pypi: TopHat | Projects | Ecosyste.ms: Papers

10.1371/journal.pone.0014040

Integrated Genetic and Epigenetic Analysis Identifies Haplotype-Specific Methylation in the FTO Type 2 Diabetes and Obesity Susceptibility Locus
Cited by: 223
Author(s): Christopher G. Bell, Sarah Finer, Cecilia M. Lindgren, Gareth A. Wilson, Vardhman K. Rakyan, Andrew E. Teschendorff, Pelin Akan, Elia Stupka, Thomas A. Down, Inga Prokopenko, Ian M. Morison, Jonathan Mill, Ruth Pidsley, Panos Deloukas, Timothy M. Frayling, Andrew T. Hattersley, Mark I. McCarthy, Stephan Beck, G. A. Hitman
Software Mentions: 1
Published: over 14 years ago

10.1371/journal.pone.0160197

Identification of Novel Transcribed Regions in Zebrafish (Danio rerio) Using RNA-Sequencing
Cited by: 3
Author(s): Jingwen Wang, Liselotte Vesterlund, Juha Kere, Hong Jiao
Software Mentions: 1
Published: about 9 years ago

10.1371/journal.pone.0030630

Transcriptome Analysis of the Model Protozoan, Tetrahymena thermophila, Using Deep RNA Sequencing
Cited by: 108
Author(s): Jie Xiong, Xianbo Lu, Zhemin Zhou, Yue Chang, Dan Yuan, Miao Tian, Zhigang Zhou, Lei Wang, Chengjie Fu, Eduardo Orias, Wei Miao
Software Mentions: 1
Published: over 13 years ago

10.1371/journal.pone.0194445

Effect of dietary restriction and subsequent re-alimentation on the transcriptional profile of bovine jejunal epithelium
Cited by: 12
Author(s): Kate Keogh, Sinéad M. Waters, Paul Cormican, A. K. Kelly, David A. Kenny
Software Mentions: 1
Published: over 7 years ago

10.1371/journal.pone.0171858

Endometrial factors similarly induced by IFNT2 and IFNTc1 through transcription factor FOXS1
Cited by: 15
Author(s): Kaoru Kusama, Rulan Bai, Keigo Nakamura, Sayaka Okada, Jiro Yasuda, Kazuhiko Imakawa
Software Mentions: 1
Published: over 8 years ago

10.1371/journal.pone.0205878

Next-Generation Sequencing and Quantitative Proteomics of Hutchinson-Gilford progeria syndrome-derived cells point to a role of nucleotide metabolism in premature aging
Cited by: 15
Author(s): Jesús Mateos, Juan Fafián-Labora, Miriam Morente-López, Iván Lesende-Rodríguez, Lorenzo Monserrat, María Antonia Odena, Eliandre de Oliveira, Javier de Toro, M.C. Arufe
Software Mentions: 1
Published: over 6 years ago

10.1371/journal.pone.0066267

Comparative Transcriptome Analysis of Adipose Tissues Reveals that ECM-Receptor Interaction Is Involved in the Depot-Specific Adipogenesis in Cattle
Cited by: 72
Author(s): Hyun-Jeong Lee, Mi Jang, Hyeongmin Kim, Woori Kwak, WonCheoul Park, Jin-Hee Hwang, Chang Kyu Lee, Gul Won Jang, Mi Na Park, Hyeong–Cheol Kim, Jin Young Jeong, Kang Seok Seo, Heebal Kim, Seoae Cho, Bo-Young Lee
Software Mentions: 1
Published: about 12 years ago

10.1371/journal.pone.0164041

The Ser82 RAGE Variant Affects Lung Function and Serum RAGE in Smokers and sRAGE Production In Vitro
Cited by: 34
Author(s): Suzanne Miller, Amanda Henry, Emily Hodge, Alexander K. Kheirallah, Charlotte K. Billington, Tracy L. Rimington, Sangita Bhaker, Ma’en Obeidat, Erik Melén, Simon Kebede Merid, Caroline Swan, Catherine Gowland, Carl P. Nelson, Ceri E. Stewart, Charlotte E Bolton, Iain Kilty, Anders Mälarstig, Stuart G. Parker, Miriam F. Moffatt, Andrew J. Wardlaw, Ian P. Hall, Ian Sayers
Software Mentions: 1
Published: almost 9 years ago

10.1371/journal.pone.0033071

Maize (Zea mays L.) Genome Diversity as Revealed by RNA-Sequencing
Cited by: 143
Author(s): Candice N. Hansey, Brieanne Vaillancourt, Rajandeep S. Sekhon, Natalia de León, Shawn M. Kaeppler, C. Robin Buell
Software Mentions: 1
Published: over 13 years ago

10.1371/journal.pone.0139134

Comparisons of the Effects of Elevated Vapor Pressure Deficit on Gene Expression in Leaves among Two Fast-Wilting and a Slow-Wilting Soybean
Cited by: 14
Author(s): Mura Jyostna Devi, Thomas R. Sinclair, Earl Taliercio
Software Mentions: 1
Published: almost 10 years ago

10.1371/journal.pone.0145836

Mitochondrial Dysfunction Plus High-Sugar Diet Provokes a Metabolic Crisis That Inhibits Growth
Cited by: 26
Author(s): Esko Kemppainen, Jack George, Görkem Garipler, Tea Tuomela, Essi Kiviranta, Tomoyoshi Soga, Cory D. Dunn, Howard T. Jacobs
Software Mentions: 1
Published: over 9 years ago

10.1371/journal.pone.0095877

Comparison of Five Major Trichome Regulatory Genes in Brassica villosa with Orthologues within the Brassicaceae
Cited by: 8
Author(s): Naghabushana K. Nayidu, Sateesh Kagale, Ali Taheri, Thushan S. Withana-Gamage, Isobel A. P. Parkin, Andrew Sharpe, Margaret Y. Gruber
Software Mentions: 1
Published: over 11 years ago

10.1371/journal.pone.0152824

Involvement of Alternative Splicing in Barley Seed Germination
Cited by: 40
Author(s): Qisen Zhang, Xiaoqi Zhang, Songbo Wang, Cong Tan, Gaofeng Zhou, Chengdao Li
Software Mentions: 1
Published: over 9 years ago

10.1038/s41598-018-34320-y

Exogenous Pi supplementation improved the salt tolerance of maize (Zea mays L.) by promoting Na+ exclusion
Cited by: 19
Author(s): Yong Sun, Chunhua Mu, Haixue Zheng, Shouping Lu, Hua Zhang, Xuecai Zhang, Xia Liu
Software Mentions: 1
Published: over 6 years ago

10.1186/s12864-020-07337-9

Comparative transcriptome analysis uncovers roles of hydrogen sulfide for alleviating cadmium toxicity in Tetrahymena thermophila
Cited by: 9
Author(s): Hongrui Lv, Jing Xu, Bo Tao, Wei Wang
Software Mentions: 1
Published: over 4 years ago

10.1371/journal.pone.0068907

Changes in the Transcriptome of the Human Endometrial Ishikawa Cancer Cell Line Induced by Estrogen, Progesterone, Tamoxifen, and Mifepristone (RU486) as Detected by RNA-Sequencing
Cited by: 40
Author(s): Karin Tamm-Rosenstein, Jaak Simm, Marina Suhorutshenko, Andres Salumets, Madis Metsis
Software Mentions: 1
Published: about 12 years ago

10.1038/s41598-018-34318-6

Drought-induced susceptibility for Cenangium ferruginosum leads to progression of Cenangium-dieback disease in Pinus koraiensis
Cited by: 13
Author(s): Minji Ryu, Ratnesh Chandra Mishra, Junhyun Jeon, Sun Keun Lee, Hyeun‐Jong Bae
Software Mentions: 1
Published: over 6 years ago

10.1186/1471-2164-11-663

Rnnotator: an automated de novo transcriptome assembly pipeline from stranded RNA-Seq reads
Cited by: 198
Author(s): Jeffrey A. Martin, Vincent M. Bruno, Zhide Fang, Xiangru Meng, Matthew J. Blow, Tao Zhang, Gavin Sherlock, M Snyder, Wang Zhong
Software Mentions: 1
Published: over 14 years ago

10.1371/journal.pone.0124597

ZNF804A Transcriptional Networks in Differentiating Neurons Derived from Induced Pluripotent Stem Cells of Human Origin
Cited by: 30
Author(s): Jian Chen, Mingyan Lin, Anastasia Hrabovsky, Erika Pedrosa, Jason Dean, Swati Jain, Deyou Zheng, Herbert M. Lachman
Software Mentions: 1
Published: over 10 years ago

10.1186/s12864-015-1922-5

Exploration of alternative splicing events in ten different grapevine cultivars
Cited by: 21
Author(s): Emilio Potenza, Marco Racchi, Lieven Sterck, E. Coller, Elisa Asquini, Silvio C. E. Tosatto, Riccardo Velasco, Yves Van de Peer, Alessandro Cestaro
Software Mentions: 1
Published: almost 10 years ago

10.1371/journal.pone.0149373

Effect of Dietary Restriction and Subsequent Re-Alimentation on the Transcriptional Profile of Bovine Skeletal Muscle
Cited by: 27
Author(s): Kate Keogh, David A. Kenny, Paul Cormican, Matthew S. McCabe, A. K. Kelly, Sinéad M. Waters
Software Mentions: 1
Published: over 9 years ago

10.1371/journal.pone.0230680

Transcriptome analysis of the edible mushroom Lentinula edodes in response to blue light
Cited by: 16
Author(s): Jae Yoon Kim, Dae Yeon Kim, Youn‐Jin Park, Myoung-Jun Jang
Software Mentions: 1
Published: over 5 years ago

10.1371/journal.pone.0180478

PLATINUM SENSITIVE 2 LIKE impacts growth, root morphology, seed set, and stress responses
Cited by: 12
Author(s): Amr R.A. Kataya, Maria T. Creighton, Toga Pangihotan Napitupulu, Christine Sætre, Behzad Shiroud Heidari, Peter Ruoff, Cathrine Lillo
Software Mentions: 1
Published: about 8 years ago

10.1371/journal.pone.0097814

Characterization of Natural Antisense Transcript, Sclerotia Development and Secondary Metabolism by Strand-Specific RNA Sequencing of Aspergillus flavus
Cited by: 14
Author(s): Xuecheng Wu, Bin Zhou, Chang Yin, Yong Guo, Ying Lin, Li Pan, Bin Wang
Software Mentions: 1
Published: about 11 years ago

10.1038/s41598-018-35202-z

Expression profiling of lncRNAs and mRNAs reveals regulation of muscle growth in the Pacific abalone, Haliotis discus hannai
Cited by: 8
Author(s): Jianfang Huang, Xuan Luo, Liting Zeng, Zekun Huang, Meng Huang, You Wang, Caihuan Ke
Software Mentions: 1
Published: over 6 years ago

10.1186/s12859-020-03824-8

Identification of novel alternative splicing biomarkers for breast cancer with LC/MS/MS and RNA-Seq
Cited by: 8
Author(s): Fan Zhang, Chris K. Deng, Mu Wang, Bin Deng, Robert C. Barber, Gang Huang
Software Mentions: 1
Published: over 4 years ago

10.1371/journal.pone.0189911

Bazedoxifene and conjugated estrogen combination maintains metabolic homeostasis and benefits liver health
Cited by: 11
Author(s): Karen Lee Ann Chen, Yijia Zhao, Kadriye Hieronymi, Brandi Patrice Smith, Zeynep Madak-Erdoğan
Software Mentions: 1
Published: over 7 years ago

10.1371/journal.pone.0165980

Glucose Starvation Alters Heat Shock Response, Leading to Death of Wild Type Cells and Survival of MAP Kinase Signaling Mutant
Cited by: 5
Author(s): Nora Plesofsky, Lee Ann Higgins, Todd W. Markowski, Robert Brambl
Software Mentions: 1
Published: over 8 years ago

10.1371/journal.pone.0149702

Comparative Transcriptomic Analysis of Primary Duck Hepatocytes Provides Insight into Differential Susceptibility to DHBV Infection
Cited by: 5
Author(s): Yan Liang, Su Qu, Gang Liu, Lei Liu, Yao Yu, Guohui Ding, Yanfeng Zhao, Yixue Li, Youhua Xie, Junqi Zhang, Di Qu
Software Mentions: 1
Published: over 9 years ago

10.1038/s41598-018-36304-4

Primula vulgaris (primrose) genome assembly, annotation and gene expression, with comparative genomics on the heterostyly supergene
Cited by: 33
Author(s): Jonathan M. Cocker, Jonathan Wright, Jinhong Li, David Swarbreck, Sarah Dyer, Mario Cáccamo, Philip M. Gilmartin
Software Mentions: 1
Published: over 6 years ago

10.1371/journal.pone.0208659

The mouse KLF1 Nan variant impairs nuclear condensation and erythroid maturation
Cited by: 9
Author(s): Ileana Cantú, Harmen J.G. van de Werken, Nynke Gillemans, Ralph Stadhouders, Steven Heshusius, Alex Maas, Fatemehsadat Esteghamat, Zeliha Őzgűr, Wilfred F. J. van IJcken, Frank Grosveld, Marieke von Lindern, Sjaak Philipsen, Thamar B. van Dijk
Software Mentions: 1
Published: over 6 years ago

10.1186/s12864-019-5430-x

Comparative transcriptomic analysis unveils interactions between the regulatory CarS protein and light response in Fusarium
Cited by: 14
Author(s): Macarena Ruger-Herreros, Obdulia Parra-Rivero, Javier Pardo-Medina, Francisco J. Romero–Campero, M. Carmen Limón, Javier Ávalos
Software Mentions: 1
Published: over 6 years ago

10.1371/journal.pone.0159638

Identification and Classification of New Transcripts in Dorper and Small-Tailed Han Sheep Skeletal Muscle Transcriptomes
Cited by: 13
Author(s): Tianle Chao, Guizhi Wang, Jianmin Wang, Zhaohua Liu, Zhibin Ji, Lei Hou, Chunlan Zhang
Software Mentions: 1
Published: about 9 years ago

10.1038/s41598-018-36484-z

Thermopriming reprograms metabolic homeostasis to confer heat tolerance
Cited by: 58
Author(s): Natalia Serrano, Lexiang Yu, Ahmed Bahieldin, Magdy M. Mahfouz
Software Mentions: 1
Published: over 6 years ago

10.1038/s41598-018-36693-6

Mitochondrial and chloroplast genomes provide insights into the evolutionary origins of quinoa (Chenopodium quinoa Willd.)
Cited by: 25
Author(s): Peter J. Maughan, Lindsay Chaney, Damien J. Lightfoot, Brian J. Cox, Mark Tester, Eric N. Jellen, David E. Jarvis
Software Mentions: 1
Published: over 6 years ago

10.1038/s41598-018-36607-6

Smooth Muscle Transcriptome Browser: offering genome-wide references and expression profiles of transcripts expressed in intestinal SMC, ICC, and PDGFRα+ cells
Cited by: 15
Author(s): Adrienne Breland, Se Eun Ha, Brian G. Jorgensen, Byungchang Jin, Treg A. Gardner, Kenton M. Sanders, Seungil Ro
Software Mentions: 1
Published: over 6 years ago

10.1371/journal.pone.0076572

RNA-Seq Reveals Differential Gene Expression in Staphylococcus aureus with Single-Nucleotide Resolution
Cited by: 16
Author(s): Joseph Osmundson, Scott Dewell, Seth A. Darst
Software Mentions: 1
Published: almost 12 years ago

10.1371/journal.pone.0188001

Developmentally regulated internal transcription initiation during meiosis in budding yeast
Cited by: 14
Author(s): Sai Zhou, Rolf Sternglanz, Aaron M. Neiman
Software Mentions: 1
Published: over 7 years ago

10.1186/s12864-016-2510-z

A transcriptomic insight into the infective juvenile stage of the insect parasitic nematode, Heterorhabditis indica
Cited by: 12
Author(s): Vishal Singh Somvanshi, Shachi Gahoi, Prakash Banakar, Prasoon Kumar Thakur, Mukesh Kumar, Manisha R. Sajnani, Priyatama Pandey, Uma Rao
Software Mentions: 1
Published: over 9 years ago

10.1371/journal.pone.0124877

RNA-Seq Analysis of the Host Response to Staphylococcus aureus Skin and Soft Tissue Infection in a Mouse Model
Cited by: 20
Author(s): Rebecca A. Brady, Vincent M. Bruno, Drusilla L Burns
Software Mentions: 1
Published: over 10 years ago

10.1371/journal.pone.0156038

Differential Expression of Extracellular Matrix and Adhesion Molecules in Fetal-Origin Amniotic Epithelial Cells of Preeclamptic Pregnancy
Cited by: 25
Author(s): Myung Sun Kim, Ji Hea Yu, Min Young Lee, Ah Leum Kim, Mi Hyun Jo, Min Gi Kim, Sung Rae Cho, Young Han Kim
Software Mentions: 1
Published: about 9 years ago

10.1371/journal.pone.0192082

Shared and organism-specific host responses to childhood diarrheal diseases revealed by whole blood transcript profiling
Cited by: 20
Author(s): Hannah A. DeBerg, Mussaret B. Zaidi, Matthew C. Altman, Prasong Khaenam, Vivian H. Gersuk, Freddy D. Campos, Iza Pérez‐Martínez, Mario Meza-Segura, Damien Chaussabel, Jacques Banchereau, Teresa Estrada-García, Peter S. Linsley
Software Mentions: 1
Published: over 7 years ago

10.1371/journal.pone.0057563

The Baboon Kidney Transcriptome: Analysis of Transcript Sequence, Splice Variants, and Abundance
Cited by: 22
Author(s): Kimberly D. Spradling, Jeremy P. Glenn, Roy Garcia, Robert E. Shade, Laura A. Cox
Software Mentions: 1
Published: over 12 years ago

10.1371/journal.pone.0117581

Discovery of Molecular Markers to Discriminate Corneal Endothelial Cells in the Human Body
Cited by: 25
Author(s): Masahito Yoshihara, Hiroko Ohmiya, Shotaro Hara, Satoshi Kawasaki, Yoshihide Hayashizaki, Masayoshi Itoh, Hideya Kawaji, Motokazu Tsujikawa, Kohji Nishida
Software Mentions: 1
Published: over 10 years ago

10.1371/journal.pone.0133923

Calorie Restriction Suppresses Age-Dependent Hippocampal Transcriptional Signatures
Cited by: 53
Author(s): Marissa J. Schafer, Igor Dolgalev, Melissa J. Alldred, Adriana Heguy, Stephen D. Ginsberg
Software Mentions: 1
Published: about 10 years ago

10.1371/journal.pone.0200914

Studying on the strictly self-compatibility mechanism of ‘Liuyefeitao’ peach (Prunus persica L.)
Cited by: 2
Author(s): Wei Liu, Mao-Song Pei, Anning Zhang
Software Mentions: 1
Published: almost 7 years ago

10.1371/journal.pone.0164959

Deciphering Transcriptional Programming during Pod and Seed Development Using RNA-Seq in Pigeonpea (Cajanus cajan)
Cited by: 10
Author(s): Lekha T. Pazhamala, Gaurav Agarwal, Prasad Bajaj, Vinay Kumar, Akanksha Kulshreshtha, Rachit K. Saxena, Rajeev K. Varshney
Software Mentions: 1
Published: almost 9 years ago

10.1186/1471-2164-15-1071

Highly expressed captured genes and cross-kingdom domains present in Helitrons create novel diversity in Pleurotus ostreatus and other fungi
Cited by: 20
Author(s): Raúl Castanera, Gúmer Pérez, Leticia Rodríguez López, Rubén Sancho, Francisco Santoyo, Manuel Alfaro, Toni Gabaldón, Antonio G. Pisabarro, José A. Oguiza, Lucı́a Ramı́rez
Software Mentions: 1
Published: over 10 years ago

10.1371/journal.pone.0137551

Bioinformatics-Based Identification of MicroRNA-Regulated and Rheumatoid Arthritis-Associated Genes
Cited by: 19
Author(s): Yi-Jiang Song, Guiling Li, Jun He, Yao Guo, Yang Li
Software Mentions: 1
Published: almost 10 years ago

10.1371/journal.pone.0141470

The TrxG Complex Mediates Cytokine Induced De Novo Enhancer Formation in Islets
Cited by: 8
Author(s): Bryan Tennant, Peter Eliol Hurley, Jasmine Dhillon, Amol Gill, Cheryl J. Whiting, Brad G. Hoffman
Software Mentions: 1
Published: almost 10 years ago

10.1371/journal.pone.0187424

Beyond the polymerase-γ theory: Production of ROS as a mode of NRTI-induced mitochondrial toxicity
Cited by: 23
Author(s): Reuben L. Smith, Josephine M.E. Tan, Martijs J. Jonker, Aldo Jongejan, Thomas Buissink, Steve Veldhuijzen, Antoine H. C. van Kampen, Stanley Brul, Hans van der Spek
Software Mentions: 1
Published: over 7 years ago

10.1371/journal.pone.0103774

MALT1 Auto-Proteolysis Is Essential for NF-κB-Dependent Gene Transcription in Activated Lymphocytes
Cited by: 61
Author(s): Mathijs Baens, Luca Bonsignore, Riet Somers, Charlotte Vanderheydt, S.D. Weeks, Jenny Gunnarsson, Elin Nilsson, Robert Roth, Margot Thome, Peter Marynen
Software Mentions: 1
Published: almost 11 years ago

10.1371/journal.pone.0092720

A Designed Experiments Approach to Optimization of Automated Data Acquisition during Characterization of Bacteria with MALDI-TOF Mass Spectrometry
Cited by: 22
Author(s): Lin Zhang, Connie M. Borror, Todd R. Sandrin
Software Mentions: 1
Published: over 11 years ago

10.1038/s41598-018-37124-2

RgsD negatively controls development, toxigenesis, stress response, and virulence in Aspergillus fumigatus
Cited by: 15
Author(s): Young Kim, Minwoo Lee, Sang-Cheol Jun, Youngjoon Choi, Jae‐Hyuk Yu, Kwang‐Soo Shin
Software Mentions: 1
Published: over 6 years ago

10.1371/journal.pone.0066131

A Novel Strategy to Increase the Proliferative Potential of Adult Human β-Cells While Maintaining Their Differentiated Phenotype
Cited by: 30
Author(s): Haytham Aly, Nidhi Rohatgi, Connie A. Marshall, Tiffani C. Grossenheider, Hiroyuki Miyoshi, Thaddeus S. Stappenbeck, Scot J. Matkovich, Michael L. McDaniel
Software Mentions: 1
Published: about 12 years ago

10.1371/journal.pone.0240279

Transcriptome analysis reveals defense-related genes and pathways against Xanthomonas campestris pv. vesicatoria in pepper (Capsicum annuum L.)
Cited by: 15
Author(s): Shenghua Gao, Fei Wang, Niran Juntawong, Ning Li, Yanxu Yin, Changlong Yu, Jiao Chen, Meicun Yao
Software Mentions: 1
Published: over 4 years ago

10.1186/s12859-016-1307-z

ChARM: Discovery of combinatorial chromatin modification patterns in hepatitis B virus X-transformed mouse liver cancer using association rule mining
Cited by: 2
Author(s): Sung Hee Park, Sun Min Lee, Young-Joon Kim, Sang Soo Kim
Software Mentions: 1
Published: over 8 years ago

10.1371/journal.pone.0180825

OsMPH1 regulates plant height and improves grain yield in rice
Cited by: 57
Author(s): Yongxing Zhang, Chunsheng Yu, Juan Lin, Jun Liu, Bin Liu, Jian Wang, Aobo Huang, Hongyu Li, Tao Zhao
Software Mentions: 1
Published: about 8 years ago

10.1371/journal.pone.0052506

Development of Transcriptomic Resources for Interrogating the Biosynthesis of Monoterpene Indole Alkaloids in Medicinal Plant Species
Cited by: 138
Author(s): Elsa Góngora-Castillo, Kevin L. Childs, Greg Fedewa, John Hamilton, David K. Liscombe, Maria Magallanes‐Lundback, Kranthi K. Mandadi, Ezekiel Nims, Weerawat Runguphan, Brieanne Vaillancourt, Marina Varbanova-Herde, Dean DellaPenna, Thomas D. McKnight, Sarah E. O’Connor, C. Robin Buell
Software Mentions: 1
Published: over 12 years ago

10.1186/1471-2164-12-516

The classification of mRNA expression levels by the phosphorylation state of RNAPII CTD based on a combined genome-wide approach
Cited by: 36
Author(s): Jun Odawara, Akihito Harada, Tomohiko Yoshimi, Kazuhira Maehara, Taro Tachibana, Seiji Okada, Koichi Akashi, Yasuyuki Ohkawa
Software Mentions: 1
Published: almost 14 years ago

10.1371/journal.pone.0187186

Arginase expression modulates nitric oxide production in Leishmania (Leishmania) amazonensis
Cited by: 31
Author(s): Stephanie Maia Acuña, Juliana Ide Aoki, Maria Fernanda Laranjeira-Silva, Ricardo Andrade Zampieri, Juliane Cristina Ribeiro Fernandes, Sandra Márcia Muxel, Lucile Maria Floeter‐Winter
Software Mentions: 1
Published: over 7 years ago

10.1371/journal.pone.0189668

Biomarkers for tissue engineering of the tendon-bone interface
Cited by: 22
Author(s): Lara Kuntz, Leone Rossetti, Elena Kunold, Andrea Schmitt, R. von Eisenhart-Rothe, Andreas R. Bausch, Rainer Burgkart
Software Mentions: 1
Published: over 7 years ago

10.1371/journal.pone.0147273

A Genome-Wide mRNA Expression Profile in Caenorhabditis elegans under Prolonged Exposure to 1750MHz Radiofrequency Fields
Cited by: 7
Author(s): Yan Gao, Yiming Lu, Jianming Yi, Zhihui Li, Dawen Gao, Zhoulong Yu, Tongning Wu, Chenggang Zhang
Software Mentions: 1
Published: over 9 years ago

10.1371/journal.pone.0129598

Transcriptomic Analysis Reveals Possible Influences of ABA on Secondary Metabolism of Pigments, Flavonoids and Antioxidants in Tomato Fruit during Ripening
Cited by: 74
Author(s): Wangshu Mou, Dongdong Li, Zisheng Luo, Linchun Mao, Tiejin Ying
Software Mentions: 1
Published: about 10 years ago

10.1371/journal.pone.0134837

Assembly and Analysis of Differential Transcriptome Responses of Hevea brasiliensis on Interaction with Microcyclus ulei
Cited by: 18
Author(s): Uriel Alonso Hurtado Páez, Ibonne Aydee García Romero, Silvia Restrepo, Fabio Ancízar Aristizábal Gutiérrez, Dolly Montoya Castaño
Software Mentions: 1
Published: almost 10 years ago

10.1186/s12864-018-5239-z

Accuracy of RNAseq based SNP discovery and genotyping in Populusnigra
Cited by: 27
Author(s): Odile Rogier, Aurélien Chateigner, Souhila Amanzougarene, Marie-Claude Lesage-Descauses, Sandrine Balzergue, Véronique Brunaud, José Caïus, Ludivine Soubigou‐Taconnat, Véronique Jorge, Vincent Segura
Software Mentions: 1
Published: over 6 years ago

10.1371/journal.pone.0051853

Genome-Wide Transcriptome and Proteome Analysis on Different Developmental Stages of Cordyceps militaris
Cited by: 74
Author(s): Yalin Yin, Guojun Yu, Yijie Chen, Shuai Jiang, Man Wang, Yifei Jin, Xianqing Lan, Yi Liang, Hui Sun
Software Mentions: 1
Published: over 12 years ago

10.1371/journal.pone.0133862

Neurogenin 3 Expressing Cells in the Human Exocrine Pancreas Have the Capacity for Endocrine Cell Fate
Cited by: 41
Author(s): Danielle L. Gomez, Marci O’Driscoll, Timothy P. Sheets, Ralph H. Hruban, José Oberholzer, James J. McGarrigle, Michael J. Shamblott
Software Mentions: 1
Published: almost 10 years ago

10.1186/1471-2164-15-1026

Comparative transcriptome sequencing of tolerant rice introgression line and its parents in response to drought stress
Cited by: 100
Author(s): Liying Huang, Fan Zhang, Wensheng Wang, Yongli Zhou, Binying Fu, Zhikang Li
Software Mentions: 1
Published: over 10 years ago

10.1371/journal.pone.0173059

A transcriptomic survey of Migdolus fryanus (sugarcane rhizome borer) larvae
Cited by: 11
Author(s): Darlan Gonçalves Nakayama, Célio Dias Santos Júnior, Luciano Takeshi Kishi, Rafael Pedezzi, A. C. Santiago, Andréa Soares-Costa, Flávio Henrique-Silva
Software Mentions: 1
Published: over 8 years ago

10.1371/journal.pone.0155304

De Novo Transcriptome Analysis and Detection of Antimicrobial Peptides of the American Cockroach Periplaneta americana (Linnaeus)
Cited by: 41
Author(s): In-Woo Kim, Joon Ha Lee, Sathiyamoorthy Subramaniyam, Eun‐Young Yun, Iksoo Kim, Jun Hyung Park, Jae Sam Hwang
Software Mentions: 1
Published: about 9 years ago

10.1038/s41598-018-38398-2

Transcriptional responses of wheat roots inoculated with Arthrobacter nitroguajacolicus to salt stress
Cited by: 71
Author(s): Maryam Safdarian, Hossein Askari, Vahid Shariati J, Ghorbanali Nematzadeh
Software Mentions: 1
Published: over 6 years ago

10.1371/journal.pone.0233962

Notch3 signaling promotes tumor cell adhesion and progression in a murine epithelial ovarian cancer model
Cited by: 9
Author(s): Jessica C. Price, Elham Azizi, L.A. Naiche, Jenny G. Parvani, Pragya Shukla, Seoyeon Kim, Jill K. Slack‐Davis, Dana Pe’er, Jan Kitajewski
Software Mentions: 1
Published: about 5 years ago

10.1371/journal.pone.0013875

HMMSplicer: A Tool for Efficient and Sensitive Discovery of Known and Novel Splice Junctions in RNA-Seq Data
Cited by: 52
Author(s): Michelle Dimon, Katherine Sorber, Joseph L. DeRisi
Software Mentions: 1
Published: over 14 years ago

10.1186/1471-2105-12-491

MAKER2: an annotation pipeline and genome-database management tool for second-generation genome projects
Cited by: 1,494
Author(s): Carson Holt, Mark Yandell
Software Mentions: 1
Published: over 13 years ago

10.1371/journal.pone.0141220

Deciphering the Developmental Dynamics of the Mouse Liver Transcriptome
Cited by: 34
Author(s): Sumedha Gunewardena, Byunggil Yoo, Lai Peng, Hong Lü, Xiao‐bo Zhong, Curtis D. Klaassen, Julia Yue Cui
Software Mentions: 1
Published: almost 10 years ago

10.1371/journal.pone.0187192

Open housing drives the expression of immune response genes in the nasal mucosa, but not the olfactory bulb
Cited by: 0
Author(s): Carolin Piotrowski, Vera Lede, Anne Butthof, Nicole Kaiser, Petra G. Hirrlinger, Matthias H. Tschöp, Torsten Schöneberg, Ingo Bechmann
Software Mentions: 1
Published: almost 8 years ago

10.1371/journal.pone.0083616

Dynamic Expression of Long Non-Coding RNAs (lncRNAs) in Adult Zebrafish
Cited by: 86
Author(s): Kriti Kaushik, Vincent Elvin Leonard, Shamsudheen Kv, Mukesh Kumar Lalwani, Saakshi Jalali, Ashok Patowary, Adita Joshi, Vinod Scaria, Sridhar Sivasubbu
Software Mentions: 1
Published: over 11 years ago

10.1371/journal.pone.0162363

Sequence Assembly of Yarrowia lipolytica Strain W29/CLIB89 Shows Transposable Element Diversity
Cited by: 64
Author(s): Christophe Magnan, James Yu, Irene Chang, Ethan D. Jahn, Yuzo Kanomata, Jihong Wu, Michael Zeller, Melanie L. Oakes, Pierre Baldi, Suzanne Sandmeyer
Software Mentions: 1
Published: almost 9 years ago

10.1371/journal.pone.0182269

Influence of acclimation to sublethal temperature on heat tolerance of Tribolium castaneum (Herbst) (Coleoptera: Tenebrionidae) exposed to 50°C
Cited by: 13
Author(s): Jianhua Lü, Shuli Liu
Software Mentions: 1
Published: almost 8 years ago

10.1038/s41598-018-37697-y

Comparative transcriptome analysis reveals differentially expressed genes related to the tissue-specific accumulation of anthocyanins in pericarp and aleurone layer for maize
Cited by: 24
Author(s): Tingchun Li, Wei Zhang, Huaying Yang, Qing Dong, Jie Ren, Honghong Fan, Xin Zhang, Yingbing Zhou
Software Mentions: 1
Published: over 6 years ago

10.1371/journal.pone.0094604

Acupuncture Promotes Angiogenesis after Myocardial Ischemia through H3K9 Acetylation Regulation at VEGF Gene
Cited by: 62
Author(s): Shu-ping Fu, Su-Yun He, Bin Xu, Chenyao Hu, Lu Shen, Weixing Shen, Yan Huang, Hao Hong, Qian Li, Ning Wang, Xuan-Liang Liu, Fanrong Liang, Bing-Mei Zhu
Software Mentions: 1
Published: over 11 years ago

10.1371/journal.pone.0065644

PPARβ Regulates Liver Regeneration by Modulating Akt and E2f Signaling
Cited by: 29
Author(s): Hui‐Xin Liu, Yaping Fang, Haoqiang Ying, Frank J. Gonzalez, Jianwen Fang, Yu‐Jui Yvonne Wan
Software Mentions: 1
Published: about 12 years ago

10.18632/oncotarget.17099

Novel transcription-induced fusion RNAs in prostate cancer
Cited by: 10
Author(s): Sen Zhao, Marthe Løvf, Kristina Totland Carm, Anne Cathrine Bakken, Andreas Hoff, Rolf Inge Skotheim
Software Mentions: 1
Published: over 8 years ago

10.1186/1471-2105-12-S11-A7

Oqtans: a Galaxy-integrated workflow for quantitative transcriptome analysis from NGS Data
Cited by: 2
Author(s): Sebastian J. Schultheiß, Géraldine Jean, Jonas Behr, Regina Bohnert, Philipp Drewe, Nico Görnitz, André Kahles, Pramod Kaushik Mudrakarta, Vipin T. Sreedharan, Georg Zeller, Gunnar Rätsch
Software Mentions: 1
Published: over 13 years ago

10.1038/s41598-019-39928-2

Transcriptome analysis of a rice cultivar reveals the differentially expressed genes in response to wild and mutant strains of Xanthomonas oryzae pv. oryzae
Cited by: 18
Author(s): Chunlian Wang, Rezwan Tariq, Zhiyuan Ji, Zheng Wei, Kaili Zheng, Rukmini Mishra, Kun Zhao
Software Mentions: 1
Published: over 6 years ago

10.1371/journal.pone.0166645

A Genome-Wide Transcriptional Analysis of Yeast-Hyphal Transition in Candida tropicalis by RNA-Seq
Cited by: 12
Author(s): Yuan Wu, Yinhu Li, Shuanbao Yu, Wenge Li, Xiao-Shu Liu, Lei Zhao, Jinxing Lu
Software Mentions: 1
Published: over 8 years ago

10.1038/s41598-019-40091-x

Amelogenic transcriptome profiling in ameloblast-like cells derived from adult gingival epithelial cells
Cited by: 7
Author(s): Sun-Yi Hyun, Seyoung Mun, Kyung-Jung Kang, Jong-Chan Lim, Shinyoung Kim, Kyudong Han, Young-Joo Jang
Software Mentions: 1
Published: over 6 years ago

10.1371/journal.pone.0172491

Activation of odorant receptor in colorectal cancer cells leads to inhibition of cell proliferation and apoptosis
Cited by: 49
Author(s): Lea Weber, Klaudia Al-Refae, Juliane Ebbert, Peter Jägers, Janine Altmüller, Christian Becker, Stephan A. Hahn, Günter Gisselmann, Hanns Hatt
Software Mentions: 1
Published: over 8 years ago

10.1186/1471-2105-15-4

Identification of RNA silencing components in soybean and sorghum
Cited by: 38
Author(s): Xiang Liu, Tao Lü, Yongchao Dou, Bin Yu, Chi Zhang
Software Mentions: 1
Published: over 11 years ago

10.1186/1471-2164-15-204

Identification of mycoparasitism-related genes against the phytopathogen Sclerotinia sclerotiorum through transcriptome and expression profile analysis in Trichoderma harzianum
Cited by: 73
Author(s): Andrei Stecca Steindorff, Marcelo Henrique Soller Ramada, Alexandre Siqueira Guedes Coelho, Robert G. Miller, George J. Pappas, Cirano José Ulhôa, Eliane Ferreira Noronha
Software Mentions: 1
Published: over 11 years ago

10.1371/journal.pone.0080816

Comparative Transcriptome Profiling of a Resistant vs. Susceptible Tomato (Solanum lycopersicum) Cultivar in Response to Infection by Tomato Yellow Leaf Curl Virus
Cited by: 104
Author(s): Tianzi Chen, Yuanda Lv, Tongming Zhao, Nan Li, Youxin Yang, Wenbao Yu, Xin He, Tingli Liu, Baolong Zhang
Software Mentions: 1
Published: over 11 years ago

10.1186/s12864-019-5830-y

Transcriptome analysis reveals differential immune related genes expression in bovine viral diarrhea virus-2 infected goat peripheral blood mononuclear cells (PBMCs)
Cited by: 24
Author(s): Wenliang Li, Mao Li, Xin Shu, Runxia Liu, Hao Fei, Jizong Li, Maojun Liu, Leilei Yang, Wenwen Zhang, Min Sun, Cheng Zhong, Jiang Ji
Software Mentions: 1
Published: about 6 years ago

10.1371/journal.pone.0156242

Differential RNA-seq, Multi-Network Analysis and Metabolic Regulation Analysis of Kluyveromyces marxianus Reveals a Compartmentalised Response to Xylose
Cited by: 29
Author(s): Du Toit W. P. Schabort, Precious K. Letebele, Laurinda Steyn, S. G. Kilian, J. C. du Preez
Software Mentions: 1
Published: about 9 years ago

10.18632/aging.102135

Frailty in middle age is associated with frailty status and race-specific changes to the transcriptome
Cited by: 17
Author(s): Calais S. Prince, Nicole Noren Hooten, Nicolle A. Mode, Yongqing Zhang, Ngozi Ejiogu, Kevin G. Becker, Alan B. Zonderman, Michele K. Evans
Software Mentions: 1
Published: almost 6 years ago

10.1186/1471-2164-12-503

De novo sequence assembly of Albugo candida reveals a small genome relative to other biotrophic oomycetes
Cited by: 119
Author(s): Matthew G. Links, Eric B. Holub, Rays H. Y. Jiang, Andrew Sharpe, Dwayne D. Hegedus, Elena Beynon, D. Sillito, Wayne E. Clarke, Shihomi Uzuhashi, M. Hossein Borhan
Software Mentions: 1
Published: almost 14 years ago

10.1038/s41598-019-41675-3

Detection of novel fusion-transcripts by RNA-Seq in T-cell lymphoblastic lymphoma
Cited by: 27
Author(s): Pilar López-Nieva, Pablo Fernández-Navarro, Osvaldo Graña‐Castro, Eduardo Andrés-León, Javíer Santos, María Villa‐Morales, María Ángeles Cobos-Fernández, Laura González-Sánchez, Marcos Malumbres, María Salazar, José Fernández‐Piqueras
Software Mentions: 1
Published: over 6 years ago

10.1371/journal.pone.0147298

Identification of Putative Biomarkers for the Early Stage of Porcine Spermatogonial Stem Cells Using Next-Generation Sequencing
Cited by: 12
Author(s): Won Young Lee, Jeong Tae, Chankyu Park, Jin‐Hoi Kim, Hak-Jae Chung, Kyung-Woon Kim, Chang-Hyun Gil, Nam‐Hyung Kim, Hyuk Song
Software Mentions: 1
Published: over 9 years ago

10.1371/journal.pone.0125745

Label-Free Protein-RNA Interactome Analysis Identifies Khsrp Signaling Downstream of the p38/Mk2 Kinase Complex as a Critical Modulator of Cell Cycle Progression
Cited by: 32
Author(s): Jorge Bouças, Christian Fritz, Anna Schmitt, Arina Riabinska, Lisa Thelen, Martin Peifer, Uschi Leeser, Peter Nüernberg, Janine Altmueller, Matthias Gaestel, Christoph Dieterich, Hans Christian Reinhardt
Software Mentions: 1
Published: about 10 years ago

10.1038/s41598-019-41748-3

Global Gene Networks in 3D4/31 Porcine Alveolar Macrophages Treated with Antigenic Epitopes of Actinobacillus pleuropneumoniae ApxIA, IIA, and IVA
Cited by: 5
Author(s): Suji Kim, Myung Whan Oh, Woo Bin Park, Han Sang Yoo
Software Mentions: 1
Published: over 6 years ago

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