pypi: HTSeq | Projects | Ecosyste.ms: Papers

10.1371/journal.pone.0152540

Gene Expression Profile in the Long-Living Lotus: Insights into the Heat Stress Response Mechanism
Cited by: 6
Author(s): Xiaojing Liu, Fengfeng Du, Naiwei Li, Yajun Chang, Dongrui Yao
Software Mentions: 2
Published: over 10 years ago

10.1371/journal.pbio.2005594

The mammalian decidual cell evolved from a cellular stress response
Cited by: 75
Author(s): Eric M. Erkenbrack, Jamie Maziarz, Oliver W. Griffith, Cong Liang, Arun R. Chavan, Mauris C. Nnamani, Günter P. Wagner
Software Mentions: 2
Published: about 8 years ago

10.1186/s12864-015-2036-9

High-throughput mRNA and miRNA profiling of epithelial-mesenchymal transition in MDCK cells
Cited by: 26
Author(s): Priyank Shukla, Claus Vogl, Barbara Wallner, Doris Rigler, Mathias Müller, Sabine Macho-Maschler
Software Mentions: 2
Published: almost 11 years ago

10.1371/journal.pone.0233789

Sevoflurane depletes macrophages from the melanoma microenvironment
Cited by: 7
Author(s): Isabella Sztwiertnia, Judith Schenz, Katharina Bomans, Dominik Schaack, Johanna Ohnesorge, Sandra Tamulyte, Markus Weigand, Florian Uhle
Software Mentions: 2
Published: over 6 years ago

10.1371/journal.pone.0116125

The Kidney Transcriptome and Proteome Defined by Transcriptomics and Antibody-Based Profiling
Cited by: 46
Author(s): Masato Habuka, Linn Fagerberg, Björn M. Hallström, Caroline Kampf, Karolina Edlund, Åsa Sivertsson, Tadashi Yamamoto, Fredrik Pontén, Mathias Uhlén, Jacob Odeberg
Software Mentions: 2
Published: almost 12 years ago

10.3390/plants9101308

Transcriptome Analyses and Antioxidant Activity Profiling Reveal the Role of a Lignin-Derived Biostimulant Seed Treatment in Enhancing Heat Stress Tolerance in Soybean
Cited by: 35
Author(s): Cristina Campobenedetto, Giuseppe Mannino, Chiara Agliassa, Alberto Acquadro, Valeria Contartese, Christian Garabello, Cinzia M. Bertea
Software Mentions: 2
Published: about 6 years ago

10.1371/journal.pone.0206379

De novo transcriptome based on next-generation sequencing reveals candidate genes with sex-specific expression in Arapaima gigas (Schinz, 1822), an ancient Amazonian freshwater fish
Cited by: 12
Author(s): Luciana Watanabe, Fátima Gomes, João L.S.G. Vianez, Márcio Roberto Teixeira Nunes, Jedson Ferreira Cardoso, Clayton Pereira da Silva de Lima, Horácio Schneider, Iracilda Sampaio
Software Mentions: 2
Published: almost 8 years ago

10.1371/journal.pone.0219163

Transcriptional profiling of Salmonella enterica serovar Enteritidis exposed to ethanolic extract of organic cranberry pomace
Cited by: 23
Author(s): Quail Das, Dion Lepp, Yin X, Kelly Ross, Jason McCallum, Keith Warriner, Massimo F. Marcone, Moussa S. Diarra
Software Mentions: 2
Published: over 7 years ago

10.1371/journal.pone.0120691

Comparative Transcriptome Profiling of the Early Infection of Wheat Roots by Gaeumannomyces graminis var. tritici
Cited by: 18
Author(s): Lirong Yang, Lin Xie, Xue Bao-guo, Paul H. Goodwin, Xin Quan, Chuanlin Zheng, Taiguo Liu, Zhensheng Lei, Xiaohong Yang, Yue-en Chao, Chao Wu
Software Mentions: 2
Published: over 11 years ago

10.3390/plants9111507

Search for New Allergens in Lolium perenne Pollen Growing under Different Air Pollution Conditions by Comparative Transcriptome Study
Cited by: 0
Author(s): Jose Antonio Lucas, Enrique Gutierrez‐Albanchez, Teresa Alfaya, Francisco Feo Brito, Francisco Javier Gutiérrez-Mañero
Software Mentions: 2
Published: almost 6 years ago

10.1371/journal.pone.0100883

A GPBAR1 (TGR5) Small Molecule Agonist Shows Specific Inhibitory Effects on Myeloid Cell Activation In Vitro and Reduces Experimental Autoimmune Encephalitis (EAE) In Vivo
Cited by: 51
Author(s): Nuruddeen D. Lewis, Lori Patnaude, Josephine Pelletier, Donald Souza, Susan Lukas, Jim King, Jonathan D. Hill, Dimitria E. Stefanopoulos, Kelli R. Ryan, Sudha Desai, Donna Skow, Stefan G. Kauschke, Andre Broermann, Daniel Kuzmich, Christian Harcken, Eugene R. Hickey, Louise K. Modis
Software Mentions: 2
Published: over 12 years ago

10.1371/journal.pone.0201628

Transcriptional profiling of two different physiological states of the yak mammary gland using RNA sequencing
Cited by: 7
Author(s): Jinjiang Fan, Yuzhu Luo, Sijiu Yu, Yan Cui, Gezhi Xu, Libin Wang, Yangyang Pan, Honghong He
Software Mentions: 2
Published: about 8 years ago

10.1371/journal.pone.0208526

Transcriptome-wide analysis links the short-term expression of the b isoforms of TIA proteins to protective proteostasis-mediated cell quiescence response
Cited by: 7
Author(s): Isabel Carrascoso, José Alcalde, Daniel Tabas-Madrid, Juan Carlos Oliveros, José M. Izquierdo
Software Mentions: 2
Published: almost 8 years ago

10.1186/s12864-020-6448-9

Transcriptomic analysis of gene expression of Verticillium dahliae upon treatment of the cotton root exudates
Cited by: 10
Author(s): Xinyu Zhang, Cheng Wei, Zhidi Feng, Qian Zhu, Yuqiang Sun, Yanjun Li, Jie Sun
Software Mentions: 2
Published: over 6 years ago

10.1371/journal.pone.0182568

Genome-wide identification of autosomal genes with allelic imbalance of chromatin state
Cited by: 7
Author(s): Andrej J. Savol, Peggy I. Wang, Yongho Jeon, David Colognori, E. Yildirim, Stefan F. Pinter, Bernhard Payer, Jeannie T. Lee, Ruslan I. Sadreyev
Software Mentions: 2
Published: about 9 years ago

10.1093/eep/dvab008

Combined exposure to polychlorinated biphenyls and high-fat diet modifies the global epitranscriptomic landscape in mouse liver.
Cited by: 12
Author(s): Carolyn M. Klinge, Kellianne M. Piell, Belinda J. Petri, Liqing He, Xiang Zhang, Jianmin Pan, N. Shesh, Kalina Andreeva, Eric C. Rouchka, Banrida Wahlang, Juliane I. Beier, Matthew C. Cave
Software Mentions: 2
Published: almost 6 years ago

10.1371/journal.pone.0130028

Defining the Human Brain Proteome Using Transcriptomics and Antibody-Based Profiling with a Focus on the Cerebral Cortex
Cited by: 43
Author(s): Evelina Sjöstedt, Linn Fagerberg, Björn M. Hallström, Anna Häggmark, Nicholas Mitsios, Peter Nilsson, Fredrik Pontén, Tomas Hökfelt, Mathias Uhlén, Jan Mulder
Software Mentions: 2
Published: over 11 years ago

10.18632/oncotarget.18117

Notch signaling regulates metabolic heterogeneity in glioblastoma stem cells
Cited by: 55
Author(s): N. Sumru Bayın, Joshua D. Frenster, Rajeev Sen, Sheng Si, Aram S. Modrek, Nataliya Galifianakis, Igor Dolgalev, Valerio Ortenzi, Irineu Illa-Bochaca, Anadjeet Khahera, Jonathan Serrano, Luis Chiriboga, David Zagzag, John G. Golfinos, Werner Doyle, Aristotelis Tsirigos, Adriana Heguy, Mitchell Chesler, Mary Helen Barcellos‐Hoff, Matija Snuderl, Dimitris G. Placantonakis
Software Mentions: 2
Published: over 9 years ago

10.1371/journal.pone.0216082

The protein elicitor Hrip1 enhances resistance to insects and early bolting and flowering in Arabidopsis thaliana
Cited by: 6
Author(s): Xin-yue Miao, Hong-pan Qu, Ya-lei Han, Congfen He, Dewen Qiu, Zhiwei Cheng
Software Mentions: 2
Published: over 7 years ago

10.1371/journal.pone.0180925

2-aminoimidazoles potentiate ß-lactam antimicrobial activity against Mycobacterium tuberculosis by reducing ß-lactamase secretion and increasing cell envelope permeability
Cited by: 17
Author(s): Albert B. Jeon, Andrés Obregón-Henao, David F. Ackart, Brendan K. Podell, Juán Manuel Belardinelli, Mary Jackson, Tuan Vu Nguyen, Meghan S. Blackledge, Roberta J. Melander, Benjamin K. Johnson, Robert B. Abramovitch, Randall J. Basaraba
Software Mentions: 2
Published: about 9 years ago

10.1371/journal.pone.0179033

Candidate genes on murine chromosome 8 are associated with susceptibility to Staphylococcus aureus infection in mice and are involved with Staphylococcus aureus septicemia in humans
Cited by: 5
Author(s): Qin Yan, Sun Hee Ahn, Felix Mba Medie, Batu K. Sharma-Kuinkel, Lawrence P. Park, William K. Scott, Hitesh Deshmukh, Ephraim L. Tsalik, Derek D. Cyr, Christopher W. Woods, Chen-Hsin Albert Yu, Carlton Adams, Robert Qi, Brenda Hansen, Vance G. Fowler
Software Mentions: 2
Published: over 9 years ago

10.1038/s41598-021-88159-x

GLUT1 overexpression enhances glucose metabolism and promotes neonatal heart regeneration
Cited by: 21
Author(s): Viviana M. Fajardo, Iris Feng, Bao Ying Chen, Cesar A. Perez-Ramirez, Baochen Shi, Peter M. Clark, Rong Tian, Ching‐Ling Lien, Matteo Pellegrini, Heather R. Christofk, Haruko Nakano, Atsushi Nakano
Software Mentions: 2
Published: over 5 years ago

10.1038/s41598-021-87842-3

An examination of skeletal muscle and hepatic tissue transcriptomes from beef cattle divergent for residual feed intake
Cited by: 9
Author(s): Clare McKenna, Kate Keogh, Richard K. Porter, Sinéad M. Waters, Paul Cormican, David A. Kenny
Software Mentions: 2
Published: over 5 years ago

10.1371/journal.pone.0136103

Impaired Cell Cycle Regulation in a Natural Equine Model of Asthma
Cited by: 22
Author(s): Alicja Pacholewska, Vidhya Jagannathan, Michaela Drögemüller, Jolanta Klukowska‐Rötzler, Simone Lanz, Eman Hamza, Emmanouil T. Dermitzakis, Eliane Marti, Tosso Leeb, Vinzenz Gerber
Software Mentions: 2
Published: about 11 years ago

10.1371/journal.pone.0216586

Aberrant gene expression by Sertoli cells in infertile men with Sertoli cell-only syndrome
Cited by: 20
Author(s): Darius A. Paduch, Stephanie Hilz, Andrew Grimson, Peter N. Schlegel, Anne Jedlicka, William W. Wright
Software Mentions: 2
Published: over 7 years ago

10.1186/s12864-019-5901-0

Independent modulation of individual genomic component transcription and a cis-acting element related to high transcriptional activity in a multipartite DNA virus
Cited by: 10
Author(s): Nana Yu, Hui Xie, Yu Liang Zhang, Jianhua Wang, Xiong Zhou, Zhi Xin Liu
Software Mentions: 2
Published: about 7 years ago

10.1371/journal.pone.0217096

Similar effects of high-fructose and high-glucose feeding in a Drosophila model of obesity and diabetes
Cited by: 29
Author(s): Laura Palanker Musselman, Jill L. Fink, Thomas J. Baranski
Software Mentions: 2
Published: over 7 years ago

10.1002/pld3.48

Ethylene causes transcriptomic changes in Synechocystis during phototaxis
Cited by: 11
Author(s): Randy F. Lacey, Cidney J. Allen, Arkadipta Bakshi, Brad M. Binder
Software Mentions: 2
Published: over 8 years ago

10.1186/s12864-017-3829-9

Transcriptomic dynamics in soybean near-isogenic lines differing in alleles for an aphid resistance gene, following infestation by soybean aphid biotype 2
Cited by: 18
Author(s): Sung‐Woo Lee, Bryan J. Cassone, Asela J. Wijeratne, Tae-Hwan Jun, Andrew P. Michel, M. A. Rouf Mian
Software Mentions: 2
Published: over 9 years ago

10.3390/ijms21218170

Whole-Transcriptome Sequencing-Based Analysis of DAZL and Its Interacting Genes during Germ Cells Specification and Zygotic Genome Activation in Chickens
Cited by: 6
Author(s): Deivendran Rengaraj, Sohyoung Won, Jong Won Han, DongAhn Yoo, Heebal Kim, Jae Yong Han
Software Mentions: 2
Published: almost 6 years ago

10.1002/pld3.292

Cytokinin isopentenyladenine and its glucoside isopentenyladenine‐9G delay leaf senescence through activation of cytokinin‐associated genes
Cited by: 10
Author(s): H Tucker Hallmark, Aaron M. Rashotte
Software Mentions: 2
Published: almost 6 years ago

10.18632/aging.203123

Hippocampal transcriptome profiling reveals common disease pathways in chronic hypoperfusion and aging
Cited by: 4
Author(s): Sang‐Ha Baik, Sharmelee Selvaraji, David Y. Fann, Luting Poh, Dong-Gyu Jo, Deron R. Herr, Shenpeng R. Zhang, Hyun Ah Kim, Michael De Silva, M.O. Lai, Christopher Chen, Grant R Drummond, Kah‐Leong Lim, Christopher G. Sobey, Thiruma V. Arumugam
Software Mentions: 2
Published: over 5 years ago

10.1186/s12864-018-5398-y

Transcriptional profiling of Pseudomonas aeruginosa and Staphylococcus aureus during in vitro co-culture
Cited by: 57
Author(s): Mikaël Tognon, Thilo Köhler, Alexandre Lüscher, Christian van Delden
Software Mentions: 2
Published: over 7 years ago

10.1002/pld3.15

Diverse contributions of MYC2 and EIN3 in the regulation of Arabidopsis jasmonate-responsive gene expression
Cited by: 7
Author(s): Yuyu Zheng, Yiheng Lan, Tieliu Shi, Ziqiang Zhu
Software Mentions: 2
Published: about 9 years ago

10.1186/1471-2164-13-S8-S2

RNA-Seq analysis implicates dysregulation of the immune system in schizophrenia
Cited by: 56
Author(s): Junzhe Xu, Jingjing Sun, Jingchun Chen, Lily Wang, Anna Li, Matthew Helm, Steven Dubovsky, Silviu‐Alin Bacanu, Zhongming Zhao, Xiangning Chen
Software Mentions: 2
Published: almost 14 years ago

10.1371/journal.pone.0178923

Comparative transcriptomics of genetically divergent lines of chickens in response to Marek’s disease virus challenge at cytolytic phase
Cited by: 4
Author(s): Kunzhe Dong, Shuang Chang, Qingmei Xie, Alexis Black-Pyrkosz, Huanmin Zhang
Software Mentions: 2
Published: over 9 years ago

10.1371/journal.pone.0170961

MicroRNA and mRNA Transcriptome Profiling in Primary Human Astrocytes Infected with Borrelia burgdorferi
Cited by: 21
Author(s): Timothy Casselli, Humaira Qureshi, Elizabeth Peterson, Danielle Perley, Emily J. Blake, Bradley Jokinen, Ata Abbas, Sergei Nechaev, John A. Watt, Archana Dhasarathy, Catherine A. Brissette
Software Mentions: 2
Published: over 9 years ago

10.3390/ijms21238888

MicroRNAs from Extracellular Vesicles Secreted by Bovine Embryos as Early Biomarkers of Developmental Competence
Cited by: 15
Author(s): B. Melo-Báez, Yat Sen Wong, C. Aguilera, J. Cabezas, Ana Carolina Furlanetto Mançanares, Gonzalo Riadi, Fidel Ovídio Castro, L. Rodríguez-Álvarez
Software Mentions: 2
Published: almost 6 years ago

10.1371/journal.pone.0237699

Analysis of miRNAs and their target genes associated with mucosal damage caused by transport stress in the mallard duck intestine
Cited by: 2
Author(s): Hao Zhang, Fang Chen, Zhen-Hua Liang, Yan Wu, Jinsong Pi, Lixia Wang, Junzheng Du, Jie Shen, Angelo Pan, Yuejin Pu
Software Mentions: 2
Published: about 6 years ago

10.1371/journal.pone.0132176

Genome-Wide Profiling of Histone Modifications (H3K9me2 and H4K12ac) and Gene Expression in Rust (Uromyces appendiculatus) Inoculated Common Bean (Phaseolus vulgaris L.)
Cited by: 30
Author(s): Vasudevan Ayyappan, Venu Kalavacharla, Jyothi Thimmapuram, Ketaki P. Bhide, Venkateswara R. Sripathi, Tomasz G. Smolinski, Muthusamy Manoharan, Yaqoob Thurston, Antonette Todd, Brewster F. Kingham
Software Mentions: 2
Published: about 11 years ago

10.1111/pbi.12548

Terpene metabolic engineering via nuclear or chloroplast genomes profoundly and globally impacts off‐target pathways through metabolite signalling
Cited by: 26
Author(s): Elise K. Pasoreck, Jin Su, Ian M. Silverman, Sager J. Gosai, Brian D. Gregory, Joshua S. Yuan, Henry Daniell
Software Mentions: 2
Published: over 10 years ago

10.3390/ijms21239124

Amino Acid and Carbohydrate Metabolism Are Coordinated to Maintain Energetic Balance during Drought in Sugarcane
Cited by: 23
Author(s): Augusto Lima Diniz, Danielle Izilda Rodrigues da Silva, Carolina Gimiliani Lembke, Maximiller Dal-Bianco, Felipe Ten Caten, Forrest Li, Romel Duarte Vilela, Marcelo Menossi, Doreen Ware, Laurício Endres, Gláucia Mendes Souza
Software Mentions: 2
Published: almost 6 years ago

10.1371/journal.pone.0185732

Transcriptome analysis of genes involved in defense against alkaline stress in roots of wild jujube (Ziziphus acidojujuba)
Cited by: 27
Author(s): Mingxin Guo, Shipeng Li, Shan Tian, Bei Wang, Xiangshan Zhao
Software Mentions: 2
Published: almost 9 years ago

10.1111/pbi.13044

Genes regulating gland development in the cotton plant
Cited by: 39
Author(s): Madhusudhana R. Janga, Devendra Pandeya, LeAnne M. Campbell, Kranti Konganti, Stephany Toinga Villafuerte, Lorraine S. Puckhaber, Alan E. Pepper, Robert D. Stipanovic, Jodi A. Scheffler, Keerti S. Rathore
Software Mentions: 2
Published: almost 8 years ago

10.1371/journal.pone.0197973

Loss of Fnip1 alters kidney developmental transcriptional program and synergizes with TSC1 loss to promote mTORC1 activation and renal cyst formation
Cited by: 17
Author(s): Ryan Michael Centini, Mark Tsang, Terri Iwata, Heon Park, Jeffrey J. Delrow, Daciana Margineantu, Brian M. Iritani, Haiwei Gu, H. Denny Liggitt, Janella Kang, Lim Kang, David M. Hockenbery, Daniel Raftery
Software Mentions: 2
Published: over 8 years ago

10.1038/s41598-021-91812-0

Cholesterol-dependent transcriptome remodeling reveals new insight into the contribution of cholesterol to Mycobacterium tuberculosis pathogenesis
Cited by: 14
Author(s): Jakub Pawełczyk, Anna Brzostek, Alina Minias, Przemysław Płociński, Anna Rumijowska-Galewicz, Dominik Strapagiel, Jolanta Zakrzewska‐Czerwińska, Jarosław Dziadek
Software Mentions: 2
Published: over 5 years ago

10.1371/journal.pone.0091353

Natural Antisense Transcripts and Long Non-Coding RNA in Neurospora crassa
Cited by: 41
Author(s): Yamini Arthanari, Christian Heintzen, Sam Griffiths-Jones, Susan K. Crosthwaite
Software Mentions: 2
Published: over 12 years ago

10.1371/journal.pone.0098578

Digital Gene-Expression Profiling Analysis of the Cholesterol-Lowering Effects of Alfalfa Saponin Extract on Laying Hens
Cited by: 14
Author(s): Lu Zhou, Shi Ya, Rui Guo, Minggen Liang, Xiaoyan Zhu, Chengzhang Wang
Software Mentions: 2
Published: over 12 years ago

10.1111/pbi.12820

Single‐base methylome analysis reveals dynamic epigenomic differences associated with water deficit in apple
Cited by: 123
Author(s): Jidi Xu, Shasha Zhou, Xiaoqing Gong, Yi Song, Steve van Nocker, Fengwang Ma, Qingmei Guan
Software Mentions: 2
Published: about 9 years ago

10.1371/journal.pone.0156453

Comprehensive RNA-Seq Analysis on the Regulation of Tomato Ripening by Exogenous Auxin
Cited by: 41
Author(s): Jiayin Li, Xiaoya Tao, Li Li, Linchun Mao, Zisheng Luo, Zia Ullah Khan, Tiejin Ying
Software Mentions: 2
Published: over 10 years ago

10.1111/pbi.13310

Deciphering the high‐quality genome sequence of coriander that causes controversial feelings
Cited by: 51
Author(s): Xiaoming Song, Jinpeng Wang, Nan Li, Jigao Yu, Fanbo Meng, Chendan Wei, Chao Liu, Wei Chen, Fulei Nie, Zhikang Zhang, Ke Gong, Xinyu Li, Jingjing Hu, Qing Yang, Yuxian Li, Chunjin Li, Shuyan Feng, He Guo, Jiaqing Yuan, Qiaoying Pei, Tong Yu, Xi Kang, Wei Zhao, Tianyu Lei, Pengchuan Sun, Li Wang, Weina Ge, Di Guo, Xiaoyang Duan, Shaoqi Shen, Chunlin Cui, Ying Yu, Yangqin Xie, Zhang Jin, Yayi Hou, Jinyu Wang, Xiuqing Li, Andrew H. Paterson, Xiyin Wang
Software Mentions: 2
Published: over 6 years ago

10.1371/journal.pone.0116309

Gene Expression Dosage Regulation in an Allopolyploid Fish
Cited by: 14
Author(s): Isa Matos, Miguel P. Machado, Manfred Schartl, M. M. Coelho
Software Mentions: 2
Published: over 11 years ago

10.3390/ijms22020781

Macrophage-Derived Inflammation Induces a Transcriptome Makeover in Mesenchymal Stromal Cells Enhancing Their Potential for Tissue Repair
Cited by: 7
Author(s): Inés Maldonado-Lasunción, Nick O’Neill, Oliver Umland, Joost Verhaagen, Martin Oudega
Software Mentions: 2
Published: over 5 years ago

10.14814/phy2.12109

Regulation of angiopoietin-like protein 4 production during and after exercise
Cited by: 35
Author(s): Frode Norheim, Marit Hjorth, Torgrim M. Langleite, Sindre Lee, Torgeir Holen, Christian Bindesbøll, Hans Kristian Stadheim, Hanne Løvdal Gulseth, Kåre I. Birkeland, Anders Kielland, Jørgen Jensen, Knut Tomas Dalen, Christian A. Drevon
Software Mentions: 2
Published: about 12 years ago

10.1371/journal.pone.0215472

UV-C treatment promotes quality of early ripening apple fruit by regulating malate metabolizing genes during postharvest storage
Cited by: 19
Author(s): Jakaria Chowdhury Onik, Yajing Xie, Yuquan Duan, Xiaojia Hu, Zhidong Wang, Qiong Lin
Software Mentions: 2
Published: over 7 years ago

10.1371/journal.pone.0244648

Transcriptomic analysis of the honey bee (Apis mellifera) queen spermathecae reveals genes that may be involved in sperm storage after mating
Cited by: 11
Author(s): Juliana Rangel, Tonya F. Shepherd, Alejandra González, Andrew Hillhouse, Kranti Konganti, Nancy H. Ing
Software Mentions: 2
Published: over 5 years ago

10.14814/phy2.12481

Perilipin 4 in human skeletal muscle: localization and effect of physical activity
Cited by: 37
Author(s): Shirin Pourteymour, Sindre Lee, Torgrim M. Langleite, Kristin Eckardt, Marit Hjorth, Christian Bindesbøll, Knut Tomas Dalen, Kåre I. Birkeland, Christian A. Drevon, Torgeir Holen, Frode Norheim
Software Mentions: 2
Published: about 11 years ago

10.14814/phy2.12450

Unique gene program of rat small resistance mesenteric arteries as revealed by deep RNA sequencing
Cited by: 8
Author(s): John J Reho, Amol C. Shetty, Rachael P. Dippold, Anup Mahurkar, Steven A. Fisher
Software Mentions: 2
Published: over 11 years ago

10.1371/journal.pone.0184974

Effects of salinity on the cellular physiological responses of Natrinema sp. J7-2
Cited by: 10
Author(s): Yadong Mei, Huan Liu, Shunxi Zhang, Ming Yang, Chun Hu, Jian Zhang, Ping Shen, Xiangdong Chen
Software Mentions: 2
Published: about 9 years ago

10.1038/s41598-021-94641-3

Transcriptome-level assessment of the impact of deformed wing virus on honey bee larvae
Cited by: 4
Author(s): Zih-Ting Chang, Yu-Feng Huang, Yuewen Chen, Ming‐Ren Yen, Po‐Ya Hsu, Tzu-Han Chen, Yi-Hsuan Li, King-Wah Chiu, Yu‐Shin Nai
Software Mentions: 2
Published: about 5 years ago

10.1371/journal.pone.0128350

Putative Regulatory Factors Associated with Intramuscular Fat Content
Cited by: 66
Author(s): A. S. M. César, Luciana Correia de Almeida Regitano, James E. Koltes, Eric R. Fritz-Waters, Dante Pazzanese Duarte Lanna, G. Gasparin, Gerson Barreto Mourão, P. S. N. Oliveira, James M. Reecy, Luiz Lehmann Coutinho
Software Mentions: 2
Published: over 11 years ago

10.1371/journal.pone.0179922

Transcriptomic analysis to uncover genes affecting cold resistance in the Chinese honey bee (Apis cerana cerana)
Cited by: 21
Author(s): Kai Xu, Qingsheng Niu, Huiting Zhao, Yali Du, Yusuo Jiang
Software Mentions: 2
Published: over 9 years ago

10.18632/oncotarget.18270

Dual effects of constitutively active androgen receptor and full-length androgen receptor for N-cadherin regulation in prostate cancer
Cited by: 6
Author(s): Félicie Cottard, Pauline Ould Madi-Berthélémy, Éva Erdmann, Frédérique Schaff-Wendling, Céline Keime, Tao Ye, Jean‐Emmanuel Kurtz, Jocelyn Céraline
Software Mentions: 2
Published: over 9 years ago

10.1371/journal.pone.0179762

Tumor Necrosis Factor dynamically regulates the mRNA stabilome in rheumatoid arthritis fibroblast-like synoviocytes
Cited by: 20
Author(s): Konstantinos Loupasakis, David Kuo, Upneet K. Sokhi, Cheol Ho Sohn, Bethany Syracuse, Ευγενία Γιαννοπούλου, Sung Ho Park, Hee‐Ju Kang, Gunnar Rätsch, Lionel B. Ivashkiv, George D. Kalliolias
Software Mentions: 2
Published: about 9 years ago

10.1371/journal.pone.0156045

Transcriptome Analysis and Gene Identification in the Pulmonary Artery of Broilers with Ascites Syndrome
Cited by: 21
Author(s): Fei Yang, Cao H, Qingyang Xiao, Xiaomin Guo, Zhuang Yu, Caiying Zhang, Tiancheng Wang, Huayuan Lin, Yan-Chun Song, Guoliang Hu, Ping Liu
Software Mentions: 2
Published: over 10 years ago

10.1186/s12864-015-1709-8

Transcriptional maturation of the mouse auditory forebrain
Cited by: 25
Author(s): Troy A. Hackett, Yan Guo, Amanda Clause, Nicholas J. Hackett, Krassimira A. Garbett, Pan Zhang, Daniel B. Polley, Károly Mirnics
Software Mentions: 2
Published: about 11 years ago

10.7717/peerj.3945

Oxygen-limited metabolism in the methanotroph Methylomicrobium buryatense 5GB1C
Cited by: 63
Author(s): Alexey Gilman, Yanfen Fu, Melissa C. Hendershott, Frances Chu, Aaron W. Puri, Amanda Lee Smith, Mitchell W. Pesesky, Rose Lieberman, David A. C. Beck, Mary E. Lidstrom
Software Mentions: 2
Published: almost 9 years ago

10.1038/s41598-021-94003-z

Transcriptomic landscape of blood platelets in healthy donors
Cited by: 21
Author(s): Anna Supernat, Marta Popęda, Krzysztof Pastuszak, Myron G. Best, Peter Grešner, Sjors In ’t Veld, Bartłomiej Siek, Natalia Bednarz‐Knoll, Matthew T. Rondina, Tomasz Stokowy, Thomas Würdinger, Jacek Jassem, Anna Żaczek
Software Mentions: 2
Published: about 5 years ago

10.7717/peerj.4537

Flavonoid biosynthesis controls fiber color in naturally colored cotton
Cited by: 20
Author(s): Haifeng Liu, Cheng Luo, Song Wu, Haitao Shen, Guoliang Li, Zhigang He, Wen-Gang Chen, Yanyan Cao, Fang Huang, Shouwu Tang, Hong Pan, Enfeng Zhao, Jianbo Zhu, Dajun He, Shaoming Wang, Guang-Ying Huo, Hailiang Liu
Software Mentions: 2
Published: over 8 years ago

10.1371/journal.pone.0217343

Identification of two molecular subtypes in canine mast cell tumours through gene expression profiling
Cited by: 6
Author(s): Lidia Hildebrand Pulz, Camila Neri Barra, Pâmela Almeida Alexandre, Greice Cestari Huete, Karine Germano Cadrobbi, Adriana Tomoko Nishiya, Sílvio Henrique de Freitas, Heidge Fukumasu, Ricardo de Francisco Strefezzi
Software Mentions: 2
Published: over 7 years ago

10.7717/peerj.1991

Transcriptomic analysis reveals distinct resistant response by physcion and chrysophanol against cucumber powdery mildew
Cited by: 17
Author(s): Yanping Li, Shilin Tian, Xiaojun Yang, Xin Wang, Yuhai Guo, Hanwen Ni
Software Mentions: 2
Published: over 10 years ago

10.3390/ijms22020940

The Grapevine E3 Ubiquitin Ligase VriATL156 Confers Resistance against the Downy Mildew Pathogen Plasmopara viticola
Cited by: 3
Author(s): Elodie Vandelle, Pietro Ariani, Alice Regaiolo, Davide Danzi, Arianna Lovato, Claudia Zadra, Nicola Vitulo, Giorgio Gambino, Annalisa Polverari
Software Mentions: 2
Published: over 5 years ago

10.1371/journal.pone.0241966

Transcripts of wheat at a target locus on chromosome 6B associated with increased yield, leaf mass and chlorophyll index under combined drought and heat stress
Cited by: 3
Author(s): Jessica Schmidt, Melissa Garcia, Chris Brien, Priyanka Kalambettu, Trevor Garnett, Delphine Fleury, Penny J. Tricker
Software Mentions: 2
Published: almost 6 years ago

10.1371/journal.pone.0165953

Genome-Wide Identification, Characterization, and Stress-Responsive Expression Profiling of Genes Encoding LEA (Late Embryogenesis Abundant) Proteins in Moso Bamboo (Phyllostachys edulis)
Cited by: 32
Author(s): Zhuo Huang, Xiaojuan Zhong, Jun He, Si-Han Jin, Han-Du Guo, Xiaofang Yu, Yujue Zhou, Xi Li, Min Ma, Qibing Chen, Hai Long
Software Mentions: 2
Published: almost 10 years ago

10.1371/journal.pone.0143378

Transcriptional Profiling Identifies Location-Specific and Breed-Specific Differentially Expressed Genes in Embryonic Myogenesis in Anas Platyrhynchos
Cited by: 9
Author(s): Rongping Zhang, Hehe Liu, Junying Liu, Jiwei Hu, Xiping Yan, Ding-min-cheng Wang, Liang Li, Jiwen Wang
Software Mentions: 2
Published: almost 11 years ago

10.7717/peerj.9172

Transcriptome profiling of avian pathogenicEscherichia coliand the mouse microvascular endothelial cell line bEnd.3 during interaction
Cited by: 6
Author(s): Peili Wang, Xianli Meng, Jianji Li, Yanfei Chen, Dong Zhang, Haoran Zhong, Pengpeng Xia, Luying Cui, Guoqiang Zhu, Heng Wang
Software Mentions: 2
Published: over 6 years ago

10.3390/ijms22031248

Integrating LCM-Based Spatio-Temporal Transcriptomics Uncovers Conceptus and Endometrial Luminal Epithelium Communication that Coordinates the Conceptus Attachment in Pigs
Cited by: 11
Author(s): Feiyu Wang, Shilei Zhao, Dadong Deng, Weiwei Wang, Xuewen Xu, Xiaolei Liu, Shuhong Zhao, Mei Yu
Software Mentions: 2
Published: over 5 years ago

10.1371/journal.pone.0160970

Whole Transcriptome Profiling Identifies CD93 and Other Plasma Cell Survival Factor Genes Associated with Measles-Specific Antibody Response after Vaccination
Cited by: 17
Author(s): Iana H. Haralambieva, Michael T. Zimmermann, Inna G. Ovsyannikova, Diane E. Grill, Ann L. Oberg, Richard B. Kennedy, Gregory A. Poland
Software Mentions: 2
Published: about 10 years ago

10.7717/peerj.1762

Epithelial, metabolic and innate immunity transcriptomic signatures differentiating the rumen from other sheep and mammalian gastrointestinal tract tissues
Cited by: 46
Author(s): Ruidong Xiang, V. H. Oddy, Alan Archibald, Phil Vercoe, Brian P. Dalrymple
Software Mentions: 2
Published: over 10 years ago

10.7717/peerj.2945

Metagenomic identification of active methanogens and methanotrophs in serpentinite springs of the Voltri Massif, Italy
Cited by: 71
Author(s): William J. Brazelton, Christopher N Thornton, Alex Hyer, Katrina I. Twing, August Longino, Susan Q. Lang, Marvin D. Lilley, Gretchen L. Früh-Green, M. O. Schrenk
Software Mentions: 2
Published: over 9 years ago

10.1371/journal.pone.0179027

Transcriptome profiling analysis reveals the role of silique in controlling seed oil content in Brassica napus
Cited by: 7
Author(s): Ke-Lin Huang, Zhang Mei-li, Guangjing Ma, Huan Wu, Xiaoming Wu, Feng Ren, Xuebao Li
Software Mentions: 2
Published: over 9 years ago

10.1371/journal.pone.0164874

Transcriptomic Variation during Spermiogenesis in Mouse Germ Cells
Cited by: 11
Author(s): Haiyang Zuo, Junfang Zhang, Liuguang Zhang, Xiaoxia Ren, Xiaoli Chen, Hao Huang, Xiao‐Fan Zhao, Dong Wang
Software Mentions: 2
Published: almost 10 years ago

10.3390/ijms22041669

The pip1s Quintuple Mutants Demonstrate the Essential Roles of PIP1s in the Plant Growth and Development of Arabidopsis
Cited by: 3
Author(s): Xing Wang, Yu Wu, Zijin Liu, Tong Liu, Lamei Zheng, Genfa Zhang
Software Mentions: 2
Published: over 5 years ago

10.1371/journal.pone.0158317

Chronic Contractile Dysfunction without Hypertrophy Does Not Provoke a Compensatory Transcriptional Response in Mouse Hearts
Cited by: 3
Author(s): Scot J. Matkovich, David R. Grubb, Julie R. McMullen, Elizabeth A. Woodcock
Software Mentions: 2
Published: over 10 years ago

10.1371/journal.pone.0221810

Desmoplasia and oncogene driven acinar-to-ductal metaplasia are concurrent events during acinar cell-derived pancreatic cancer initiation in young adult mice
Cited by: 13
Author(s): B. Lamar Johnson, Marcela d’Alincourt Salazar, Sarah Mackenzie-Dyck, Massimo D’Apuzzo, Hung Ping Shih, Edwin R. Manuel, Don J. Diamond
Software Mentions: 2
Published: about 7 years ago

10.7717/peerj.5103

Transcriptomic evidence for involvement of reactive oxygen species in Rhizoctonia solani AG1 IA sclerotia maturation
Cited by: 9
Author(s): Bo Liu, Haode Wang, Zhoujie Ma, Xiaotong Gai, Yanqiu Sun, Shidao He, Xian Liu, Yanfeng Wang, Yue Xuan, Zhen Gao
Software Mentions: 2
Published: over 8 years ago

10.1371/journal.pone.0179491

Comparative transcriptome analysis provides insights into molecular mechanisms for parthenocarpic fruit development in eggplant (Solanum melongena L.)
Cited by: 16
Author(s): Xia Chen, Min Zhang, Jie Tan, Shuping Huang, Chunli Wang, Hongyuan Zhang, Taiming Tan
Software Mentions: 2
Published: over 9 years ago

10.1186/s12864-018-4467-6

Identification of usual interstitial pneumonia pattern using RNA-Seq and machine learning: challenges and solutions
Cited by: 22
Author(s): Yoonha Choi, Tiffany Ting Liu, Daniel G. Pankratz, Thomas V. Colby, Neil M. Barth, David A. Lynch, P. Sean Walsh, Ganesh Raghu, Giulia C. Kennedy, Jing Huang
Software Mentions: 2
Published: over 8 years ago

10.1371/journal.pone.0175943

Transcriptome and proteome responses in RNAlater preserved tissue of Arabidopsis thaliana
Cited by: 34
Author(s): Colin Kruse, Proma Basu, Darron R. Luesse, Sarah E. Wyatt
Software Mentions: 2
Published: over 9 years ago

10.1371/journal.pone.0192147

Evaluation of changes arising in the pig mesenchymal stromal cells transcriptome following cryopreservation and Trichostatin A treatment
Cited by: 5
Author(s): Artur Gurgul, Joanna Romanek, Klaudia Pawlina-Tyszko, Tomasz Szmatoła, Jolanta Opiela
Software Mentions: 2
Published: over 8 years ago

10.1371/journal.pone.0141590

AmpliconDuo: A Split-Sample Filtering Protocol for High-Throughput Amplicon Sequencing of Microbial Communities
Cited by: 35
Author(s): Anja Lange, Steffen Jost, Dominik Heider, Christina Böck, Bettina Budeus, Elmar Schilling, Axel Strittmatter, Jens Boenigk, Daniel Hoffmann
Software Mentions: 2
Published: almost 11 years ago

10.7717/peerj.10500

Transcriptional profile in rat muscle: down-regulation networks in acute strenuous exercise
Cited by: 1
Author(s): Stela Mirla da Silva Felipe, Raquel Martins de Freitas, Emanuel Diego dos Santos Penha, Christina Pacheco, Daniel Freitas Freire Martins, Juliana Osório Alves, Paula Matias Soares, Adriano César Carneiro Loureiro, Tanes I. Lima, Leonardo R. Silveira, Alex Soares Marreiros Ferraz, Jorge Estefano Santana de Souza, José Henrique Leal-Cardoso, Denise Pires de Carvalho, Vânia Marilande Ceccatto
Software Mentions: 2
Published: over 5 years ago

10.1371/journal.pone.0152574

Genomic Characterization and Comparison of Multi-Regional and Pooled Tumor Biopsy Specimens
Cited by: 13
Author(s): Je‐Gun Joung, Joon Seol Bae, Sang Cheol Kim, Hyunchul Jung, Woong-Yang Park, Sang‐Yong Song
Software Mentions: 2
Published: over 10 years ago

10.1038/s41598-021-97515-w

Molecular underpinnings of division of labour among workers in a socially complex termite
Cited by: 5
Author(s): D. Elsner, Klaus Hartfelder, Judith Korb
Software Mentions: 2
Published: about 5 years ago

10.1371/journal.pone.0084651

Intestinal Subepithelial Myofibroblasts Support the Growth of Intestinal Epithelial Stem Cells
Cited by: 89
Author(s): Nan Li, Ziyad Jabaji, Jiafang Wang, Vaidehi S. Joshi, Garrett J. Brinkley, Hassan A. Khalil, Fengchao Wang, Artur Jaroszewicz, Matteo Pellegrini, Linheng Li, Michael Lewis, Matthias Stelzner, James C.Y. Dunn, Martı́n G. Martı́n
Software Mentions: 2
Published: over 12 years ago

10.1371/journal.pone.0158471

Bioinformatics Prediction of Polyketide Synthase Gene Clusters from Mycosphaerella fijiensis
Cited by: 19
Author(s): Roslyn D. Noar, Margaret E. Daub
Software Mentions: 2
Published: about 10 years ago

10.1371/journal.pone.0137797

Embryonic Lethality Due to Arrested Cardiac Development in Psip1/Hdgfrp2 Double-Deficient Mice
Cited by: 9
Author(s): Hao Wang, Ming-Chieh Shun, Amy K. Dickson, Alan Engelman
Software Mentions: 2
Published: about 11 years ago

10.3390/cancers12030697

Oxaliplatin-Induced DHX9 Phosphorylation Promotes Oncogenic Circular RNA CCDC66 Expression and Development of Chemoresistance
Cited by: 39
Author(s): Ya-Chi Lin, Ya-Shan Yu, Hongchin Lin, Kuei‐Yang Hsiao
Software Mentions: 2
Published: over 6 years ago

10.7717/peerj.2664

Whole-genome single-nucleotide polymorphism (SNP) marker discovery and association analysis with the eicosapentaenoic acid (EPA) and docosahexaenoic acid (DHA) content inLarimichthys crocea
Cited by: 18
Author(s): Shijun Xiao, Panpan Wang, Linsong Dong, Yaguang Zhang, Zhaofang Han, Qiurong Wang, Zhiyong Wang
Software Mentions: 2
Published: almost 10 years ago

10.3390/cancers12051148

A Novel 4-gene Score to Predict Survival, Distant Metastasis and Response to Neoadjuvant Therapy in Breast Cancer
Cited by: 46
Author(s): Masanori Oshi, Eriko Katsuta, Li Yan, John M.L. Ebos, Omar M. Rashid, Ryusei Matsuyama, Itaru Endo, Kazuaki Takabe
Software Mentions: 2
Published: over 6 years ago

Projects: pypi: HTSeq

Science Score: 65/100

Bonuses:

Penalties:

Papers Mentioning HTSeq 3,071