pypi: TopHat | Projects | Ecosyste.ms: Papers

10.1038/s41598-019-41703-2

RNA-seq reveals the involvement of key genes for aerobic adaptation in rice
Cited by: 23
Author(s): Amol S. Phule, Kalyani M. Barbadikar, Sheshu Madhav Maganti, P. Seguttuvel, D. Subrahmanyam, M.B.B. Prasad Babu, Polumetla Ananda Kumar
Software Mentions: 1
Published: over 7 years ago

10.1038/s41598-019-41796-9

Transcriptional response of grapevine to infection with the fungal pathogen Lasiodiplodia theobromae
Cited by: 11
Author(s): Wei Zhang, Jiye Yan, Xinghong Li, Qikai Xing, K. W. Thilini Chethana, Wensheng Zhao
Software Mentions: 1
Published: over 7 years ago

10.1038/s41598-019-41778-x

Environmental interactions are regulated by temperature in Burkholderia seminalis TC3.4.2R3
Cited by: 3
Author(s): Priscila Jane Romano de Oliveira Gonçalves, Carmen C. Denman, Almir José Ferreira, Sarina Tsui, Marcelo Brocchi, Brendan W. Wren, Welington Luiz Araújo
Software Mentions: 1
Published: over 7 years ago

10.3390/ijms20092235

Nitrate Reductase-Mediated Nitric Oxide Regulates the Leaf Shape in Arabidopsis by Mediating the Homeostasis of Reactive Oxygen Species
Cited by: 18
Author(s): Qiaona Pan, Chen-Chen Geng, Dandan Li, Shiwen Xu, Dandan Mao, Saima Umbreen, Gary J. Loake, Beimi Cui
Software Mentions: 1
Published: over 7 years ago

10.1186/s12870-014-0355-7

Potential functions of microRNAs in starch metabolism and development revealed by miRNA transcriptome profiling of cassava cultivars and their wild progenitor
Cited by: 46
Author(s): Xin Chen, Jing Xia, Zhiqiang Xia, Hefang Zhang, Chen Zeng, Cheng Lü, Weixiong Zhang, Wenquan Wang
Software Mentions: 1
Published: over 11 years ago

10.1038/s41598-019-42393-6

Comparative RNA sequencing reveals that HPV16 E6 abrogates the effect of E6*I on ROS metabolism
Cited by: 15
Author(s): Philippe Paget-Bailly, Koceila Meznad, Diane Bruyère, Jérôme Perrard, Michaël Herfs, Alain C. Jung, Christiane Mougin, Jean‐Luc Prétet, Aurélie Baguet
Software Mentions: 1
Published: over 7 years ago

10.1186/s12870-020-02350-2

Novel low-nitrogen stress-responsive long non-coding RNAs (lncRNA) in barley landrace B968 (Liuzhutouzidamai) at seedling stage
Cited by: 18
Author(s): Zhiwei Chen, Qi Jiang, Panpan Jiang, Wan Zhang, Jianhua Huang, Chenghong Liu, Nigel G. Halford, Ruiju Lu
Software Mentions: 1
Published: over 6 years ago

10.1186/s12868-018-0458-4

Expression of alternatively spliced variants of the Dclk1 gene is regulated by psychotropic drugs
Cited by: 8
Author(s): Magdalena Zygmunt, Dżesika Hoinkis, Jacek Hajto, Marcin Piechota, Bożena Skupień-Rabian, Urszula Jankowska, Sylwia Kędracka–Krok, Jan Rodriguez Parkitna, Michał Korostyński
Software Mentions: 1
Published: about 8 years ago

10.1038/s41598-019-42179-w

Maternal DCAF13 Regulates Chromatin Tightness to Contribute to Embryonic Development
Cited by: 11
Author(s): Yang Liu, Long‐Wen Zhao, Jingling Shen, Heng‐Yu Fan, Yan Jin
Software Mentions: 1
Published: over 7 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: over 13 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 5 years ago

10.1186/s12868-015-0157-3

Methamphetamine induces alterations in the long non-coding RNAs expression profile in the nucleus accumbens of the mouse
Cited by: 36
Author(s): Li Zhu, Jie Zhu, Yufeng Liu, Yanjiong Chen, Yanlin Liu, Li-Ren Huang, Sisi Chen, Tao Li, Yonghui Dang, Teng Chen
Software Mentions: 1
Published: over 11 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 9 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: about 12 years ago

10.1038/s41598-019-43259-7

The implication of plastid transcriptome analysis in petaloid monocotyledons: A case study of Lilium lancifolium (Liliaceae, Liliales)
Cited by: 3
Author(s): Hoang Dang Khoa, Joohwan Kim
Software Mentions: 1
Published: over 7 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: almost 9 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 8 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 11 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: about 11 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: about 11 years ago

10.1038/s41598-019-43578-9

Differences in the molecular signatures of mucosal-associated invariant T cells and conventional T cells
Cited by: 25
Author(s): Daeui Park, Hong Gi Kim, Miok Kim, Tamina Park, Hyung‐Ho Ha, Dong Hoon Lee, Kang-Seo Park, Seong Jun Park, Hae Ja Lim, Chang Hoon Lee
Software Mentions: 1
Published: over 7 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: almost 14 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: about 11 years ago

10.1186/s12860-020-00284-z

Functional analyses of miRNA-146b-5p during myogenic proliferation and differentiation in chicken myoblasts
Cited by: 13
Author(s): Jeong Hyo Lee, Seo Woo Kim, Ji Seon Han, Seung Pyo Shin, Sang In Lee, Tae Sub Park
Software Mentions: 1
Published: over 6 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 9 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: over 10 years ago

10.1186/s12867-018-0113-8

Analyses of changes in myocardial long non-coding RNA and mRNA profiles after severe hemorrhagic shock and resuscitation via RNA sequencing in a rat model
Cited by: 9
Author(s): Lin Lin, Zhengfei Yang, Guanghui Zheng, Yongxun Zhuansun, Yue Wang, Jianguo Li, Rui Chen, Wanchun Tang
Software Mentions: 1
Published: almost 8 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: over 6 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: almost 16 years ago

10.3390/ijms20102394

Identification and Characterization of Novel Fusion Genes with Potential Clinical Applications in Mexican Children with Acute Lymphoblastic Leukemia
Cited by: 12
Author(s): Minerva Mata-Rocha, Angélica Rangel-López, Elva Jiménez‐Hernández, Blanca Angélica Morales-Castillo, Carolina González-Torres, Javier Gaytán-Cervantes, Enrique Álvarez-Olmos, Juan Carlos Núñez-Enríquez, Arturo Fajardo-Gutiérrez, Jorge Alfonso Martín-Trejo, Karina Anastacia Solís-Labastida, Aurora Medina-Sansón, Janet Flores-Lujano, Omar Alejandro Sepúlveda-Robles, José Gabriel Peñaloza-González, Laura Eugenia Espinoza-Hernández, Nora Nancy Núñez-Villegas, Rosa Martha Espinosa-Elizondo, Beatriz Cortés-Herrera, José Refugio Torres-Nava, Luz Victoria Flores-Villegas, Laura Elizabeth Merino-Pasaye, Carolina Bekker-Méndez, Martha Margarita Velázquez-Aviña, María Luisa Pérez-Saldivar, Benito Alejandro Bautista-Martínez, Raquel Amador-Sánchez, Ana Itamar González‐Ávila, Silvia Jiménez-Morales, David Aldebarán Duarte-Rodríguez, Jessica Denisse Santillán-Juárez, Alejandra Jimena García-Velázquez, Haydeé Rosas-Vargas, Juan Manuel Mejı́a-Aranguré
Software Mentions: 1
Published: over 7 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 11 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 9 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: almost 13 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: about 10 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: about 9 years ago

10.1038/s41598-019-43979-w

Transcriptional profiling of coaggregation interactions between Streptococcus gordonii and Veillonella parvula by Dual RNA-Seq
Cited by: 19
Author(s): Naresh V.R. Mutha, Waleed K. Mohammed, Natalio Krasnogor, Geok Yuan Annie Tan, Wei Yee Wee, Yongming Li, Siew Woh Choo, Nicholas S. Jakubovics
Software Mentions: 1
Published: over 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 10 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: over 13 years ago

10.1186/1471-2164-15-759

Systematic transcriptome analysis of the zebrafish model of diamond-blackfan anemia induced by RPS24 deficiency
Cited by: 15
Author(s): Binfeng Song, Qian Zhang, Zhaojun Zhang, Yang Wan, Qiong Jia, Xiaomin Wang, Xiaofan Zhu, Anskar Y. H. Leung, Tao Cheng, Xiangdong Fang, Weiping Yuan, Haibo Jia
Software Mentions: 1
Published: about 12 years ago

10.1186/s12864-017-4123-6

The dynamic landscape of gene regulation during Bombyx mori oogenesis
Cited by: 10
Author(s): Qiang Zhang, Wei Sun, Bangyong Sun, Yang Xiao, Ze Zhang
Software Mentions: 1
Published: about 9 years ago

10.1186/1471-2164-15-287

Species-specific alternative splicing leads to unique expression of sno-lncRNAs
Cited by: 44
Author(s): Xiao‐Ou Zhang, Qingrui Yin, Haibin Wang, Yang Zhang, Chen Tian, Ping Zheng, Xuhua Lu, Lingling Chen, Li Yang
Software Mentions: 1
Published: over 12 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: almost 10 years ago

10.1098/rsob.180029

Cultured cells and wing disc size of silkworm can be controlled by the Hippo pathway
Cited by: 9
Author(s): Zi Liang, Yingjie Lu, Ying Qian, Liyuan Zhu, Sulan Kuang, Fei Chen, Yongjie Feng, Xiaolong Hu, Guangwen Cao, Renyu Xue, Chengliang Gong
Software Mentions: 1
Published: over 8 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: about 8 years ago

10.1186/s12864-015-1598-x

The Eucalyptus terpene synthase gene family
Cited by: 115
Author(s): Carsten Külheim, Amanda Padovan, Charles A. Hefer, Sandra T. Krause, Tobias G. Köllner, Alexander Andrew Myburg, Jörg Degenhardt, William J. Foley
Software Mentions: 1
Published: over 11 years ago

10.1186/s12864-019-6062-x

‘Candidatus Phytoplasma solani’ interferes with the distribution and uptake of iron in tomato
Cited by: 16
Author(s): Sara Buoso, Laura Pagliari, Rita Musetti, Marta Martini, Fabio Marroni, Wolfgang Schmidt, Simonetta Santi
Software Mentions: 1
Published: about 7 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: almost 13 years ago

10.1038/s41598-019-45089-z

Divergent age-dependent peripheral immune transcriptomic profile following traumatic brain injury
Cited by: 10
Author(s): Amanda Hazy, Lauren Bochicchio, Andrea Oliver, Eric Xie, Shuo Geng, Thomas Brickler, Hehuang Xie, Liwu Li, Irving C. Allen, Michelle H. Theus
Software Mentions: 1
Published: over 7 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: over 10 years ago

10.1007/s00204-021-03084-2

Dynamic alteration in miRNA and mRNA expression profiles at different stages of chronic arsenic exposure-induced carcinogenesis in a human cell culture model of skin cancer
Cited by: 18
Author(s): Mayukh Banerjee, Ana Paula Ferragut Cardoso, Laila Al-Eryani, Jianmin Pan, Theodore S. Kalbfleisch, Sudhir Srivastava, N. Shesh, J. Christopher States
Software Mentions: 1
Published: over 5 years ago

10.1038/s41598-019-45600-6

Healthy adiposity and extended lifespan in obese mice fed a diet supplemented with a polyphenol-rich plant extract
Cited by: 24
Author(s): Virginie Aires, Jérôme Labbé, Valérie Deckert, Jean‐Paul Pais de Barros, Romain Boidot, Marc Haumont, Guillaume Maquart, Naïg Le Guern, David Masson, Emmanuelle Prost-Camus, Michel Prost, Laurent Lagrost
Software Mentions: 1
Published: over 7 years ago

10.3390/ijms20122929

Next-Generation Sequencing in Acute Lymphoblastic Leukemia
Cited by: 55
Author(s): Nicoletta Coccaro, Luisa Anelli, Antonella Zagaria, Giorgina Specchia, Francesco Albano
Software Mentions: 1
Published: over 7 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 10 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: over 11 years ago

10.1186/s12864-018-4857-9

Two divergent Symbiodinium genomes reveal conservation of a gene cluster for sunscreen biosynthesis and recently lost genes
Cited by: 105
Author(s): Eiichi Shoguchi, Girish Beedessee, Isao Tada, Kanako Hisata, Takeshi Kawashima, Takeshi Takeuchi, Nana Arakaki, Manabu Fujie, Ryo Koyanagi, Michael C. Roy, Masanobu Kawachi, Michio Hidaka, Noriyuki Satoh, Chuya Shinzato
Software Mentions: 1
Published: over 8 years ago

10.3390/cancers11020251

Pan-Cancer Analyses Reveal Genomic Features of FOXM1 Overexpression in Cancer
Cited by: 125
Author(s): Carter J. Barger, Connor Branick, Linda Chee, Adam R. Karpf
Software Mentions: 1
Published: over 7 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 11 years ago

10.3390/cancers12071936

DEK Expression in Breast Cancer Cells Leads to the Alternative Activation of Tumor Associated Macrophages
Cited by: 13
Author(s): Nicholas A. Pease, Miranda S. Shephard, Mathieu Sertorio, Susan E. Waltz, Lisa M. Privette Vinnedge
Software Mentions: 1
Published: about 6 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 11 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 13 years ago

10.1038/s41598-019-47003-z

The anti-aflatoxigenic mechanism of cinnamaldehyde in Aspergillus flavus
Cited by: 36
Author(s): Ping Wang, Longxue Ma, Jing Jin, Mao Zheng, Lin Pan, Yang Zhao, Xiulan Sun, Yang Liu, Fuguo Xing
Software Mentions: 1
Published: about 7 years ago

10.1038/s41598-019-47985-w

A chromosome-anchored eggplant genome sequence reveals key events in Solanaceae evolution
Cited by: 131
Author(s): Lorenzo Barchi, Marco Pietrella, Luca Venturini, Andrea Minio, L. Toppino, Alberto Acquadro, Giuseppe Andolfo, Giuseppe Aprea, C. Avanzato, Laura Bassolino, Cinzia Comino, Alessandra Dal Molin, Alberto Ferrarini, L. Maor, Ezio Portis, Sebastian Reyes-Chin-Wo, Riccardo Rinaldi, T. Sala, Davide Scaglione, Prashant Sonawane, Paola Tononi, Efrat Almekias-Siegl, Elisa Zago, Maria Raffaella Ercolano, Asaph Aharoni, Massimo Delledonne, Giovanni Giuliano, Sergio Lanteri, Giuseppe Leonardo Rotino
Software Mentions: 1
Published: about 7 years ago

10.3390/cancers13020351

EGR1/GADD45α Activation by ROS of Non-Thermal Plasma Mediates Cell Death in Thyroid Carcinoma
Cited by: 11
Author(s): Seung-Hyun Jung, Chahyun Oh, Jae Won Chang, Lihua Liu, Mi Ae Lim, Yan Jin, Yudan Piao, Hae Jong Kim, Ho-Ryun Won, Seong Eun Lee, Min Joung Lee, Jun Young Heo, Sangmi Jun, Doheon Lee, Woo Seok Kang, Dong Wook Kim, Ki-Sang Rha, Young Il Kim, Yea Eun Kang, Bon Seok Koo
Software Mentions: 1
Published: over 5 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 8 years ago

10.1038/s41598-019-48309-8

Transcriptional alterations reveal Bacillus amyloliquefaciens-rice cooperation under salt stress
Cited by: 68
Author(s): Puneet Singh Chauhan, Charu Lata, Shalini Tiwari, Abhishek Chauhan, Shaunak Mishra, Lalit Agrawal, Debasis Chakrabarty, Puneet Singh Chauhan
Software Mentions: 1
Published: about 7 years ago

10.3390/cancers12071772

The ATF6-EGF Pathway Mediates the Awakening of Slow-Cycling Chemoresistant Cells and Tumor Recurrence by Stimulating Tumor Angiogenesis
Cited by: 15
Author(s): Jaebeom Cho, Hye‐Young Min, Honglan Pei, Wei Xuan, Jeong Yeon Sim, Shin‐Hyung Park, Su Jung Hwang, Lee Hj, Sang Hyun Hong, Young Kee Shin, Ho‐Young Lee
Software Mentions: 1
Published: over 6 years ago

10.3390/cancers13184614

CBP/p300 Bromodomain Inhibitor–I–CBP112 Declines Transcription of the Key ABC Transporters and Sensitizes Cancer Cells to Chemotherapy Drugs
Cited by: 9
Author(s): Magdalena Strachowska, Karolina Gronkowska, Sylwia Michlewska, Agnieszka Robaszkiewicz
Software Mentions: 1
Published: about 5 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: over 10 years ago

10.1186/s12864-015-1813-9

Transcriptome analysis of the Holly mangrove Acanthus ilicifolius and its terrestrial relative, Acanthus leucostachyus, provides insights into adaptation to intertidal zones
Cited by: 33
Author(s): Yuchen Yang, Shuhuan Yang, Jianfang Li, Yunfei Deng, Zhang Zhang, Shaohua Xu, Wuxia Guo, Cairong Zhong, Renchao Zhou, Suhua Shi
Software Mentions: 1
Published: about 11 years ago

10.1038/s41598-019-48867-x

Construction of complete Tupaia belangeri transcriptome database by whole-genome and comprehensive RNA sequencing
Cited by: 16
Author(s): Takahiro Sanada, Kyoko Tsukiyama-Kohara, Tadasu Shin-I, Naoki Yamamoto, Mohammad Enamul Hoque Kayesh, Daisuke Yamane, Junichiro Takano, Yumiko Shiogama, Yasuhiro Yasutomi, Kazuho Ikeo, Takashi Gojobori, Masashi Mizokami, Michinori Kohara
Software Mentions: 1
Published: about 7 years ago

10.1038/s41598-019-48533-2

Mapping insoluble indole metabolites in the gastrointestinal environment of a murine colorectal cancer model using desorption/ionisation on porous silicon imaging
Cited by: 13
Author(s): David Rudd, Kirsten Benkendorff, Charndeep Chahal, Taryn Guinan, Ove Gustafsson, Babak Esmaeelian, Hanna Krysinska, Lisa D. Pogson, Nicolas H. Voelcker, Catherine A. Abbott
Software Mentions: 1
Published: about 7 years ago

10.3390/cancers13174276

Usp22 Overexpression Leads to Aberrant Signal Transduction of Cancer-Related Pathways but Is Not Sufficient to Drive Tumor Formation in Mice
Cited by: 1
Author(s): Xi Kuang, Michael McAndrew, Lisa Maria Mustachio, Yi Jen Chen, Boyko S. Atanassov, Kevin Lin, Yao Lu, Jianjun Shen, Andrew P. Salinger, Timothy L. Macatee, Sharon Y.R. Dent, Evangelia Koutelou
Software Mentions: 1
Published: about 5 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: almost 9 years ago

10.1038/s41598-019-48983-8

Transcriptional profiling of corneal stromal cells derived from patients with keratoconus
Cited by: 19
Author(s): Rabab Sharif, Mariam Lotfy Khaled, Tina B. McKay, Yutao Liu, Dimitrios Karamichos
Software Mentions: 1
Published: about 7 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 10 years ago

10.1038/s41598-019-49089-x

Muscle transcriptome analysis reveals genes and metabolic pathways related to mineral concentration in Bos indicus
Cited by: 14
Author(s): Juliana Afonso, Luiz Lehmann Coutinho, P. C. Tizioto, Wellison J. S. Diniz, A. O. de Lima, M. I. P. Rocha, C. E. Buss, Bruno de Bezerril Andrade, Otávio Piaya, Juliana Virginio da Silva, Laura A B Lins, Caio Fernando Gromboni, Ana Rita Nogueira, M. R. S. Fortes, Gérson Barreto Mourão, Luciana Correia de Almeida Regitano
Software Mentions: 1
Published: about 7 years ago

10.1016/j.cell.2015.12.025

Trim28 Haploinsufficiency Triggers Bi-stable Epigenetic Obesity
Cited by: 153
Author(s): Kevin Dalgaard, Kathrin Landgraf, Steffen Heyne, Adelheid Lempradl, John Longinotto, Klaus Gossens, Marius Ruf, Michael Orthofer, Ruslan Strogantsev, Madhan Selvaraj, Tess Tsai Hsiu Lu, Eduard Casas, Raffaele Teperino, M. Azim Surani, Ilona Zvetkova, Debra Rimmington, Y.C. Loraine Tung, Brian Y.H. Lam, Rachel Larder, Giles S.H. Yeo, Stephen O’Rahilly, Tanya Vavouri, Emma Whitelaw, Josef Penninger, Thomas Jenuwein, Ching‐Lung Cheung, Anne C. Ferguson-Smith, Anthony P. Coll, Antje Körner, J. Andrew Pospisilik
Software Mentions: 1
Published: almost 11 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 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: almost 10 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: almost 9 years ago

10.1038/s41598-019-48977-6

Innate immune responses to paraquat exposure in a Drosophila model of Parkinson’s disease
Cited by: 35
Author(s): Urmila Maitra, Michael N. Scaglione, Stanislava Chtarbanova, Janis M. O’Donnell
Software Mentions: 1
Published: about 7 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 6 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 11 years ago

10.1186/s13578-019-0287-x

The Y-linked proto-oncogene TSPY contributes to poor prognosis of the male hepatocellular carcinoma patients by promoting the pro-oncogenic and suppressing the anti-oncogenic gene expression
Cited by: 11
Author(s): Tatsuo Kido, Yun‐Fai Chris Lau
Software Mentions: 1
Published: over 7 years ago

10.1186/s13578-021-00590-9

Neuromuscular junction-specific genes screening by deep RNA-seq analysis
Cited by: 4
Author(s): Hui Tao, Hongyang Jing, Xiaojing Lai
Software Mentions: 1
Published: over 5 years ago

10.18632/aging.203292

Yiqi Jiemin decoction alleviates allergic rhinitis in a guinea pig model by suppressing inflammation, restoring Th1/Th2 balance, and improving cellular metabolism
Cited by: 7
Author(s): Zhonghua Yan, Huan Liu, Jingjing Yuan, Lulu Jiao, Mo Zhou, Jinfeng Liu, Xiaohui Wen, Siming Liu, Pengpeng Hao, Jianhua Liu, Wei Wu
Software Mentions: 1
Published: about 5 years ago

10.1186/s13578-021-00559-8

Deletion at an 1q24 locus reveals a critical role of long noncoding RNA DNM3OS in skeletal development
Cited by: 3
Author(s): Ting Yu, Qiu fan Xu, Si Yang Li, Hui Huang, Sarah Dugan, Lei Shao, Jennifer A. Roggenbuck, Xiao tong Liu, Huai ze Liu, Betsy A. Hirsch, Ya Shen, Chen Liu, Steven Y. Cheng
Software Mentions: 1
Published: over 5 years ago

10.3390/ijms20174303

Transcriptome Analysis Reveals Key Seed-Development Genes in Common Buckwheat (Fagopyrum esculentum)
Cited by: 15
Author(s): Hongyou Li, Qiuyu Lv, Jiao Deng, Juan Huang, Fang Cai, Chenggang Liang, Qijiao Chen, Yan Wang, Lingjun Zhu, Xiaona Zhang
Software Mentions: 1
Published: about 7 years ago

10.1186/s12864-017-4367-1

Genome-wide analyses of direct target genes of four rice NAC-domain transcription factors involved in drought tolerance
Cited by: 52
Author(s): Phil Hyun Chung, Harin Jung, Yang Do Choi, Ju-Kon Kim
Software Mentions: 1
Published: over 8 years ago

10.1186/2045-3701-2-37

Strategies to identify long noncoding RNAs involved in gene regulation
Cited by: 69
Author(s): Catherine Lee, Nobuaki Kikyo
Software Mentions: 1
Published: almost 15 years ago

10.1186/s13578-018-0251-1

A role of Pumilio 1 in mammalian oocyte maturation and maternal phase of embryogenesis
Cited by: 15
Author(s): Winifred Mak, Jing Xia, Ee Chun Cheng, Katie M. Lowther, Haifan Lin
Software Mentions: 1
Published: almost 8 years ago

10.1186/2045-3701-2-43

RNA-seq analysis of synovial fibroblasts brings new insights into rheumatoid arthritis
Cited by: 40
Author(s): Daniel P. Heruth, Margaret Gibson, Dmitry N. Grigoryev, Li Qin Zhang, Shui Qing Ye
Software Mentions: 1
Published: almost 15 years ago

10.1186/s12964-015-0106-x

Stimulus-dependent differences in signalling regulate epithelial-mesenchymal plasticity and change the effects of drugs in breast cancer cell lines
Cited by: 43
Author(s): Joseph Cursons, Karl Johan Leuchowius, Mark Waltham, Eva Tomaskovic-Crook, Momeneh Foroutan, Cameron P. Bracken, Andrew Redfern, Edmund J. Crampin, Ian P. Street, Melissa J. Davis, Erik W. Thompson
Software Mentions: 1
Published: over 11 years ago

10.1186/s12964-020-00678-8

Reprogramming of synovial macrophage metabolism by synovial fibroblasts under inflammatory conditions
Cited by: 28
Author(s): Noritaka Saeki, Yuuki Imai
Software Mentions: 1
Published: almost 6 years ago

10.1186/s12964-016-0146-x

Neurogenin 3 is regulated by neurotrophic tyrosine kinase receptor type 2 (TRKB) signaling in the adult human exocrine pancreas
Cited by: 8
Author(s): Michael J. Shamblott, Marci O’Driscoll, Danielle L. Gomez, Dustin L. McGuire
Software Mentions: 1
Published: about 10 years ago

10.1038/s41418-018-0243-z

miR-92b-3p-TSC1 axis is critical for mTOR signaling-mediated vascular smooth muscle cell proliferation induced by hypoxia
Cited by: 40
Author(s): Jihui Lee, Jeongyeon Heo, Hyunjin Kang
Software Mentions: 1
Published: almost 8 years ago

10.1038/cdd.2016.135

Chromatin remodeling during in vivo neural stem cells differentiating to neurons in early Drosophila embryos
Cited by: 20
Author(s): Youqiong Ye, Min Li, Liang Gu, Xiaolong Chen, Jiejun Shi, Xiaobai Zhang, Cizhong Jiang
Software Mentions: 1
Published: almost 10 years ago

10.1038/s41418-019-0433-3

Autologous micrograft accelerates endogenous wound healing response through ERK-induced cell migration
Cited by: 26
Author(s): Martina Balli, Francesca Vitali, Adrian Janiszewski, Ellen Caluwé, Álvaro Cortés-Calabuig, Sébastien Carpentier, Robin Duelen, Flavio Lorenzo Ronzoni, Lukas Marcelis, Francesca Maria Bosisio, Riccardo Bellazzi, Aernout Luttun, Maria Gabriella Cusella De Angelis, Gabriele Ceccarelli, Frederic Lluı́s, Maurilio Sampaolesi
Software Mentions: 1
Published: almost 7 years ago

10.1038/s41418-020-00694-8

Kdm6a suppresses the alternative activation of macrophages and impairs energy expenditure in obesity
Cited by: 17
Author(s): Jun Chen, Xing Xu, Yan Li, Li Fan, Jianjun Zhang, Qin Xu, Wantao Chen, Wei Yan, Xu Wang
Software Mentions: 1
Published: almost 6 years ago

10.1038/s41418-019-0289-6

Thymidylate synthase maintains the de-differentiated state of triple negative breast cancers
Cited by: 30
Author(s): Aarif Siddiqui, Paradesi Naidu Gollavilli, Annemarie Schwab, Maria Eleni Vazakidou, Pelin G. Ersan, Mallika Ramakrishnan, Dick Pluim, Si’Ana A. Coggins, Özge Saatçi, Laura Annaratone, Jan H.M. Schellens, Baek Kim, Irfan A. Asangani, Suhail Ahmed Kabeer Rasheed, Caterina Marchiò, Özgür Şahin, Paolo Ceppi
Software Mentions: 1
Published: over 7 years ago

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Papers Mentioning TopHat 5,017