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 9 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 9 years ago

10.7554/eLife.60481

Identification of PARP-7 substrates reveals a role for MARylation in microtubule control in ovarian cancer cells
Cited by: 35
Author(s): Lori Parsons, Sridevi Challa, Bryan A. Gibson, Tulip Nandu, MiKayla S Stokes, Dan Huang, Jayanthi Lea, W. Lee Kraus
Software Mentions: 3
Published: almost 6 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 9 years ago

10.1371/journal.pone.0192362

Transporter genes identified in landraces associated with high zinc in polished rice through panicle transcriptome for biofortification
Cited by: 21
Author(s): C. N. Neeraja, Kalyani S. Kulkarni, P. Madhu Babu, D. N. Rao, K. Surekha, V. Ravindra Babu
Software Mentions: 3
Published: almost 9 years ago

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 9 years ago

10.7554/eLife.47990

Accelerated phosphatidylcholine turnover in macrophages promotes adipose tissue inflammation in obesity
Cited by: 40
Author(s): Kasparas Petkevicius, Samuel Virtue, Guillaume Bidault, Benjamin Jenkins, Cankut Çubuk, Cecilia Morgantini, Myriam Aouadi, Joaquín Dopazo, Mireille J. Serlie, Albert Koulman, António Vidal-Puig
Software Mentions: 3
Published: about 7 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 7 years ago

10.7554/eLife.26575

Human embryonic lung epithelial tips are multipotent progenitors that can be expanded in vitro as long-term self-renewing organoids
Cited by: 206
Author(s): Marko Nikolić, Oriol Caritg, Quitz Jeng, Jo-Anne Johnson, Dawei Sun, Kate J. Howell, Jane Brady, Usua Laresgoiti, George E. Allen, Richard J. Butler, Matthias Zilbauer, Adam Giangreco, Emma L. Rawlins
Software Mentions: 3
Published: over 9 years ago

10.3390/cells9010090

PP2A Deficiency Enhances Carcinogenesis of Lgr5+ Intestinal Stem Cells Both in Organoids and In Vivo
Cited by: 3
Author(s): Yu–Ting Yen, May B. Chien, Yung-Chih Lai, Dao-Peng Chen, Cheng‐Ming Chuong, Mien‐Chie Hung, Shih‐Chieh Hung
Software Mentions: 3
Published: almost 7 years ago

10.7554/eLife.13328

Thousands of novel translated open reading frames in humans inferred by ribosome footprint profiling
Cited by: 108
Author(s): Anil Raj, Sidney H. Wang, Heejung Shim, Arbel Harpak, Yang Li, Brett W. Engelmann, Matthew Stephens, Yoav Gilad, Jonathan K. Pritchard
Software Mentions: 3
Published: over 10 years ago

10.1371/journal.pone.0201854

Genome-wide analysis of DNA polymorphisms, the methylome and transcriptome revealed that multiple factors are associated with low pollen fertility in autotetraploid rice
Cited by: 21
Author(s): Xiang Li, Hang Yu, Yamin Jiao, Muhammad Qasim Shahid, Jinwen Wu, Xiangdong Liu
Software Mentions: 3
Published: over 8 years ago

10.7554/eLife.33333

Zfp281 is essential for mouse epiblast maturation through transcriptional and epigenetic control of Nodal signaling
Cited by: 25
Author(s): Xin Huang, Sophie Balmer, Fan Yang, Miguel Fidalgo, Dan Li, Diana Guallar, Anna-Katerina Hadjantonakis, Jianlong Wang
Software Mentions: 3
Published: almost 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: about 5 years ago

10.1080/21505594.2020.1839231

A new regulator in the crossroads of oxidative stress resistance and virulence in <i>Candida glabrata</i>: The transcription factor CgTog1
Cited by: 5
Author(s): Pedro Pais, Susana Vagueiro, Dalila Mil‐Homens, Andreia I. Pimenta, Romeu Viana, Michiyo Okamoto, Hiroji Chibana, Arsénio M. Fialho, Miguel C. Teixeira
Software Mentions: 3
Published: about 6 years ago

10.1172/jci.insight.141690

Aging imparts cell-autonomous dysfunction to regulatory T cells during recovery from influenza pneumonia
Cited by: 20
Author(s): Luisa Morales‐Nebreda, Kathryn A. Helmin, Manuel A. Torres Acosta, Nikolay S. Markov, Jennifer Yuan Shih Hu, Anthony M. Joudi, Raul Piseaux‐Aillon, Hiam Abdala‐Valencia, Yuliya Politanska, Benjamin D. Singer
Software Mentions: 3
Published: over 5 years ago

10.7554/eLife.08298

Starvation promotes concerted modulation of appetitive olfactory behavior via parallel neuromodulatory circuits
Cited by: 142
Author(s): Kang I. Ko, Cory M. Root, Scott A. Lindsay, Orel A. Zaninovich, Andrew K. Shepherd, Steven A. Wasserman, Susy M. Kim, Jing W. Wang
Software Mentions: 3
Published: over 11 years ago

10.1371/journal.pone.0128041

Transcriptome Profiling of the Potato (Solanum tuberosum L.) Plant under Drought Stress and Water-Stimulus Conditions
Cited by: 85
Author(s): Lei Gong, Hongxia Zhang, Xiaoyan Gan, Li Zhang, Yuchao Chen, Fengjie Nie, Lei Shi, Miao Li, Zhiqian Guo, Guohui Zhang, Song Yao
Software Mentions: 3
Published: over 11 years ago

10.7554/eLife.54572

Building the vertebrate codex using the gene breaking protein trap library
Cited by: 10
Author(s): Noriko Ichino, MaKayla R Serres, Rhianna Urban, Mark D. Urban, Anthony J. Treichel, Kyle Schaefbauer, Lauren E Greif, Gaurav K. Varshney, Kimberly J. Skuster, Melissa McNulty, Camden L Daby, Ying Wang, Hsin-Kai Liao, Suzan El‐Rass, Yonghe Ding, Weibin Liu, Jennifer L. Anderson, Mark D Wishman, Ankit Sabharwal, Lisa A. Schimmenti, Sridhar Sivasubbu, Darius Balciunas, Matthias Hammerschmidt, Steven A. Farber, Xiang Wen, Xiaolei Xu, Maura McGrail, Jeffrey J. Essner, Shawn M. Burgess, Karl J. Clark, Stephen C. Ekker
Software Mentions: 3
Published: about 6 years ago

10.1038/s41598-017-17000-1

Modulation of Immune Signaling and Metabolism Highlights Host and Fungal Transcriptional Responses in Mouse Models of Invasive Pulmonary Aspergillosis
Cited by: 25
Author(s): Shiv D. Kale, Tariq Ayubi, Dawoon Chung, Nuria Tubau-Juni, Andrew Leber, Ha X. Dang, Saikumar Karyala, Raquel Hontecillas, Christopher B. Lawrence, Robert A. Cramer, Josep Bassaganya‐Riera
Software Mentions: 3
Published: almost 9 years ago

10.7554/eLife.01630

A proteomic chronology of gene expression through the cell cycle in human myeloid leukemia cells
Cited by: 123
Author(s): Tony Ly, Yasmeen Ahmad, Adam Shlien, Dominique N. Soroka, Allie Mills, Michael J. Emanuele, Michael R. Stratton, Angus I. Lamond
Software Mentions: 3
Published: over 12 years ago

10.3389/fcell.2021.698442

Long Non-coding RNA Signatures Associated With Liver Aging in Senescence-Accelerated Mouse Prone 8 Model
Cited by: 3
Author(s): Shuai Zhang, Juan-Juan Duan, Yuguang Du, Jinlu Xie, Haijing Zhang, Changyu Li, Wensheng Zhang
Software Mentions: 3
Published: over 5 years ago

10.7554/eLife.43352

Identification of EOMES-expressing spermatogonial stem cells and their regulation by PLZF
Cited by: 39
Author(s): Manju Sharma, Anuj Srivastava, Heather Fairfield, David E. Bergstrom, William F. Flynn, Robert E. Braun
Software Mentions: 3
Published: over 7 years ago

10.7554/eLife.09406

An internal promoter underlies the difference in disease severity between N- and C-terminal truncation mutations of Titin in zebrafish
Cited by: 83
Author(s): Jun Zou, Diana A. Tran, Mai Baalbaki, Ling Tang, Annie Poon, Angelo Pelonero, Erron W. Titus, Christiana Yuan, Chenxu Shi, Shruthi Patchava, Elizabeth Halper, Jasmine Garg, Irina Movsesyan, Chaoying Yin, Roland S. Wu, Lisa D. Wilsbacher, Jiandong Liu, Ron Hager, Shaun R. Coughlin, Martin Jinek, Clive R. Pullinger, John P. Kane, Daniel Hart, Pui Yan Kwok, Rahul C. Deo
Software Mentions: 3
Published: about 11 years ago

10.1371/journal.pone.0202309

Comparison of gene co-networks analysis provide a systems view of rice (Oryza sativa L.) response to Tilletia horrida infection
Cited by: 6
Author(s): aijun wang, Xinyue Shu, Xianyu Niu, Wenjuan Zhao, Peng Ai, Ping Li, Aiping Zheng
Software Mentions: 3
Published: about 8 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: about 7 years ago

10.7554/eLife.64212

Loss of MGA repression mediated by an atypical polycomb complex promotes tumor progression and invasiveness
Cited by: 24
Author(s): Haritha Mathsyaraja, Jonathen Catchpole, Brian Freie, Emily Eastwood, Ekaterina Babaeva, Michael Geuenich, Pei Feng Cheng, Jessica Ayers, Ming Yu, Nan Wu, Sitapriya Moorthi, Kumud R. Poudel, Amanda Koehne, William M. Grady, A. McGarry Houghton, Alice H. Berger, Yuzuru Shiio, David MacPherson, Robert N. Eisenman
Software Mentions: 3
Published: over 5 years ago

10.3389/fcell.2021.655201

Polycomb Factor PHF19 Controls Cell Growth and Differentiation Toward Erythroid Pathway in Chronic Myeloid Leukemia Cells
Cited by: 6
Author(s): Marc García-Montolio, Cecilia Ballaré, Enrique Blanco, Arantxa Gutiérrez, Sergi Aranda, Antonio Gómez, Chung Hoow Kok, David T. Yeung, Timothy P. Hughes, Pedro Vizán, Luciano Di Croce
Software Mentions: 3
Published: over 5 years ago

10.7554/eLife.00348

Epigenetic conservation at gene regulatory elements revealed by non-methylated DNA profiling in seven vertebrates
Cited by: 188
Author(s): Hannah K. Long, David Sims, Andreas Heger, Neil P. Blackledge, Claudia Kutter, Megan Lynne Wright, Frank Grützner, Duncan T. Odom, Roger Patient, Chris P. Ponting, Robert J. Klose
Software Mentions: 3
Published: over 13 years ago

10.7554/eLife.52962

A complex regulatory landscape involved in the development of mammalian external genitals
Cited by: 23
Author(s): Ana Rita Amândio, Lucille Lopez-Delisle, Christopher Chase Bolt, Bénédicte Mascrez, Denis Duboule
Software Mentions: 3
Published: over 6 years ago

10.1371/journal.pone.0162402

Comprehensive Transcriptome Analyses of the Fructose-Fed Syrian Golden Hamster Liver Provides Novel Insights into Lipid Metabolism
Cited by: 8
Author(s): Ziyang Li, Chaoliang Xiong, Suo Mo, Haiying Tian, Mengqian Yu, Tingting Mao, Qian Chen, Huai‐Rong Luo, Quan-Zhen Li, Jianxin Lü, Yi Zhao, Wei Li
Software Mentions: 3
Published: about 10 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 7 years ago

10.7554/eLife.24523

Synergistic interactions with PI3K inhibition that induce apoptosis
Cited by: 23
Author(s): Yaara Zwang, Oliver Jonas, Casandra Chen, Mikael L. Rinne, John G. Doench, Federica Piccioni, Tan Li, Hai‐Tsang Huang, Jinhua Wang, Young Jin Ham, Joyce T. O’Connell, Patrick Bhola, Mihir B. Doshi, Matthew A. Whitman, Michael J. Cima, Anthony Letaï, David E. Root, Robert Langer, Nathanael S. Gray, William C. Hahn
Software Mentions: 3
Published: over 9 years ago

10.3389/fcell.2021.648209

Melatonin Modulates Lipid Metabolism in Porcine Cumulus–Oocyte Complex via Its Receptors
Cited by: 4
Author(s): Tianqi Zhu, Shengyu Guan, Dongying Lv, Mengmeng Zhao, Laiqing Yan, Li Shi, Pengyun Ji, Lu Zhang, Guoshi Liu
Software Mentions: 3
Published: over 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 7 years ago

10.3389/fcell.2020.00448

miR-205 Expression Elevated With EDS Treatment and Induced Leydig Cell Apoptosis by Targeting RAP2B via the PI3K/AKT Signaling Pathway
Cited by: 3
Author(s): Chunrong Yang, Rui Chen, Lin Ma, Wenjing Yang, Mingyue Chen, Yanghai Zhang, Shuai Yu, Wuzi Dong, Wenxian Zeng, Xianyong Lan, Chuanying Pan
Software Mentions: 3
Published: over 6 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 8 years ago

10.3389/fcell.2021.700290

Structural and Functional Characterization of a Testicular Long Non-coding RNA (4930463O16Rik) Identified in the Meiotic Arrest of the Mouse Topaz1–/– Testes
Cited by: 6
Author(s): Manon Chadourne, Elodie Poumerol, Luc Jouneau, Bruno Passet, Johan Castille, Eli Sellem, Eric Pailhoux, Béatrice Mandon‐Pepin
Software Mentions: 3
Published: over 5 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 8 years ago

10.1038/s41598-017-17735-x

Transcriptomic signatures of cellular and humoral immune responses in older adults after seasonal influenza vaccination identified by data-driven clustering
Cited by: 25
Author(s): Emily A. Voigt, Diane E. Grill, Michael T. Zimmermann, Whitney L. Simon, Inna G. Ovsyannikova, Richard B. Kennedy, Gregory A. Poland
Software Mentions: 3
Published: almost 9 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 8 years ago

10.1038/s41598-017-17386-y

Loss of disease tolerance during Citrobacter rodentium infection is associated with impaired epithelial differentiation and hyperactivation of T cell responses
Cited by: 14
Author(s): Ellen S. Kang, Guohui Zhou, Mitra Yousefi, Romain Cayrol, Jianguo Xia, Samantha Gruenheid
Software Mentions: 3
Published: almost 9 years ago

10.18632/oncotarget.25998

Bladder cancer detection by urinary extracellular vesicle mRNA analysis
Cited by: 21
Author(s): Taku Murakami, Cindy M. Yamamoto, Tomoshige Akino, Hiroshi Tanaka, Nobuyuki Fukuzawa, Hiroyoshi Suzuki, Takahiro Osawa, Takeshi Tsuji, Toshimori Seki, Hiroshi Harada
Software Mentions: 3
Published: about 8 years ago

10.3390/cells9010025

Depolarization-Associated CircRNA Regulate Neural Gene Expression and in Some Cases May Function as Templates for Translation
Cited by: 28
Author(s): Elena Mahmoudi, Dylan Kiltschewskij, Chantel Fitzsimmons, Murray J. Cairns
Software Mentions: 3
Published: almost 7 years ago

10.1038/s41598-018-20458-2

SMARCA2-regulated host cell factors are required for MxA restriction of influenza A viruses
Cited by: 10
Author(s): Dominik Dornfeld, Alexandra H. Dudek, Thibaut Vausselin, Sira C. Günther, Judd F. Hultquist, Sebastian Giese, Daria Khokhlova-Cubberley, Yap Ching Chew, Lars Pache, Nevan J. Krogan, Adolfo Garcı́a-Sastre, Martin Schwemmle, Megan L. Shaw
Software Mentions: 3
Published: almost 9 years ago

10.1186/s13018-020-01994-y

Differential gene expression in skin RNA of horses affected with degenerative suspensory ligament desmitis
Cited by: 7
Author(s): Abigail Haythorn, M.F. Young, James B. Stanton, Jian Zhang, P. O. E. Mueller, Jaroslava Halper
Software Mentions: 3
Published: about 6 years ago

10.1038/s41598-018-21065-x

RNA-seq transcriptome analysis of breast cancer cell lines under shikonin treatment
Cited by: 25
Author(s): Kuo‐Hua Lin, Ming‐Yii Huang, Wei‐Chung Cheng, Shu-Chi Wang, Shih-Hua Fang, Hung-Pin Tu, Chin-Chuan Su, Yung-Li Hung, Po-Len Liu, Chi-Shuo Chen, Yuting Wang, Chia-Yang Li
Software Mentions: 3
Published: over 8 years ago

10.3390/cells10030635

Genome-Wide Identification of U-To-C RNA Editing Events for Nuclear Genes in Arabidopsis thaliana
Cited by: 12
Author(s): Ruchika, Chisato Okudaira, Matomo Sakari, Toshifumi Tsukahara
Software Mentions: 3
Published: over 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 7 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 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 6 years ago

10.1098/rsob.190141

Identification of a novel regulatory pathway for PPARα by RNA-seq characterization of the endothelial cell lipid peroxidative injury transcriptome
Cited by: 4
Author(s): Fangfang Dou, Beiling Wu, Sun Liang, Jiulin Chen, Te Liu, Zhihua Yu, Chuan Chen
Software Mentions: 3
Published: almost 7 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 6 years ago

10.1038/s41598-018-21770-7

Complementarity of assembly-first and mapping-first approaches for alternative splicing annotation and differential analysis from RNAseq data
Cited by: 29
Author(s): Clara Benoit‐Pilven, Camille Marchet, Émilie Chautard, Leandro Lima, Marie-Pierre Lambert, Gustavo Sacomoto, Amandine E. Rey, Audric Cologne, Sophie Terrone, Louis Dulaurier, Jean‐Baptiste Claude, Cyril F. Bourgeois, Didier Auboeuf, Vincent Lacroix
Software Mentions: 3
Published: over 8 years ago

10.1371/journal.pone.0079118

Discovering Transcription and Splicing Networks in Myelodysplastic Syndromes
Cited by: 11
Author(s): Hongyan Wang, Jianguo Wen, Chung‐Che Chang, Xiaobo Zhou
Software Mentions: 3
Published: almost 13 years ago

10.1038/s41598-018-23334-1

Genome-wide identification, putative functionality and interactions between lncRNAs and miRNAs in Brassica species
Cited by: 32
Author(s): Jinfang Zhang, Lijuan Wei, Jun Jiang, Annaliese S. Mason, Haojie Li, Cheng Cui, Linna Chai, Beibei Zheng, Yongqing Zhu, Qing Xia, Long Jiang, Donghui Fu
Software Mentions: 3
Published: over 8 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 15 years ago

10.1186/s12967-016-1083-6

Targeted myocardial gene expression in failing hearts by RNA sequencing
Cited by: 20
Author(s): Kajari Dhar, Anthony L. Moulton, Eric Rome, Fang Qiu, Jeff Kittrell, Eugenia Raichlin, Ronald Zolty, J. Um, Michael J. Moulton, Hesham Basma, Daniel R. Anderson, James D. Eudy, Brian D. Lowes
Software Mentions: 3
Published: almost 10 years ago

10.3389/fcimb.2017.00176

Human Neutrophils Produce CCL23 in Response to Various TLR-Agonists and TNFα
Cited by: 41
Author(s): Fábio Arruda-Silva, Francisco M. Bianchetto-Aguilera, Sara Gasperini, Sara Polletti, Emanuela Cosentino, Nicola Tamassia, Marco A. Cassatella
Software Mentions: 3
Published: over 9 years ago

10.1371/journal.pone.0234029

An investigation into the beneficial effects and molecular mechanisms of humic acid on foxtail millet under drought conditions
Cited by: 8
Author(s): Jie Shen, Meijun Guo, Yuguo Wang, Xiangyang Yuan, Shuqi Dong, Xi-e Song, Peng Guo
Software Mentions: 3
Published: over 6 years ago

10.1038/s41598-018-25434-4

Identification and application of exogenous dsRNA confers plant protection against Sclerotinia sclerotiorum and Botrytis cinerea
Cited by: 135
Author(s): Austein McLoughlin, Nick Wytinck, P.L. Walker, Ian J. Girard, K. Y. Rashid, Teresa de Kievit, W. G. Dilantha Fernando, Steve Whyard, Mark F. Belmonte
Software Mentions: 3
Published: over 8 years ago

10.3389/fncel.2017.00434

Systematic Analysis of mRNA and miRNA Expression of 3D-Cultured Neural Stem Cells (NSCs) in Spaceflight
Cited by: 9
Author(s): Yi Cui, Jin Soo Han, Zhifeng Xiao, Yiduo Qi, Yannan Zhao, Bing Chen, Yongxiang Fang, Sumei Liu, Xianming Wu, Jianwu Dai
Software Mentions: 3
Published: almost 9 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 11 years ago

10.1186/s13148-020-00916-3

The fusiform gyrus exhibits an epigenetic signature for Alzheimer’s disease
Cited by: 11
Author(s): Dingailu Ma, Irfete S. Fetahu, Mei Wang, Rui Fang, Jia-hui Li, Huan Liu, Tobin Gramyk, Isabella Iwanicki, Sophie Zhaotao Gu, Winnie Xu, Li Tan, Feizhen Wu, Yujiang Geno Shi
Software Mentions: 3
Published: about 6 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 12 years ago

10.3389/fendo.2017.00373

Prepubertal Ovariectomy Exaggerates Adult Affective Behaviors and Alters the Hippocampal Transcriptome in a Genetic Rat Model of Depression
Cited by: 8
Author(s): Neha Raghavan, Hao Chen, Matthew J. Schipma, Wendy Luo, Sam Chung, Lei Wang, Eva E. Redei
Software Mentions: 3
Published: almost 9 years ago

10.3389/fgene.2020.00352

Identification and Analysis of Dysfunctional Genes and Pathways in CD8+ T Cells of Non-Small Cell Lung Cancer Based on RNA Sequencing
Cited by: 5
Author(s): Xuefang Tao, Xiaotang Wu, Tao Huang, Deguang Mu
Software Mentions: 3
Published: over 6 years ago

10.1038/celldisc.2016.41

NANOG reprograms prostate cancer cells to castration resistance via dynamically repressing and engaging the AR/FOXA1 signaling axis
Cited by: 40
Author(s): Collene Jeter, Bigang Liu, Yue Lu, Hsueh-Ping Chao, Dingxiao Zhang, Xin Liu, Xin Chen, Qiuhui Li, Kiera Rycaj, Tammy Calhoun-Davis, Li Yan, Qiang Hu, Jianmin Wang, Jianjun Shen, Song Liu, Dean G. Tang
Software Mentions: 3
Published: almost 10 years ago

10.3389/fgene.2021.655900

Genome-Wide DNA Methylation and Transcriptome Analyses Reveal Epigenetic and Genetic Mechanisms Underlying Sex Maintenance of Adult Chinese Alligator
Cited by: 4
Author(s): Jianqing Lin, Jun Yu, Li Sun, Sheng‐Guo Fang
Software Mentions: 3
Published: over 5 years ago

10.3389/fgene.2021.648158

Identification and Comparative Analysis of Long Non-coding RNAs in High- and Low-Fecundity Goat Ovaries During Estrus
Cited by: 3
Author(s): Yaokun Li, Xiangping Xu, Ming Deng, Xian Zou, Zhifeng Zhao, Sixiu Huang, Dewu Liu, Guangbin Liu
Software Mentions: 3
Published: over 5 years ago

10.1186/s13071-020-04476-6

Major SCP/TAPS protein expansion in Lucilia cuprina is associated with novel tandem array organisation and domain architecture
Cited by: 1
Author(s): Yair D J Prawer, Andreas J. Stroehlein, Neil D. Young, Shilpa Kapoor, Ross S. Hall, Razi Ghazali, Philip Batterham, Robin B. Gasser, Trent Perry, Clare A. Anstead
Software Mentions: 3
Published: almost 6 years ago

10.3389/fgene.2019.00117

RNA-Seq of Liver From Pigs Divergent in Feed Efficiency Highlights Shifts in Macronutrient Metabolism, Hepatic Growth and Immune Response
Cited by: 35
Author(s): Justyna Horodyska, Ruth M. Hamill, Henry Reyer, Nares Trakooljul, Peadar G. Lawlor, Ursula M. McCormack, Klaus Wimmers
Software Mentions: 3
Published: over 7 years ago

10.1038/s41598-018-26841-3

Screening and characterisation of sex differentiation-related long non-coding RNAs in Chinese soft-shell turtle (Pelodiscus sinensis)
Cited by: 19
Author(s): Jun Zhang, Peng Yu, Qinyan Zhou, Xilei Li, Shuquan Ding, Shiping Su, Xiaohua Zhang, Xiaoli Yang, Weicheng Zhou, Qing Wan, Jian‐Fang Gui
Software Mentions: 3
Published: over 8 years ago

10.3389/fgene.2019.00036

Integrative Analysis of Transcriptome and GWAS Data to Identify the Hub Genes Associated With Milk Yield Trait in Buffalo
Cited by: 45
Author(s): Tingxian Deng, Aixin Liang, Shasha Liang, Xiaoya Ma, Xingrong Lu, Anqin Duan, Chaoyou Pang, Guohua Hua, Shenhe Liu, Giuseppe Campanile, Angela Salzano, B. Gasparrini, Xianwei Liang, Liguo Yang
Software Mentions: 3
Published: almost 8 years ago

10.3389/fgene.2014.00277

Insights into the epigenomic landscape of the human malaria vector Anopheles gambiae
Cited by: 14
Author(s): Elena Gómez-Díaz, Ana Rivero, Fabrice Chandre, Victor G. Corcés
Software Mentions: 3
Published: about 12 years ago

10.1371/journal.pone.0074912

Gaucher Disease: Transcriptome Analyses Using Microarray or mRNA Sequencing in a Gba1 Mutant Mouse Model Treated with Velaglucerase alfa or Imiglucerase
Cited by: 17
Author(s): Nupur Dasgupta, You-Hai Xu, Sangwon Oh, Ying Sun, Jia Li, Mehdi Keddache, Gregory A. Grabowski
Software Mentions: 3
Published: about 13 years ago

10.1371/journal.pone.0078868

Inferring Polymorphism-Induced Regulatory Gene Networks Active in Human Lymphocyte Cell Lines by Weighted Linear Mixed Model Analysis of Multiple RNA-Seq Datasets
Cited by: 4
Author(s): Wensheng Zhang, Andrea Edwards, Erik K. Flemington, Kun Zhang
Software Mentions: 3
Published: about 13 years ago

10.3389/fmicb.2018.01026

Comparative Methylome Analysis Reveals Perturbation of Host Epigenome in Chestnut Blight Fungus by a Hypovirus
Cited by: 10
Author(s): Ru Li, Sisi Zhou, Yongbing Li, Xiaorui Shen, Qinnan Wang, Baoshan Chen
Software Mentions: 3
Published: over 8 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 7 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 10 years ago

10.3389/fmicb.2018.01374

Investigation of Citrinin and Pigment Biosynthesis Mechanisms in Monascus purpureus by Transcriptomic Analysis
Cited by: 39
Author(s): Bin Liang, Xinjun Du, Ping Li, Chanchan Sun, Shuo Wang
Software Mentions: 3
Published: over 8 years ago

10.3389/fmicb.2019.02411

A Short-Term Feeding of Dietary Casein Increases Abundance of Lactococcus lactis and Upregulates Gene Expression Involving Obesity Prevention in Cecum of Young Rats Compared With Dietary Chicken Protein
Cited by: 12
Author(s): Zhanming Fan, Shangxin Song, Yafang Ma, Xinglian Xu
Software Mentions: 3
Published: about 7 years ago

10.1371/journal.pone.0177814

ANK1 is up-regulated in laser captured microglia in Alzheimer’s brain; the importance of addressing cellular heterogeneity
Cited by: 35
Author(s): Diego Mastroeni, Shobana Sekar, Jennifer Nolz, Elaine Delvaux, Katie Lunnon, Jonathan Mill, Winnie S. Liang, Paul D. Coleman
Software Mentions: 3
Published: over 9 years ago

10.1038/s41598-018-28299-9

Identification of Biomarkers Based on Differentially Expressed Genes in Papillary Thyroid Carcinoma
Cited by: 38
Author(s): Jun Han, Meijun Chen, Yihan Wang, Boxuan Gong, Tianwei Zhuang, Lingyu Liang, Hong Qiao
Software Mentions: 3
Published: over 8 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 11 years ago

10.3389/fmicb.2020.02069

Transcriptomic Analysis and Functional Characterization Reveal the Duck Interferon Regulatory Factor 1 as an Important Restriction Factor in the Replication of Tembusu Virus
Cited by: 8
Author(s): Chengwei Xiang, Mei Huang, Tingting Xiong, Rong Fang, Linyu Li, Ding Xiang Liu, Rui Ai Chen
Software Mentions: 3
Published: about 6 years ago

10.1074/jbc.M116.751644

Bromodomain and extraterminal inhibitors block the Epstein-Barr virus lytic cycle at two distinct steps
Cited by: 25
Author(s): Kristin M. Keck, S. Moquin, Amanda He, Samantha G. Fernandez, Jessica J. Somberg, Stephanie M. Liu, Delsy M. Martinez, JJ L. Miranda
Software Mentions: 3
Published: over 9 years ago

10.1038/s42003-021-02242-7

A human isogenic iPSC-derived cell line panel identifies major regulators of aberrant astrocyte proliferation in Down syndrome
Cited by: 11
Author(s): Keiji Kawatani, Toshihiko Nambara, Nobutoshi Nawa, Hidetaka Yoshimatsu, Haruna Kusakabe, Katsuya Hirata, Akira Tanave, Kenta Sumiyama, Kimihiko Banno, Hidetoshi Taniguchi, Hitomi Arahori, Keiichi Ozono, Yasuji Kitabatake
Software Mentions: 3
Published: over 5 years ago

10.1016/j.omto.2021.04.014

Induction of cell death in ovarian cancer cells by doxorubicin and oncolytic vaccinia virus is associated with CREB3L1 activation
Cited by: 8
Author(s): Anna Mistarz, Matthew A. Graczyk, M. Winkler, Prashant Singh, Eduardo Cortes, Anthony Miliotto, Song Liu, Mark D. Long, Yan Li, Aimee Stablewski, Kieran L. O’Loughlin, Hans Minderman, Kunle Odunsi, Hanna Rokita, AJ Robert McGray, Emese Zsíros, Danuta Kozbor
Software Mentions: 3
Published: almost 5 years ago

10.7717/peerj.1527

Genome-wide identification of hypoxia-induced enhancer regions
Cited by: 8
Author(s): Nick Kamps-Hughes, Jessica L. Preston, Melissa A Randel, Eric A. Johnson
Software Mentions: 3
Published: almost 11 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: about 11 years ago

10.1038/s41598-018-29912-7

Transcriptional profiles of crossbred embryos derived from yak oocytes in vitro fertilized with cattle sperm
Cited by: 2
Author(s): Xiang-Dong Zi, Shuang Liu, Wei Xia, Xianrong Xiong, Bin Luo
Software Mentions: 3
Published: over 8 years ago

10.3389/fmicb.2017.02683

Desert Dust as a Source of Iron to the Globally Important Diazotroph Trichodesmium
Cited by: 19
Author(s): Despo Polyviou, Alison J. Baylay, Andrew Hitchcock, Julie Robidart, C. Mark Moore, Thomas S. Bibby
Software Mentions: 3
Published: almost 9 years ago

10.1371/journal.pone.0156723

Genome-Wide Analysis of Long Noncoding RNAs and Their Responses to Drought Stress in Cotton (Gossypium hirsutum L.)
Cited by: 76
Author(s): Xuke Lu, Xiugui Chen, Mingchun Mu, Junjuan Wang, Xiaoge Wang, Delong Wang, Zujun Yin, Weili Fan, Shuai Wang, Lixue Guo, Wuwei Ye
Software Mentions: 3
Published: over 10 years ago

10.3389/fmicb.2020.555306

Copper Homeostasis in Aspergillus nidulans Involves Coordinated Transporter Function, Expression and Cellular Dynamics
Cited by: 4
Author(s): Martzel Antsotegi-Uskola, Ane Markina-Iñarrairaegui, Unai Ugalde
Software Mentions: 3
Published: almost 6 years ago

10.1186/s13567-018-0545-7

Comparative liver transcriptome analysis in ducklings infected with duck hepatitis A virus 3 (DHAV-3) at 12 and 48 hours post-infection through RNA-seq
Cited by: 11
Author(s): Xuelian Zhang, Chen Cao, Yue Liu, Haihui Qi, Wenjing Zhang, Chunxue Hao, Haotian Chen, Qi Zhang, Wenlong Zhang, Mingchun Gao, Junwei Wang, Bo Ma
Software Mentions: 3
Published: over 8 years ago

10.1038/s41419-020-2333-3

UHRF1-repressed 5’-hydroxymethylcytosine is essential for the male meiotic prophase I
Cited by: 9
Author(s): Hongjie Pan, Ning Jiang, Shenfei Sun, Hanwei Jiang, Jianze Xu, Xiaohua Jiang, Qian Gao, Liang Li, Haili Wu, Huajun Zheng, Qi Qi, Tianqi Li, Meixing Zhang, Lingling Zhang, Xiaofeng Wan, Xinhua Lin, Jiemin Wong, Qinghua Shi, Li R
Software Mentions: 3
Published: over 6 years ago

10.1186/s12985-018-1044-1

Transcriptome analysis of Nicotiana benthamiana infected by Tobacco curly shoot virus
Cited by: 35
Author(s): Ke Li, Gentu Wu, Mingjun Li, Mingge Ma, Jie Du, Miao Sun, Xianchao Sun, Ling Qing
Software Mentions: 3
Published: about 8 years ago

10.3389/fmicb.2020.535673

Transcriptome and miRNome Analysis Provide New Insight Into Host Lipid Accumulation, Innate Immunity, and Viral Persistence in Hepatitis C Virus Infection in vitro
Cited by: 5
Author(s): Chong Li, Lungen Lu, Zhongtian Qi, Yaping Zhu, Fengtao Su, Ping Zhao
Software Mentions: 3
Published: about 6 years ago

10.3389/fmicb.2020.02075

Sodium New Houttuyfonate Inhibits Candida albicans Biofilm Formation by Inhibiting the Ras1-cAMP-Efg1 Pathway Revealed by RNA-seq
Cited by: 21
Author(s): Jiadi Wu, Donghui Wu, Yeye Zhao, Yuanqing Si, Longfei Mei, Jing Shao, Tianming Wang, Yan Ge, Changzhong Wang
Software Mentions: 3
Published: about 6 years ago