Ecosyste.ms: Papers

10.1038/s41598-017-15145-7

Comparison of Transcriptomic Platforms for Analysis of Whole Blood from Ebola-Infected Cynomolgus Macaques
Cited by: 28
Author(s): Emily Speranza, Louis A. Altamura, Kirsten A. Kulcsar, Sandra L. Bixler, Cynthia A. Rossi, Randal J. Schoepp, Elyse R. Nagle, William Aguilar, Christina E. Douglas, Korey L. Delp, Timothy D. Minogue, Gustavo Palacios, Arthur J. Goff, John H. Connor
Software Mentions: 3
Published: about 7 years ago

10.1038/s41598-017-13844-9

Genome-wide discovery of long intergenic noncoding RNAs and their epigenetic signatures in the rat
Cited by: 3
Author(s): Aimin Li, Zhongyin Zhou, Xinhong Hei, Newton O. Otecko, Junying Zhang, Yajun Liu, Huanfu Zhou, Zhiqiang Zhao, Lei Wang
Software Mentions: 3
Published: about 7 years ago

10.1038/s41598-017-14083-8

Profiling of miRNAs and target genes related to cystogenesis in ADPKD mouse models
Cited by: 32
Author(s): Yu Mi Woo, Do Yeon Kim, Nam Jin Koo, Yong Min Kim, Sun Young Lee, Je Yeong Ko, Yubin Shin, Bo Hye Kim, Hyowon Mun, Seonju Choi, Eun Ji Lee, Jeong Oh Shin, Eun Young Park, Jinwoong Bok, Jong Hoon Park
Software Mentions: 3
Published: about 7 years ago

10.1038/s41598-017-14239-6

Gene expression atlas of fruit ripening and transcriptome assembly from RNA-seq data in octoploid strawberry (Fragaria × ananassa)
Cited by: 82
Author(s): José F. Sánchez-Sevilla, José G. Vallarino, Sonia Osorio, Aureliano Bombarely, David Posé, Catharina Merchante, Miguel A. Botella, Iraida Amaya, Victoriano Valpuesta
Software Mentions: 3
Published: about 7 years ago

10.1038/s41598-017-13186-6

Genome-wide open chromatin regions and their effects on the regulation of silk protein genes in Bombyx mori
Cited by: 13
Author(s): Quan Zhang, Tingcai Cheng, Shengkai Jin, Youbing Guo, Yuqian Wu, Duolian Liu, Xiaomin Xu, Yueting Sun, Zhiqing Li, Huawei He, Qingyou Xia
Software Mentions: 3
Published: about 7 years ago

10.1038/s41598-017-12747-z

Role of autophagy in cell-penetrating peptide transfection model
Cited by: 23
Author(s): Moataz Dowaidar, Maxime Gestin, Carmine Pasquale Cerrato, Mohammed Hakim Jafferali, Helerin Margus, Paula Ann Kivistik, Kariem Ezzat, Einar Hallberg, Margus Pooga, Mattias Hällbrink, Ülo Langel
Software Mentions: 3
Published: about 7 years ago

10.1038/s41598-017-11304-y

Dynamic Changes in the Splenic Transcriptome of Chickens during the Early Infection and Progress of Marek’s Disease
Cited by: 5
Author(s): Di Lu, Maikun Teng, Huawei Li, Huizhen Li, Shenglin Ma, Pengwei Zhao, Xiujie Li, Ruiguang Deng, Gaiping Zhang, Jun Luo
Software Mentions: 3
Published: about 7 years ago

10.18632/oncotarget.25764

Lyophilized human cells stored at room temperature preserve multiple RNA species at excellent quality for RNA sequencing
Cited by: 5
Author(s): Lilla Ozgyin, Attila Horváth, Bálint László Bálint
Software Mentions: 3
Published: over 6 years ago

10.7717/peerj.201

Characterization of RNA in exosomes secreted by human breast cancer cell lines using next-generation sequencing
Cited by: 173
Author(s): Piroon Jenjaroenpun, Yuliya Kremenska, Vrundha M. Nair, Maksym Kremenskoy, Baby Joseph, Igor V. Kurochkin
Software Mentions: 3
Published: about 11 years ago

10.1186/s12870-014-0188-4

Metabolite and transcript profiling of berry skin during fruit development elucidates differential regulation between Cabernet Sauvignon and Shiraz cultivars at branching points in the polyphenol pathway
Cited by: 109
Author(s): Asfaw Degu, Uri Hochberg, Noga Sikron, Luca Venturini, Genny Buson, Ryan Ghan, Inbar Plaschkes, Albert Batushansky, Vered Chalifa‐Caspi, Fulvio Mattivi, Massimo Delledonne, Mario Pezzotti, Shimon Rachmilevitch, Grant R. Cramer, Aaron Fait
Software Mentions: 3
Published: over 10 years ago

10.1530/JME-15-0119

Gene expression changes in subcutaneous adipose tissue due to Cushing's disease
Cited by: 24
Author(s): Irit Hochberg, Innocence Harvey, Quynh Tran, Erin J. Stephenson, Ariel L. Barkan, Alan R. Saltiel, William F. Chandler, Dave Bridges
Software Mentions: 3
Published: over 9 years ago

10.7717/peerj.11919

The whole-genome and expression profile analysis of <i>WRKY</i> and <i>RGAs</i> in <i>Dactylis glomerata</i> showed that <i>DG6C02319.1</i> and Dg<i>WRKYs</i> may cooperate in the immunity against rust
Cited by: 4
Author(s): Juncai Ren, Jialing Hu, Ailing Zhang, Shuping Ren, Tingting Jing, Xiaoshan Wang, Min Sun, Linkai Huang, Bing Zeng
Software Mentions: 3
Published: over 3 years ago

10.1186/1479-5876-9-155

SITC/iSBTc Cancer Immunotherapy Biomarkers Resource Document: Online resources and useful tools - a compass in the land of biomarker discovery
Cited by: 26
Author(s): Davide Bedognetti, James M Balwit, Ena Wang, Mary L. Disis, Cedrik M. Britten, Lucia Gemma Delogu, Sara Tomei, Bernard A. Fox, Thomas F. Gajewski, Francesco M. Marincola, Lisa H. Butterfield
Software Mentions: 3
Published: about 13 years ago

10.1038/s41598-017-10376-0

Genomic and transcriptomic analyses reveal differential regulation of diverse terpenoid and polyketides secondary metabolites in Hericium erinaceus
Cited by: 28
Author(s): Juan Chen, Zhiai Xu, Yan Yang, Yong Xing, Qi Zhang, Jia Mei Li, Ke Ma, Hong Wei Liu, Shun Guo
Software Mentions: 3
Published: about 7 years ago

10.7717/peerj.8947

Transcriptomic changes across the life cycle of <i>Trypanosoma cruzi II</i>
Cited by: 8
Author(s): Lissa Cruz-Saavedra, Gustavo Adolfo Vallejo, Felipe Guhl, Juan David Ramírez
Software Mentions: 3
Published: over 4 years ago

10.1038/s41598-017-07872-8

A Genome-Wide Identification of the WRKY Family Genes and a Survey of Potential WRKY Target Genes in Dendrobium officinale
Cited by: 28
Author(s): Chunmei He, Jaime A. Teixeira da Silva, Jian‐Wen Tan, Jianxia Zhang, Xiaoping Pan, Mingzhi Li, Jian‐Ping Luo, Jun Duan
Software Mentions: 3
Published: over 7 years ago

10.1038/s41598-017-09680-6

Genome-wide comparative analysis of H3K4me3 profiles between diploid and allotetraploid cotton to refine genome annotation
Cited by: 10
Author(s): Qi You, Xin Yi, Kang Zhang, Chunchao Wang, Xuelian Ma, Xueyan Zhang, Wenying Xu, Fuguang Li, Zhen Su
Software Mentions: 3
Published: over 7 years ago

10.1038/s41598-017-08239-9

The Candida albicans HIR histone chaperone regulates the yeast-to-hyphae transition by controlling the sensitivity to morphogenesis signals
Cited by: 17
Author(s): Sabrina Jenull, Michael Tscherner, Megha Gulati, Clarissa J. Nobile, Neeraj Chauhan, Karl Kuchler
Software Mentions: 3
Published: over 7 years ago

10.1186/s12870-016-0775-7

B chromosome contains active genes and impacts the transcription of A chromosomes in maize (Zea mays L.)
Cited by: 53
Author(s): Wei Huang, Yan Du, Xin Zhao, Weiwei Jin
Software Mentions: 3
Published: over 8 years ago

10.1038/s41389-019-0178-3

Repression of transcription factor AP-2 alpha by PPARγ reveals a novel transcriptional circuit in basal-squamous bladder cancer
Cited by: 21
Author(s): Haruo Yamashita, Yuka Imamura Kawasawa, Lauren Shuman, Zongyu Zheng, Tracy S. Tran, Vonn Walter, Joshua I. Warrick, Guoli Chen, Hikmat Al‐Ahmadie, Matthew Kaag, Pak Kin Wong, Jay D. Raman, David J. DeGraff
Software Mentions: 3
Published: almost 5 years ago

10.7717/peerj.382

Characterisation of the horse transcriptome from immunologically active tissues
Cited by: 6
Author(s): Joanna Moreton, Sunir Malla, A. Aziz Aboobaker, Rachael Tarlinton, Richard D. Emes
Software Mentions: 3
Published: over 10 years ago

10.1038/s41388-020-01614-3

Comprehensive characterisation of intronic mis-splicing mutations in human cancers
Cited by: 20
Author(s): Hyunchul Jung, Kang Seon Lee, Jung Kyoon Choi
Software Mentions: 3
Published: almost 4 years ago

10.7717/peerj.8144

Navigating oxygen deprivation: liver transcriptomic responses of the red eared slider turtle to environmental anoxia
Cited by: 10
Author(s): Kyle K. Biggar, Jing Zhang, Kenneth B. Storey
Software Mentions: 3
Published: almost 5 years ago

10.7717/peerj.2829

Hydrogel scaffolds promote neural gene expression and structural reorganization in human astrocyte cultures
Cited by: 12
Author(s): V. Bleu Knight, Elba E. Serrano
Software Mentions: 3
Published: almost 8 years ago

10.18632/oncotarget.25672

The calcium channel proteins ORAI3 and STIM1 mediate TGF-β induced<i>Snai1</i>expression
Cited by: 21
Author(s): Atrayee Bhattacharya, Janani Kumar, Kole Hermanson, Yuyang Sun, Humaira Qureshi, Danielle Perley, Adam Scheidegger, Brij B. Singh, Archana Dhasarathy
Software Mentions: 3
Published: over 6 years ago

10.1038/srep27640

Comprehensive analysis of multi-tissue transcriptome data and the genome-wide investigation of GRAS family in Phyllostachys edulis
Cited by: 11
Author(s): Hansheng Zhao, Lili Dong, Huayu Sun, Lichao Li, Yonggen Lou, Lili Wang, Zuyao Li, Zhimin Gao
Software Mentions: 3
Published: over 8 years ago

10.1038/srep27357

Identification of differentially expressed genes from multipotent epithelia at the onset of an asexual development
Cited by: 16
Author(s): Lorenzo Ricci, Ankita Chaurasia, Pascal Lapébie, Philippe Dru, Rebecca R. Helm, Richard R. Copley, Stefano Tiozzo
Software Mentions: 3
Published: over 8 years ago

10.1186/s12870-021-03129-9

Tomato transcriptomic response to Tuta absoluta infestation
Cited by: 11
Author(s): Daniela D’Esposito, Daniele Manzo, Alessandro Ricciardi, Antonio P. Garonna, Antonino De Natale, Luigi Frusciante, Francesco Pennacchio, Maria Raffaella Ercolano
Software Mentions: 3
Published: over 3 years ago

10.1002/prp2.386

Rifampin modulation of xeno- and endobiotic conjugating enzyme mRNA expression and associated microRNAs in human hepatocytes
Cited by: 16
Author(s): Brandon T. Gufford, Jason Robarge, Michael T. Eadon, Hongyu Gao, Hai Lin, Yunlong Liu, Zeruesenay Desta, Todd C. Skaar
Software Mentions: 3
Published: over 6 years ago

10.1038/srep26813

RNA-Seq reveals 10 novel promising candidate genes affecting milk protein concentration in the Chinese Holstein population
Cited by: 59
Author(s): Cong Li, Wentao Cai, Chixing Zhou, Hongwei Yin, Ziqi Zhang, Juan J. Loor, Dongxiao Sun, Qin Zhang, Jianfeng Liu, Shengli Zhang
Software Mentions: 3
Published: over 8 years ago

10.1038/srep26090

The nitrogen responsive transcriptome in potato (Solanum tuberosum L.) reveals significant gene regulatory motifs
Cited by: 31
Author(s): José Héctor Gálvez, Helen H. Tai, M. Lagüe, Bernie J. Zebarth, Martina V. Strömvik
Software Mentions: 3
Published: over 8 years ago

10.1038/srep26114

Comparative analysis of the integument transcriptomes of the black dilute mutant and the wild-type silkworm Bombyx mori
Cited by: 17
Author(s): Songyuan Wu, Xiaoling Tong, Chenxing Peng, Xiong Guan, Kunpeng Lu, Hai Hu, Tan D, Chunlin Li, Minjin Han, Cheng Lü, Fangyin Dai
Software Mentions: 3
Published: over 8 years ago

10.1038/srep25619

Integrative analysis of extracellular and intracellular bladder cancer cell line proteome with transcriptome: improving coverage and validity of –omics findings
Cited by: 12
Author(s): Agnieszka Latosinska, Manousos Makridakis, Maria Frantzi, Daniel Borràs, Bart Janssen, William Mullen, Jérôme Zoidakis, Axel S. Merseburger, Vera Jankowski, Harald Mischak, Antonia Vlahou
Software Mentions: 3
Published: over 8 years ago

10.14814/phy2.13534

Human hair follicle transcriptome profiling: a minimally invasive tool to assess molecular adaptations upon low‐volume, high‐intensity interval training
Cited by: 7
Author(s): Jing Zhang, Sarah J. Wallace, Maria Y. Shiu, Ingrid Smith, Shawn G. Rhind, Valérie S. Langlois
Software Mentions: 3
Published: almost 7 years ago

10.1038/srep23219

Identification of genes for controlling swine adipose deposition by integrating transcriptome, whole-genome resequencing, and quantitative trait loci data
Cited by: 42
Author(s): Kai Xing, Feng Zhu, Lichao Zhai, ShaoKang Chen, Zhen Tan, Yangyang Sun, Zhuocheng Hou, ChuDuan Wang
Software Mentions: 3
Published: over 8 years ago

10.1038/srep20837

Differential Expression of Genes and DNA Methylation associated with Prenatal Protein Undernutrition by Albumen Removal in an avian model
Cited by: 15
Author(s): Els Willems, Carlos Guerrero-Bosagna, Eddy Decuypere, Steven Janssens, Johan Buyse, Nadine Buys, Per Jensen, Nadia Everaert
Software Mentions: 3
Published: almost 9 years ago

10.1371/journal.pgen.1009370

Hybrid seed incompatibility in Capsella is connected to chromatin condensation defects in the endosperm
Cited by: 13
Author(s): Katarzyna Dziasek, Lauriane Simon, Clément Lafon‐Placette, Benjamin Laenen, Cecilia Wärdig, Juan Santos‐González, Tanja Slotte, Claudia Köhler
Software Mentions: 3
Published: almost 4 years ago

10.1186/s12870-020-02673-0

Resistance analysis of cherry rootstock ‘CDR-1’ (Prunus mahaleb) to crown gall disease
Cited by: 5
Author(s): Chengcheng Liang, Tian Wang, Rendun Wu, Mei Zhao, Yong Zhao, Yuliang Cai
Software Mentions: 3
Published: about 4 years ago

10.1038/srep21507

Comprehensive transcriptomic and proteomic characterization of human mesenchymal stem cells reveals source specific cellular markers
Cited by: 98
Author(s): Anja M. Billing, Hisham Ben Hamidane, Shaima S. Dib, Richard Cotton, Aditya Bhagwat, Pankaj Kumar, Shahina Hayat, Noha A. Yousri, Neha Goswami, Karsten Suhre, Arash Rafii, Johannes Graumann
Software Mentions: 3
Published: almost 9 years ago

10.1038/srep17978

Identifying transcription start sites and active enhancer elements using BruUV-seq
Cited by: 26
Author(s): Brian Magnuson, Artur Veloso, Killeen S. Kirkconnell, Leonardo Carmo de Andrade Lima, Michelle T. Paulsen, Emily A. Ljungman, Karan Bedi, J.K. Prasad, Thomas E. Wilson, Mats Ljungman
Software Mentions: 3
Published: almost 9 years ago

10.1038/srep17328

Genome-wide DNA methylation map of human neutrophils reveals widespread inter-individual epigenetic variation
Cited by: 54
Author(s): Aniruddha Chatterjee, Peter A. Stockwell, Euan J. Rodger, Elizabeth J. Duncan, Matthew Parry, Robert J. Weeks, Ian M. Morison
Software Mentions: 3
Published: almost 9 years ago

10.1038/srep16932

Dual transcriptome sequencing reveals resistance of TLR4 ligand-activated bone marrow-derived macrophages to inflammation mediated by the BET inhibitor JQ1
Cited by: 22
Author(s): Amitabh Das, Jin Choul Chai, Chul‐Su Yang, Young Seek Lee, Nando Dulal Das, Kyoung Hwa Jung, Young Gyu Chai
Software Mentions: 3
Published: about 9 years ago

10.1186/s12870-020-2309-6

A transcriptomic view of the ability of nascent hexaploid wheat to tolerate aneuploidy
Cited by: 6
Author(s): Deying Zeng, Jiantao Guan, Jiangtao Luo, Laibin Zhao, Yazhou Li, Wenshuai Chen, Lianquan Zhang, Shunzong Ning, Zhongwei Yuan, Aili Li, Youliang Zheng, Long Mao, Dengcai Liu, Ming Hao
Software Mentions: 3
Published: over 4 years ago

10.1128/JVI.01869-20

The Human Adenovirus 2 Transcriptome: an Amazing Complexity of Alternatively Spliced mRNAs
Cited by: 11
Author(s): Amanda Westergren Jakobsson, Bo Segerman, Ola Wallerman, Sara Bergström Lind, Hongxing Zhao, Carl-Johan Rubin, Ulf Pettersson, Göran Akusjärvi
Software Mentions: 3
Published: almost 4 years ago

10.1186/s12870-021-02825-w

Transcriptional and proteomic insights into phytotoxic activity of interspecific potato hybrids with low glycoalkaloid contents
Cited by: 5
Author(s): Katarzyna Szajko, Jarosław Ciekot, Iwona Wasilewicz‐Flis, Waldemar Marczewski, Dorota Sołtys‐Kalina
Software Mentions: 3
Published: almost 4 years ago

10.1038/srep13456

TRIM32 modulates pluripotency entry and exit by directly regulating Oct4 stability
Cited by: 15
Author(s): Lamiaa Bahnassawy, Thanneer M. Perumal, Laura González-Cano, Anna-Lena Hillje, Leila Taher, Wojciech Makałowski, Yutaka Suzuki, Georg Fuellen, Antonio del Sol, Jens Christian Schwamborn
Software Mentions: 3
Published: about 9 years ago

10.1038/srep16324

Revisiting the reference genomes of human pathogenic Cryptosporidium species: reannotation of C. parvum Iowa and a new C. hominis reference
Cited by: 42
Author(s): Juan Pablo Isaza, Ana Luz Galván, Víctor Polanco, Bernice Huang, Andrey V. Matveyev, Myrna G. Serrano, Patrício Manque, Gregory A. Buck, Juan F. Alzate
Software Mentions: 3
Published: about 9 years ago

10.1371/journal.pgen.1004562

A Genome-Wide Association Study of the Maize Hypersensitive Defense Response Identifies Genes That Cluster in Related Pathways
Cited by: 60
Author(s): Bode A. Olukolu, Guan‐Feng Wang, Vijay Vontimitta, Bala P. Venkata, Sandeep Marla, Jiabing Ji, Emma W. Gachomo, Kevin Chu, Adisu Negeri, Jacqueline Benson, Rebecca Nelson, Peter J. Bradbury, Dahlia M. Nielsen, James B. Holland, Peter Balint‐Kurti, Gurmukh S. Johal
Software Mentions: 3
Published: about 10 years ago

10.1038/srep13336

Extensive shift in placental transcriptome profile in preeclampsia and placental origin of adverse pregnancy outcomes
Cited by: 81
Author(s): Siim Sõber, Mario Reiman, Triin Kikas, Kristiina Rull, Rain Inno, Pille Vaas, Pille Teesalu, Jesus M. Lopez Marti, Pirkko Mattila, Maris Laan
Software Mentions: 3
Published: over 9 years ago

10.1038/srep12524

Transcriptional profiling of macrophages derived from monocytes and iPS cells identifies a conserved response to LPS and novel alternative transcription
Cited by: 79
Author(s): Kaur Alasoo, Fernando O. Martínez, Christine Hale, Siamon Gordon, Fiona Powrie, Gordon Dougan, Subhankar Mukhopadhyay, Daniel J. Gaffney
Software Mentions: 3
Published: over 9 years ago

10.1186/s12870-020-02450-z

Comparative transcriptome profiling reveals cold stress responsiveness in two contrasting Chinese jujube cultivars
Cited by: 21
Author(s): Heng Zhou, Ying He, Yu Cheng Zhu, Meiyu Li, Shuang Song, Wenhao Bo, Yingyue Li, Xiaoming Pang
Software Mentions: 3
Published: over 4 years ago

10.1038/s41388-018-0661-x

Lineage-specific control of TFIIH by MITF determines transcriptional homeostasis and DNA repair
Cited by: 17
Author(s): Marcos Seoane, Sophia Buhs, Pablo A. Iglesias, Julia Strauß, Ann-Christin Puller, Jürgen Müller, Helwe Gerull, Susanne Feldhaus, Malik Alawi, Johanna M. Brandner, Dennis Eggert, Jinyan Du, Jürgen Thomale, Peter J. Wild, Martin Zimmermann, Thomas Sternsdorf, Udo Schumacher, Peter Nollau, David E. Fisher, Martin Horstmann
Software Mentions: 3
Published: almost 6 years ago

10.1038/srep08957

Systematic identification and characterization of long intergenic non-coding RNAs in fetal porcine skeletal muscle development
Cited by: 84
Author(s): Weimin Zhao, Yulian Mu, Lei Ma, Chen Wang, Zhonglin Tang, Shulin Yang, Rong Zhou, Xiaoju Hu, Menghua Li, Kui Li
Software Mentions: 3
Published: over 9 years ago

10.1038/s41597-019-0291-3

A de novo genome assembly of the dwarfing pear rootstock Zhongai 1
Cited by: 23
Author(s): C. Ou, Fei Wang, Jiahong Wang, Li Song, Yanjie Zhang, Ming Fang, Li Ma, Yanan Zhao, Shuling Jiang
Software Mentions: 3
Published: almost 5 years ago

10.1038/s41597-019-0253-9

Prenatal hypoxia-induced epigenomic and transcriptomic reprogramming in rat fetal and adult offspring hearts
Cited by: 16
Author(s): Xin Chen, Li Zhang, Charles Wang
Software Mentions: 3
Published: about 5 years ago

10.1038/s41597-019-0231-2

Comparative transcriptome profiling of immune response against Vibrio harveyi infection in Chinese tongue sole
Cited by: 17
Author(s): Hao Xu, Xiwen Xu, Xihong Li, Lei Wang, Jiayu Cheng, Qian Zhou, Songlin Chen
Software Mentions: 3
Published: about 5 years ago

10.1038/s41597-019-0194-3

The sequencing and de novo assembly of the Larimichthys crocea genome using PacBio and Hi-C technologies
Cited by: 30
Author(s): Baohua Chen, Zhixiong Zhou, Qiaozhen Ke, Yidi Wu, Haili Bai, Fei Pu, Peng Xu
Software Mentions: 3
Published: about 5 years ago

10.1038/s41597-019-0162-y

Global tissue-specific transcriptome analysis of Citrus sinensis fruit across six developmental stages
Cited by: 12
Author(s): Guizhi Feng, Juxun Wu, Hualin Yi
Software Mentions: 3
Published: over 5 years ago

10.1038/s41597-019-0014-9

Genome-wide identification and characterization of long noncoding and circular RNAs in germline stem cells
Cited by: 14
Author(s): Xiaoyong Li, Geng Tian, Yue Zhao, Ji Wu
Software Mentions: 3
Published: over 5 years ago

10.1186/s12870-019-1802-2

Transcript analyses reveal a comprehensive role of abscisic acid in modulating fruit ripening in Chinese jujube
Cited by: 8
Author(s): Zhang Zhong, C.K. Kang, Shuyi Zhang, Xingang Li
Software Mentions: 3
Published: over 5 years ago

10.18632/oncotarget.25646

Collaborating genomic, transcriptomic and microbiomic alterations lead to canine extreme intestinal polyposis
Cited by: 16
Author(s): Jin Wang, Tianfang Wang, Micah A. Bishop, John F. Edwards, Hang Yin, Stephen Dalton, Laura K. Bryan, Shaying Zhao
Software Mentions: 3
Published: over 6 years ago

10.1371/journal.pgen.1007617

Tudor-domain containing protein 5-like promotes male sexual identity in the Drosophila germline and is repressed in females by Sex lethal
Cited by: 21
Author(s): Shekerah Primus, Caitlin Pozmanter, Kelly Baxter, Mark Van Doren
Software Mentions: 3
Published: over 5 years ago

10.1038/sdata.2017.118

A gene expression atlas of adult Schistosoma mansoni and their gonads
Cited by: 44
Author(s): Zhigang Lu, Florian Sessler, Nancy Holroyd, Steffen Hahnel, Thomas Quack, Matthew Berriman, Christoph G. Grevelding
Software Mentions: 3
Published: over 7 years ago

10.1038/sdata.2016.19

Genome-scale DNA methylome and transcriptome profiling of human neutrophils
Cited by: 17
Author(s): Aniruddha Chatterjee, Peter A. Stockwell, Euan J. Rodger, Ian M. Morison
Software Mentions: 3
Published: over 8 years ago

10.1371/journal.pgen.1002962

A Comparison of Brain Gene Expression Levels in Domesticated and Wild Animals
Cited by: 119
Author(s): Frank W. Albert, Mehmet Somel, Miguel Carneiro, Ayinuer Aximu‐Petri, Michael Halbwax, Olaf Thalmann, José Antonio Blanco‐Aguiar, I. Z. Plyusnina, Lyudmila N. Trut, Rafael Villafuerte, Nuno Ferrand, Sylvia Kaiser, Per Jensen, Svante Pääbo
Software Mentions: 3
Published: about 12 years ago

10.1371/journal.pone.0149640

Preferentially Expressed Antigen of Melanoma Prevents Lung Cancer Metastasis
Cited by: 14
Author(s): Quan Huang, Haifeng Wei, Zhipeng Wu, Lin Li, Liangfang Yao, Zhengwang Sun, Lei Li, Lin Zx, Wei Xu, Shuai Han, Wenjiao Cao, Yunfei Xu, Dianwen Song, Xianghong Yang, Jianru Xiao
Software Mentions: 3
Published: over 8 years ago

10.1371/journal.pgen.1008510

STK-12 acts as a transcriptional brake to control the expression of cellulase-encoding genes in Neurospora crassa
Cited by: 17
Author(s): Liangcai Lin, Shanshan Wang, Xin Li, Qun He, J. Philipp Benz, Chaoguang Tian
Software Mentions: 3
Published: almost 5 years ago

10.1371/journal.pgen.1008861

Adaptive evolution among cytoplasmic piRNA proteins leads to decreased genomic auto-immunity
Cited by: 12
Author(s): Luyang Wang, Daniel A. Barbash, Erin S. Kelleher
Software Mentions: 3
Published: over 4 years ago

10.1371/journal.pgen.1006224

Downstream Antisense Transcription Predicts Genomic Features That Define the Specific Chromatin Environment at Mammalian Promoters
Cited by: 16
Author(s): Christopher A. Lavender, Kimberly R. Cannady, Jackson A. Hoffman, Kevin W. Trotter, Daniel A. Gilchrist, Brian D. Bennett, Adam Burkholder, Craig J. Burd, David C. Fargo, Trevor Archer
Software Mentions: 3
Published: over 8 years ago

10.1126/sciadv.abe5357

S100A8/S100A9 cytokine acts as a transcriptional coactivator during breast cellular transformation
Cited by: 24
Author(s): Ruisheng Song, Kevin Struhl
Software Mentions: 3
Published: almost 4 years ago

10.1155/2016/1562041

Transcript Polymorphism Rates in Soybean Seed Tissue Are Increased in a Single Transformant of Glycine max
Cited by: 2
Author(s): Kevin Lambirth, Adam M. Whaley, Jessica A. Schlueter, Kenneth J. Piller, Kenneth L. Bost
Software Mentions: 3
Published: almost 8 years ago

10.1186/s12284-021-00515-7

A Genome Doubling Event Reshapes Rice Morphology and Products by Modulating Chromatin Signatures and Gene Expression Profiling
Cited by: 5
Author(s): Chao Zhou, Xiaoyun Liu, Xinglei Li, Hanlin Zhou, Sijia Wang, Yanfei Zhu, Yonghong Zhang, Sanhe Li, Aiqing You, Lei Zhou, Zhengquan He
Software Mentions: 3
Published: over 3 years ago

10.1371/journal.pgen.1006294

The Impact of Endurance Training on Human Skeletal Muscle Memory, Global Isoform Expression and Novel Transcripts
Cited by: 44
Author(s): Maléne E. Lindholm, Stefania Giacomello, Beata Werne Solnestam, Håkan Fischer, Mikael Huss, Sanela Kjellqvist, Carl Johan Sundberg
Software Mentions: 3
Published: about 8 years ago

10.1155/2020/8831331

Differential Expression and PAH Degradation: What <i>Burkholderia vietnamiensi</i>s G4 Can Tell Us?
Cited by: 7
Author(s): Guilherme Pinto Cauduro, Ana Lusia Leal, Tiago Falcón Lopes, Marcela Marmitt, Victor Hugo Valiati
Software Mentions: 3
Published: about 4 years ago

10.1186/s12977-018-0417-2

CLIP-related methodologies and their application to retrovirology
Cited by: 10
Author(s): Paul D. Bieniasz, Sebla B. Kutluay
Software Mentions: 3
Published: over 6 years ago

10.1186/s12870-015-0468-7

Specific pools of endogenous peptides are present in gametophore, protonema, and protoplast cells of the moss Physcomitrella patens
Cited by: 37
Author(s): Igor Fesenko, Georgij Arapidi, Alexander Skripnikov, Dmitry Alexeev, Elena S. Kostryukova, Alexander I. Manolov, Ilya Altukhov, Regina Khazigaleeva, A. V. Seredina, Sergey I. Kovalchuk, Rustam H. Ziganshin, В. Г. Згода, Svetlana E. Novikova, Tatiana A. Semashko, D. K. Slizhikova, Vasilij V Ptushenko, A. Yu. Gorbachev, Vadim M. Govorun, В. Т. Иванов
Software Mentions: 3
Published: almost 10 years ago

10.1093/gigascience/giz070

Pseudomolecule-level assembly of the Chinese oil tree yellowhorn (Xanthoceras sorbifolium) genome
Cited by: 42
Author(s): Quanxin Bi, Yang Zhao, Wei Du, Ying Lu, Gui Liu, Zhimin Zheng, Haiyan Yu, Yubo Cui, Zhi Liu, Tianpeng Cui, Deshi Cui, Xiaojuan Liu, Yingchao Li, Fan Siqi, Xiaoyu Hu, Guanghui Fu, Jian Ding, Chengjiang Ruan, Libing Wang
Software Mentions: 3
Published: over 5 years ago

10.1093/gigascience/giz036

The genomes of pecan and Chinese hickory provide insights into Carya evolution and nut nutrition
Cited by: 78
Author(s): Yajiang Huang, Li Xiao, Zhongren Zhang, Rui Zhang, Zhengjia Wang, Chun-Ying Huang, Ren Huang, Yumeng Luan, Tongqiang Fan, Jianhua Wang, Chen Shen, Shenmei Zhang, Xinwang Wang, Jennifer J. Randall, Bingsong Zheng, Jiasheng Wu, Qixiang Zhang, Guohua Xia, Chao Xu, Ming Chen, Liangsheng Zhang, Wenkai Jiang, Li‐Zhi Gao, Zhiduan Chen, Charles A. Leslie, L.J. Grauke, Jianqin Huang
Software Mentions: 3
Published: over 5 years ago

10.1093/gigascience/giy120

Chromosomal-level assembly of yellow catfish genome using third-generation DNA sequencing and Hi-C analysis
Cited by: 59
Author(s): Gaorui Gong, Dan Cheng, Shijun Xiao, Wenjie Guo, Peipei Huang, Yang Xiong, Junjie Wu, Yan He, Jicheng Zhang, Xiaohui Li, Nansheng Chen, Jian‐Fang Gui, Jie Mei
Software Mentions: 3
Published: about 6 years ago

10.7554/eLife.61406

The kinase PDK1 is critical for promoting T follicular helper cell differentiation
Cited by: 12
Author(s): Zhen Sun, Yingpeng Yao, Menghao You, Jingjing Liu, Wenhui Guo, Zhihong Qi, Zhao Wang, Fang Wang, Weiping Yuan, Shuyang Yu
Software Mentions: 3
Published: almost 4 years ago

10.1371/journal.pgen.1005940

The Chromatin Remodelling Enzymes SNF2H and SNF2L Position Nucleosomes adjacent to CTCF and Other Transcription Factors
Cited by: 91
Author(s): Nicola Wiechens, Vijender Singh, Triantafyllos Gkikopoulos, Pietà Schofield, Sónia Rocha, Tom Owen-Hughes
Software Mentions: 3
Published: over 8 years ago

10.1155/2015/206937

Comprehensive Analysis of Transcriptome Sequencing Data in the Lung Tissues of COPD Subjects
Cited by: 52
Author(s): Woo Jin Kim, Jae Hyun Lim, Jae Seung Lee, Sang Do Lee, Ju Han Kim, Yeon Mok Oh
Software Mentions: 3
Published: almost 10 years ago

10.1093/gigascience/gix028

Hybrid de novo genome assembly of the Chinese herbal fleabane Erigeron breviscapus
Cited by: 18
Author(s): Jing Yang, Guanghui Zhang, Jing Zhang, Hui Liu, Wei Chen, Xiao Wang, Yahe Li, Yang Dong, Shengchao Yang
Software Mentions: 3
Published: over 7 years ago

10.1371/journal.pgen.1007273

Ethylene induced plant stress tolerance by Enterobacter sp. SA187 is mediated by 2‐keto‐4‐methylthiobutyric acid production
Cited by: 80
Author(s): Axel de Zélicourt, Lukáš Synek, Maged M. Saad, Hanin S. Alzubaidy, Rewaa S. Jalal, Yakun Xie, Cristina Andrés‐Barrao, Eleonora Rolli, Florence Guérard, Kadarkaraisamy Mariappan, İhsanullah Daur, Jean Colcombet, Moussa Benhamed, Thomas Depaepe, Dominique Van Der Straeten, Heribert Hirt
Software Mentions: 3
Published: over 6 years ago

10.1093/gigascience/giw004

Genome sequence of a rice pest, the white-backed planthopper (Sogatella furcifera)
Cited by: 35
Author(s): Lin Wang, Nan Tang, Xinlei Gao, Zhaoxia Chang, Liqin Zhang, Guohui Zhou, Dongyang Guo, Zhen Zeng, Wenjie Li, Ibukun A. Akinyemi, Huanming Yang, Qingfa Wu
Software Mentions: 3
Published: almost 8 years ago

10.1371/journal.pgen.1007903

Genomic insights into neonicotinoid sensitivity in the solitary bee Osmia bicornis
Cited by: 57
Author(s): Katherine Beadle, Kumar Saurabh Singh, Bartlomiej J. Troczka, Emma Randall, Marion Zaworra, Christoph Zimmer, Angela Hayward, R. J. Reid, Laura Kor, Maxie Kohler, Benjamin Buer, David R. Nelson, Martin S. Williamson, T.G. Emyr Davies, L. M. Field, Ralf Nauen, Chris Bass
Software Mentions: 3
Published: almost 6 years ago

10.1371/journal.pgen.1007999

Transcription-dependent spreading of the Dal80 yeast GATA factor across the body of highly expressed genes
Cited by: 7
Author(s): Aria Ronsmans, Maxime Wéry, Ugo Szachnowski, Camille Gautier, Marc Descrimes, Evelyne Dubois, Antonin Morillon, Isabelle Georis
Software Mentions: 3
Published: over 5 years ago

10.1186/2047-217X-3-25

A comprehensive resource of genomic, epigenomic and transcriptomic sequencing data for the black truffle Tuber melanosporum
Cited by: 9
Author(s): Pao‐Yang Chen, Barbara Montanini, Wen‐Wei Liao, Marco Morselli, Artur Jaroszewicz, David López, Simone Ottonello, Matteo Pellegrini
Software Mentions: 3
Published: about 10 years ago

10.7554/eLife.30809

The role of microglia and their CX3CR1 signaling in adult neurogenesis in the olfactory bulb
Cited by: 73
Author(s): R. Reshef, Elena Kudryavitskaya, Haran Shani-Narkiss, Batya Isaacson, Neta Rimmerman, Adi Mizrahi, Raz Yirmiya
Software Mentions: 3
Published: almost 7 years ago

10.5808/GI.2020.18.1.e8

Bioinformatics services for analyzing massive genomic datasets
Cited by: 6
Author(s): Gunhwan Ko, Pan-Gyu Kim, Youngbum Cho, Seongmun Jeong, Jae-Yoon Kim, Kyoung Hyoun Kim, Hoyeon Lee, Jiyeon Han, Namhee Yu, Seokjin Ham, Insoon Jang, Byung Ha Kang, Sunguk Shin, Lian Kim, Seungwon Lee, Dougu Nam, Jihyun F. Kim, Namshin Kim, Seon‐Young Kim, Sanghyuk Lee, Tae-Young Roh, Byung-Wook Lee
Software Mentions: 3
Published: over 4 years ago

10.1371/journal.pgen.1006704

Meioc maintains an extended meiotic prophase I in mice
Cited by: 85
Author(s): Y. Q. Shirleen Soh, Maria M. Mikedis, Mina Kojima, Alexander K. Godfrey, Dirk G. de Rooij, David C. Page
Software Mentions: 3
Published: over 7 years ago

10.1186/s13073-018-0534-5

Exposure to the gut microbiota drives distinct methylome and transcriptome changes in intestinal epithelial cells during postnatal development
Cited by: 108
Author(s): Wei-Hung Pan, Felix Sommer, Maren Falk-Paulsen, Thomas Ulas, Lena Best, Antonella Fazio, Priyadarshini Kachroo, Anne Luzius, Marlene Jentzsch, Ateequr Rehman, Fabian Müller, Thomas Lengauer, Joern Walter, Sven Künzel, John F. Baines, Stefan Schreiber, André Franke, Joachim L. Schultze, Fredrik Bäckhed, Philip Rosenstiel
Software Mentions: 3
Published: over 6 years ago

10.1371/journal.pgen.1007806

Conserved mRNA-granule component Scd6 targets Dhh1 to repress translation initiation and activates Dcp2-mediated mRNA decay in vivo
Cited by: 27
Author(s): Quira Zeidan, Feng He, Fan Zhang, Hongen Zhang, Allan Jacobson, Alan G. Hinnebusch
Software Mentions: 3
Published: almost 6 years ago

10.1371/journal.pgen.1004922

Genome-wide Association Study Identifies Shared Risk Loci Common to Two Malignancies in Golden Retrievers
Cited by: 60
Author(s): Noriko Tonomura, Ingegerd Elvers, Rachael Thomas, Kate Megquier, Jason Turner-Maier, Cédric Howald, Aaron L. Sarver, Ross Swofford, Aric M. Frantz, Daisuke Ito, Evan Mauceli, Maja L. Arendt, Hyun Ji Noh, Michele Koltookian, Tara Biagi, Sarah Fryc, Christina L. Williams, Anne C. Avery, Jong Hyuk Kim, Lisa G. Barber, Kristine Burgess, Eric S. Lander, Elinor K. Karlsson, Chieko Azuma, Jaime F. Modiano, Matthew Breen, Kerstin Lindblad‐Toh
Software Mentions: 3
Published: almost 10 years ago

10.1186/s13073-015-0168-9

Widespread intron retention diversifies most cancer transcriptomes
Cited by: 254
Author(s): Heidi Dvinge, Robert K. Bradley
Software Mentions: 3
Published: over 9 years ago

10.1186/s13046-020-01622-x

Non-coding RNAs in cancer: platforms and strategies for investigating the genomic “dark matter”
Cited by: 110
Author(s): Katia Grillone, Caterina Riillo, Francesca Scionti, Roberta Rocca, Giuseppe Tradigo, Pietro Hiram Guzzi, Stefano Alcaro, Maria Teresa Di Martino, Pierosandro Tagliaferri, Pierfrancesco Tassone
Software Mentions: 3
Published: over 4 years ago

10.1371/journal.pgen.1008562

Mutations on ent-kaurene oxidase 1 encoding gene attenuate its enzyme activity of catalyzing the reaction from ent-kaurene to ent-kaurenoic acid and lead to delayed germination in rice
Cited by: 20
Author(s): Hui Zhang, Ming Li, Dongli He, Kun Wang, Pingfang Yang
Software Mentions: 3
Published: almost 5 years ago

10.1371/journal.pgen.1009069

Mesenchyme-derived IGF2 is a major paracrine regulator of pancreatic growth and function
Cited by: 16
Author(s): Constanze M. Hammerle, Ionel Sandovici, Gemma V. Brierley, Nicola Smith, Warren E. Zimmer, Ilona Zvetkova, Haydn M. Prosser, Yoichi Sekita, Brian Lam, Marcella Ma, Wendy N. Cooper, Antonio Vidal‐Puig, Susan E. Ozanne, Gema Medina‐Gómez, Miguel Constância
Software Mentions: 3
Published: about 4 years ago

10.1371/journal.pgen.1007672

The genomic basis of environmental adaptation in house mice
Cited by: 53
Author(s): Megan Phifer‐Rixey, Ke Bi, Kathleen G. Ferris, Michael J. Sheehan, Diane C. Lin, Katya L. Mack, Sara Keeble, Tomohiro Suzuki, Jeffrey M. Good, Michael W. Nachman
Software Mentions: 3
Published: about 6 years ago

10.1371/journal.pgen.1003067

CELF4 Regulates Translation and Local Abundance of a Vast Set of mRNAs, Including Genes Associated with Regulation of Synaptic Function
Cited by: 102
Author(s): Jacy L. Wagnon, Michael Briese, Wenzhi Sun, Connie L. Mahaffey, Tomaž Curk, Gregor Rot, Jernej Ule, Wayne N. Frankel
Software Mentions: 3
Published: almost 12 years ago