeng Zhou, Ivan Rusyn, Fred A. Wright
Software Mentions: 5
Published: almost 9 years ago

10.1038/s42003-021-01892-x

Transcriptomic analyses of the termite, Cryptotermes secundus, reveal a gene network underlying a long lifespan and high fecundity
Cited by: 15
Author(s): Silu Lin, Jana Werle, Judith Korb
Software Mentions: 5
Published: over 5 years ago

10.3389/fgene.2019.00766

Machine Learning Classifiers for Endometriosis Using Transcriptomics and Methylomics Data
Cited by: 30
Author(s): Sharmin Akter, Dong Xu, Susan C. Nagel, John J. Bromfield, Katherine E. Pelch, Gilbert B Wilshire, Trupti Joshi
Software Mentions: 5
Published: about 7 years ago

10.1038/s41396-020-00794-w

Phage gene expression and host responses lead to infection-dependent costs of CRISPR immunity
Cited by: 17
Author(s): Sean Meaden, Loris Capria, Ellinor O. Alseth, Sylvain Gandon, Ambarish Biswas, Luca Lenzi, Stineke van Houte, Edze R. Westra
Software Mentions: 5
Published: about 6 years ago

10.18632/oncotarget.23280

Validation of a hypoxia related gene signature in multiple soft tissue sarcoma cohorts
Cited by: 32
Author(s): Lingjian Yang, Laura Forker, Joely J. Irlam, Nischalan Pillay, Ananya Choudhury, Catharine M L West
Software Mentions: 4
Published: almost 9 years ago

10.1016/j.devcel.2020.09.025

Functional Diversification of SRSF Protein Kinase to Control Ubiquitin-Dependent Neurodevelopmental Signaling
Cited by: 27
Author(s): Francisco Bustos, Anna Segarra-Fas, Gino Nardocci, Andrew Cassidy, Odetta Antico, L. S. P. Davidson, Lennart Brandenburg, Thomas Macartney, Rachel Toth, Claire Hastie, Jennifer L. Moran, Robert Gourlay, Joby Varghese, Renata Soares, Martín Montecino, Greg M. Findlay
Software Mentions: 4
Published: almost 6 years ago

10.3389/fgene.2018.00330

Across-Experiment Transcriptomics of Sheep Rumen Identifies Expression of Lipid/Oxo-Acid Metabolism and Muscle Cell Junction Genes Associated With Variation in Methane-Related Phenotypes
Cited by: 7
Author(s): Ruidong Xiang, Jody McNally, J. J. Bond, David J. Tucker, Cameron McCarthy, A. J. Donaldson, K. L. Austin, Suzanne Rowe, Arjan Jonker, C. S. Pinares-Patiño, John C. McEwan, Phil Vercoe, V. H. Oddy, Brian P. Dalrymple
Software Mentions: 4
Published: about 8 years ago

10.1007/s13238-019-0648-6

Core transcriptional signatures of phase change in the migratory locust
Cited by: 26
Author(s): Pengcheng Yang, Hou Li, Xianhui Wang, Le Kang
Software Mentions: 4
Published: over 7 years ago

10.1186/s13287-019-1323-9

Long noncoding RNA CCDC144NL-AS1 knockdown induces naïve-like state conversion of human pluripotent stem cells
Cited by: 8
Author(s): Yingying Wang, Baosen Guo, Zengrong Xiao, Haijun Lin, Xi Zhang, Yueqiang Song, Yalei Li, Xuehu Gao, Jin-Jun Yu, Zhihua Shao, Xuekun Li, Yuan Luo, Siguang Li
Software Mentions: 4
Published: about 7 years ago

Projects: pypi: HTSeq

Science Score: 65/100

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Papers Mentioning HTSeq 3,071