pypi: HTSeq | Projects | Ecosyste.ms: Papers

10.7554/eLife.32697

A switch in transcription and cell fate governs the onset of an epigenetically-deregulated tumor in Drosophila
Cited by: 13
Author(s): Joana Torres, Remo Monti, Ariane L. Moore, Makiko Seimiya, Yanrui Jiang, Niko Beerenwinkel, Christian Beisel, Jorge V. Beira, Renato Paro
Software Mentions: 3
Published: over 8 years ago

10.1038/s41598-018-34636-9

Gene set enrichment analysis of the bronchial epithelium implicates contribution of cell cycle and tissue repair processes in equine asthma
Cited by: 13
Author(s): Laurence Tessier, Olivier Côté, Mary E. Clark, Laurent Viel, Andrés Diaz-Méndez, Simon Anders, Dorothee Bienzle
Software Mentions: 3
Published: about 8 years ago

10.7554/eLife.02510

MicroRNAs shape circadian hepatic gene expression on a transcriptome-wide scale
Cited by: 93
Author(s): Ngoc-Hien Du, Alaaddin Bulak Arpat, Mara De Matos, David Gatfield
Software Mentions: 3
Published: over 12 years ago

10.1186/s13059-021-02439-3

Nanopore sequencing reveals endogenous NMD-targeted isoforms in human cells
Cited by: 23
Author(s): Evangelos D. Karousis, Foivos Gypas, Mihaela Zavolan, Oliver Mühlemann
Software Mentions: 3
Published: about 5 years ago

10.7554/eLife.43352

Identification of EOMES-expressing spermatogonial stem cells and their regulation by PLZF
Cited by: 39
Author(s): Manju Sharma, Anuj Srivastava, Heather Fairfield, David E. Bergstrom, William F. Flynn, Robert E. Braun
Software Mentions: 3
Published: over 7 years ago

10.1371/journal.pone.0222081

Differential gene expression in bovine endometrial epithelial cells after challenge with LPS; specific implications for genes involved in embryo maternal interactions
Cited by: 18
Author(s): Yongkang Guo, Tom van Schaik, Naveed Jhamat, Adnan Niazi, M. Chanrot, Gilles Charpigny, J. F. Valarcher, Erik Bongcam‐Rudloff, Gerhard Andersson, P. Humblot
Software Mentions: 3
Published: about 7 years ago

10.3389/fmicb.2017.02683

Desert Dust as a Source of Iron to the Globally Important Diazotroph Trichodesmium
Cited by: 19
Author(s): Despo Polyviou, Alison J. Baylay, Andrew Hitchcock, Julie Robidart, C. Mark Moore, Thomas S. Bibby
Software Mentions: 3
Published: almost 9 years ago

10.1038/s41598-018-34591-5

Brassica yellows virus’ movement protein upregulates anthocyanin accumulation, leading to the development of purple leaf symptoms on Arabidopsis thaliana
Cited by: 18
Author(s): Xiangru Chen, Ying Wang, Hang-Hai Zhao, Xiaoyan Zhang, Xianbing Wang, Dawei Li, Jialin Yu, Chenggui Han
Software Mentions: 3
Published: about 8 years ago

10.1371/journal.pone.0231285

Blood co-expression modules identify potential modifier genes of diabetes and lung function in cystic fibrosis
Cited by: 6
Author(s): Fanny Pineau, Davide Caimmi, Milena Magalhães, Enora Fremy, Abdillah Mohamed, Laurent Mély, Sylvie Leroy, Marlène Murris, Mireille Claustres, R. Chiron, Albertina De Sario
Software Mentions: 3
Published: over 6 years ago

10.1038/s41598-018-34015-4

ERK1/2-dependent gene expression in the bovine ovulating follicle
Cited by: 15
Author(s): Yasmin Schuermann, Monique Tomazele Rovani, Bernardo Garziera Gasperin, Rogério Ferreira, Juliana Germano Ferst, Ejimedo Madogwe, Paulo Bayard Dias Gonçalves, Vilceu Bordignon, Raj Duggavathi
Software Mentions: 3
Published: about 8 years ago

10.3389/fmicb.2016.00636

Transcriptomic Analysis Reveals Adaptive Responses of an Enterobacteriaceae Strain LSJC7 to Arsenic Exposure
Cited by: 17
Author(s): Yingjiao Zhang, Songcan Chen, Xiuli Hao, Jian‐Qiang Su, Xudong Xue, Yu Yan, Yan Zhu, Jun Ye
Software Mentions: 3
Published: over 10 years ago

10.1371/journal.pone.0209300

Angiopoietin-2 promotes osteogenic differentiation of thoracic ligamentum flavum cells via modulating the Notch signaling pathway
Cited by: 9
Author(s): Xiaoxi Yang, Zhongqiang Chen, Xiangyu Meng, Chuiguo Sun, Mengtao Li, Shu Li, Dongwei Fan, Tianqi Fan, Ann Yehong Huang, Chi Zhang
Software Mentions: 3
Published: almost 8 years ago

10.3389/fmicb.2017.00716

Effects of Inhibitors on the Transcriptional Profiling of Gluconobater oxydans NL71 Genes after Biooxidation of Xylose into Xylonate
Cited by: 16
Author(s): Yuanyuan Miao, Yi Shen, Yong Xu
Software Mentions: 3
Published: over 9 years ago

10.7554/eLife.24523

Synergistic interactions with PI3K inhibition that induce apoptosis
Cited by: 23
Author(s): Yaara Zwang, Oliver Jonas, Casandra Chen, Mikael L. Rinne, John G. Doench, Federica Piccioni, Tan Li, Hai‐Tsang Huang, Jinhua Wang, Young Jin Ham, Joyce T. O’Connell, Patrick Bhola, Mihir B. Doshi, Matthew A. Whitman, Michael J. Cima, Anthony Letaï, David E. Root, Robert Langer, Nathanael S. Gray, William C. Hahn
Software Mentions: 3
Published: over 9 years ago

10.1038/s41598-018-33744-w

Genome-wide identification of AP2/ERF superfamily genes and their expression during fruit ripening of Chinese jujube
Cited by: 42
Author(s): Zhijun Zhong, Xingang Li
Software Mentions: 3
Published: about 8 years ago

10.1038/s41598-017-14083-8

Profiling of miRNAs and target genes related to cystogenesis in ADPKD mouse models
Cited by: 32
Author(s): Yu Mi Woo, Do Yeon Kim, Nam Jin Koo, Yong Min Kim, Sun Young Lee, Je Yeong Ko, Yubin Shin, Bo Hye Kim, Hyowon Mun, Seonju Choi, Eun Ji Lee, Jeong Oh Shin, Eun Young Park, Jinwoong Bok, Jong Hoon Park
Software Mentions: 3
Published: about 9 years ago

10.7554/eLife.19027

Ongoing resolution of duplicate gene functions shapes the diversification of a metabolic network
Cited by: 27
Author(s): Meihua Christina Kuang, Paul D. Hutchins, John N. Russell, Joshua J. Coon, Chris Todd Hittinger
Software Mentions: 3
Published: about 10 years ago

10.3389/fmicb.2019.02064

Immediate Effects of Ammonia Shock on Transcription and Composition of a Biogas Reactor Microbiome
Cited by: 16
Author(s): Martin Fischer, Andrea Ulbricht, Sven C. Neulinger, Sarah Refai, Kati Waßmann, Sven Künzel, Ruth A. Schmitz
Software Mentions: 3
Published: about 7 years ago

10.3389/fmicb.2021.681911

Effect of Temperature on Metronidazole Resistance in Helicobacter pylori
Cited by: 8
Author(s): Meiliang Gong, Yan Han, Xuning Wang, Hai Tao, Fansen Meng, Baicun Hou, Benjamin B. Sun, Gangshi Wang
Software Mentions: 3
Published: over 5 years ago

10.7554/eLife.33057

ZFP36 RNA-binding proteins restrain T cell activation and anti-viral immunity
Cited by: 83
Author(s): Michael J. Moore, Nathalie E. Blachère, John Fak, Christopher Y. Park, Kirsty Sawicka, Salina Parveen, Ilana Zucker-Scharff, Bruno Moltedo, Alexander Y. Rudensky, Robert B. Darnell
Software Mentions: 3
Published: over 8 years ago

10.7554/eLife.33178

ICE1 promotes the link between splicing and nonsense-mediated mRNA decay
Cited by: 48
Author(s): T. Baird, Ken Chih-Chien Cheng, Yu‐Chi Chen, Eugen Buehler, Scott E. Martin, James Inglese, J. Robert Hogg
Software Mentions: 3
Published: over 8 years ago

10.1038/s41422-018-0103-x

Expansion and differentiation of human hepatocyte-derived liver progenitor-like cells and their use for the study of hepatotropic pathogens
Cited by: 105
Author(s): Gongbo Fu, Weijian Huang, Min Zeng, Zhou Xu, Hongping Wu, Changcheng Liu, Han Wu, Jun Weng, Hong‐Dan Zhang, Yongchao Cai, Charles Ashton, Min Ding, Dan Tang, Baohua Zhang, Yi Gao, Weifeng Yu, Bo Zhai, Zhiying He, Hongyang Wang, He‐Xin Yan
Software Mentions: 3
Published: about 8 years ago

10.7554/eLife.13463

Neural stem cell-encoded temporal patterning delineates an early window of malignant susceptibility in Drosophila
Cited by: 63
Author(s): Karine Narbonne-Reveau, Elodie Lanet, Caroline Dillard, Sophie Foppolo, Ching-Huan Chen, Hugues Parrinello, Stéphanie Rialle, Nicholas S. Sokol, Cédric Maurange
Software Mentions: 3
Published: over 10 years ago

10.1038/s41598-017-11304-y

Dynamic Changes in the Splenic Transcriptome of Chickens during the Early Infection and Progress of Marek’s Disease
Cited by: 5
Author(s): Di Lu, Maikun Teng, Huawei Li, Huizhen Li, Shenglin Ma, Pengwei Zhao, Xiujie Li, Ruiguang Deng, Gaiping Zhang, Jun Luo
Software Mentions: 3
Published: about 9 years ago

10.7554/eLife.63726

The Hippo pathway controls myofibril assembly and muscle fiber growth by regulating sarcomeric gene expression
Cited by: 27
Author(s): Aynur Kaya-Çopur, Fabio Marchianò, Marco Y. Hein, Daniel Alpern, Julie Russeil, Nuno Miguel Luis, Matthias Mann, Bart Deplancke, Bianca Habermann, Frank Schnorrer
Software Mentions: 3
Published: almost 6 years ago

10.7554/eLife.23623

The dynamic three-dimensional organization of the diploid yeast genome
Cited by: 55
Author(s): Seungsoo Kim, Ivan Liachko, Donna Garvey Brickner, Kate B. Cook, William Stafford Noble, Jason H. Brickner, Jay Shendure, Maitreya J. Dunham
Software Mentions: 3
Published: over 9 years ago

10.1371/journal.pone.0132310

Assessing Dissimilarity Measures for Sample-Based Hierarchical Clustering of RNA Sequencing Data Using Plasmode Datasets
Cited by: 20
Author(s): Pablo Reeb, Sergio Jorge Bramardi, Juan P. Steibel
Software Mentions: 3
Published: over 11 years ago

10.3389/fmicb.2017.01830

A Laboratory Methodology for Dual RNA-Sequencing of Bacteria and their Host Cells In Vitro
Cited by: 18
Author(s): J. Wallis Marsh, Michael S. Humphrys, Garry Myers
Software Mentions: 3
Published: about 9 years ago

10.1038/s41598-017-10376-0

Genomic and transcriptomic analyses reveal differential regulation of diverse terpenoid and polyketides secondary metabolites in Hericium erinaceus
Cited by: 28
Author(s): Juan Chen, Zhiai Xu, Yan Yang, Yong Xing, Qi Zhang, Jia Mei Li, Ke Ma, Hong Wei Liu, Shun Guo
Software Mentions: 3
Published: about 9 years ago

10.7554/eLife.59545

Specific Neuroligin3–αNeurexin1 signaling regulates GABAergic synaptic function in mouse hippocampus
Cited by: 18
Author(s): Motokazu Uchigashima, Kohtarou Konno, Emily Demchak, Amy Cheung, Takuya Watanabe, David G Keener, Manabu Abe, Timmy Le, Kenji Sakimura, Toshikuni Sasaoka, Takeshi Uemura, Yuka Imamura Kawasawa, Masahiko Watanabe, Kensuke Futai
Software Mentions: 3
Published: almost 6 years ago

10.7554/eLife.53403

Zebrafish macrophage developmental arrest underlies depletion of microglia and reveals Csf1r-independent metaphocytes
Cited by: 36
Author(s): Laura E. Kuil, Nynke Oosterhof, Giuliano Ferrero, Tereza Mikulášová, Martina Hason, Jordy Dekker, Mireia Rovira, Herma C. van der Linde, Paulina Mh van Strien, Emma de Pater, Gerben Schaaf, Erik Mj Bindels, Valérie Wittamer, Tjakko J. van Ham
Software Mentions: 3
Published: over 6 years ago

10.1016/j.celrep.2019.03.080

lncRNA Spehd Regulates Hematopoietic Stem and Progenitor Cells and Is Required for Multilineage Differentiation
Cited by: 25
Author(s): M. Joaquina Delás, Benjamin T. Jackson, Tatjana Kovačević, Silvia Vangelisti, Ester Munera Maravilla, Sophia A Wild, Eva Maria Stork, Nicolas Erard, Simon Knott, Gregory J. Hannon
Software Mentions: 3
Published: over 7 years ago

10.1038/s41421-021-00248-3

Integrated characterization of SARS-CoV-2 genome, microbiome, antibiotic resistance and host response from single throat swabs
Cited by: 10
Author(s): Bo Lu, Yi Yan, Liting Dong, Lingling Han, Yawei Liu, Junping Yu, Jianjun Chen, Danyang Yi, Meiling Zhang, Xin Deng, Chao Wang, Runkun Wang, Dengpeng Wang, Hongping Wei, Di Liu, Chengqi Yi
Software Mentions: 3
Published: over 5 years ago

10.1038/s41598-018-32116-8

Permissiveness to form pluripotent stem cells may be an evolutionarily derived characteristic in Mus musculus
Cited by: 10
Author(s): Tiffany A. Garbutt, Thomas I. Konneker, Kranti Konganti, Andrew Hillhouse, Francis Swift-Haire, Alexis Jones, Drake Phelps, David L. Aylor, David W. Threadgill
Software Mentions: 3
Published: about 8 years ago

10.3389/fmicb.2021.725403

The Perception of Rhizosphere Bacterial Communication Signals Leads to Transcriptome Reprogramming in Lysobacter capsici AZ78, a Plant Beneficial Bacterium
Cited by: 1
Author(s): Ana Bejarano, Michele Perazzolli, I. Pertot, Gerardo Puopolo
Software Mentions: 3
Published: about 5 years ago

10.1038/s41418-021-00771-6

MECOM permits pancreatic acinar cell dedifferentiation avoiding cell death under stress conditions
Cited by: 19
Author(s): Elyne Backx, Elke Wauters, Jonathan Baldan, Mathias Van Bulck, Ellis Michiels, Yves Heremans, Diedert Luc De Paep, Mineo Kurokawa, Susumu Goyama, Luc Bouwens, Patrick Jacquemin, Isabelle Houbracken, Ilse Rooman
Software Mentions: 3
Published: over 5 years ago

10.3389/fmicb.2015.00569

RNA-Seq analysis of isolate- and growth phase-specific differences in the global transcriptomes of enteropathogenic Escherichia coli prototype isolates
Cited by: 27
Author(s): Tracy H. Hazen, Sean C. Daugherty, Amol C. Shetty, Anup Mahurkar, Owen White, James B. Kaper, David A. Rasko
Software Mentions: 3
Published: over 11 years ago

10.1038/s41419-021-03401-8

Cdk5rap3 is essential for intestinal Paneth cell development and maintenance
Cited by: 13
Author(s): Michaela Quintero, Siyang Liu, Yanhua Xia, Yonghong Huang, Yi Zou, Ge Li, Ling Hu, Nagendra Singh, Richard S. Blumberg, Yafei Cai, Hong Xu, Honglin Li
Software Mentions: 3
Published: almost 6 years ago

10.3389/fmicb.2018.01261

Transcriptional Regulation of Cysteine and Methionine Metabolism in Lactobacillus paracasei FAM18149
Cited by: 17
Author(s): Daniel Wüthrich, Claudia Wenzel, Tharmatha Bavan, Rémy Bruggmann, Hélène Berthoud, Stefan Irmler
Software Mentions: 3
Published: over 8 years ago

10.7554/eLife.44306

PAX8 regulon in human ovarian cancer links lineage dependency with epigenetic vulnerability to HDAC inhibitors
Cited by: 31
Author(s): Kaixuan Shi, Xiang Yin, Mei-Chun Cai, Yan Yan, Chenqiang Jia, Ping Ma, Shengzhe Zhang, Zhenfeng Zhang, Zhenyu Gu, Meiying Zhang, Wen Di, Guanglei Zhuang
Software Mentions: 3
Published: over 7 years ago

10.7554/eLife.39234

Transition between fermentation and respiration determines history-dependent behavior in fluctuating carbon sources
Cited by: 38
Author(s): Bram Cerulus, Abbas Jariani, Gemma Perez-Samper, Lieselotte Vermeersch, Julian Pietsch, Matthew M. Crane, Aaron M. New, Brigida Gallone, Miguel Roncoroni, Maria C. Dzialo, Sander K. Govers, Jhana O. Hendrickx, Eva Galle, Maarten Coomans, Pieter Berden, Sara Verbandt, Peter S. Swain, Kevin J. Verstrepen
Software Mentions: 3
Published: about 8 years ago

10.3389/fmicb.2015.01199

A detailed view of the intracellular transcriptome of Listeria monocytogenes in murine macrophages using RNA-seq
Cited by: 23
Author(s): Tilman Schultze, Rolf Hilker, Gopala Krishna Mannala, Katrin Gentil, Markus Weigel, Neda Farmani, Anita Windhorst, Alexander Goesmann, Trinad Chakraborty, Torsten Hain
Software Mentions: 3
Published: about 11 years ago

10.1038/s41419-021-03641-8

LDHA induces EMT gene transcription and regulates autophagy to promote the metastasis and tumorigenesis of papillary thyroid carcinoma
Cited by: 44
Author(s): Xiukun Hou, Xianle Shi, Wei Zhang, Dapeng Li, Linfei Hu, Jihong Yang, Jingzhu Zhao, Songfeng Wei, Xi Wei, Xianhui Ruan, Xiangqian Zheng, Ming Gao
Software Mentions: 3
Published: over 5 years ago

10.1038/s41598-017-10648-9

Genome-wide DNA methylation and transcriptome analyses reveal genes involved in immune responses of pig peripheral blood mononuclear cells to poly I:C
Cited by: 31
Author(s): Haifei Wang, Jiying Wang, Chao Ning, Xianrui Zheng, Jinlian Fu, Aiguo Wang, Qin Zhang, Jianfeng Liu
Software Mentions: 3
Published: about 9 years ago

10.1371/journal.pone.0172884

Ion channel expression patterns in glioblastoma stem cells with functional and therapeutic implications for malignancy
Cited by: 36
Author(s): Julia Pollak, Goutam Karan, Cory C. Funk, Sonali Arora, Eunjee Lee, Jun Zhu, Nathan D. Price, Patrick J. Paddison, Jan‐Marino Ramirez, Robert Rostomily
Software Mentions: 3
Published: over 9 years ago

10.1042/BSR20210495

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

10.1038/s41598-021-97013-z

Electronic cigarette smoke reduces ribosomal protein gene expression to impair protein synthesis in primary human airway epithelial cells
Cited by: 5
Author(s): Hae-Ryung Park, Jose Vallarino, Michael J. O’Sullivan, Charlotte Wirth, Ronald Allan M Panganiban, Gabrielle Webb, Maya Shumyatcher, Blanca E. Himes, Jin‐Ah Park, David C. Christiani, Joseph G. Allen, Quan Lu
Software Mentions: 3
Published: about 5 years ago

10.1186/s13072-015-0039-z

Tip60 complex binds to active Pol II promoters and a subset of enhancers and co-regulates the c-Myc network in mouse embryonic stem cells
Cited by: 46
Author(s): Sarina Ravens, Changwei Yu, Ye Tao, Matthieu Stierlé, László Tora
Software Mentions: 3
Published: about 11 years ago

10.1038/s41598-021-98420-y

Short-term transcriptomic response to plasma membrane injury
Cited by: 3
Author(s): Swantje Christin Häger, Catarina Dias, Stine Lauritzen Sønder, André Vidas Olsen, Isabelle da Piedade, Anne Sofie Busk Heitmann, Elena Papaleo, Jesper Nylandsted
Software Mentions: 3
Published: about 5 years ago

10.1038/s41598-021-94386-z

An epigenetic GPI anchor defect impairs TLR4 signaling in the B cell transdifferentiation model for primary human monocytes BLaER1
Cited by: 3
Author(s): Julia Wegner, Thomas Zillinger, Thais Marina Schlee-Guimarães, Eva Bartok, Martin Schlee
Software Mentions: 3
Published: over 5 years ago

10.1038/s41598-021-91924-7

Mutant p53s and chromosome 19 microRNA cluster overexpression regulate cancer testis antigen expression and cellular transformation in hepatocellular carcinoma
Cited by: 4
Author(s): Goodwin G. Jinesh, Marco Napoli, Marian T. Smallin, Andrew John Davis, Hayley D. Ackerman, Payal Raulji, Nicole Montey, Elsa R. Flores, Andrew S. Brohl
Software Mentions: 3
Published: over 5 years ago

10.1186/s13072-020-00363-7

Characterization of universal features of partially methylated domains across tissues and species
Cited by: 12
Author(s): Benjamin E. Decato, Jianghan Qu, Xiaojing Ji, Elvin Wagenblast, Simon Knott, Gregory J. Hannon, Andrew D. Smith
Software Mentions: 3
Published: about 6 years ago

10.1186/s12915-018-0579-3

Food perception without ingestion leads to metabolic changes and irreversible developmental arrest in C. elegans
Cited by: 14
Author(s): Rebecca E. W. Kaplan, Amy K. Webster, Rojin Chitrakar, Joseph A. Dent, L. Ryan Baugh
Software Mentions: 3
Published: about 8 years ago

10.1186/s13072-018-0187-z

Deletion of HP1γ in cardiac myocytes affects H4K20me3 levels but does not impact cardiac growth
Cited by: 12
Author(s): Kyohei Oyama, Danny El‐Nachef, Fang Chen, Hidemi Kajimoto, Jeremy Brown, Prim B. Singh, W. Robb MacLellan
Software Mentions: 3
Published: over 8 years ago

10.1038/s41598-021-96263-1

Dynamic landscape of chromatin accessibility and transcriptomic changes during differentiation of human embryonic stem cells into dopaminergic neurons
Cited by: 7
Author(s): César Meléndez-Ramírez, Raquel Cuevas-Diaz Duran, Tonatiuh Barrios-García, Mayela Giacoman-Lozano, Adolfo López-Ornelas, Jessica Herrera-Gamboa, Enrique Estudillo, Ernesto Soto-Reyes, Iván Velasco, Víctor Treviño
Software Mentions: 3
Published: about 5 years ago

10.1038/s41392-018-0028-3

USP7 deubiquitinates and stabilizes NOTCH1 in T-cell acute lymphoblastic leukemia
Cited by: 36
Author(s): Huizhuang Shan, Xiangyun Li, Xinhua Xiao, Yuting Dai, Jinyan Huang, Junjun Song, Meng Liu, Li Yang, Lei Hu, Tong Yin, Li Zhou, Hanzhang Xu, Yingli Wu
Software Mentions: 3
Published: about 8 years ago

10.1038/s41598-021-89175-7

Concurrent X chromosome inactivation and upregulation during non-human primate preimplantation development revealed by single-cell RNA-sequencing
Cited by: 2
Author(s): Ana Luíza Cidral, Joana Carvalho Moreira de Mello, Joost Gribnau, Lygia V. Pereira
Software Mentions: 3
Published: over 5 years ago

10.1186/s12915-017-0419-x

Genome sequencing of the staple food crop white Guinea yam enables the development of a molecular marker for sex determination
Cited by: 95
Author(s): Muluneh Tamiru, Satoshi Natsume, Hiroki Takagi, Ben White, Hiroki Yaegashi, Mitsuru Shimizu, Kentaro Yoshida, Aiko Uemura, Kanta Oikawa, Akira Abe, Naoya Urasaki, Hideo Matsumura, Babil Pachakkil, Shinşuke Yamanaka, Ryo Matsumoto, Satoru Muranaka, Gezahegn Girma, Antonio Lopez-Montes, Melaku Gedil, Ranjana Bhattacharjee, Michael T. Abberton, P. Lava Kumar, Ismail Rabbi, Mai Tsujimura, Toru Terachi, Wilfried Haerty, Manuel Corpas, Sophien Kamoun, Günter Kahl, H. Takagi, Robert Asiedu, Ryohei Terauchi
Software Mentions: 3
Published: about 9 years ago

10.1038/s41598-021-86612-5

Potential impact of celiac disease genetic risk factors on T cell receptor signaling in gluten-specific CD4+ T cells
Cited by: 4
Author(s): Olivier B. Bakker, Aarón D. Ramírez-Sánchez, Z Borek, Nigel Klein, Yang Li, Rutger Modderman, Yvonne Kooy–Winkelaar, Marie K. Johannesen, Filomena Matarese, Joost H.A. Martens, Vinod Kumar, Jeroen van Bergen, Shuo‐Wang Qiao, Knut E.A. Lundin, Ludvig M. Sollid, Frits Koning, Cisca Wijmenga, Sebo Withoff, Iris Jonkers
Software Mentions: 3
Published: over 5 years ago

10.1371/journal.pone.0187966

RNA-seq reveals transcriptome changes in goats following myostatin gene knockout
Cited by: 24
Author(s): Lamei Wang, Bei Cai, Shiwei Zhou, Haijing Zhu, Qu Liu, Xiaolong Wang
Software Mentions: 3
Published: almost 9 years ago

10.1186/s12864-018-4856-x

Genome-wide expression profiling of leaves and roots of watermelon in response to low nitrogen
Cited by: 25
Author(s): Muhammad Azher Nawaz, Chen Chen, Fareeha Shireen, Zhuhua Zheng, Hamza Sohail, Muhammad Afzal, Muhammad Amjad Ali, Zhilong Bie, Yuan Huang
Software Mentions: 3
Published: over 8 years ago

10.1038/s41598-021-91503-w

Colonisation dynamics of Listeria monocytogenes strains isolated from food production environments
Cited by: 12
Author(s): Jessica Gray, P. Scott Chandry, Mandeep Kaur, Chawalit Kocharunchitt, Séamus Fanning, John P. Bowman, Edward M. Fox
Software Mentions: 3
Published: over 5 years ago

10.1155/2020/1705387

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

10.1186/1471-2164-15-905

Limited sex-biased neural gene expression patterns across strains in Zebrafish (Danio rerio)
Cited by: 54
Author(s): Ryan Y. Wong, Melissa M McLeod, John Godwin
Software Mentions: 3
Published: almost 13 years ago

10.1038/s41598-021-86795-x

Distinct transcriptomic response to Newcastle disease virus infection during heat stress in chicken tracheal epithelial tissue
Cited by: 2
Author(s): Perot Saelao, Ying Wang, Ganrea Chanthavixay, Vivian M. Yu, Rodrigo A. Gallardo, Jack C. M. Dekkers, Susan J. Lamont, T. Ross Kelly, Huaijun Zhou
Software Mentions: 3
Published: over 5 years ago

10.1371/journal.pone.0181761

The integrated analysis of RNA-seq and microRNA-seq depicts miRNA-mRNA networks involved in Japanese flounder (Paralichthys olivaceus) albinism
Cited by: 12
Author(s): Na Wang, Ruoqing Wang, Renkai Wang, Yongsheng Tian, Changwei Shao, Xiaodong Jia, Songlin Chen
Software Mentions: 3
Published: over 9 years ago

10.1038/s41598-021-87278-9

Analysis of the gene transcription patterns and DNA methylation characteristics of triploid sea cucumbers (Apostichopus japonicus)
Cited by: 8
Author(s): Lingshu Han, Yuena Sun, Yue Cao, Peng Gao, Zijiao Quan, Yaqing Chang, Jun Ding
Software Mentions: 3
Published: over 5 years ago

10.1038/s41598-021-91811-1

Identifying molecular targets for reverse aging using integrated network analysis of transcriptomic and epigenomic changes during aging
Cited by: 7
Author(s): Hwang-Yeol Lee, Yeonsu Jeon, Yeon Kyung Kim, Jae Young Jang, Yun Sung Cho, Jong Bhak, Kwang-Hyun Cho
Software Mentions: 3
Published: over 5 years ago

10.1016/j.stemcr.2020.01.004

Activin A and BMP4 Signaling Expands Potency of Mouse Embryonic Stem Cells in Serum-Free Media
Cited by: 13
Author(s): Baojiang Wu, Lin Li, Bojiang Li, Junpeng Gao, Yanglin Chen, Mengyi Wei, Zhiqing Yang, Baojing Zhang, Shudong Li, Kexin Li, Changshan Wang, M. Azim Surani, Xihe Li, Fuchou Tang, Siqin Bao
Software Mentions: 3
Published: almost 7 years ago

10.1038/s41598-021-82905-x

Transcriptional response to the host cell environment of a multidrug-resistant Mycobacterium tuberculosis clonal outbreak Beijing strain reveals its pathogenic features
Cited by: 9
Author(s): Pakorn Aiewsakun, Pinidphon Prombutara, Tegar Adriansyah Putra Siregar, Thanida Laopanupong, Phongthon Kanjanasirirat, Tanawadee Khumpanied, Suparerk Borwornpinyo, Pirut Tong-ngam, Alisa Tubsuwan, Prapaporn Srilohasin, Angkana Chaiprasert, Wuthiwat Ruangchai, Prasit Palittapongarnpim, Therdsak Prammananan, Brian C. VanderVen, Marisa Ponpuak
Software Mentions: 3
Published: almost 6 years ago

10.1371/journal.pone.0225466

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

10.1186/s12864-020-06870-x

Shedding light on cashmere goat hair follicle biology: from morphology analyses to transcriptomic landascape
Cited by: 8
Author(s): Cristina Nocelli, Katia Cappelli, Stefano Capomaccio, Luisa Pascucci, Francesca Mercati, Irene Pazzaglia, Samanta Mecocci, Marco Antonini, Carlo Renieri
Software Mentions: 3
Published: over 6 years ago

10.1371/journal.pone.0206055

Transcriptome profiling of transgenic potato plants provides insights into variability caused by plant transformation
Cited by: 9
Author(s): Dae Kwan Ko, Satya Swathi Nadakuduti, David S. Douches, C. Robin Buell
Software Mentions: 3
Published: about 8 years ago

10.1038/s41598-020-80168-6

Global tissue transcriptomic analysis to improve genome annotation and unravel skin pigmentation in goldfish
Cited by: 14
Author(s): Wei Gan, Yu Wen Chung-Davidson, Zelin Chen, Shiying Song, Weicheng Cui, Wei He, Qinghua Zhang, Weiming Li, Mingyou Li, Jianfeng Ren
Software Mentions: 3
Published: almost 6 years ago

10.1038/s41598-021-83541-1

Characterization of the nuclear and cytosolic transcriptomes in human brain tissue reveals new insights into the subcellular distribution of RNA transcripts
Cited by: 23
Author(s): Ammar Zaghlool, Adnan Niazi, Åsa K. Björklund, Jakub Orzechowski Westholm, Adam Ameur, Lars Feuk
Software Mentions: 3
Published: over 5 years ago

10.1038/s41598-020-79082-8

Human extrahepatic and intrahepatic cholangiocyte organoids show region-specific differentiation potential and model cystic fibrosis-related bile duct disease
Cited by: 37
Author(s): Monique M A Verstegen, Floris J.M. Roos, Ksenia Burka, Helmuth Gehart, Myrthe Jager, Maaike de Wolf, Marcel J. C. Bijvelds, Hugo R. de Jonge, Arif Ibrahim Ardisasmita, Nick A. van Huizen, Henk P. Roest, Jeroen de Jonge, Michael Koch, Francesco Pampaloni, Sabine A. Fuchs, Imre F. Schene, Theo M. Luider, Hubert P.J. van der Doef, Frank Bodewes, Ruben H J de Kleine, Bart Spee, Gert‐Jan Kremers, Hans Clevers, Jan N. M. IJzermans, Edwin Cuppen, Luc J. W. van der Laan
Software Mentions: 3
Published: almost 6 years ago

10.1007/s12020-020-02523-x

Diagnosis of thyroid neoplasm using support vector machine algorithms based on platelet RNA-seq
Cited by: 11
Author(s): Yanwei Shen, Yi Lai, Dong Xu, Le Cun Xu, Lin Frank Song, Jun Zhou, Chengwen Song, Jiadong Wang
Software Mentions: 3
Published: almost 6 years ago

10.1093/bioinformatics/btv488

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

10.1371/journal.pone.0219272

Global gene expression analysis in etiolated and de-etiolated seedlings in conifers
Cited by: 9
Author(s): Sonali Sachin Ranade, Nicolas Delhomme, María Rosario García‐Gil
Software Mentions: 3
Published: over 7 years ago

10.1093/bioinformatics/btz433

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

10.1186/s12864-021-07366-y

PacBio full-length transcriptome of wild apple (Malus sieversii) provides insights into canker disease dynamic response
Cited by: 18
Author(s): Xiaojie Liu, Xiaoshuang Li, Xiangying Wen, Yan Zhang, Yu Ding, Yiheng Zhang, Bei Gao, Daoyuan Zhang
Software Mentions: 3
Published: almost 6 years ago

10.1038/s41598-020-75438-2

Gene expression of the heat stress response in bovine peripheral white blood cells and milk somatic cells in vivo
Cited by: 30
Author(s): Josie B. Garner, Amanda J. Chamberlain, Christy Vander Jagt, Thuy Thi Thu Nguyen, Brett Mason, L. C. Marett, Brian J Leury, William J. Wales, Ben J. Hayes
Software Mentions: 3
Published: about 6 years ago

10.1371/journal.pone.0221634

Comparative multi-omics systems analysis reveal the glycolysis / gluconeogenesis signal pathway play an important role in virulence attenuation in fish-derived GBS YM001
Cited by: 2
Author(s): Yu Liu, Liping Li, Ting Huang, Rui Wang, Weizheng Liang, Qiong Yang, Aiying Lei, Ming Chen
Software Mentions: 3
Published: about 7 years ago

10.1371/journal.pone.0081925

Gene Expression, Single Nucleotide Variant and Fusion Transcript Discovery in Archival Material from Breast Tumors
Cited by: 51
Author(s): Nadine Norton, Zhifu Sun, Yan W. Asmann, Daniel J. Serie, Brian M. Necela, Aditya Bhagwate, Jin Jen, Bruce W. Eckloff, Krishna R. Kalari, Kevin J. Thompson, Jennifer M. Carr, Jennifer M. Kachergus, Xochiquetzal J. Geiger, Edith A. Perez, E. Aubrey Thompson
Software Mentions: 3
Published: almost 13 years ago

10.1371/journal.pone.0160168

New Cell Adhesion Molecules in Human Ischemic Cardiomyopathy. PCDHGA3 Implications in Decreased Stroke Volume and Ventricular Dysfunction
Cited by: 14
Author(s): Ana Ortega, Carolina Gil-Cayuela, Estefanía Tarazón, María García‐Manzanares, José Montero, Juan Cinca, Manuel Portolés, Miguel Rivera, Esther Roselló‐Lletí
Software Mentions: 3
Published: over 10 years ago

10.1155/2018/4767328

Digital Gene Expression Profiling Analysis of Aged Mice under Moxibustion Treatment
Cited by: 6
Author(s): Nan Liu, Yunyao Jiang, Min Xing, Baixiao Zhao, Jincai Hou, Minyee Lim, Jian Huang, Xue Li, Li Han
Software Mentions: 3
Published: almost 9 years ago

10.1038/s41598-020-77178-9

LOXL2 promotes aggrecan and gender-specific anabolic differences to TMJ cartilage
Cited by: 7
Author(s): Mustafa Tashkandi, Saqer F. Alsaqer, Thabet Alhousami, Faiza Ali, Yaotang Wu, Jennifer Shin, Pushkar Mehra, Larry M. Wolford, Louis C. Gerstenfeld, Mary B. Goldring, Manish V. Bais
Software Mentions: 3
Published: almost 6 years ago

10.1371/journal.pone.0207715

Distinct genes and pathways associated with transcriptome differences in early cardiac development between fast- and slow-growing broilers
Cited by: 9
Author(s): J. Zhang, Carl J. Schmidt, Susan J. Lamont
Software Mentions: 3
Published: almost 8 years ago

10.1080/22221751.2020.1821581

mRNA and miRNA profiling of Zika virus-infected human umbilical cord mesenchymal stem cells identifies miR-142-5p as an antiviral factor
Cited by: 23
Author(s): Rak Kyun Seong, Jae Kwan Lee, Geum Joon Cho, Mukesh Kumar, Ok Sarah Shin
Software Mentions: 3
Published: almost 7 years ago

10.1371/journal.pone.0240253

Systems genetics analysis of the LXS recombinant inbred mouse strains:Genetic and molecular insights into acute ethanol tolerance
Cited by: 0
Author(s): Richard A. Radcliffe, Robin D. Dowell, Aaron Odell, Phillip A. Richmond, Beth Bennett, Colin Larson, Katerina Kechris, Laura Saba, Pratyaydipta Rudra, Wenmei Shi
Software Mentions: 3
Published: about 6 years ago

10.1371/journal.pone.0079874

Phenotypic and Transcriptional Fidelity of Patient-Derived Colon Cancer Xenografts in Immune-Deficient Mice
Cited by: 31
Author(s): Jeffrey Chou, Matthew Fitzgibbon, Christie-Lynn Mortales, Andrea M. H. Towlerton, Melissa P. Upton, Raymond S. Yeung, Martin W. McIntosh, Edus H. Warren
Software Mentions: 3
Published: almost 13 years ago

10.1186/s12917-016-0881-7

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

10.1186/s12915-017-0453-8

Telomere heterogeneity linked to metabolism and pluripotency state revealed by simultaneous analysis of telomere length and RNA-seq in the same human embryonic stem cell
Cited by: 16
Author(s): Hua Wang, Kunshan Zhang, Yifei Liu, Yudong Fu, Shan Gao, Peng Gong, Haiying Wang, Zhongli Zhou, Ming Zeng, Zhenfeng Wu, Yu Sun, Tong Chen, Siguang Li, Lin Liu
Software Mentions: 3
Published: almost 9 years ago

10.1080/15592294.2018.1429857

Genome-wide oxidative bisulfite sequencing identifies sex-specific methylation differences in the human placenta
Cited by: 34
Author(s): Sungsam Gong, Michelle D. Johnson, Justyna Dopierała, Francesca Gaccioli, Ulla Sovio, Miguel Constância, Gordon C. S. Smith, D. Stephen Charnock-Jones
Software Mentions: 3
Published: over 8 years ago

10.1038/s41598-021-84138-4

Transcriptome analysis of ciliary-dependent MCH signaling in differentiating 3T3-L1 pre-adipocytes
Cited by: 4
Author(s): Lloyd Allen Cook, Henry D. Ophardt, Rongkun Shen, Bryan H. Pratt, Lucas A. Galbier
Software Mentions: 3
Published: over 5 years ago

10.1186/s13287-016-0370-8

Identification and validation of multiple cell surface markers of clinical-grade adipose-derived mesenchymal stromal cells as novel release criteria for good manufacturing practice-compliant production
Cited by: 120
Author(s): Emily T. Camilleri, Michael P. Gustafson, Amel Dudakovic, Scott M. Riester, Catalina Galeano Garces, Christopher R. Paradise, Hideki Takai, Marcel Karperien, Simon M. Cool, Hee Jeong Im Sampen, A. Noelle Larson, Wenchun Qu, Jay Smith, Allan B. Dietz, André J. van Wijnen
Software Mentions: 3
Published: over 10 years ago

10.1186/s12864-021-07959-7

Dual RNA-seq transcriptome analysis of caecal tissue during primary Eimeria tenella infection in chickens
Cited by: 7
Author(s): Arnar K. S. Sandholt, Eva Wattrang, Tobias Lilja, Harri Ahola, Anna Lundén, Karin Troell, Staffan G. Svärd, Robert Söderlund
Software Mentions: 3
Published: about 5 years ago

10.1186/s12917-017-1279-x

RNA sequencing reveals candidate genes and polymorphisms related to sperm DNA integrity in testis tissue from boars
Cited by: 14
Author(s): Maren van Son, Nina Hårdnes Tremoen, Ann Helen Gaustad, Frøydis Deinboll Myromslien, Dag Inge Våge, Else‐Berit Stenseth, Teklu T Zeremichael, Eli Grindflek
Software Mentions: 3
Published: almost 9 years ago

10.1371/journal.pone.0148039

Reduced CYFIP1 in Human Neural Progenitors Results in Dysregulation of Schizophrenia and Epilepsy Gene Networks
Cited by: 27
Author(s): Rebecca A. Nebel, Dejian Zhao, Erika Pedrosa, Jill Kirschen, Herbert M. Lachman, Deyou Zheng, Brett S. Abrahams
Software Mentions: 3
Published: almost 11 years ago

10.1038/s41598-020-69884-1

Selective dysregulation of ROCK2 activity promotes aberrant transcriptional networks in ABC diffuse large B-cell lymphoma
Cited by: 4
Author(s): Edd Ricker, Akanksha Verma, Rossella Marullo, Sanjay Gupta, Chao Ye, Tania Pannellini, Michela Manni, Wayne Tam, Giorgio Inghirami, Olivier Elemento, Leandro Cerchietti, Alessandra B. Pernis
Software Mentions: 3
Published: over 6 years ago

Projects: pypi: HTSeq

Science Score: 65/100

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Papers Mentioning HTSeq 3,071