pypi: TopHat | Projects | Ecosyste.ms: Papers

10.1186/s12864-018-4821-8

Evolutionary divergence of 3’ UTRs in cichlid fishes
Cited by: 19
Author(s): Xiong Peng, C. Darrin Hulsey, Axel Meyer, Paolo Franchini
Software Mentions: 1
Published: over 6 years ago

Transcriptional landscape of pathogen‐responsive lnc <scp>RNA</scp> s in rice unveils the role of <scp>ALEX</scp> 1 in jasmonate pathway and disease resistance
Cited by: 76
Author(s): Yang Yu, Yufan Zhou, Yan-Zhao Feng, He Huang, Jianping Lian, Yuwei Yang, Meng-Qi Lei, Yuchan Zhang, Yue‐Qin Chen
Software Mentions: 1
Published: over 5 years ago

10.1016/j.stemcr.2013.09.005

Analysis of SOX2-Expressing Cell Populations Derived from Human Pluripotent Stem Cells
Cited by: 30
Author(s): David A. Brafman, Noel Moya, Stephanie Allen-Soltero, Thomas Fellner, Megan Robinson, Zoë L. McMillen, Terry Gaasterland, Karl Willert
Software Mentions: 1
Published: over 11 years ago

10.1093/pcp/pcu188

Plant Omics Data Center: An Integrated Web Repository for Interspecies Gene Expression Networks with NLP-Based Curation
Cited by: 54
Author(s): Hajime Ohyanagi, Tomoyuki Takano, Shin Terashima, Mariko Kobayashi, Maasa Kanno, Kanehisa Morimoto, Hiromi Kitano, Yohei Sasaki, Misa Saito, Satomi Asano, Soichi Ozaki, Toru Kudo, Koji Yokoyama, Koichiro Aya, Keita Suwabe, Go Suzuki, Koh Aoki, Yasutaka Kubo, Masao Watanabe, Makoto Matsuoka, Kentarô Yano
Software Mentions: 1
Published: about 10 years ago

10.1007/s00299-016-2065-0

Comparative transcriptome profiling of upland (VS16) and lowland (AP13) ecotypes of switchgrass
Cited by: 13
Author(s): Vasudevan Ayyappan, Malay C. Saha, Jyothi Thimmapuram, Venkateswara R. Sripathi, Ketaki P. Bhide, Elizabeth Fiedler, Rita K. Hayford, Venu Kalavacharla
Software Mentions: 1
Published: over 8 years ago

10.1016/j.stemcr.2018.01.002

Comparison of Non-human Primate versus Human Induced Pluripotent Stem Cell-Derived Cardiomyocytes for Treatment of Myocardial Infarction
Cited by: 43
Author(s): Xin Zhao, Haodong Chen, Dan Xiao, Huaxiao Yang, Ilanit Itzhaki, Xulei Qin, Tony Chour, Aitor Aguirre, Kim A. Lehmann, Young-Kyun Kim, Praveen Shukla, Alexandra Holmström, Joe Z. Zhang, Yan Zhuge, B Ndoye, Mingtao Zhao, Evgenios Neofytou, Wolfram‐Hubertus Zimmermann, Mohit Jain, Joseph C. Wu
Software Mentions: 1
Published: about 7 years ago

10.1002/pld3.136

Many rice genes are differentially spliced between roots and shoots but cytokinin has minimal effect on splicing
Cited by: 3
Author(s): Nowlan H. Freese, April R. Estrada, Ivory C. Blakley, Jinjie Duan, Ann E. Loraine
Software Mentions: 1
Published: almost 6 years ago

10.1016/j.stemcr.2017.09.012

Oocyte-Specific Homeobox 1, Obox1, Facilitates Reprogramming by Promoting Mesenchymal-to-Epithelial Transition and Mitigating Cell Hyperproliferation
Cited by: 13
Author(s): Lijun Wu, You Wu, Bing Peng, Zhenzhen Hou, Yu Dong, Kang Chen, Mingyue Guo, Han Li, Xia Chen, Xiaochen Kou, Yanhong Zhao, Yan Bi, Yixuan Wang, Hong Wang, Rongrong Le, Lan Kang, Shaorong Gao
Software Mentions: 1
Published: over 7 years ago

10.1186/s12864-021-07723-x

Genetic analysis of three maize husk traits by QTL mapping in a maize-teosinte population
Cited by: 4
Author(s): Xiaolei Zhang, Lu Ming, Aiai Xia, Tao Xu, Zhenhai Cui, Ruiying Zhang, Wenguo Liu, Yan He
Software Mentions: 1
Published: over 3 years ago

10.1111/tpj.14976

BdWRKY38 is required for the incompatible interaction of <i>Brachypodium distachyon</i> with the necrotrophic fungus <i>Rhizoctonia solani</i>
Cited by: 15
Author(s): Yusuke Kouzai, Minami Shimizu, Komaki Inoue, Yukiko Uehara‐Yamaguchi, Kotaro Takahagi, Risa Nakayama, Takakazu Matsuura, Izumi C. Mori, Takashi Hirayama, Sobhy S. H. Abdelsalam, Yoshiteru Noutoshi, Keiichi Mochida
Software Mentions: 1
Published: over 4 years ago

10.1111/tpj.14728

Disturbance of floral colour pattern by activation of an endogenous pararetrovirus, petunia vein clearing virus, in aged petunia plants
Cited by: 20
Author(s): Kazunori Kuriyama, Midori Tabara, Hiromitsu Moriyama, Akira Kanazawa, Hisashi Koiwa, Hideki Takahashi, Teruyuki Fukuhara
Software Mentions: 1
Published: almost 5 years ago

10.1007/s11103-020-01005-y

Transcriptional and metabolite analysis reveal a shift in direct and indirect defences in response to spider-mite infestation in cucumber (Cucumis sativus)
Cited by: 18
Author(s): Jun He, Harro J. Bouwmeester, Marcel Dicke, Iris F. Kappers
Software Mentions: 1
Published: almost 5 years ago

10.1007/s11105-018-1088-9

Genomic and Transcriptomic Analysis Identified Gene Clusters and Candidate Genes for Oil Content in Peanut (Arachis hypogaea L.)
Cited by: 16
Author(s): Xiaohua Wang, Ping Xu, Yin Liang, Yan Ren, Shuangling Li, Yùzhēn Shí, Thomas D. Alcock, Qing Xiong, Wei Qian, Xiaoyuan Chi, Manish K. Pandey, Rajeev K. Varshney, Ming Yüan
Software Mentions: 1
Published: over 6 years ago

10.1007/s00497-019-00362-z

Comparative transcriptome analysis reveals new molecular pathways for cucumber genes related to sex determination
Cited by: 21
Author(s): Magdalena Pawełkowicz, Leszek P. Pryszcz, Agnieszka Skarzyńska, Rafał Wóycicki, Kacper Posyniak, Jacek Rymuszka, Zbigniew Przybecki, Wojciech Pląder
Software Mentions: 1
Published: about 6 years ago

10.3390/plants9050596

Comparative Analysis of Root Transcriptome Reveals Candidate Genes and Expression Divergence of Homoeologous Genes in Response to Water Stress in Wheat
Cited by: 10
Author(s): Behnam Derakhshani, Habtamu Ayalew, Kohei Mishina, Tsuyoshi Tanaka, Yoshihiro Kawahara, Hossein Jafary, Youko Oono
Software Mentions: 1
Published: almost 5 years ago

10.3390/plants8040101

Transcriptomic Analysis of Orange Fruit Treated with Pomegranate Peel Extract (PGE)
Cited by: 19
Author(s): Imen Belgacem, Sonia Pangallo, Ahmed Abdelfattah, Flora V. Romeo, S. O. Cacciola, Maria Giulia Li Destri Nicosia, Gabriele Ballistreri, Leonardo Schena
Software Mentions: 1
Published: almost 6 years ago

10.1186/1471-2164-12-587

Directional gene expression and antisense transcripts in sexual and asexual stages of Plasmodium falciparum
Cited by: 301
Author(s): María José López-Barragán, Jacob E. Lemieux, Mariam Quiñones, Kim C. Williamson, Alvaro Molina-Cruz, Kairong Cui, Carolina Barillas‐Mury, Keji Zhao, Xin-zhuan Su
Software Mentions: 1
Published: about 13 years ago

10.3390/plants9020204

Transcriptome and Phytochemical Analysis Reveals the Alteration of Plant Hormones, Characteristic Metabolites, and Related Gene Expression in Tea (Camellia sinensis L.) Leaves During Withering
Cited by: 16
Author(s): Ping Xu, Hui Su, Sheng Zhao, Rong Jin, Haiyan Cheng, Anan Xu, Wanyi Lai, Yin X, Yuefei Wang
Software Mentions: 1
Published: about 5 years ago

10.3390/plants8090302

Circular and Micro RNAs from Arabidopsis thaliana Flowers Are Simultaneously Isolated from AGO-IP Libraries
Cited by: 15
Author(s): Érika Frydrych Capelari, Guilherme Cordenonsi da Fonseca, Frank Guzmán, Rogério Margis
Software Mentions: 1
Published: over 5 years ago

10.3390/plants9091112

Transcriptomic Analysis of a Susceptible African Maize Line to Fusarium verticillioides Infection
Cited by: 9
Author(s): Humaira Lambarey, Naadirah Moola, Amy Veenstra, Shane L. Murray, Mohamed Suhail Rafudeen
Software Mentions: 1
Published: over 4 years ago

10.3390/plants9030344

Transcriptome Analysis Reveals Candidate Genes Related to Anthocyanin Biosynthesis in Different Carrot Genotypes and Tissues
Cited by: 19
Author(s): Meng Geng, Sabine K. Clausen, Søren K. Rasmussen
Software Mentions: 1
Published: almost 5 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: about 4 years ago

10.1016/j.stemcr.2018.02.014

A Critical Role of TET1/2 Proteins in Cell-Cycle Progression of Trophoblast Stem Cells
Cited by: 35
Author(s): Stephanie Chrysanthou, Claire E. Senner, Laura Woods, Elena Fineberg, Hanneke Okkenhaug, Sarah Burge, Vicente Pérez-García, Myriam Hemberger
Software Mentions: 1
Published: almost 7 years ago

10.3390/plants10050823

Transcriptional Changes of Cell Wall Organization Genes and Soluble Carbohydrate Alteration during Leaf Blade Development of Rice Seedlings
Cited by: 1
Author(s): Jae-Yeon Joo, Me-Sun Kim, Jwakyung Sung
Software Mentions: 1
Published: almost 4 years ago

10.3390/plants9101298

Overexpression of OsC3H10, a CCCH-Zinc Finger, Improves Drought Tolerance in Rice by Regulating Stress-Related Genes
Cited by: 22
Author(s): So Yoon Seong, Jae Sung Shim, Seung Woon Bang, Ju-Kon Kim
Software Mentions: 1
Published: over 4 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: about 14 years ago

10.1016/j.stemcr.2020.08.003

A p53-Dependent Checkpoint Induced upon DNA Damage Alters Cell Fate during hiPSC Differentiation
Cited by: 4
Author(s): Cara Bernadette Eldridge, Finian J. Allen, Alastair Crisp, Rodrigo A. Grandy, Ludovic Vallier, Julian E. Sale
Software Mentions: 1
Published: over 4 years ago

10.1371/journal.pbio.3000563

Mediator MED23 regulates inflammatory responses and liver fibrosis
Cited by: 7
Author(s): Zhichao Wang, Dan Cao, Chonghui Li, Lihua Min, Gang Wang
Software Mentions: 1
Published: about 5 years ago

10.1371/journal.pbio.2006966

Environment-induced same-sex mating in the yeast Candida albicans through the Hsf1–Hsp90 pathway
Cited by: 17
Author(s): Guijian Guan, Tao Li, Huizhen Yue, Weihong Liang, Jiao Gong, Bing Jian, Qiushi Zheng, Amanda O. Veri, Shuru Fan, Nicole Robbins, Leah E. Cowen, Guanghua Huang
Software Mentions: 1
Published: almost 6 years ago

10.1371/journal.pbio.2004049

Reporters to mark and eliminate basal or luminal epithelial cells in culture and in vivo
Cited by: 16
Author(s): O. Sonzogni, Jennifer Haynes, Laurie A. Seifried, Yahia M. Kamel, Kai Huang, Michael D. BeGora, Faith Au Yeung, Céline Robert-Tissot, Yujing J. Heng, Xin Yuan, Gerbug M. Wulf, Ken J. Kron, Elvin Wagenblast, Mathieu Lupien, Thomas Kislinger, Gregory J. Hannon, Senthil K. Muthuswamy
Software Mentions: 1
Published: over 6 years ago

10.1371/journal.pbio.3000452

A hormone receptor pathway cell-autonomously delays neuron morphological aging by suppressing endocytosis
Cited by: 10
Author(s): Charlotte Richardson, Callista Yee, Kang Shen
Software Mentions: 1
Published: over 5 years ago

10.1371/journal.pbio.1001647

Analysis of the RelA:CBP/p300 Interaction Reveals Its Involvement in NF-κB-Driven Transcription
Cited by: 113
Author(s): Sulakshana Mukherjee, Marcelo Behar, Harry Birnbaum, Alexander Hoffmann, Peter E. Wright, Gourisankar Ghosh
Software Mentions: 1
Published: over 11 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: over 9 years ago

10.1371/journal.pbio.3000418

Activation of the intrinsic fibroinflammatory program in adult pancreatic acinar cells triggered by Hippo signaling disruption
Cited by: 26
Author(s): Jun Li, Ming Gao, Michael Nipper, Janice Jianhong Deng, Francis E. Sharkey, Randy L. Johnson, Howard C. Crawford, Yidong Chen, Pei Wang
Software Mentions: 1
Published: over 5 years ago

10.1371/journal.pbio.1001806

Phosphoinositide Metabolism Links cGMP-Dependent Protein Kinase G to Essential Ca2+ Signals at Key Decision Points in the Life Cycle of Malaria Parasites
Cited by: 180
Author(s): Mathieu Brochet, Mark O. Collins, Terry Smith, Eloise Thompson, Sarah Sebastian, Katrin Volkmann, Frank Schwach, Lia Chappell, Ana Gomes, Matthew Berriman, Julian C. Rayner, David A. Baker, Jyoti S. Choudhary, Oliver Billker
Software Mentions: 1
Published: almost 11 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: about 6 years ago

10.1371/journal.pbio.1000625

The Reality of Pervasive Transcription
Cited by: 379
Author(s): Michael B. Clark, Paulo Amaral, Felix Schlesinger, Marcel E. Dinger, Ryan J. Taft, John L. Rinn, Chris P. Ponting, Peter F. Stadler, Kevin V. Morris, Antonin Morillon, Joel Rozowsky, Mark Gerstein, Claes Wahlestedt, Yoshihide Hayashizaki, Piero Carninci, T Gingeras, John S. Mattick
Software Mentions: 1
Published: over 13 years ago

10.1371/journal.pbio.2006522

H3K36 trimethylation mediated by SETD2 regulates the fate of bone marrow mesenchymal stem cells
Cited by: 65
Author(s): Lijun Wang, Ningning Niu, Li Li, Rui Shao, Huiling Ouyang, Weiguo Zou
Software Mentions: 1
Published: over 6 years ago

10.18632/oncotarget.22552

Glucose impairs tamoxifen responsiveness modulating connective tissue growth factor in breast cancer cells
Cited by: 30
Author(s): Maria Rosaria Ambrosio, Vittoria D’Esposito, Valerio Costa, Domenico Liguoro, Francesca Collina, Monica Cantile, Nella Prevete, Carmela Passaro, G. Mosca, Michelino De Laurentiis, Maurizio Di Bonito, Gerardo Botti, Renato Franco, Francesco Béguinot, Alfredo Ciccodicola, Pietro Formisano
Software Mentions: 1
Published: over 7 years ago

10.1371/journal.pbio.3000782

Phase separation of Arabidopsis EMB1579 controls transcription, mRNA splicing, and development
Cited by: 28
Author(s): Shujun Zhang, Zhankun Li, Naizhi Chen, Yao Huang, Shanjin Huang
Software Mentions: 1
Published: over 4 years ago

10.1371/journal.pbio.1001518

Selecting One of Several Mating Types through Gene Segment Joining and Deletion in Tetrahymena thermophila
Cited by: 78
Author(s): Marcella D. Cervantes, Eileen P. Hamilton, Jie Xiong, Michael J. Lawson, Dan Yuan, Michalis Hadjithomas, Wei Miao, Eduardo Orias
Software Mentions: 1
Published: almost 12 years ago

10.1186/s13568-018-0697-x

Genome-wide identification of the fatty acid desaturases gene family in four Aspergillus species and their expression profile in Aspergillus oryzae
Cited by: 6
Author(s): Wen Tang, Changsheng Ouyang, Lanlan Liu, Haoran Li, Chuanhui Zeng, Jie Wang, Lijun Fu, WU Qing, Bin Zeng
Software Mentions: 1
Published: over 6 years ago

10.1371/journal.pbio.3000294

Hidden genomic evolution in a morphospecies—The landscape of rapidly evolving genes in Tetrahymena
Cited by: 23
Author(s): Jie Xiong, Wentao Yang, Kai Chen, Chuanqi Jiang, Yang Ma, Xiaocui Chai, Guangwu Yan, Guangying Wang, Dan Yuan, Yifan Liu, Shelby L. Bidwell, Nikhat Zafar, Michalis Hadjithomas, Vivek Krishnakumar, Robert S. Coyne, Eduardo Orias, Wei Miao
Software Mentions: 1
Published: over 5 years ago

10.1371/journal.pbio.3000630

Cell-autonomous light sensitivity via Opsin3 regulates fuel utilization in brown adipocytes
Cited by: 33
Author(s): Mari Sato, Taichi Tsuji, Kunyan Yang, Xiaozhi Ren, Jonathan M. Dreyfuss, Tian Lian Huang, Chih-Hao Wang, Farnaz Shamsi, Luiz O. Leiria, Matthew D. Lynes, King Wai Yau, Yu–Hua Tseng
Software Mentions: 1
Published: about 5 years ago

10.1371/journal.pbio.1000590

Noncanonical Compensation of Zygotic X Transcription in Early Drosophila melanogaster Development Revealed through Single-Embryo RNA-Seq
Cited by: 193
Author(s): Susan E. Lott, Jacqueline E. Villalta, Gary P. Schroth, Shujun Luo, Leath A. Tonkin, Michael B. Eisen
Software Mentions: 1
Published: about 14 years ago

10.1371/journal.pcbi.1003314

Systematically Differentiating Functions for Alternatively Spliced Isoforms through Integrating RNA-seq Data
Cited by: 75
Author(s): Ridvan Eksi, Hong Dong Li, Rajasree Menon, Yuchen Wen, Gilbert S. Omenn, Matthias Kretzler, Yuanfang Guan
Software Mentions: 1
Published: over 11 years ago

10.1371/journal.pcbi.1004441

Analysis of Nearly One Thousand Mammalian Mirtrons Reveals Novel Features of Dicer Substrates
Cited by: 64
Author(s): Jiayu Wen, Erik Ladewig, Stephen H. Shenker, Jaaved Mohammed, Eric C. Lai
Software Mentions: 1
Published: over 9 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: almost 9 years ago

10.1371/journal.pcbi.1008325

Twelve quick steps for genome assembly and annotation in the classroom
Cited by: 27
Author(s): Hyungtaek Jung, Tomer Ventura, J. Sook Chung, Woo Jin Kim, Bo‐Hye Nam, Hee Jeong Kong, Young‐Ok Kim, Min-Seung Jeon, Seong‐il Eyun
Software Mentions: 1
Published: over 4 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: about 10 years ago

10.1371/journal.pcbi.1004821

Ups and Downs of Poised RNA Polymerase II in B-Cells
Cited by: 2
Author(s): Phuong Dao, Damian Wójtowicz, Stacy A. C. Nelson, David Levens, Teresa M. Przytycka
Software Mentions: 1
Published: almost 9 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: over 13 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: about 6 years ago

10.1186/s13287-018-0850-0

Three-dimensional printed PLA scaffold and human gingival stem cell-derived extracellular vesicles: a new tool for bone defect repair
Cited by: 179
Author(s): Francesca Diomede, Agnese Gugliandolo, Paolo Cardelli, Ilaria Merciaro, Valeria Ettorre, Tonino Traini, Rossella Bedini, Domenico Scionti, Alessia Bramanti, Antonio Nanci, Sergio Caputi, Antonella Fontana, Emanuela Mazzon, Oriana Trubiani
Software Mentions: 1
Published: almost 7 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: about 10 years ago

10.1371/journal.pcbi.1007204

A cell-based probabilistic approach unveils the concerted action of miRNAs
Cited by: 5
Author(s): Shelly Mahlab-Aviv, Michal Linial
Software Mentions: 1
Published: about 5 years ago

10.1371/journal.pcbi.1006163

2018 ISCB Overton Prize awarded to Cole Trapnell
Cited by: 0
Author(s): Christiana N. Fogg, Diane E. Kovats, Ron Shamir
Software Mentions: 1
Published: over 6 years ago

10.1371/journal.pcbi.1003737

A Scalable and Accurate Targeted Gene Assembly Tool (SAT-Assembler) for Next-Generation Sequencing Data
Cited by: 29
Author(s): Yuan Zhang, Yanni Sun, James R. Cole
Software Mentions: 1
Published: over 10 years ago

10.1371/journal.pcbi.1004465

Network-Based Isoform Quantification with RNA-Seq Data for Cancer Transcriptome Analysis
Cited by: 15
Author(s): Wei Zhang, Ju Young Chang, Liangyu Lin, Kay Minn, Baolin Wu, Jeremy Chien, Jeongsik Yong, Hui Zheng, Rui Kuang
Software Mentions: 1
Published: about 9 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: almost 11 years ago

10.1371/journal.pcbi.1007344

Systematically understanding the immunity leading to CRPC progression
Cited by: 23
Author(s): Ji Z, Weiling Zhao, Hui-Kuan Lin, Xiaobo Zhou
Software Mentions: 1
Published: over 5 years ago

10.1371/journal.pcbi.1002917

The Vast, Conserved Mammalian lincRNome
Cited by: 50
Author(s): David Managadze, Alexander E. Lobkovsky, Yuri I. Wolf, Svetlana A. Shabalina, Igor B. Rogozin, Eugene V. Koonin
Software Mentions: 1
Published: almost 12 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: over 5 years ago

10.1371/journal.pcbi.1003611

Histone Modifications Are Associated with Transcript Isoform Diversity in Normal and Cancer Cells
Cited by: 23
Author(s): Ondřej Podlaha, Subhajyoti De, Mithat Gönen, Franziska Michor
Software Mentions: 1
Published: over 10 years ago

10.1371/journal.pgen.1003116

Systematic Identification of Rhythmic Genes Reveals camk1gb as a New Element in the Circadian Clockwork
Cited by: 39
Author(s): Adi Tovin, Shahar Alon, Zohar Ben-Moshe, Philipp Mracek, Gad D. Vatine, Nicholas S. Foulkes, Jasmine Jacob‐Hirsch, Gideon Rechavi, Reiko Toyama, Steven L. Coon, David C. Klein, Eli Eisenberg, Yoav Gothilf
Software Mentions: 1
Published: about 12 years ago

10.1371/journal.pgen.1007208

A molecular basis behind heterophylly in an amphibious plant, Ranunculus trichophyllus
Cited by: 34
Author(s): Juhyun Kim, Youngsung Joo, Jinseul Kyung, Minu Jeon, Jong Yoon Park, Ho Gyun Lee, Doo Soo Chung, Eun‐Ju Lee, Ilha Lee
Software Mentions: 1
Published: about 7 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: over 13 years ago

10.1371/journal.pgen.1004159

Sex-Specific Embryonic Gene Expression in Species with Newly Evolved Sex Chromosomes
Cited by: 25
Author(s): Susan E. Lott, Jacqueline E. Villalta, Qi Zhou, Doris Bachtrog, Michael B. Eisen
Software Mentions: 1
Published: about 11 years ago

10.18632/oncotarget.13167

SNHG8 is identified as a key regulator of epstein-barr virus(EBV)-associated gastric cancer by an integrative analysis of lncRNA and mRNA expression
Cited by: 42
Author(s): Tao Huang, Yan Ji, Dan Hu, Baozheng Chen, Hejun Zhang, Chao Li, Gang Chen, Xingguang Luο, Zheng Xiao, Xiandong Lin
Software Mentions: 1
Published: over 8 years ago

10.1186/s12864-015-1692-0

Global transcriptional analysis of Burkholderia pseudomallei high and low biofilm producers reveals insights into biofilm production and virulence
Cited by: 44
Author(s): Chui Yoke Chin, Yuka Hara, Ahmad Kamal Ghazali, Soon Joo Yap, Cin Kong, Yee Chin Wong, Naufal Rozali, Seng Fook Koh, Chee Choong Hoh, S. D. Puthucheary, Sheila Nathan
Software Mentions: 1
Published: over 9 years ago

10.1371/journal.pgen.1005277

Canine Spontaneous Head and Neck Squamous Cell Carcinomas Represent Their Human Counterparts at the Molecular Level
Cited by: 33
Author(s): Liu D, Huan Xiong, Angela E. Ellis, Nicole C. Northrup, Kevin K. Dobbin, Dong M. Shin, Shaying Zhao
Software Mentions: 1
Published: over 9 years ago

10.1371/journal.pgen.1006026

Two Components of the RNA-Directed DNA Methylation Pathway Associate with MORC6 and Silence Loci Targeted by MORC6 in Arabidopsis
Cited by: 40
Author(s): Zhang-Wei Liu, Jin‐Xing Zhou, Huanwei Huang, Yongqiang Li, Chen Shao, Lin Li, Tao Cai, She Chen, Xin‐Jian He
Software Mentions: 1
Published: almost 9 years ago

10.1371/journal.pgen.1004701

Ethylene-Induced Inhibition of Root Growth Requires Abscisic Acid Function in Rice (Oryza sativa L.) Seedlings
Cited by: 92
Author(s): Biao Ma, Cui‐Cui Yin, Shiying He, Xiang Lü, Wan–Ke Zhang, Tiegang Lu, Shouyi Chen, Jinsong Zhang
Software Mentions: 1
Published: over 10 years ago

10.1371/journal.pgen.1008543

The Lid/KDM5 histone demethylase complex activates a critical effector of the oocyte-to-zygote transition
Cited by: 10
Author(s): Daniela Torres-Campana, Shuhei Kimura, Guillermo A. Orsi, Béatrice Horard, Benoît Galand, Benjamin Loppin
Software Mentions: 1
Published: almost 5 years ago

10.1186/s13287-019-1437-0

Age-related transcriptome changes in Sox2+ supporting cells in the mouse cochlea
Cited by: 62
Author(s): Cheng Cheng, Yunfeng Wang, Luo Guo, Xiaoling Lü, Weijie Zhu, Muhammad Waqas, Liyan Zhang, Ling Lü, Junyan Gao, Mingliang Tang, Fangyi Chen, Xia Gao, Huawei Li, Renjie Chai
Software Mentions: 1
Published: about 5 years ago

10.1371/journal.pgen.1004135

Integrated Genomic Characterization Reveals Novel, Therapeutically Relevant Drug Targets in FGFR and EGFR Pathways in Sporadic Intrahepatic Cholangiocarcinoma
Cited by: 290
Author(s): Mitesh J. Borad, Mia D. Champion, Jan B. Egan, Winnie S. Liang, Rafaël Fonseca, Alan H. Bryce, Ann E. McCullough, Michael T. Barrett, Katherine S. Hunt, Maitray D. Patel, Scott W. Young, Joseph M. Collins, Alvin C. Silva, Rachel Condjella, Matthew S. Block, Robert R. McWilliams, Konstantinos N. Lazaridis, Eric W. Klee, Keith C. Bible, Pamela Jo Harris, Gavin R. Oliver, Jaysheel Bhavsar, Asha Nair, Sumit Middha, Yan W. Asmann, Jean Pierre A. Kocher, Kimberly A. Schahl, Benjamin R. Kipp, Emily G. Barr Fritcher, Angela Baker, Jessica Aldrich, Ahmet Kurdoglu, Tyler Izatt, Alexis Christoforides, Irene Cherni, Sara Nasser, Rebecca Reiman, L Taylor Phillips, Jackie McDonald, Jonathan Adkins, Stephen D. Mastrian, Pamela Placek, Aprill Watanabe, Janine LoBello, Haiyong Han, Daniel D. Von Hoff, David W. Craig, A. Keith Stewart, John D. Carpten
Software Mentions: 1
Published: about 11 years ago

10.1186/s12864-017-3619-4

Cross-talk of the biotrophic pathogen Claviceps purpurea and its host Secale cereale
Cited by: 19
Author(s): Birgitt Oeser, Sabine Kind, Selma Schurack, Thomas Schmutzer, Paul Tudzynski, Janine Hinsch
Software Mentions: 1
Published: almost 8 years ago

10.1186/s12864-020-06983-3

Systematic analysis of the Capsicum ERF transcription factor family: identification of regulatory factors involved in the regulation of species-specific metabolites
Cited by: 23
Author(s): Jiangfeng Song, Changming Chen, Shuanglin Zhang, Juntao Wang, Zhong Huang, Muxi Chen, Bihao Cao, Zhiwen Zhu, Jing Liu
Software Mentions: 1
Published: over 4 years ago

10.1371/journal.pgen.1005744

CFLAP1 and CFLAP2 Are Two bHLH Transcription Factors Participating in Synergistic Regulation of AtCFL1-Mediated Cuticle Development in Arabidopsis
Cited by: 20
Author(s): Shibai Li, Xiaochen Wang, Shuyuan He, Jieru Li, Huang Qing, Takato Imaizumi, Le-Qing Qu, Genji Qin, Qu Liu, Hongya Gu
Software Mentions: 1
Published: about 9 years ago

10.1186/s12864-017-3874-4

Comparative transcriptomics uncovers alternative splicing and molecular marker development in radish (Raphanus sativus L.)
Cited by: 15
Author(s): Xiaobo Luo, Liang Xu, Dongyi Liang, Yan Wang, Wei Zhang, Xiaoming Zhu, Yuelin Zhu, Haiyan Jiang, Mingjia Tang, Liwang Liu
Software Mentions: 1
Published: over 7 years ago

10.1371/journal.pgen.1006019

Overexpression of Latent TGFβ Binding Protein 4 in Muscle Ameliorates Muscular Dystrophy through Myostatin and TGFβ
Cited by: 33
Author(s): Kay Marie Lamar, Sasha Bogdanovich, Brandon Gardner, Quan Gao, Tamari Miller, Judy U. Earley, Michele Hadhazy, Andy H. Vo, Lisa Wren, Jeffery D. Molkentin, Elizabeth M. McNally
Software Mentions: 1
Published: almost 9 years ago

10.1371/journal.pgen.1004334

The Proper Splicing of RNAi Factors Is Critical for Pericentric Heterochromatin Assembly in Fission Yeast
Cited by: 27
Author(s): Scott P. Kallgren, Stuart Andrews, Xavier Tadeo, Haitong Hou, James J. Moresco, Patricia G. Tu, John R. Yates, Péter L. Nagy, Songtao Jia
Software Mentions: 1
Published: over 10 years ago

10.1371/journal.pgen.1005013

Essential Role for Endogenous siRNAs during Meiosis in Mouse Oocytes
Cited by: 92
Author(s): Paula Stein, Nikolay V. Rozhkov, Liancheng Fan, Fabián L. Cárdenas, Olga Davydenk, Lee E. Vandivier, Brian D. Gregory, Gregory J. Hannon, Richard M. Schultz
Software Mentions: 1
Published: about 10 years ago

10.1371/journal.pgen.1009113

Impaired tumor immune response in metastatic tumors is a selective pressure for neutral evolution in CRC cases
Cited by: 7
Author(s): Shotaro Sakimura, Satoshi Nagayama, Mitsuko Fukunaga, Qingjiang Hu, Akihiro Kitagawa, Yuta Kobayashi, Takanori Hasegawa, Manjiro Noda, Yuta Kouyama, Dai Shimizu, Tomoko Saito, Atsushi Niida, Yusuke Tsuruda, Hajime Otsu, Yoshihiro Matsumoto, Hajime Uchida, Takaaki Masuda, Keizō Sugimachi, Shin Sasaki, Kazutaka Yamada, Kuniyuki Takahashi, Hideki Innan, Yutaka Suzuki, Hiromi Nakamura, Yasushi Totoki, Shinichi Mizuno, Masanobu Ohshima, Tatsuhiro Shibata, Koshi Mimori
Software Mentions: 1
Published: about 4 years ago

10.1371/journal.pgen.1006823

Allelic variants of OsHKT1;1 underlie the divergence between indica and japonica subspecies of rice (Oryza sativa) for root sodium content
Cited by: 86
Author(s): Malachy T. Campbell, Nonoy Bandillo, Fouad Razzaq Al Shiblawi, Sandeep Sharma, Kan Liu, Qian Du, Aaron J. Schmitz, Chi Zhang, Anne Aliénor Véry, Aaron J. Lorenz, Harkamal Walia
Software Mentions: 1
Published: over 7 years ago

10.1371/journal.pgen.1007773

Spen limits intestinal stem cell self-renewal
Cited by: 9
Author(s): Mahéva Andriatsilavo, Marine Stefanutti, Katarzyna Siudeja, Carolina N. Perdigoto, Benjamin Boumard, Louis Gervais, Alexandre Gillet-Markowska, Lara Al zouabi, François Schweisguth, Allison J. Bardin
Software Mentions: 1
Published: over 6 years ago

10.1371/journal.pgen.1009751

Bracoviruses recruit host integrases for their integration into caterpillar’s genome
Cited by: 12
Author(s): Zehua Wang, Xi-qian Ye, Yuenan Zhou, Xiaotong Wu, Rongmin Hu, Jiachen Zhu, Ting Chen, Elisabeth Huguet, Min Shi, Jean‐Michel Drezen, Jianhua Huang, Xue-Xin Chen
Software Mentions: 1
Published: over 3 years ago

10.1371/journal.pgen.1002930

Phylogenetic and Transcriptomic Analysis of Chemosensory Receptors in a Pair of Divergent Ant Species Reveals Sex-Specific Signatures of Odor Coding
Cited by: 183
Author(s): Xiaofan Zhou, Jesse Slone, Antonis Rokas, Shelley L. Berger, Jürgen Liebig, Anandasankar Ray, Danny Reinberg, Laurence J. Zwiebel
Software Mentions: 1
Published: over 12 years ago

10.1371/journal.pgen.1003543

RSR-2, the Caenorhabditis elegans Ortholog of Human Spliceosomal Component SRm300/SRRM2, Regulates Development by Influencing the Transcriptional Machinery
Cited by: 15
Author(s): Laura Fontrodona, Montserrat Porta-de-la-Riva, Tomás Morán, Wei Niu, Mònica Dı́az, David Aristizábal-Corrales, Alberto Villanueva, Simó Schwartz, V Reinke, Julián Cerón
Software Mentions: 1
Published: over 11 years ago

10.1371/journal.pgen.1006307

Altered mRNA Splicing, Chondrocyte Gene Expression and Abnormal Skeletal Development due to SF3B4 Mutations in Rodriguez Acrofacial Dysostosis
Cited by: 33
Author(s): Felipe Albuquerque Marques, Jessica Tenney, Iván Durán, Jorge Martı́n, Lisette Nevarez, Robert Pogue, Deborah Krakow, Daniel H. Cohn, Bing Li
Software Mentions: 1
Published: over 8 years ago

10.1371/journal.pgen.1006818

Analysis of DNA polymerase ν function in meiotic recombination, immunoglobulin class-switching, and DNA damage tolerance
Cited by: 10
Author(s): Kei-ichi Takata, Shelley Reh, Matthew J. Yousefzadeh, Maciej Jakub Żelazowski, Sarita Bhetawal, David Trono, Megan G. Lowery, Maria Sandoval, Yoko Takata, Yue Lu, Kevin Lin, Jianjun Shen, Donna F. Kusewitt, Kevin M. McBride, Francesca Cole, Richard D. Wood
Software Mentions: 1
Published: over 7 years ago

10.1371/journal.pgen.1002879

Dynamic Distribution of Linker Histone H1.5 in Cellular Differentiation
Cited by: 69
Author(s): Jingyu Li, Michaela Patterson, Hanna Mikkola, William E. Lowry, Siavash K. Kurdistani
Software Mentions: 1
Published: over 12 years ago

10.1371/journal.pgen.1002449

An siRNA Screen in Pancreatic Beta Cells Reveals a Role for Gpr27 in Insulin Production
Cited by: 49
Author(s): Gregory Ku, Zachary Pappalardo, Chun Chieh Luo, Michael S. German, Michael T. McManus
Software Mentions: 1
Published: about 13 years ago

10.1371/journal.pgen.1005647

Genome-Wide Association Study of Golden Retrievers Identifies Germ-Line Risk Factors Predisposing to Mast Cell Tumours
Cited by: 39
Author(s): Maja L. Arendt, Malin Melin, Noriko Tonomura, Michele Koltookian, Céline Courtay-Cahen, Netty Flindall, Joyce Bass, Kim M. Boerkamp, Katherine Megquir, Lisa Youell, Sue Murphy, Colleen E. McCarthy, Cheryl A. London, Gerard R. Rutteman, Mike Starkey, Kerstin Lindblad‐Toh
Software Mentions: 1
Published: over 9 years ago

10.1371/journal.pgen.1004100

Regulation of Synaptic nlg-1/Neuroligin Abundance by the skn-1/Nrf Stress Response Pathway Protects against Oxidative Stress
Cited by: 41
Author(s): Trisha A. Staab, Oleg Egrafov, James A. Knowles, Derek Sieburth
Software Mentions: 1
Published: about 11 years ago

10.1371/journal.pgen.1005444

Trans-Reactivation: A New Epigenetic Phenomenon Underlying Transcriptional Reactivation of Silenced Genes
Cited by: 1
Author(s): Maria Cristina Onorati, Walter Arancio, Vincenzo Cavalieri, Antonia Maria Rita Ingrassia, Giulio Pavesi, Davide Corona
Software Mentions: 1
Published: over 9 years ago

10.1371/journal.pgen.1003354

The Conserved SKN-1/Nrf2 Stress Response Pathway Regulates Synaptic Function in Caenorhabditis elegans
Cited by: 57
Author(s): Trisha A. Staab, Trevor C. Griffen, Connor Corcoran, Oleg V. Evgrafov, James A. Knowles, Derek Sieburth
Software Mentions: 1
Published: almost 12 years ago

10.1186/s12864-015-1793-9

A global analysis of the complex landscape of isoforms and regulatory networks of p63 in human cells and tissues
Cited by: 50
Author(s): Isha Sethi, Rose‐Anne Romano, Christian Gluck, Kirsten Smalley, Bořivoj Vojtěšek, Michael Buck, Satrajit Sinha
Software Mentions: 1
Published: over 9 years ago

10.1186/1471-2164-14-310

Discovering chromatin motifs using FAIRE sequencing and the human diploid genome
Cited by: 5
Author(s): Chi Yang, Michael Buck, Min-Hsuan Chen, Yun-Fan Chen, Hsin-Chi Lan, Jeremy J.W. Chen, Chao Cheng, Chun-Chi Liu
Software Mentions: 1
Published: almost 12 years ago

10.1186/1471-2164-14-150

Determination of dosage compensation of the mammalian X chromosome by RNA-seq is dependent on analytical approach
Cited by: 38
Author(s): Nathaniel K. Jue, Michael Murphy, Seth D. Kasowitz, Sohaib M Qureshi, Craig Obergfell, Sahar Elsisi, Robert J. Foley, Rachel J. O’Neill, Michael O’Neill
Software Mentions: 1
Published: almost 12 years ago

Projects: pypi: TopHat

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