10.1186/s12864-019-6095-1

Genomic characteristics and comparative genomics analysis of the endophytic fungus Sarocladium brachiariae
Cited by: 20
Author(s): Yang Yang, Xiaobao Liu, Jing Cai, Yipeng Chen, Boxun Li, Zhi‐Kai Guo, Huang Guixiu
Software Mentions: 1
Published: almost 7 years ago

10.1186/s12864-020-6732-8

A chromosome-scale assembly of the smallest Dothideomycete genome reveals a unique genome compaction mechanism in filamentous fungi
Cited by: 6
Author(s): Bo Wang, Xiaofei Liang, Mark L. Gleason, Tom Hsiang, Rong Zhang
Software Mentions: 1
Published: over 6 years ago

10.1186/s12864-019-5481-z

Rootstock-induced molecular responses associated with drought tolerance in sweet orange as revealed by RNA-Seq
Cited by: 21
Author(s): Luana Pereira Gonçalves, Raquel L. Boscariol-Camargo, Marco Aurélio Takita, Marcos Antônio Machado, Walter S. dos Soares Filho, Márcio Gilberto Cardoso Costa
Software Mentions: 1
Published: over 7 years ago

10.1186/s12864-017-4407-x

Analysis of the hybrid genomes of two field isolates of the soil-borne fungal species Verticillium longisporum
Cited by: 18
Author(s): Johan Fogelqvist, Georgios Tzelepis, Sarosh Bejai, Jonas Ilbäck, Arne Schwelm, Christina Dixelius
Software Mentions: 1
Published: over 8 years ago

10.1186/1471-2164-15-60

RNA-Seq transcriptome analysis of Spirodela dormancy without reproduction
Cited by: 32
Author(s): Wenqin Wang, Yongrui Wu, Joachim Messing
Software Mentions: 1
Published: over 12 years ago

10.1186/s12864-019-6276-y

Enhancement of de novo sequencing, assembly and annotation of the Mongolian gerbil genome with transcriptome sequencing and assembly from several different tissues
Cited by: 4
Author(s): Shifeng Cheng, Yuan Fu, Yaolei Zhang, Wenfei Xian, Hongli Wang, Benedikt Grothe, Xin Liu, Xun Xu, Achim Klug, Elizabeth A. McCullagh
Software Mentions: 1
Published: almost 7 years ago

10.1186/s12864-015-1541-1

Estrogen receptor beta impacts hormone-induced alternative mRNA splicing in breast cancer cells
Cited by: 28
Author(s): Dougba Noel Dago, Claudio Scafoglio, Antonio Rinaldi, Domenico Memoli, Giorgio Giurato, Giovanni Nassa, Maria Ravo, Francesca Rizzo, Roberta Tarallo, Alessandro Weisz
Software Mentions: 1
Published: over 11 years ago

10.1186/1471-2164-15-578

Identification of cucurbitacins and assembly of a draft genome for Aquilaria agallocha
Cited by: 35
Author(s): Chuan-Hung Chen, Tony Kuo, Ming Yang, Ting-Ying Chien, Mei-Ju Chu, Li-Chun Huang, Chien‐Yu Chen, Hsiao-Feng Lo, Shih‐Tong Jeng, Long‐Fang O. Chen
Software Mentions: 1
Published: over 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: over 13 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: over 13 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: about 9 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: about 6 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: about 11 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 15 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 12 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: almost 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 15 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 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: over 7 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: about 11 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: 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: over 6 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: over 12 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: over 10 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 12 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: over 5 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: about 9 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: almost 14 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: about 13 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: about 9 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: almost 14 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: almost 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: about 11 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: over 13 years ago

10.1371/journal.pgen.1003428

An Essential Role for Zygotic Expression in the Pre-Cellular Drosophila Embryo
Cited by: 57
Author(s): Zehra Ali-Murthy, Susan E. Lott, Michael B. Eisen, Thomas B. Kornberg
Software Mentions: 1
Published: over 13 years ago

10.1371/journal.pgen.1006949

Integration of the tricarboxylic acid (TCA) cycle with cAMP signaling and Sfl2 pathways in the regulation of CO2 sensing and hyphal development in Candida albicans
Cited by: 47
Author(s): Tao Li, Yulong Zhang, Shuru Fan, Clarissa J. Nobile, Guijian Guan, Guanghua Huang
Software Mentions: 1
Published: about 9 years ago

10.1371/journal.pgen.1003948

The SET Domain Proteins SUVH2 and SUVH9 Are Required for Pol V Occupancy at RNA-Directed DNA Methylation Loci
Cited by: 147
Author(s): Zhang-Wei Liu, Chen Shao, Cui‐Jun Zhang, Jin‐Xing Zhou, Suwei Zhang, Lin Li, She Chen, Huanwei Huang, Tao Cai, Xin‐Jian He
Software Mentions: 1
Published: over 12 years ago

10.1371/journal.pgen.1008642

The genomic landscape of undifferentiated embryonal sarcoma of the liver is typified by C19MC structural rearrangement and overexpression combined with TP53 mutation or loss
Cited by: 16
Author(s): Bhuvana Setty, Goodwin G. Jinesh, Michael A. Arnold, Fredrik Pettersson, Chia-Ho Cheng, Ling Cen, Sean Yoder, Jamie K. Teer, Elsa R. Flores, Damon R. Reed, Andrew S. Brohl
Software Mentions: 1
Published: over 6 years ago

10.1371/journal.pgen.1005768

Prp4 Kinase Grants the License to Splice: Control of Weak Splice Sites during Spliceosome Activation
Cited by: 25
Author(s): Daniela Eckert, Nicole Andrée, Aleh Razanau, Susanne Zock-Emmenthal, Martin Lützelberger, Susann Plath, Henning Schmidt, Ángel Guerra-Moreno, Luca Cozzuto, José Ayté, Norbert F. Käufer
Software Mentions: 1
Published: over 10 years ago

10.1371/journal.pgen.1003853

Genetic Architecture of Skewed X Inactivation in the Laboratory Mouse
Cited by: 42
Author(s): John D. Calaway, Alan B. Lenarcic, John P. Didion, Jeremy Wang, Jeremy B. Searle, Leonard McMillan, William Valdar, Fernando Pardo-Manuel de Villena
Software Mentions: 1
Published: almost 13 years ago

10.1371/journal.pgen.1008563

BLISTER-regulated vegetative growth is dependent on the protein kinase domain of ER stress modulator IRE1A in Arabidopsis thaliana
Cited by: 14
Author(s): Zheng-Hui Hong, Tao Qing, Daniel Schubert, Julia A. Kleinmanns, Jian‐Xiang Liu
Software Mentions: 1
Published: over 6 years ago

10.1371/journal.pgen.1003705

The Intronic Long Noncoding RNA ANRASSF1 Recruits PRC2 to the RASSF1A Promoter, Reducing the Expression of RASSF1A and Increasing Cell Proliferation
Cited by: 164
Author(s): Felipe Beckedorff, Ana C. Ayupe, Renan Crocci-Souza, Murilo Sena Amaral, Hidehiko Nakaya, Daniela T. Soltys, Carlos Frederico Martins Menck, Eduardo M. Reis, Sérgio Verjovski-Almeida
Software Mentions: 1
Published: about 13 years ago

10.1371/journal.pgen.1007042

Role of UHRF1 in de novo DNA methylation in oocytes and maintenance methylation in preimplantation embryos
Cited by: 91
Author(s): Shoji Maenohara, Motoko Unoki, Y. Toh, Hiroaki Ohishi, Jafar Sharif, Haruhiko Koseki, Hidetada Sasaki
Software Mentions: 1
Published: almost 9 years ago

10.1371/journal.pgen.1004893

Transcriptional Control of an Essential Ribozyme in Drosophila Reveals an Ancient Evolutionary Divide in Animals
Cited by: 5
Author(s): Sathiyanarayanan Manivannan, Lien B. Lai, Venkat Gopalan, Amanda Simcox
Software Mentions: 1
Published: over 11 years ago

10.1371/journal.pgen.1005713

Hnrnph1 Is A Quantitative Trait Gene for Methamphetamine Sensitivity
Cited by: 56
Author(s): Neema Yazdani, Clarissa C. Parker, Ying Shen, Eric Reed, Michael A. Guido, Loren A. Kole, Stacey L Kirkpatrick, Jackie E. Lim, Greta Sokoloff, Riyan Cheng, W. Evan Johnson, Abraham A. Palmer, Camron D. Bryant
Software Mentions: 1
Published: over 10 years ago

10.1371/journal.pgen.1003875

A KH-Domain RNA-Binding Protein Interacts with FIERY2/CTD Phosphatase-Like 1 and Splicing Factors and Is Important for Pre-mRNA Splicing in Arabidopsis
Cited by: 87
Author(s): Tao Chen, Peng Cui, Hao Chen, Shahjahan Ali, Shoudong Zhang, Liming Xiong
Software Mentions: 1
Published: almost 13 years ago

10.1371/journal.pgen.1003001

Calpain-5 Mutations Cause Autoimmune Uveitis, Retinal Neovascularization, and Photoreceptor Degeneration
Cited by: 76
Author(s): Vinit B. Mahajan, Jessica M. Skeie, Alexander G. Bassuk, John H. Fingert, Terry A. Braun, Heather T. Daggett, James C. Folk, Val C. Sheffield, Edwin M. Stone
Software Mentions: 1
Published: almost 14 years ago

10.1371/journal.pgen.1006820

Identification of a Sjögren's syndrome susceptibility locus at OAS1 that influences isoform switching, protein expression, and responsiveness to type I interferons
Cited by: 55
Author(s): He Li, Tove Ragna Reksten, John A. Ice, Jennifer A. Kelly, Indra Adrianto, Astrid Rasmussen, Shaofeng Wang, Bo He, Kiely Grundahl, Stuart B. Glenn, Corinne Miceli‐Richard, Simon Bowman, Sue Lester, Per Eriksson, Maija‐Leena Eloranta, Johan G. Brun, Lasse Gunnar Gøransson, Erna Harboe, Joel M. Guthridge, Kenneth M. Kaufman, Marika Kvarnström, Deborah S. Cunninghame Graham, Ketan Patel, Adam J. Adler, A. Darise Farris, Michael T. Brennan, James Chodosh, Rajaram Gopalakrishnan, Michael H. Weisman, Swamy Venuturupalli, Daniel J. Wallace, Kimberly S. Hefner, Glen D. Houston, Andrew J.W. Huang, Pamela J. Hughes, David M. Lewis, Lida Radfar, Evan S. Vista, Contessa E. Edgar, Michael D. Rohrer, Donald U. Stone, Timothy J. Vyse, John B. Harley, Patrick M. Gaffney, Judith A. James, Seán Turner, Ilias Alevizos, Juan-Manuel Anaya, Nelson L. Rhodus, Barbara Segal, Courtney G. Montgomery, R. Hal Scofield, Susan Kovats, Xavier Mariette, Lars Rönnblom, Torsten Witte, Maureen Rischmueller, Marie Wahren‐Herlenius, Roald Omdal, Roland Jönsson, Wan‐Fai Ng, Gunnel Nordmark, Christopher J. Lessard, Kathy L. Sivils
Software Mentions: 1
Published: about 9 years ago

10.1371/journal.pgen.1004292

Molecular Mechanisms of Hypoxic Responses via Unique Roles of Ras1, Cdc24 and Ptp3 in a Human Fungal Pathogen Cryptococcus neoformans
Cited by: 14
Author(s): Yun C. Chang, Ami Khanal Lamichhane, H. Martin Garraffo, Peter J. Walter, Maarten Leerkes, Kyung J. Kwon‐Chung
Software Mentions: 1
Published: over 12 years ago

10.1371/journal.pgen.1008818

Interaction of YAP with the Myb-MuvB (MMB) complex defines a transcriptional program to promote the proliferation of cardiomyocytes
Cited by: 19
Author(s): Marco Gründl, Susanne Walz, Laura Hauf, Melissa Schwab, Kerstin Marcela Werner, Susanne Spahr, Clemens Schulte, Hans Michael Maric, Carsten P. Ade, Stefan Gaubatz
Software Mentions: 1
Published: over 6 years ago

10.1371/journal.pgen.1004746

COE Loss-of-Function Analysis Reveals a Genetic Program Underlying Maintenance and Regeneration of the Nervous System in Planarians
Cited by: 42
Author(s): Martis W. Cowles, Kerilyn C. Omuro, Brianna N. Stanley, Carlo Giovanni Quintanilla, Ricardo M. Zayas
Software Mentions: 1
Published: almost 12 years ago

10.1371/journal.pgen.1004049

A 660-Kb Deletion with Antagonistic Effects on Fertility and Milk Production Segregates at High Frequency in Nordic Red Cattle: Additional Evidence for the Common Occurrence of Balancing Selection in Livestock
Cited by: 126
Author(s): Naveen Kumar Kadri, Goutam Sahana, Carole Charlier, Terhi Iso-Touru, Bernt Guldbrandtsen, Latifa Karim, U. Nielsen, Frank Panitz, G.P. Aamand, Nina Schulman, Michel Georges, Johanna Vilkki, Mogens Sandø Lund, Tom Druet
Software Mentions: 1
Published: over 12 years ago

10.1371/journal.pgen.1005379

A Splice Region Variant in LDLR Lowers Non-high Density Lipoprotein Cholesterol and Protects against Coronary Artery Disease
Cited by: 22
Author(s): Sólveig Grétarsdóttir, Hannes Helgason, Anna Helgadóttir, Ásgeir Sigurðsson, Guðmar Þorleifsson, Audur Magnusdottir, Ásmundur Oddsson, Valgerður Steinthórsdóttir, Thorunn Rafnar, Jacqueline de Graaf, Maryam S. Daneshpour, Mehdi Hedayati, Fereidoun Azizi, Niels Grarup, Torben Jørgensen, Henrik Vestergaard, Torben Hansen, Gudmundur I. Eyjolfsson, Ólöf Sigurðardóttir, Ísleifur Ólafsson, Lambertus A. Kiemeney, Oluf Pedersen, Patrick Sulem, Guðmundur Þorgeirsson, Daníel F. Guðbjartsson, Hilma Hólm, Unnur Þorsteinsdóttir, Kári Stefánsson
Software Mentions: 1
Published: almost 11 years ago

10.1371/journal.pgen.1006106

Dynamics of Chloroplast Translation during Chloroplast Differentiation in Maize
Cited by: 91
Author(s): Prakitchai Chotewutmontri, Alice Barkan
Software Mentions: 1
Published: about 10 years ago

10.1371/journal.pgen.1009402

NCK-associated protein 1 like (nckap1l) minor splice variant regulates intrahepatic biliary network morphogenesis
Cited by: 3
Author(s): Kimia Ghaffari, Lain X. Pierce, Maria Roufaeil, Isabel Gibson, Kevin Tae, Saswat Sahoo, James R. Cantrell, Olov Andersson, Jasmine Lau, Takuya Sakaguchi
Software Mentions: 1
Published: over 5 years ago

10.1371/journal.pmed.1001888

P2RX7 Purinoceptor: A Therapeutic Target for Ameliorating the Symptoms of Duchenne Muscular Dystrophy
Cited by: 50
Author(s): Anthony Sinadinos, Chris Young, Rasha Al-Khalidi, Anna Teti, Paweł Kaliński, Shafini Mohamad, Léonore Floriot, Tiphaine Henry, Gianluca Tozzi, Taiwen Jiang, Olivier Wurtz, Alexis Lefebvre, Mikhail Shugay, Jie Tong, David Vaudry, S. Arkle, Jean-Claude do-Rego, Dariusz C. Górecki
Software Mentions: 1
Published: almost 11 years ago

10.1371/journal.pntd.0002467

Proteomic Analysis of the Excretory-Secretory Products from Larval Stages of Ascaris suum Reveals High Abundance of Glycosyl Hydrolases
Cited by: 56
Author(s): Tao Wang, Katleen Van Steendam, Maarten Dhaenens, Johnny Vlaminck, Dieter Deforce, Aaron R. Jex, Robin B. Gasser, Peter Geldhof
Software Mentions: 1
Published: almost 13 years ago

10.1371/journal.pntd.0006025

L-arginine availability and arginase activity: Characterization of amino acid permease 3 in Leishmania amazonensis
Cited by: 28
Author(s): Juliana Ide Aoki, Sandra Márcia Muxel, Ricardo Andrade Zampieri, Stephanie Maia Acuña, Juliane Cristina Ribeiro Fernandes, Rubia Heloisa Vanderlinde, Maria Carmen Oliveira de Pinho Sales, Lucile Maria Floeter‐Winter
Software Mentions: 1
Published: almost 9 years ago

10.1371/journal.pntd.0005313

Comparative and functional triatomine genomics reveals reductions and expansions in insecticide resistance-related gene families
Cited by: 43
Author(s): Lucila Traverso, Andrés Lavore, Ivana Sierra, Victorio Palacio, Jesús Martínez-Barnetche, José Manuel Latorre-Estivalis, Gastón Mougabure‐Cueto, Flavio Francini, Marcelo G. Lorenzo, Mario H. Rodrı́guez, Sheila Ons, Rolando Rivera‐Pomar
Software Mentions: 1
Published: over 9 years ago

10.1371/journal.pntd.0001854

RNAseq Analysis of the Parasitic Nematode Strongyloides stercoralis Reveals Divergent Regulation of Canonical Dauer Pathways
Cited by: 77
Author(s): Jonathan D. Stoltzfus, Samuel S. Minot, Matthew Berriman, Thomas J. Nolan, James B. Lok
Software Mentions: 1
Published: almost 14 years ago

10.1371/journal.pone.0148940

Genome-Wide Discovery of Long Non-Coding RNAs in Rainbow Trout
Cited by: 74
Author(s): Rafet Al-Tobasei, Bam Paneru, Mohamed Salem
Software Mentions: 1
Published: over 10 years ago

10.1371/journal.pone.0099625

RNA-Seq Transcriptome Profiling Identifies CRISPLD2 as a Glucocorticoid Responsive Gene that Modulates Cytokine Function in Airway Smooth Muscle Cells
Cited by: 127
Author(s): Blanca E. Himes, Xiaofeng Jiang, Peter J. Wagner, Ruoxi Hu, Qiyu Wang, Barbara J. Klanderman, Reid M. Whitaker, Qingling Duan, Jessica Lasky‐Su, Christina Nikolos, William F. Jester, Martin Johnson, Reynold A. Panettieri, Kelan G. Tantisira, Scott T. Weiss, Quan Lu
Software Mentions: 1
Published: about 12 years ago

10.1371/journal.pone.0085284

Deep Sequencing–Based Transcriptome Profiling Reveals Comprehensive Insights into the Responses of Nicotiana benthamiana to Beet necrotic yellow vein virus Infections Containing or Lacking RNA4
Cited by: 24
Author(s): Haojun Fan, Haiwen Sun, Ying Wang, Yong Liang Zhang, Xianbing Wang, Dawei Li, Jialin Yu, Chenggui Han
Software Mentions: 1
Published: over 12 years ago

10.1371/journal.pone.0127755

In Vitro Model for Studying Esophageal Epithelial Differentiation and Allergic Inflammatory Responses Identifies Keratin Involvement in Eosinophilic Esophagitis
Cited by: 39
Author(s): Kiran Kc, Marc E. Rothenberg, Joseph D. Sherrill
Software Mentions: 1
Published: about 11 years ago

10.1371/journal.pone.0102868

Sequence, Structural and Expression Divergence of Duplicate Genes in the Bovine Genome
Cited by: 13
Author(s): Xiaoping Liao, Hua Bao, Yan Meng, Graham Plastow, S. S. Moore, Paul Stothard
Software Mentions: 1
Published: about 12 years ago

10.1371/journal.pone.0125890

Integrating Transcriptome and Genome Re-Sequencing Data to Identify Key Genes and Mutations Affecting Chicken Eggshell Qualities
Cited by: 18
Author(s): Quan Zhang, Feng Zhu, Long Liu, Chuan Zheng, De He Wang, Zhuo Cheng Hou, Zhiliang Ning
Software Mentions: 1
Published: over 11 years ago

10.1371/journal.pone.0198323

Genome wide analysis of TLR1/2- and TLR4-activated SZ95 sebocytes reveals a complex immune-competence and identifies serum amyloid A as a marker for activated sebaceous glands
Cited by: 24
Author(s): Dániel Törőcsik, Dóra Kovács, Szilárd Póliska, Zita Szentkereszty-Kovács, Marianna Lovászi, Katalin Hegyi, Andrea Szegedi, Christos C. Zouboulis, Mona Ståhle
Software Mentions: 1
Published: about 8 years ago

10.1371/journal.pone.0080306

Comprehensive Analysis of Long Non-Coding RNAs in Ovarian Cancer Reveals Global Patterns and Targeted DNA Amplification
Cited by: 72
Author(s): Rozita Akrami, Anders Jacobsen, Jessica I. Hoell, Nikolaus Schultz, Chris Sander, Erik Larsson
Software Mentions: 1
Published: almost 13 years ago

10.1371/journal.pone.0138982

Whose Gene Is It Anyway? The Effect of Preparation Purity on Neutrophil Transcriptome Studies
Cited by: 36
Author(s): Huw B. Thomas, Robert J. Moots, Steven W. Edwards, Helen L. Wright
Software Mentions: 1
Published: almost 11 years ago

10.1371/journal.pone.0219413

Transcriptional Differences in Peanut (Arachis hypogaea L.) Seeds at the Freshly Harvested, After-ripening and Newly Germinated Seed Stages: Insights into the Regulatory Networks of Seed Dormancy Release and Germination
Cited by: 13
Author(s): Pingli Xu, Guiying Tang, Weipei Cui, Guangxia Chen, Changle Ma, Jieqiong Zhu, Pengxiang Li, Lei Shan, Zhanji Liu, Shubo Wan
Software Mentions: 1
Published: over 6 years ago

10.1371/journal.pone.0136932

Network Modeling Reveals Cross Talk of MAP Kinases during Adaptation to Caspofungin Stress in Aspergillus fumigatus
Cited by: 57
Author(s): Robert Altwasser, Clara Baldin, Jakob Weber, Reinhard Guthke, Olaf Kniemeyer, Axel A. Brakhage, Jörg Linde, Vito Valiante
Software Mentions: 1
Published: almost 11 years ago

10.1371/journal.pone.0090989

Deep RNA Sequencing Reveals Hidden Features and Dynamics of Early Gene Transcription in Paramecium bursaria Chlorella Virus 1
Cited by: 37
Author(s): Guillaume Blanc, Michael Mozar, Irina V. Agarkova, James R. Gurnon, Giane M. Yanai-Balser, Janet M. Rowe, Yuannan Xia, Jean-Jack M. Riethoven, David D. Dunigan, James L. Van Etten
Software Mentions: 1
Published: over 12 years ago

10.1371/journal.pone.0161256

The Genome-Wide Analysis of Carcinoembryonic Antigen Signaling by Colorectal Cancer Cells Using RNA Sequencing
Cited by: 16
Author(s): Olga Bajenova, А. В. Горбунова, Igor Evsyukov, Mikhail Rayko, Svetlana Gapon, Ekaterina Bozhokina, A.A. Shishkin, Stephen J. O’Brien
Software Mentions: 1
Published: almost 10 years ago

10.1371/journal.pone.0105267

Genomic Distribution of H3K9me2 and DNA Methylation in a Maize Genome
Cited by: 127
Author(s): Patrick T. West, Qing Li, Lexiang Ji, Steven R. Eichten, Jawon Song, Matthew Vaughn, Robert J. Schmitz, Nathan M. Springer
Software Mentions: 1
Published: about 12 years ago

10.1371/journal.pone.0168744

Signatures of Crested Ibis MHC Revealed by Recombination Screening and Short-Reads Assembly Strategy
Cited by: 2
Author(s): Liao Chang, Shiyang He, Danqing Mao, Yuanhong Liu, Zijun Xiong, Deliang Fu, Bo Li, Shuguang Wei, Xun Xu, Shengbin Li, Hui Yuan
Software Mentions: 1
Published: over 9 years ago

10.1371/journal.pone.0158279

Transcriptome Profiling Reveals the Antitumor Mechanism of Polysaccharide from Marine Algae Gracilariopsis lemaneiformis
Cited by: 26
Author(s): Yani Kang, Hua Li, Jun Wu, Xiaoting Xu, Xue Sun, Xiaodong Zhao, Nianjun Xu
Software Mentions: 1
Published: about 10 years ago

10.1371/journal.pone.0140487

Alternative Splicing in Next Generation Sequencing Data of Saccharomyces cerevisiae
Cited by: 36
Author(s): Konrad Schreiber, Gergely Csaba, Martin Haslbeck, Ralf Zimmer
Software Mentions: 1
Published: almost 11 years ago

10.1371/journal.pone.0190935

Relaxin reverses inflammatory and immune signals in aged hearts
Cited by: 25
Author(s): Brian Martin, Beth A Gabris-Weber, Rajiv P. Reddy, Guillermo Romero, Ansuman Chattopadhyay, Guy Salama
Software Mentions: 1
Published: over 8 years ago

10.1371/journal.pone.0182032

Identification of RNA biomarkers for chemical safety screening in mouse embryonic stem cells using RNA deep sequencing analysis
Cited by: 6
Author(s): Hidenori Tani, Jun-ichi Takeshita, Hiroshi Aoki, Kaoru Nakamura, Ryosuke Abe, Akinobu Toyoda, Yasunori Endo, Sadaaki Miyamoto, Masashi Gamo, Hiroaki Sato, Masaki Takasu
Software Mentions: 1
Published: about 9 years ago

10.1371/journal.pone.0148558

GAD2 Alternative Transcripts in the Human Prefrontal Cortex, and in Schizophrenia and Affective Disorders
Cited by: 23
Author(s): Kasey Davis, Ran Tao, Chao Li, Yuan Gao, Marjorie C. Gondré‐Lewis, Barbara K. Lipska, Joo Heon Shin, Bin Xie, Tianzhang Ye, Daniel R. Weinberger, Joel E. Kleinman, Thomas M. Hyde
Software Mentions: 1
Published: over 10 years ago

10.1371/journal.pone.0131559

Genome-, Transcriptome- and Proteome-Wide Analyses of the Gliadin Gene Families in Triticum urartu
Cited by: 23
Author(s): Yanlin Zhang, Guangbin Luo, Dongcheng Liu, Dongzhi Wang, Wenlong Yang, Jiazhu Sun, Aimin Zhang, Kai Zhan
Software Mentions: 1
Published: about 11 years ago

10.1371/journal.pone.0173438

RNA-sequence analysis of gene expression from honeybees (Apis mellifera) infected with Nosema ceranae
Cited by: 43
Author(s): Bouabid Badaoui, A. Fougeroux, Fabien Petit, Anna Anselmo, C. Gorni, Marco Cucurachi, Antonella Cersini, Anna Granato, G. Cardeti, Giovanni Formato, Franco Mutinelli, Elisabetta Giuffra, J. L. Williams, Sara Botti
Software Mentions: 1
Published: over 9 years ago

10.1371/journal.pone.0144118

Comparative Transcriptome Analysis of Recessive Male Sterility (RGMS) in Sterile and Fertile Brassica napus Lines
Cited by: 36
Author(s): Cunmin Qu, Fuyou Fu, Miao Liu, Hongwei Zhao, Chuan-Chuan Liu, Jiana Li, Zhongjie Tang, Xinhua Xu, Xiao‐Yang Qiu, Rui Wang, Kun Lu
Software Mentions: 1
Published: over 10 years ago

10.1371/journal.pone.0135337

Rapid Characterization of Microalgae and Microalgae Mixtures Using Matrix-Assisted Laser Desorption Ionization Time-Of-Flight Mass Spectrometry (MALDI-TOF MS)
Cited by: 26
Author(s): Duane Barbano, Regina Diaz, Lin Zhang, Todd R. Sandrin, Henri Gerken, Thomas A. Dempster
Software Mentions: 1
Published: about 11 years ago

10.1371/journal.pone.0170441

Testicular Dysgenesis Syndrome and Long-Lasting Epigenetic Silencing of Mouse Sperm Genes Involved in the Reproductive System after Prenatal Exposure to DEHP
Cited by: 50
Author(s): Ludwig Stenz, Jessica Escoffier, Rita Rahban, Serge Nef, Ariane Paoloni-Giacobino
Software Mentions: 1
Published: over 9 years ago

10.1371/journal.pone.0118295

RNA-Seq Analysis Identifies New Genes Regulated by the Histone-Like Nucleoid Structuring Protein (H-NS) Affecting Vibrio cholerae Virulence, Stress Response and Chemotaxis
Cited by: 53
Author(s): Hongxia Wang, Julio C. Ayala, Jorge A. Benítez, Alcino J. Silva
Software Mentions: 1
Published: over 11 years ago

10.1371/journal.pone.0158349

Supervillin Is a Component of the Hair Cell’s Cuticular Plate and the Head Plates of Organ of Corti Supporting Cells
Cited by: 6
Author(s): Lana M. Pollock, Nilay Gupta, Xi Chen, Elizabeth J. Luna, Brian M. McDermott
Software Mentions: 1
Published: about 10 years ago

10.1371/journal.pone.0236823

Unraveling the mechanisms of resistance to Sclerotium rolfsii in peanut (Arachis hypogaea L.) using comparative RNA-Seq analysis of resistant and susceptible genotypes
Cited by: 25
Author(s): Tejas C. Bosamia, Sneha M. Dodia, Gyan P. Mishra, Suhail Ahmad, Binal Joshi, Polavakkalipalayam P. Thirumalaisamy, Narendra Kumar, A. L. Rathnakumar, Chandramohan Sangh, Abhay Kumar, Radhakrishnan Thankappan
Software Mentions: 1
Published: about 6 years ago

10.1371/journal.pone.0140756

Functional Analysis and RNA Sequencing Indicate the Regulatory Role of Argonaute1 in Tomato Compound Leaf Development
Cited by: 7
Author(s): Tian Wang, Rui Lin, Liwei Wen, Daqi Fu, Beiwei Zhu, Yunbo Luo, Hongliang Zhu
Software Mentions: 1
Published: almost 11 years ago

10.1371/journal.pone.0199437

Comparative analysis of the male inflorescence transcriptome profiles of an ms22 mutant of maize
Cited by: 2
Author(s): Yanni Gao, Lijuan Zhang, ShengChao Zhao, Yongjun Yan
Software Mentions: 1
Published: about 8 years ago

10.1371/journal.pone.0173824

Transcriptomic profile of leg muscle during early growth in chicken
Cited by: 52
Author(s): Qingwu Xue, Genxi Zhang, Tingting Li, Jiaojiao Ling, Xiangqian Zhang, Jinyu Wang
Software Mentions: 1
Published: over 9 years ago

10.1371/journal.pone.0213305

Transcriptome response of roots to salt stress in a salinity-tolerant bread wheat cultivar
Cited by: 61
Author(s): Nazanin Amirbakhtiar, Ahmad Ismaili, Mohammad Reza Ghaffari, Farhad Nazarian Firouzabadi, Zahra‐Sadat Shobbar
Software Mentions: 1
Published: over 7 years ago

10.1371/journal.pone.0106818

Transcriptome Profiling of Spinal Muscular Atrophy Motor Neurons Derived from Mouse Embryonic Stem Cells
Cited by: 36
Author(s): Miho Matsushima, Ashlee W. Harris, Brewster F. Kingham, Casey J. Lumpkin, Lynn M. Opdenaker, Suzanne M. McCahan, Wenlan Wang, Matthew E.R. Butchbach
Software Mentions: 1
Published: almost 12 years ago

10.1371/journal.pone.0142434

Digital Gene Expression Analysis Based on De Novo Transcriptome Assembly Reveals New Genes Associated with Floral Organ Differentiation of the Orchid Plant Cymbidium ensifolium
Cited by: 12
Author(s): Fengming Yang, Genfa Zhu
Software Mentions: 1
Published: almost 11 years ago

10.1371/journal.pone.0161410

Elevating CLIC4 in Multiple Cell Types Reveals a TGF-β Dependent Induction of a Dominant Negative Smad7 Splice Variant
Cited by: 11
Author(s): Anjali Shukla, Yihan Yang, Sara Madanikia, Yan Ho, Mangmang Li, Vanesa C. Sanchez, Christophe Cataisson, Jing Huang, Stuart H. Yuspa
Software Mentions: 1
Published: about 10 years ago

10.1371/journal.pone.0177066

Characterization of joining sites of a viral histone H4 on host insect chromosomes
Cited by: 4
Author(s): Sunil Kumar, Jin Kyo Jung, Yonggyun Kim
Software Mentions: 1
Published: over 9 years ago

10.1371/journal.pone.0206765

An integrated analysis of mRNA and sRNA transcriptional profiles in tomato root: Insights on tomato wilt disease
Cited by: 15
Author(s): Min Zhao, Huimin Ji, Ying Gao, Xin-Xin Cao, Hui‐Ying Mao, Shan Ouyang, Peng Liu
Software Mentions: 1
Published: almost 8 years ago

10.1371/journal.pone.0060837

Generation of Mast Cells from Mouse Fetus: Analysis of Differentiation and Functionality, and Transcriptome Profiling Using Next Generation Sequencer
Cited by: 8
Author(s): Nobuyuki Fukuishi, Yuusuke Igawa, Tomoyo Kunimi, Hirofumi Hamano, Masao Toyota, Hironobu Takahashi, Hiromichi Kenmoku, Yasuyuki Yagi, Nobuaki Matsui, Masaaki Akagi
Software Mentions: 1
Published: over 13 years ago

10.1371/journal.pone.0137157

Transcriptome Characterization of Developing Bean (Phaseolus vulgaris L.) Pods from Two Genotypes with Contrasting Seed Zinc Concentrations
Cited by: 13
Author(s): Carolina Astudillo-Reyes, Andrea C. Fernandez, Karen A. Cichy
Software Mentions: 1
Published: almost 11 years ago

10.1371/journal.pone.0181656

The exported chaperone Hsp70-x supports virulence functions for Plasmodium falciparum blood stage parasites
Cited by: 43
Author(s): Sarah C. Charnaud, Matthew W. A. Dixon, Catherine Q Nie, Lia Chappell, Paul R Sanders, Thomas Nebl, Eric Hanssen, Matthew Berriman, Jo‐Anne Chan, Adam J. Blanch, James G. Beeson, Julian C. Rayner, Jude M. Przyborski, Leann Tilley, Brendan S. Crabb, Paul R. Gilson
Software Mentions: 1
Published: about 9 years ago