pypi: HTSeq | Projects | Ecosyste.ms: Papers

10.1186/s12864-017-4374-2

A survey on cellular RNA editing activity in response to Candida albicans infections
Cited by: 3
Author(s): Yao‐Wei Huang, Yingying Cao, Jiarui Li, Yuanhua Liu, Zhong Wu, Xuan Li, Chen Chen, Pei Hao
Software Mentions: 3
Published: almost 9 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

10.1002/2211-5463.13199

Identification of differentially expressed genes in diabetic kidney disease by RNA‐Seq analysis of venous blood platelets
Cited by: 0
Author(s): Bao Long Zhang, Xiu Hong Yang, Hui Jin, Xiao Li Zhan
Software Mentions: 3
Published: over 5 years ago

10.1038/s41389-018-0108-9

Atypical GATA transcription factor TRPS1 represses gene expression by recruiting CHD4/NuRD(MTA2) and suppresses cell migration and invasion by repressing TP63 expression
Cited by: 24
Author(s): Yuzhi Wang, Xue Lü, Xue Gong, Lixian Wu, Jun Zhang, Weiguang Li, Jian Li, Liming Chen
Software Mentions: 3
Published: almost 8 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

10.1186/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

10.1371/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

10.1371/journal.pone.0155061

Comparative Analysis of Transcriptomes among Bombyx mori Strains and Sexes Reveals the Genes Regulating Melanic Morph and the Related Phenotypes
Cited by: 3
Author(s): Songzhen He, Xiaoling Tong, Kunpeng Lu, Yaru Lu, Jiangwen Luo, Wenhao Yang, Min Chen, Minjin Han, Hai Hu, Cheng Lü, Fangyin Dai
Software Mentions: 3
Published: over 10 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

10.1371/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

10.1038/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

10.1038/s41389-020-0210-7

Chromatin remodeling protein HELLS is critical for retinoblastoma tumor initiation and progression
Cited by: 28
Author(s): Loredana Zocchi, Aditi Mehta, Stephanie Wu, Jie Wu, Yijun Gu, Jingtian Wang, Suk-Hwan Suh, Robert C. Spitale, Claudia A. Benavente
Software Mentions: 3
Published: over 6 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

10.1038/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

10.1038/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/s41598-021-89175-7

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

10.1038/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

10.1371/journal.pone.0222325

Fe limitation decreases transcriptional regulation over the diel cycle in the model diatom Thalassiosira pseudonana
Cited by: 13
Author(s): Johanna A. L. Goldman, Megan J. Schatz, Chris T. Berthiaume, Sacha Coesel, Mónica V. Orellana, E. Virginia Armbrust
Software Mentions: 3
Published: about 7 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

10.1186/s12915-019-0633-9

Analysis of sea star larval regeneration reveals conserved processes of whole-body regeneration across the metazoa
Cited by: 36
Author(s): Gregory A. Cary, Andrew Wolff, Olga Zueva, Joseph Pattinato
Software Mentions: 3
Published: over 7 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/s41598-021-86612-5

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

10.1038/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/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.0095987

Dissection of Estrogen Receptor Alpha Signaling Pathways in Osteoblasts Using RNA-Sequencing
Cited by: 22
Author(s): Matthew M. Roforth, Elizabeth J. Atkinson, Ellis R. Levin, Sundeep Khosla, David G. Monroe
Software Mentions: 3
Published: over 12 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/s41598-021-84138-4

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

10.1371/journal.pone.0192253

Transcriptional profiling of liver tissues in chicken embryo at day 16 and 20 using RNA sequencing reveals differential antioxidant enzyme activity
Cited by: 10
Author(s): Shaohua Yang, Lu Lu Wang, Zhaoyuan Shi, Xiaoqian Ou, Wei Wang, Chen Xue, Guoqing Liu
Software Mentions: 3
Published: almost 9 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

10.1371/journal.pone.0207497

Response of Tribolium castaneum to dietary mannitol, with remarks on its possible nutritive effects
Cited by: 8
Author(s): Shingo Kikuta
Software Mentions: 3
Published: almost 8 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

10.1093/femsle/fny082

Fermentation products in the cystic fibrosis airways induce aggregation and dormancy-associated expression profiles in a CF clinical isolate of Pseudomonas aeruginosa
Cited by: 18
Author(s): Joann Phan, Tara Gallagher, Andrew Oliver, Whitney England, Katrine Whiteson
Software Mentions: 3
Published: over 8 years ago

10.1038/s41598-021-96374-9

Integrative genetic, genomic and transcriptomic analysis of heat shock protein and nuclear hormone receptor gene associations with spontaneous preterm birth
Cited by: 10
Author(s): Johanna M. Huusko, Heli Tiensuu, Antti M. Haapalainen, Anu Pasanen, Pinja Tissarinen, Minna K. Karjalainen, Ge Zhang, Kaare Christensen, Kelli K. Ryckman, Bo Jacobsson, Jeffrey C. Murray, Stephen F. Kingsmore, Mikko Hallman, Louis J. Muglia, Mika Rämet
Software Mentions: 3
Published: about 5 years ago

10.1111/jipb.13037

Roles of DEMETER in regulating DNA methylation in vegetative tissues and pathogen resistance
Cited by: 20
Author(s): Wenjie Zhang, Huan Huang, Xin Lin, Zhu C, Ken‐ichi Kosami, Chao‐Feng Huang, Huiming Zhang, Cheng‐Guo Duan, Jian‐Kang Zhu, Daisuke Miki
Software Mentions: 3
Published: over 5 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

10.1038/s41598-021-81611-y

Absence of S100A4 in the mouse lens induces an aberrant retina-specific differentiation program and cataract
Cited by: 3
Author(s): Rupalatha Maddala, Junyuan Gao, Richard T. Mathias, Tylor R. Lewis, Vadim Y. Arshavsky, Adriana Levine, Jonathan M. Backer, Anne R. Bresnick, Ponugoti Vasantha Rao
Software Mentions: 3
Published: almost 6 years ago

10.1371/journal.pone.0159197

Comparative Transcriptome Profiling of Human Foreskin Fibroblasts Infected with the Sylvio and Y Strains of Trypanosoma cruzi
Cited by: 22
Author(s): Genevieve A. Houston-Ludlam, Ashton T. Belew, Najib M. El-Sayed
Software Mentions: 3
Published: over 10 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

10.1038/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/s41598-021-82905-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

10.1038/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.0147950

Differential Gene Expression Patterns in Chicken Cardiomyocytes during Hydrogen Peroxide-Induced Apoptosis
Cited by: 8
Author(s): Chunyun Wan, Jinmei Xiang, Youwen Li, Deliang Guo
Software Mentions: 3
Published: almost 11 years ago

10.1371/journal.pone.0239701

Transcriptomic and metabolomic profiling of melatonin treated soybean (Glycine max L.) under drought stress during grain filling period through regulation of secondary metabolite biosynthesis pathways
Cited by: 14
Author(s): Liang Cao, Xijun Jin, Yuxian Zhang, Mingcong Zhang, Yanhong Wang
Software Mentions: 3
Published: about 6 years ago

10.3390/ani9080523

Global Mapping of H3K4 Trimethylation (H3K4me3) and Transcriptome Analysis Reveal Genes Involved in the Response to Epidemic Diarrhea Virus Infections in Pigs
Cited by: 12
Author(s): Haifei Wang, Yang Li, Huan Qu, Hanping Feng, Shenglong Wu, Wenbin Bao
Software Mentions: 3
Published: over 7 years ago

10.1186/s13072-018-0212-2

CRX directs photoreceptor differentiation by accelerating chromatin remodeling at specific target sites
Cited by: 31
Author(s): Philip A. Ruzycki, Xiaodong Zhang, Shiming Chen
Software Mentions: 3
Published: over 8 years ago

10.1371/journal.pone.0143811

The Clinical Significance and Molecular Features of the Spatial Tumor Shapes in Breast Cancers
Cited by: 14
Author(s): Hyeong‐Gon Moon, Namshin Kim, Seongmun Jeong, Min-Ju Lee, Hyunhye Moon, Jong-Jin Kim, Tae-Kyung Yoo, Han‐Byoel Lee, Ji Sun Kim, Dong‐Young Noh, Wonshik Han
Software Mentions: 3
Published: almost 11 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

10.1371/journal.pone.0172141

Transcriptome analysis of two recombinant inbred lines of common bean contrasting for symbiotic nitrogen fixation
Cited by: 11
Author(s): Kelvin Kamfwa, Dongyan Zhao, James D. Kelly, Karen A. Cichy
Software Mentions: 3
Published: over 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

10.1186/s12864-020-6507-2

Transcriptomic profiles of Dunaliella salina in response to hypersaline stress
Cited by: 18
Author(s): Qinghua He, Yaqiu Lin, Hong Kee Tan, Yu Zhou, Yan Wen, Jiajia Gan, Ruiwen Li, Qinglian Zhang
Software Mentions: 3
Published: almost 7 years ago

10.1038/s41598-020-74051-7

Integrative transcriptomic analysis for linking acute stress responses to squamous cell carcinoma development
Cited by: 4
Author(s): Tran Nguyen, Kimal Rajapakshe, Courtney Nicholas, Leticia Tordesillas, Erik A. Ehli, Christel M. Davis, Cristian Coarfa, Elsa R. Flores, Sally E. Dickinson, Clara Curiel‐Lewandrowski, Kenneth Y. Tsai
Software Mentions: 3
Published: about 6 years ago

10.1038/s41598-020-70248-y

Transcriptome sequencing supports a conservation of macrophage polarization in fish
Cited by: 24
Author(s): Annelieke S. Wentzel, Jules Petit, Wouter G. van Veen, I.R. Fink, Marleen Scheer, M. Carla Piazzon, Maria Forlenza, Herman P. Spaink, G.F. Wiegertjes
Software Mentions: 3
Published: over 6 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

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

10.1371/journal.pone.0202309

Comparison of gene co-networks analysis provide a systems view of rice (Oryza sativa L.) response to Tilletia horrida infection
Cited by: 6
Author(s): aijun wang, Xinyue Shu, Xianyu Niu, Wenjuan Zhao, Peng Ai, Ping Li, Aiping Zheng
Software Mentions: 3
Published: about 8 years ago

10.1038/s41598-020-69179-5

Regulation of MYO18B mRNA by a network of C19MC miRNA-520G, IFN-γ, CEBPB, p53 and bFGF in hepatocellular carcinoma
Cited by: 9
Author(s): Goodwin G. Jinesh, Marco Napoli, Hayley D. Ackerman, Payal Raulji, Nicole Montey, Elsa R. Flores, Andrew S. Brohl
Software Mentions: 3
Published: over 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

10.1038/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/s41598-020-66988-6

A Transcriptome Analysis Reveals that Hepatic Glycolysis and Lipid Synthesis Are Negatively Associated with Feed Efficiency in DLY Pigs
Cited by: 8
Author(s): Cineng Xu, Xingwang Wang, Zhanwei Zhuang, Jie Wu, Shenping Zhou, Jianping Quan, Rongrong Ding, Yong Ye, Longlong Peng, Zhenfang Wu, Enqin Zheng, Jie Yang
Software Mentions: 3
Published: over 6 years ago

10.1186/s12870-015-0468-7

Specific pools of endogenous peptides are present in gametophore, protonema, and protoplast cells of the moss Physcomitrella patens
Cited by: 37
Author(s): Igor Fesenko, Georgij Arapidi, Alexander Skripnikov, Dmitry Alexeev, Elena S. Kostryukova, Alexander I. Manolov, Ilya Altukhov, Regina Khazigaleeva, A. V. Seredina, Sergey I. Kovalchuk, Rustam H. Ziganshin, В. Г. Згода, Svetlana E. Novikova, Tatiana A. Semashko, D. K. Slizhikova, Vasilij V Ptushenko, A. Yu. Gorbachev, Vadim M. Govorun, В. Т. Иванов
Software Mentions: 3
Published: almost 12 years ago

10.1038/s41598-020-65593-x

Detrimental effects of flame retardant, PBB153, exposure on sperm and future generations
Cited by: 29
Author(s): Katherine W. Greeson, Kristen L. Fowler, Paige M. Estave, S. Kate Thompson, Chelsea Wagner, R. Clayton Edenfield, Krista Maye Symosko, Alyse N. Steves, M. Elizabeth Marder, Metrecia L. Terrell, Hillary Barton, Michael Koval, Michele Marcus, Charles A. Easley
Software Mentions: 3
Published: over 6 years ago

10.1371/journal.pone.0183526

Transcriptomic profile of cystic fibrosis patients identifies type I interferon response and ribosomal stalk proteins as potential modifiers of disease severity
Cited by: 23
Author(s): Michael Kormann, Alexander Dewerth, Felizitas A. Eichner, Praveen Baskaran, Andreas Hector, Nicolas Regamey, Dominik Hartl, Rupert Handgretinger, Justin S. Antony
Software Mentions: 3
Published: about 9 years ago

10.1186/s12864-021-07407-6

High-pressure processing-induced transcriptome response during recovery of Listeria monocytogenes
Cited by: 14
Author(s): Ilhan Cem Duru, Florentina Ionela Bucur, Margarita Andreevskaya, Bahareh Nikparvar, Anne Ylinen, Leontina Grigore‐Gurgu, Tone Mari Rode, Peter Crauwels, Pia Laine, Lars Paulín, Trond Løvdal, Christian U. Riedel, Nadav Bar, Daniela Borda, Anca Loana Nicolau, Petri Auvinen
Software Mentions: 3
Published: over 5 years ago

10.1038/s41598-020-68187-9

Prostate cancer-derived holoclones: a novel and effective model for evaluating cancer stemness
Cited by: 9
Author(s): Louise Flynn, Martin P. Barr, Anne‐Marie Baird, Paul Smyth, Órla Casey, Gordon Blackshields, John Greene, Stephen R. Pennington, Emily Hams, Padraic G. Fallon, John O’Leary, Orla Sheils, Stephen Finn
Software Mentions: 3
Published: over 6 years ago

10.1186/s12870-019-1802-2

Transcript analyses reveal a comprehensive role of abscisic acid in modulating fruit ripening in Chinese jujube
Cited by: 8
Author(s): Zhang Zhong, C.K. Kang, Shuyi Zhang, Xingang Li
Software Mentions: 3
Published: over 7 years ago

10.1371/journal.pone.0183128

Anguillicola crassus infection affects mRNA expression levels in gas gland tissue of European yellow and silver eel
Cited by: 16
Author(s): Gabriel Schneebauer, Ron P. Dirks, Bernd Pelster
Software Mentions: 3
Published: about 9 years ago

10.1038/s41598-020-61305-7

Root transcriptome reveals efficient cell signaling and energy conservation key to aluminum toxicity tolerance in acidic soil adapted rice genotype
Cited by: 12
Author(s): Wricha Tyagi, Julia S. Yumnam, Debashish Sen, Mayank Rai
Software Mentions: 3
Published: over 6 years ago

10.1186/s12870-021-02825-w

Transcriptional and proteomic insights into phytotoxic activity of interspecific potato hybrids with low glycoalkaloid contents
Cited by: 5
Author(s): Katarzyna Szajko, Jarosław Ciekot, Iwona Wasilewicz‐Flis, Waldemar Marczewski, Dorota Sołtys‐Kalina
Software Mentions: 3
Published: almost 6 years ago

10.1371/journal.pone.0209061

Exploring differentially expressed key genes related to development of follicle by RNA-seq in Peking ducks (Anas Platyrhynchos)
Cited by: 14
Author(s): Jinjun Ren, Changsen Sun, Li Chen, Jianhong Hu, Xuetao Huang, Xiaolin Liu, Lizhi Liu
Software Mentions: 3
Published: over 7 years ago

10.1371/journal.pone.0181399

The antenna transcriptome changes in mosquito Anopheles sinensis, pre- and post- blood meal
Cited by: 14
Author(s): Qian Chen, Di Pei, Jianyong Li, Chengyu Jing, Wenjian Wu, Yahui Man
Software Mentions: 3
Published: over 9 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

10.1038/s41598-020-62150-4

Genome sequencing of Rigidoporus microporus provides insights on genes important for wood decay, latex tolerance and interspecific fungal interactions
Cited by: 15
Author(s): Abbot O. Oghenekaro, Andriy Kovalchuk, Tommaso Raffaello, Susana Camarero, Markus Gressler, Bernard Henrissat, Juna Lee, Mengxia Liu, Ángel T. Martı́nez, Otto Miettinen, Sirma Mihaltcheva, Jasmyn Pangilinan, Fei Ren, Robert Riley, Francisco J. Ruiz‐Dueñas, Ana Serrano, Michael R. Thon, Zilan Wen, Zhen Zeng, Kerrie Barry, I. V. Grigoriev, Francis Martin, Fred O. Asiegbu
Software Mentions: 3
Published: over 6 years ago

10.1371/journal.pone.0185062

Intercalated disc in failing hearts from patients with dilated cardiomyopathy: Its role in the depressed left ventricular function
Cited by: 13
Author(s): Ana Ortega, Estefanía Tarazón, Carolina Gil-Cayuela, María García‐Manzanares, Luis Martínez‐Dolz, Francisca Lago, José Ramón González-Juanatey, Juan Cinca, Esther Jorge, Manuel Portolés, Esther Roselló‐Lletí, Miguel Rivera
Software Mentions: 3
Published: about 9 years ago

10.1038/s41598-019-50618-x

Comparisons of lung and gluteus transcriptome profiles between yaks at different ages
Cited by: 1
Author(s): Jinwei Xin, Zhixin Chai, Chengfu Zhang, Qiang Zhang, Yong Zhu, Hanwen Cao, Qiumei Ji, Jincheng Zhong
Software Mentions: 3
Published: about 7 years ago

10.1186/s12864-020-6477-4

Transcriptome profiling of laser-captured germ cells and functional characterization of zbtb40 during 17alpha-methyltestosterone-induced spermatogenesis in orange-spotted grouper (Epinephelus coioides)
Cited by: 12
Author(s): Xi Wu, Yang Yang, Chaoyue Zhong, Yin Guo, Shuisheng Li, Haoran Lin, Xiaochun Liu
Software Mentions: 3
Published: almost 7 years ago

10.1038/s41598-019-51535-9

Transcriptomic analysis reveals potential genes involved in tanshinone biosynthesis in Salvia miltiorrhiza
Cited by: 29
Author(s): Yuan‐Jen Chang, Meizhen Wang, Jiang Li, Shanfa Lu
Software Mentions: 3
Published: about 7 years ago

10.1371/journal.pone.0214703

Characterization of genes and alleles involved in the control of flowering time in grapevine
Cited by: 7
Author(s): Nadia Kamal, Iris Ochßner, Anna Schwandner, Prisca Viehöver, Ludger Hausmann, Reinhard Töpfer, Bernd Weißhaar, Daniela Holtgräwe
Software Mentions: 3
Published: over 7 years ago

10.1371/journal.pone.0105004

Transcriptomic Analysis of Tail Regeneration in the Lizard Anolis carolinensis Reveals Activation of Conserved Vertebrate Developmental and Repair Mechanisms
Cited by: 111
Author(s): Elizabeth Hutchins, Glenn J. Markov, Walter L. Eckalbar, Rajani M. George, Jesse M. King, Minami Tokuyama, Lauren A. Geiger, Nataliya Emmert, Michael Ammar, April N. Allen, Ashley L. Siniard, Jason J. Corneveaux, Rebecca E. Fisher, Juli Wade, Dale F. DeNardo, J. Alan Rawls, Matthew J. Huentelman, Jeanne Wilson‐Rawls, Kenro Kusumi
Software Mentions: 3
Published: about 12 years ago

10.1371/journal.pone.0169646

TGF-β3 Inhibits Antibody Production by Human B Cells
Cited by: 28
Author(s): Yoshiaki Tsuchida, Shuji Sumitomo, Kazuyoshi Ishigaki, Akari Suzuki, Yuta Kochi, Haruka Tsuchiya, Ota M, Takashi Komai, Mariko Inoue, Kaoru Morita, Tomohisa Okamura, Kazuhiko Yamamoto, Keishi Fujio
Software Mentions: 3
Published: almost 10 years ago

10.1371/journal.pone.0211913

Comparative transcriptome analysis of resistant and susceptible kiwifruits in response to Pseudomonas syringae pv. Actinidiae during early infection
Cited by: 17
Author(s): Yun‐Chun Song, Lei Sun, Miaomiao Lin, Jinyong Chen, Xiujuan Qi, Chun-Gen Hu, Jinbao Fang
Software Mentions: 3
Published: over 7 years ago

10.1186/s12870-017-1188-y

Physiological and transcriptomic responses in the seed coat of field-grown soybean (Glycine max L. Merr.) to abiotic stress
Cited by: 25
Author(s): Courtney P. Leisner, Craig R. Yendrek, Elizabeth A. Ainsworth
Software Mentions: 3
Published: almost 9 years ago

10.1038/s41598-020-60656-5

Genomic alterations and abnormal expression of APE2 in multiple cancers
Cited by: 20
Author(s): Katherine A. Jensen, Xinghua Shi, Yan Shen Shan
Software Mentions: 3
Published: over 6 years ago

10.1038/s41598-020-68437-w

Injection of seminal fluid into the hemocoel of honey bee queens (Apis mellifera) can stimulate post-mating changes
Cited by: 9
Author(s): W. Cameron Jasper, Laura M. Brutscher, Christina M. Grozinger, Elina L. Niño
Software Mentions: 3
Published: over 6 years ago

10.1038/s41598-019-44600-w

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

10.1038/s41598-019-43277-5

Comparative transcriptome profiling of multi-ovary wheat under heterogeneous cytoplasm suppression
Cited by: 1
Author(s): Jialin Guo, Gaisheng Zhang, Yulong Song, Shen Ma, Na Niu, Junwei Wang
Software Mentions: 3
Published: over 7 years ago

10.1038/s41598-019-45126-x

Combating viral contaminants in CHO cells by engineering innate immunity
Cited by: 13
Author(s): Austin W. T. Chiang, Shangzhong Li, Benjamin P. Kellman, Gouri Chattopadhyay, Yaqin Zhang, Chih Chung Kuo, Jahir M. Gutierrez, Faezeh Ghazi, Hana Schmeisser, Patrice Ménard, Sara Petersen Bjørn, Bjørn Gunnar Voldborg, Amy S. Rosenberg, Montserrat Puig, Nathan E. Lewis
Software Mentions: 3
Published: over 7 years ago

10.1038/s41598-019-44305-0

Variable protein homeostasis in housekeeping and non-housekeeping pathways under mycotoxins stress
Cited by: 6
Author(s): Yu Sun, Jikai Wen, Ruohong Chen, Yiqun Deng
Software Mentions: 3
Published: over 7 years ago

10.1371/journal.pone.0100930

Response of the Hepatic Transcriptome to Aflatoxin B1 in Domestic Turkey (Meleagris gallopavo)
Cited by: 28
Author(s): Melissa S. Monson, Robert E. Settlage, K. Wyatt McMahon, Kristelle M. Mendoza, Sumit Rawal, Hani El-Nezami, Roger A. Coulombe, Kent M. Reed
Software Mentions: 3
Published: over 12 years ago

10.1002/ece3.4573

Social environment affects the transcriptomic response to bacteria in ant queens
Cited by: 6
Author(s): Lumi Viljakainen, Jaana Jurvansuu, Ida Holmberg, Tobias Pamminger, Silvio Erler, Sylvia Cremer
Software Mentions: 3
Published: about 8 years ago

10.1038/s41598-019-45817-5

The Fungal Histone Acetyl Transferase Gcn5 Controls Virulence of the Human Pathogen Candida albicans through Multiple Pathways
Cited by: 34
Author(s): Raju Shivarathri, Michael Tscherner, Florian Zwolanek, Nitesh Kumar Singh, Neeraj Chauhan, Karl Kuchler
Software Mentions: 3
Published: over 7 years ago

10.1038/s41598-019-42608-w

Gene co-expression networks contributing to the expression of compensatory growth in metabolically active tissues in cattle
Cited by: 9
Author(s): Kate Keogh, David A. Kenny, Sinéad M. Waters
Software Mentions: 3
Published: over 7 years ago

10.1186/1471-2164-15-960

Lassa and Marburg viruses elicit distinct host transcriptional responses early after infection
Cited by: 27
Author(s): Ignacio Caballero, Judy Yen, Lisa E. Hensley, Anna N. Honko, Arthur J. Goff, John H. Connor
Software Mentions: 3
Published: almost 13 years ago

10.1038/s41598-019-42170-5

Comparative transcriptome profiling of low light tolerant and sensitive rice varieties induced by low light stress at active tillering stage
Cited by: 30
Author(s): Sudhanshu Sekhar, Darshan Panda, Jitendra Kumar, Nihar Nalini Mohanty, Monalisha Biswal, M. J. Baig, Awadhesh Kumar, Umakanta Ngangkham, Sanghamitra Samantaray, Sharat Kumar Pradhan, Birendra Prasad Shaw, Padmini Swain, Lambodar Behera
Software Mentions: 3
Published: over 7 years ago

10.1371/journal.pone.0180824

An integrative genomics approach identifies novel pathways that influence candidaemia susceptibility
Cited by: 20
Author(s): Vasiliki Matzaraki, Mark S. Gresnigt, Martin Jaeger, Isis Ricaño-Ponce, Melissa D. Johnson, Marije Oosting, Lude Franke, Sebo Withoff, John R. Perfect, Leo A. B. Joosten, Bart Jan Kullberg, Frank L. van de Veerdonk, Iris Jonkers, Yang Li, Cisca Wijmenga, Mihai G. Netea, Vinod Kumar
Software Mentions: 3
Published: over 9 years ago

10.1186/s12870-021-03041-2

Genome-wide association study and transcriptome analysis discover new genes for bacterial leaf blight resistance in rice (Oryza sativa L.)
Cited by: 10
Author(s): Xinyue Shu, Ai‐Jun Wang, Bo Jiang, Yuqi Jiang, Xiang Xiao, Xiaoqun Yi, Shuangcheng Li, Qi Deng, Yunlong Wang, Jun Zhu, Yueyang Liang, Huainian Liu, Ting Zou, Lingxia Wang, Ping Li, Aiping Zheng
Software Mentions: 3
Published: over 5 years ago

10.18632/aging.101485

Regulatory RNA binding proteins contribute to the transcriptome-wide splicing alterations in human cellular senescence
Cited by: 13
Author(s): Qiongye Dong, Lei Wei, Michael Q. Zhang, Xiaowo Wang
Software Mentions: 3
Published: over 8 years ago

10.1038/s41598-019-43354-9

Analysis by RNA-seq of transcriptomic changes elicited by heat shock in Leishmania major
Cited by: 20
Author(s): Alberto Rastrojo, Laura Corvo, Rodrigo Lombraña, José Carlos Solana, Begoña Aguado, José Marı́a Requena
Software Mentions: 3
Published: over 7 years ago

10.1186/s12870-016-0836-y

Vine nitrogen status and volatile thiols and their precursors from plot to transcriptome level
Cited by: 24
Author(s): Pierre Helwi, Sabine Guillaumie, Cécile Thibon, Céline Keime, Aude Habran, Ghislaine Hilbert, Éric Gomès, Philippe Darriet, Serge Delrot, Cornelis van Leeuwen
Software Mentions: 3
Published: over 10 years ago

Projects: pypi: HTSeq

Science Score: 65/100

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Papers Mentioning HTSeq 3,071