pypi: cufflinks | Projects | Ecosyste.ms: Papers

10.3390/ani11092558

Novel Facets of the Liver Transcriptome Are Associated with the Susceptibility and Resistance to Lipid-Related Metabolic Disorders in Periparturient Holstein Cows
Cited by: 2
Author(s): Ryan S. Pralle, Wenli Li, Brianna Murphy, H.T. Holdorf, H.M. White
Software Mentions: 2
Published: about 3 years ago

10.1186/s12859-017-1777-7

ODG: Omics database generator - a tool for generating, querying, and analyzing multi-omics comparative databases to facilitate biological understanding
Cited by: 13
Author(s): Joseph Guhlin, Kevin A.T. Silverstein, Peng Zhou, Peter Tiffin, Nevin D. Young
Software Mentions: 2
Published: over 7 years ago

10.1186/s12859-015-0704-z

EMSAR: estimation of transcript abundance from RNA-seq data by mappability-based segmentation and reclustering
Cited by: 18
Author(s): Mi Kyung Lee, Chae Hwa Seo, B. Alver, Sanghyuk Lee, Peter J. Park
Software Mentions: 2
Published: about 9 years ago

10.1186/1471-2105-13-331

Prediction of novel long non-coding RNAs based on RNA-Seq data of mouse Klf1 knockout study
Cited by: 110
Author(s): Lei Sun, Zhihua Zhang, Timothy L. Bailey, Andrew C. Perkins, Michael R. Tallack, Zhao‐Xu Xu, Hui Liu
Software Mentions: 2
Published: almost 12 years ago

10.1186/s12859-018-2390-0

Accurate prediction of protein-lncRNA interactions by diffusion and HeteSim features across heterogeneous network
Cited by: 24
Author(s): Lei Deng, Junqiang Wang, Yun Xiao, Zixiang Wang, Hui Liu
Software Mentions: 2
Published: about 6 years ago

10.1186/s12896-017-0356-3

Improved n-butanol production via co-expression of membrane-targeted tilapia metallothionein and the clostridial metabolic pathway in Escherichia coli
Cited by: 18
Author(s): Wei-Chih Chin, Kuo-Hsing Lin, Chun-Chi Liu, Kenji Tsuge, Chieh-Chen Huang
Software Mentions: 2
Published: over 7 years ago

10.1186/s12861-019-0200-1

YWHA (14-3-3) protein isoforms and their interactions with CDC25B phosphatase in mouse oogenesis and oocyte maturation
Cited by: 21
Author(s): Alaa Eisa, Santanu De, Ariana C. Detwiler, Eva Gilker, Alexander C. Ignatious, Srinivasan Vijayaraghavan, Douglas Kline
Software Mentions: 2
Published: about 5 years ago

10.1186/s12862-016-0740-y

First insights into the nature and evolution of antisense transcription in nematodes
Cited by: 12
Author(s): Christian Rödelsperger, Kevin Menden, Vahan Serobyan, Hanh Witte, Praveen Baskaran
Software Mentions: 2
Published: over 8 years ago

10.1186/1471-2164-14-607

RNA-seq analyses of gene expression in the microsclerotia of Verticillium dahliae
Cited by: 69
Author(s): Dechassa Duressa, Amy Anchieta, Dongquan Chen, Anna Klimes, Maria D. García-Pedrajas, Katherine F. Dobinson, Steven J. Klosterman
Software Mentions: 2
Published: about 11 years ago

10.1186/1471-2164-14-843

Analysis of porcine adipose tissue transcriptome reveals differences in de novo fatty acid synthesis in pigs with divergent muscle fatty acid composition
Cited by: 73
Author(s): Jordi Corominas, Yuliaxis Ramayo-Caldas, Anna Puig-Oliveras, Jordi Estellé, Anna Castelló, E. Alves, Ramona N. Pena, María Ballester, Josep María Folch
Software Mentions: 2
Published: almost 12 years ago

10.1186/1471-2164-15-1131

Interspecific and intraspecific gene variability in a 1-Mb region containing the highest density of NBS-LRR genes found in the melon genome
Cited by: 15
Author(s): Víctor González, Núria Aventín, Emilio Centeno, Pere Puigdomènech
Software Mentions: 2
Published: almost 10 years ago

10.1186/s12864-015-1547-8

Transciptome analysis reveals flavonoid biosynthesis regulation and simple sequence repeats in yam (Dioscorea alata L.) tubers
Cited by: 41
Author(s): Zhi Gang Wu, Jiang Wu, Nitin Mantri, Xiao Qing Bao, Songlin Chen, Zheng Ming Tao
Software Mentions: 2
Published: over 9 years ago

10.1186/s12864-019-5585-5

Strand-specific RNA-seq based identification and functional prediction of drought-responsive lncRNAs in cassava
Cited by: 41
Author(s): Zehong Ding, Weiwei Tie, Lili Fu, Yan Yan, Guanghua Liu, Wei Yan, Yanan Li, Chunlai Wu, Jiaming Zhang, Wei Hu
Software Mentions: 2
Published: over 5 years ago

10.1186/s12864-020-07069-w

Genome-wide identification and expression patterns analysis of the RPD3/HDA1 gene family in cotton
Cited by: 9
Author(s): Jingjing Zhang, Aimin Wu, Hengling Wei, Pengbo Hao, Qi Zhang, Miaomiao Tian, Yongsheng Xu, Shuaishuai Cheng, Xiaokang Fu, Liang Ma, Hantao Wang, Shuang Yu
Software Mentions: 2
Published: about 4 years ago

10.1186/s12864-015-1554-9

Identification and distribution of the NBS-LRR gene family in the Cassava genome
Cited by: 125
Author(s): Roberto Lozano, Martha T. Hamblin, Simon Prochnik, Jean‐Luc Jannink
Software Mentions: 2
Published: over 9 years ago

10.1186/s12864-020-07192-8

Integrated analysis of lncRNAs and mRNAs reveals key trans-target genes associated with ETEC-F4ac adhesion phenotype in porcine small intestine epithelial cells
Cited by: 9
Author(s): Serafino M. A. Augustino, Qiang Xu, Xueqin Liu, Siyuan Mi, Liangyu Shi, Yibing Liu, Hui Wen, Di Wang, Lei Liu, Qin Zhang, Ying Yu
Software Mentions: 2
Published: about 4 years ago

10.1186/s12864-017-4078-7

Expression dynamics and relations with nearby genes of rat transposable elements across 11 organs, 4 developmental stages and both sexes
Cited by: 6
Author(s): Yongcheng Dong, Ziyan Huang, Qifan Kuang, Zhining Wen, Zhibin Liu, Yizhou Li, Yi Yang, Menglong Li
Software Mentions: 2
Published: about 7 years ago

10.1186/s12864-017-3699-1

Comparative analysis of the predicted secretomes of Rosaceae scab pathogens Venturia inaequalis and V. pirina reveals expanded effector families and putative determinants of host range
Cited by: 48
Author(s): Cecilia Deng, Kim M. Plummer, Darcy A. B. Jones, Carl H. Mesarich, Jason Shiller, Adam P. Taranto, Andrew Robinson, P. Kastner, Nathan E. Hall, Matthew D. Templeton, Joanna K. Bowen
Software Mentions: 2
Published: over 7 years ago

10.1186/1471-2164-15-842

New gene models and alternative splicing in the maize pathogen Colletotrichum graminicola revealed by RNA-Seq analysis
Cited by: 29
Author(s): Ivo Schliebner, Rayko Becher, Marcus Hempel, H. B. Deising, Ralf Horbach
Software Mentions: 2
Published: about 10 years ago

10.1186/s12864-015-2138-4

Integrated genomics approach to identify biologically relevant alterations in fewer samples
Cited by: 8
Author(s): Pratik Chandrani, Pawan Upadhyay, Prajish Iyer, Mayur Tanna, Madhur Shetty, Gorantala Venkata Raghuram, Ninad Oak, Ankita Singh, Rohan Chaubal, Manoj P. Ramteke, Sudeep Gupta, Amit Dutt
Software Mentions: 2
Published: about 9 years ago

10.1186/s12920-018-0414-2

Gene Ontology-based function prediction of long non-coding RNAs using bi-random walk
Cited by: 18
Author(s): Jingpu Zhang, Shuai Zou, Lei Deng
Software Mentions: 2
Published: about 6 years ago

10.1186/s12920-018-0394-2

Comprehensive off-target analysis of dCas9-SAM-mediated HIV reactivation via long noncoding RNA and mRNA profiling
Cited by: 13
Author(s): Yonggang Zhang, Gustavo Arango, Fang Li, Xiao Xiao, Raj Putatunda, Jun Yu, Xiao Feng Yang, Hong Wang, Layne T. Watson, Liqing Zhang, Wenhui Hu
Software Mentions: 2
Published: about 6 years ago

10.1186/1471-2229-13-229

Four distinct types of dehydration stress memory genes in Arabidopsis thaliana
Cited by: 191
Author(s): Yong Ding, Ning Liu, Laëtitia Virlouvet, Jean-Jack M. Riethoven, Michael Fromm, Zoya Avramova
Software Mentions: 2
Published: almost 11 years ago

10.1186/1471-2229-14-76

Over-expression of Arabidopsis AtCHR23 chromatin remodeling ATPase results in increased variability of growth and gene expression
Cited by: 21
Author(s): Adam Folta, Edouard Severing, Julian Krauskopf, Henri van de Geest, J. Verver, Jan-Peter Nap, Ľudmila Mlynárová
Software Mentions: 2
Published: over 10 years ago

10.1186/s12870-018-1603-z

The transcriptome of zinc deficient maize roots and its relationship to DNA methylation loss
Cited by: 24
Author(s): Svenja Mager, Brigitte Schönberger, Uwe Ludewig
Software Mentions: 2
Published: almost 6 years ago

10.1186/s12870-021-02939-1

Comprehensive transcriptional analysis reveals salt stress-regulated key pathways, hub genes and time-specific responsive gene categories in common bermudagrass (Cynodon dactylon (L.) Pers.) roots
Cited by: 13
Author(s): An Shao, Wei Wang, Shugao Fan, Xiao Xu, Yanling Yin, Erick Amombo, Xiaoning Li, Guangyang Wang, Hongli Wang, Jinmin Fu
Software Mentions: 2
Published: over 3 years ago

10.1186/s12870-017-1124-1

Metabolic pathways and genes identified by RNA-seq analysis of barley near-isogenic lines differing by allelic state of the Black lemma and pericarp (Blp) gene
Cited by: 19
Author(s): Anastasiya Y. Glagoleva, Nikolay A. Shmakov, O. Y. Shoeva, Gennady V. Vasiliev, Natalia V. Shatskaya, Andreas Börner, D. A. Afonnikov, Elena K. Khlestkina
Software Mentions: 2
Published: about 7 years ago

10.1186/s12870-016-0953-7

Whole genome-wide transcript profiling to identify differentially expressed genes associated with seed field emergence in two soybean low phytate mutants
Cited by: 15
Author(s): Fengjie Yuan, Xiaomin Yu, Dekun Dong, Qinghua Yang, Xujun Fu, Shenlong Zhu, Derui Zhu
Software Mentions: 2
Published: almost 8 years ago

10.1186/s12870-018-1362-x

Arabidopsis thaliana ambient temperature responsive lncRNAs
Cited by: 43
Author(s): Edouard Severing, Luigi Faino, Suraj Jamge, Marco Busscher, Yang Kuijer-Zhang, Francesca Bellinazzo, Jacqueline Busscher-Lange, Virgínia Fernández, Gerco C. Angenent, Richard G. H. Immink, Alice Pajoro
Software Mentions: 2
Published: over 6 years ago

10.1186/s13104-020-4883-y

DNA methylation and expression analyses reveal epialleles for the foliar disease resistance genes in peanut (Arachis hypogaea L.)
Cited by: 6
Author(s): Ramesh Bhat, Jonathan Rockey, Kenta Shirasawa, I. S. Tilak, M. P. Brijesh Patil, V. B. Reddy Lachagari
Software Mentions: 2
Published: almost 5 years ago

10.1007/s10549-021-06127-5

Differential gene expression analysis of palbociclib-resistant TNBC via RNA-seq
Cited by: 4
Author(s): Lilibeth Lanceta, Nadiia Lypova, Conor O’Neill, Xiaohong Li, Eric C. Rouchka, Jason Chesney, Yoannis Imbert-Fernandez
Software Mentions: 2
Published: almost 4 years ago

10.3390/md19040217

Transcriptome Analysis Reveals Possible Immunomodulatory Activity Mechanism of Chlorella sp. Exopolysaccharides on RAW264.7 Macrophages
Cited by: 2
Author(s): Siwei Wu, Hongquan Liu, Siyu Li, Han Sun, Xiumiao He, Ying Huang, Liang Han
Software Mentions: 2
Published: over 3 years ago

10.1007/s11033-021-06277-1

Differential expression of protein disulfide-isomerase A3 isoforms, PDIA3 and PDIA3N, in human prostate cancer cell lines representing different stages of prostate cancer
Cited by: 5
Author(s): Maria Araceli Diaz Cruz, Sandra Karlsson, Ferenc Szekeres, Maria Faresjö, Dan Lund, Dennis Larsson
Software Mentions: 2
Published: over 3 years ago

10.3390/molecules22122126

Biochemical, Physiological and Transcriptomic Comparison between Burley and Flue-Cured Tobacco Seedlings in Relation to Carbohydrates and Nitrate Content
Cited by: 17
Author(s): Yafei Li, Huijuan Yang, Dong Chil Chang, Shuzhen Lin, Yuqing Feng, Jingjing Li, Hongzhi Shi
Software Mentions: 2
Published: almost 7 years ago

10.3390/v12040463

RNAseq Reveals the Contribution of Interferon Stimulated Genes to the Increased Host Defense and Decreased PPR Viral Replication in Cattle
Cited by: 8
Author(s): K.G. Tirumurugaan, Rahul Mohanchandra Pawar, G. Dhinakar Raj, A. Thangavelu, John A. Hammond, Satya Parida
Software Mentions: 2
Published: over 4 years ago

10.7717/peerj.2223

Transcriptome analysis ofPseudomonas aeruginosaPAO1 grown at both body and elevated temperatures
Cited by: 19
Author(s): Kok-Gan Chan, Kumutha Priya, Chien‐Yi Chang, Azimah Abd Rahman, Kok Keng Tee, Wai‐Fong Yin
Software Mentions: 2
Published: over 8 years ago

10.1371/journal.pcbi.1005457

Transcriptomics technologies
Cited by: 589
Author(s): Russell Lowe, Neil J. Shirley, Mark R. Bleackley, Stephen K. Dolan, Thomas Shafee
Software Mentions: 2
Published: over 7 years ago

10.1371/journal.pgen.1007130

Gene duplicates cause hybrid lethality between sympatric species of Mimulus
Cited by: 56
Author(s): Matthew P. Zuellig, Andrea L. Sweigart
Software Mentions: 2
Published: over 6 years ago

10.1371/journal.pgen.1009085

DNA supercoiling differences in bacteria result from disparate DNA gyrase activation by polyamines
Cited by: 10
Author(s): Alexandre Duprey, Eduardo A. Groisman
Software Mentions: 2
Published: about 4 years ago

10.1371/journal.pone.0091172

An Improved Canine Genome and a Comprehensive Catalogue of Coding Genes and Non-Coding Transcripts
Cited by: 190
Author(s): Marc P. Hoeppner, Andrew L. Lundquist, Mono Pirun, Jennifer R. S. Meadows, Neda Zamani, Jeremy Johnson, Görel Sundström, April Cook, Michael G. FitzGerald, Ross Swofford, Evan Mauceli, Behrooz Torabi Moghadam, Anna Greka, Jessica Alföldi, Amr Abouelleil, Lynne Aftuck, Daniel Bessette, Aaron M. Berlin, Adam D. Brown, Gary Gearin, Annie Lui, J. Pendexter Macdonald, Margaret Priest, Terrance Shea, Jason Turner-Maier, Andrew Zimmer, Eric S. Lander, Federica Di Palma, Kerstin Lindblad‐Toh, Manfred Grabherr
Software Mentions: 2
Published: over 10 years ago

10.1371/journal.pone.0240662

Transcriptome analysis reveals Nitrogen deficiency induced alterations in leaf and root of three cultivars of potato (Solanum tuberosum L.)
Cited by: 34
Author(s): Jingying Zhang, Yaping Wang, Yanyan Zhao, Zhang Yun, Jia-Yue Zhang, Huanzhi Ma, Yuzhu Han
Software Mentions: 2
Published: about 4 years ago

10.1371/journal.pone.0201270

A user-friendly platform for yeast two-hybrid library screening using next generation sequencing
Cited by: 31
Author(s): Marie‐Laure Erffelinck, Bianca Ribeiro, Marı́a Perassolo, Laurens Pauwels, Jacob Pollier, Véronique Storme, Alain Goossens
Software Mentions: 2
Published: almost 6 years ago

10.1371/journal.pone.0176768

Induction of endogenous retroelements as a potential mechanism for mouse-specific drug-induced carcinogenicity
Cited by: 3
Author(s): Timothy Coskran, Zhijie Jiang, James E. Klaunig, Dixie L. Mager, Leslie Obert, Andrew W. Robertson, Nicholas F. Tsinoremas, Zemin Wang, Mark Gosink
Software Mentions: 2
Published: over 7 years ago

10.1371/journal.pone.0221751

Helicase-like transcription factor (Hltf) gene-deletion promotes oxidative phosphorylation (OXPHOS) in colorectal tumors of AOM/DSS-treated mice
Cited by: 7
Author(s): Rebecca A. Helmer, Gurvinder Kaur, Lisa A. Smith, Beverly S. Chilton
Software Mentions: 2
Published: about 5 years ago

10.1371/journal.pone.0164881

Life History Responses and Gene Expression Profiles of the Nematode Pristionchus pacificus Cultured on Cryptococcus Yeasts
Cited by: 22
Author(s): Gaurav Sanghvi, Praveen Baskaran, Waltraud Röseler, Bogdan Sieriebriennikov, Christian Rödelsperger, Ralf J. Sommer
Software Mentions: 2
Published: about 8 years ago

10.1371/journal.pone.0176675

Optimized approach for Ion Proton RNA sequencing reveals details of RNA splicing and editing features of the transcriptome
Cited by: 13
Author(s): Roger B. Brown, Nathaniel J. Madrid, Hideaki Suzuki, Scott A. Ness
Software Mentions: 2
Published: over 7 years ago

10.1371/journal.pone.0057625

In Silico Estimation of Translation Efficiency in Human Cell Lines: Potential Evidence for Widespread Translational Control
Cited by: 20
Author(s): Stewart G. Stevens, Chris M. Brown
Software Mentions: 2
Published: over 11 years ago

10.1371/journal.pone.0103270

Long Intergenic Non-Coding RNAs (LincRNAs) Identified by RNA-Seq in Breast Cancer
Cited by: 45
Author(s): Xiaohu Ding, Limin Zhu, Ting Ji, Xiping Zhang, Fengmei Wang, Shaoju Gan, Ming Zhao, Hongjian Yang
Software Mentions: 2
Published: over 10 years ago

10.1371/journal.pone.0172950

Splicing-related genes are alternatively spliced upon changes in ambient temperatures in plants
Cited by: 44
Author(s): Leonie Verhage, Edouard Severing, Johan Bucher, Michiel Lammers, Jacqueline Busscher-Lange, Guusje Bonnema, Nicole Rodenburg, Marcel Proveniers, Gerco C. Angenent, Richard G. H. Immink
Software Mentions: 2
Published: over 7 years ago

10.1371/journal.pone.0172547

Cyclin Y-mediated transcript profiling reveals several important functional pathways regulated by Cyclin Y in hippocampal neurons
Cited by: 9
Author(s): I-Seul Joe, Jong-Hwan Kim, Hanna Kim, Junghwa Hong, Mirang Kim, Mikyoung Park
Software Mentions: 2
Published: over 7 years ago

10.1038/s41419-019-1774-z

The Kindlin2-p53-SerpinB2 signaling axis is required for cellular senescence in breast cancer
Cited by: 21
Author(s): Khalid Sossey‐Alaoui, Elżbieta Pluskota, Dorota Szpak, Edward F. Plow
Software Mentions: 2
Published: over 5 years ago

10.1186/s11658-018-0120-2

Systematic analysis of genes involved in oral cancer metastasis to lymph nodes
Cited by: 22
Author(s): Xingâan Zhang, Lanfang Zhang, Xiaoyao Tan, Ying Li, Xiaojiao Han, Hua-dong Wang, Huawei Ming, Qiujiang Li, Kang Liu, Gang Feng
Software Mentions: 2
Published: about 6 years ago

10.1038/cr.2017.106

5-Hydroxymethylcytosine signatures in cell-free DNA provide information about tumor types and stages
Cited by: 181
Author(s): Chun-Xiao Song, Senlin Yin, Li Ma, Amanda Wheeler, Yu Chen, Yan Zhang, Bin Liu, Junjie Xiong, Weihan Zhang, Jian-Kun Hu, Zong-Guang Zhou, Biao Dong, Ze Tian, Stefanie S. Jeffrey, Mei-Sze Chua, Samuel So, Weimin Liu, Yuquan Wei, Jiajie Diao, Dan Xie, Stephen R. Quake
Software Mentions: 2
Published: over 7 years ago

10.3390/cells10010076

Identification of Targets from LRRK2 Rescue Phenotypes
Cited by: 3
Author(s): Joanne Toh, Ling Ling Chua, Patrick Ho, Edwin Sandanaraj, Carol Tang, Hongyan Wang, Eng King Tan
Software Mentions: 2
Published: almost 4 years ago

10.1038/s42003-020-0805-8

Variant phasing and haplotypic expression from long-read sequencing in maize
Cited by: 16
Author(s): Bo Wang, Elizabeth Tseng, Primo Baybayan, Kevin Eng, Michael Regulski, Yinping Jiao, Liya Wang, Andrew Olson, Kapeel Chougule, Peter Van Buren, Doreen Ware
Software Mentions: 2
Published: almost 5 years ago

10.1016/j.dib.2016.03.012

Data set for transcriptional response to depletion of the Shoc2 scaffolding protein
Cited by: 5
Author(s): Eric C. Rouchka, Myoungkun Jeoung, Eun Ryoung Jang, Jinpeng Liu, Chi Wang, Xiaohong Li, Emilia Galperin
Software Mentions: 2
Published: over 8 years ago

10.1242/dmm.036764

Developmental origins for semilunar valve stenosis identified in mice harboring congenital heart disease-associated GATA4 mutation
Cited by: 15
Author(s): Stephanie LaHaye, Uddalak Majumdar, Jun Yasuhara, Sara N. Koenig, Adrianna Matos‐Nieves, Rahul Kumar, Vidu Garg
Software Mentions: 2
Published: almost 6 years ago

10.1186/s13072-015-0029-1

A comprehensive epigenome map of Plasmodium falciparum reveals unique mechanisms of transcriptional regulation and identifies H3K36me2 as a global mark of gene suppression
Cited by: 52
Author(s): Krishanpal Karmodiya, Saurabh J. Pradhan, Bhagyashree S. Joshi, Rahul Jangid, Puli Chandramouli Reddy, Sanjeev Galande
Software Mentions: 2
Published: about 9 years ago

10.3389/fimmu.2020.609456

Innovation in Nucleotide-Binding Oligomerization-Like Receptor and Toll-Like Receptor Sensing Drives the Major Histocompatibility Complex-II Free Atlantic Cod Immune System
Cited by: 5
Author(s): Xing‐Kun Jin, Bernat Morro, Ole K. Tørresen, Visila Moiche, Monica Hongrø Solbakken, Kjetill S. Jakobsen, Sissel Jentoft, Simon Mackenzie
Software Mentions: 2
Published: almost 4 years ago

10.3389/fmicb.2019.00967

Salmonella Establishment in Agricultural Soil and Colonization of Crop Plants Depend on Soil Type and Plant Species
Cited by: 84
Author(s): Sven Jechalke, Jasper Schierstaedt, Marlies Becker, Burkhardt Flemer, Rita Grosch, Kornelia Smalla, Adam Schikora
Software Mentions: 2
Published: over 5 years ago

10.3389/fmicb.2019.02708

Vesicles From Vibrio cholerae Contain AT-Rich DNA and Shorter mRNAs That Do Not Correlate With Their Protein Products
Cited by: 15
Author(s): Petter Langlete, Anders K. Krabberød, Hanne C. Winther‐Larsen
Software Mentions: 2
Published: about 5 years ago

10.3389/fneur.2015.00100

Gene Expression Associated with Early and Late Chronotypes in Drosophila melanogaster
Cited by: 14
Author(s): Mirko Pegoraro, Emma Picot, Celia Napier Hansen, Charalambos P. Kyriacou, Ezio Rosato, Eran Tauber
Software Mentions: 2
Published: over 9 years ago

10.3389/fnut.2021.751388

Transcriptomic Analysis Reveals a Sex-Dimorphic Influence of GAT-2 on Murine Liver Function
Cited by: 1
Author(s): Jian Fu, Qingzhuo Zhang, Zebiao Wu, Changming Hong, Congrui Zhu
Software Mentions: 2
Published: about 3 years ago

10.3389/fpls.2016.01445

Genome-Wide Identification and Evolution Analysis of Trehalose-6-Phosphate Synthase Gene Family in Nelumbo nucifera
Cited by: 17
Author(s): Qijiang Jin, Xin Hu, Xin Li, Bei Wang, Yanjie Wang, Hongwei Jiang, Neil S. Mattson, Yingchun Xu
Software Mentions: 2
Published: about 8 years ago

10.3389/fpls.2017.00093

Understanding Host-Pathogen Interactions with Expression Profiling of NILs Carrying Rice-Blast Resistance Pi9 Gene
Cited by: 44
Author(s): Priyanka Jain, Pankaj Kumar Singh, Ritu Kapoor, Apurva Khanna, Amolkumar U. Solanke, S. Gopala Krishnan, Ashok Kumar Singh, Vinay Sharma, Tilak Raj Sharma
Software Mentions: 2
Published: over 7 years ago

10.3389/fpls.2020.577274

Single-Parent Expression of Anti-sense RNA Contributes to Transcriptome Complementation in Maize Hybrid
Cited by: 0
Author(s): Xiangbo Zhang, Yongwen Qi
Software Mentions: 2
Published: almost 4 years ago

10.3389/fpsyt.2018.00778

Dynamic Patterns of Threat-Associated Gene Expression in the Amygdala and Blood
Cited by: 13
Author(s): Adriana Lori, Stephanie A. Maddox, Sumeet K. Sharma, Raül Andero, Kerry J. Ressler, Alicia K. Smith
Software Mentions: 2
Published: almost 6 years ago

10.1534/g3.117.300224

Filamentation Involves Two Overlapping, but Distinct, Programs of Filamentation in the Pathogenic Fungus Candida albicans
Cited by: 50
Author(s): Jahaun Azadmanesh, Austin Gowen, Paul E. Creger, Nichole D. Schafer, Jill R. Blankenship
Software Mentions: 2
Published: about 7 years ago

10.3390/genes10030224

Differential Alternative Splicing Genes in Response to Boron Deficiency in Brassica napus
Cited by: 12
Author(s): Jin Gu, Wei Li, Sheliang Wang, Xiaoyan Zhang, A. Coules, Guangda Ding, Fangsen Xu, Jian Ren, Chungui Lu, Lei Shi
Software Mentions: 2
Published: over 5 years ago

10.3390/genes11040467

Transcriptomic Profiling Identifies Differentially Expressed Genes in Palbociclib-Resistant ER+ MCF7 Breast Cancer Cells
Cited by: 10
Author(s): Lilibeth Lanceta, Conor O’Neill, Nadiia Lypova, Xiahong Li, Eric C. Rouchka, Sabine Waigel, Jorge G. Gómez-Gutiérrez, Jason Chesney, Yoannis Imbert-Fernandez
Software Mentions: 2
Published: over 4 years ago

10.3390/genes12010031

Genome-Wide Analysis of LysM-Containing Gene Family in Wheat: Structural and Phylogenetic Analysis during Development and Defense
Cited by: 13
Author(s): Zheng Chen, Zijie Shen, Zhao Da, Lei Xu, Lijun Zhang, Quan Zou
Software Mentions: 2
Published: almost 4 years ago

10.1111/gtc.12178

Quality control method for RNA ‐seq using single nucleotide polymorphism allele frequency
Cited by: 6
Author(s): Takaho A. Endo
Software Mentions: 2
Published: about 10 years ago

10.1007/s13258-018-0677-1

Genetic structure of six cattle populations revealed by transcriptome-wide SNPs and gene expression
Cited by: 5
Author(s): Wei Wang, Huai Wang, Hui Tang, Jia Gan, Changgeng Shi, Qing Lu, Donghui Fang, Jun Yi, Maozhong Fu
Software Mentions: 2
Published: over 6 years ago

10.1016/j.gdata.2016.03.004

Analyzing the temporal regulation of translation efficiency in mouse liver
Cited by: 6
Author(s): Peggy Janich, Alaaddin Bulak Arpat, Violeta Castelo-Szekely, David Gatfield
Software Mentions: 2
Published: over 8 years ago

10.1186/s13059-017-1221-3

The histone H3 variant H3.3 regulates gene body DNA methylation in Arabidopsis thaliana
Cited by: 105
Author(s): Heike Wollmann, Hume Stroud, Ramesh Yelagandula, Yoshiaki Tarutani, Dazong Jiang, Jing Li, Bhagyshree Jamge, Hidenori Takeuchi, Sarah Holec, Xin Nie, Tetsuji Kakutani, Steven E. Jacobsen, Frédéric Berger
Software Mentions: 2
Published: over 7 years ago

10.1186/s13059-020-1927-5

Genome-wide MNase hypersensitivity assay unveils distinct classes of open chromatin associated with H3K27me3 and DNA methylation in Arabidopsis thaliana
Cited by: 28
Author(s): Hainan Zhao, Wenli Zhang, Tao Zhang, Yuan Lin, Yaodong Hu, Chao Fang, Jiming Jiang
Software Mentions: 2
Published: almost 5 years ago

10.1093/gigascience/giy046

Chromosome-scale assembly of the Monopterus genome
Cited by: 28
Author(s): Xueya Zhao, Majing Luo, Zhigang Li, Zhong Pei, Yang Cheng, Fengling Lai, Xin Wang, Min Jiang, Mingzhou Bai, Yulan Yang, Hanhua Cheng, Rongjia Zhou
Software Mentions: 2
Published: over 6 years ago

10.1038/s41438-018-0018-1

Transcriptome profiling reveals regulatory mechanisms underlying corolla senescence in petunia
Cited by: 25
Author(s): Hong Wang, Xiaoxiao Chang, Jing Lin, Chang YouHong, Jen-Chih Chen, Michael Reid, Cai‐Zhong Jiang
Software Mentions: 2
Published: over 6 years ago

10.1186/s40781-018-0177-5

Examination of the xanthosine response on gene expression of mammary epithelial cells using RNA-seq technology
Cited by: 3
Author(s): Shanti Choudhary, Wenli Li, Derek M. Bickhart, Ramneek Verma, R. S. Sethi, Chandra Sekhar Mukhopadhyay, Ratan K. Choudhary
Software Mentions: 2
Published: over 6 years ago

10.1093/jxb/erv554

Brevis plant1, a putative inositol polyphosphate 5-phosphatase, is required for internode elongation in maize
Cited by: 25
Author(s): Luis Miguel Sosa Ávila, Diego Cerrudo, Clarence J. Swanton, Lewis Lukens
Software Mentions: 2
Published: almost 9 years ago

10.1093/jxb/ery110

Distinct gene networks modulate floral induction of autonomous maize and photoperiod-dependent teosinte
Cited by: 35
Author(s): Mark A A Minow, Luis Miguel Sosa Ávila, Katie J. Turner, Elena Ponzoni, Iride Mascheretti, Forest Dussault, Lewis Lukens, Vincenzo Rossi, Joseph Colasanti
Software Mentions: 2
Published: over 6 years ago

10.1371/journal.ppat.1007008

Atrophy of skin-draining lymph nodes predisposes for impaired immune responses to secondary infection in mice with chronic intestinal nematode infection
Cited by: 13
Author(s): Xiaogang Feng, Cajsa Classon, Graciela Terán, Yunlong Yang, Lei Li, Sherwin Chan, Ulf Ribacke, Antonio Gigliotti Rothfuchs, Jonathan M. Coquet, Susanne Nylén
Software Mentions: 2
Published: over 6 years ago

10.1098/rspb.2019.0470

Uncovering a mitochondrial unfolded protein response in corals and its role in adapting to a changing world
Cited by: 11
Author(s): Bradford A. Dimos, Siraje Arif Mahmud, Lauren E. Fuess, Laura D. Mydlarz, Mark W. Pellegrino
Software Mentions: 2
Published: over 5 years ago

10.1080/15476286.2016.1232238

A novel role for the 3′-5′ exoribonuclease Dis3L2 in controlling cell proliferation and tissue growth
Cited by: 21
Author(s): Benjamin P. Towler, Christopher Iain Jones, Kirsty L. Harper, Joseph A. Waldron, Sarah F. Newbury
Software Mentions: 2
Published: about 8 years ago

10.1186/s12284-014-0020-7

Differentially-expressed genes in rice infected by Xanthomonas oryzae pv. oryzae relative to a flagellin-deficient mutant reveal potential functions of flagellin in host–pathogen interactions
Cited by: 17
Author(s): Chao Yu, Huamin Chen, Tian Fang, Jan E. Leach, Chenyang He
Software Mentions: 2
Published: about 10 years ago

10.1038/srep10339

Target of Rapamycin Complex 2 regulates cell growth via Myc in Drosophila
Cited by: 18
Author(s): Ying Kuo, Huanwei Huang, Tao Cai, Tao Wang
Software Mentions: 2
Published: over 9 years ago

10.1038/srep24141

Implication of Long noncoding RNAs in the endothelial cell response to hypoxia revealed by RNA-sequencing
Cited by: 113
Author(s): Christine Voellenkle, José Manuel García-Manteiga, Simona Pedrotti, Alessandra Perfetti, Ilario De Toma, D. Da Silva, Biagina Maimone, Simona Greco, Pasquale Fasanaro, Pasquale Creo, Germana Zaccagnini, Carlo Gaetano, Fabio Martelli
Software Mentions: 2
Published: over 8 years ago

10.1038/srep29933

The myocardial regenerative potential of three-dimensional engineered cardiac tissues composed of multiple human iPS cell-derived cardiovascular cell lineages
Cited by: 87
Author(s): Hidetoshi Masumoto, Takeichiro Nakane, Joseph P. Tinney, Fangping Yuan, Fei Ye, William J. Kowalski, Kenji Minakata, Ryuzo Sakata, Jun Yamashita, Bradley B. Keller
Software Mentions: 2
Published: over 8 years ago

10.3934/microbiol.2018.1.123

Analysis of immune-related genes during Nora virus infection of Drosophila melanogaster using next generation sequencing
Cited by: 21
Author(s): Wilfredo A. López, Alexis M. Page, Darby J. Carlson, Brad L. Ericson, Mátyás Cserháti, Chittibabu Guda, Kimberly A. Carlson
Software Mentions: 2
Published: almost 7 years ago

10.1038/s41598-018-21601-9

Understanding the functional role of genistein in the bone differentiation in mouse osteoblastic cell line MC3T3-E1 by RNA-seq analysis
Cited by: 17
Author(s): Myungsuk Kim, Jae‐Hak Lim, Jung‐Hee Lee, Kyung-Mi Lee, Suji Kim, Kye Won Park, Chu Won Nho, Yoon Shin Cho
Software Mentions: 2
Published: almost 7 years ago

10.1038/s41598-018-23655-1

Integrated transcriptomes throughout swine oestrous cycle reveal dynamic changes in reproductive tissues interacting networks
Cited by: 24
Author(s): Junmo Kim, Jong-Eun Park, Inkyu Yoo, Jisoo Han, Namshin Kim, Won-Jun Lim, Eun Seok Cho, Bong-Hwan Choi, Suna Choi, Tae-Hun Kim, M.F.W. te Pas, Hakhyun Ka, Kyung-Tai Lee
Software Mentions: 2
Published: over 6 years ago

10.1038/s41598-018-24341-y

Deciphering the mechanism of action of 089, a compound impairing the fungal cell cycle
Cited by: 6
Author(s): Irene Stefanini, Lisa Rizzetto, Damaríz Rivero, Sílvia Carbonell, Marta Gut, Simon Heath, Andrea Trabocchi, Antonio Guarna, Nagwa Ben Ghazzi, Paul Bowyer, Misha Kapushesky, Duccio Cavalieri
Software Mentions: 2
Published: over 6 years ago

10.1038/s41598-018-26429-x

Transcriptomic response of breast cancer cells to anacardic acid
Cited by: 30
Author(s): David J. Schultz, Abirami Krishna, Stephany L. Vittitow, Negin Alizadeh-Rad, Penn Muluhngwi, Eric C. Rouchka, Carolyn M. Klinge
Software Mentions: 2
Published: over 6 years ago

10.1038/s41598-018-29477-5

Immunophenotyping and transcriptional profiling of in vitro cultured human adipose tissue derived stem cells
Cited by: 28
Author(s): Alina Mieczkowska, Adriana Schumacher, Natalia Filipowicz, Anna Wardowska, Maciej Zieliński, Piotr Madanecki, Ewa Nowicka, Paulina Langa, Milena Deptuła, Jacek Zieliński, Karolina Kondej, Alicja Renkielska, Patrick G. Buckley, David K. Crossman, Michael R. Crowley, Artur Czupryn, Piotr Mucha, Paweł Sachadyn, Łukasz Janus, Piotr M. Skowron, Sylwia Rodziewicz‐Motowidło, M Cichorek, Michał Pikuła, Arkadiusz Piotrowski
Software Mentions: 2
Published: over 6 years ago

10.1038/s41598-018-31432-3

Metabolome and molecular basis for carbohydrate increase and nitrate reduction in burley tobacco seedlings by glycerol through upregulating carbon and nitrogen metabolism
Cited by: 8
Author(s): Yafei Li, Dong Chil Chang, Huijuan Yang, Jing Wang, Hongzhi Shi
Software Mentions: 2
Published: about 6 years ago

10.1038/s41598-019-39141-1

Transcriptomic profiles of retinal ganglion cells are defined by the magnitude of intraocular pressure elevation in adult mice
Cited by: 16
Author(s): Yong H. Park, Joshua D. Snook, Edwin J. Ostrin, Sangbae Kim, Rui Chen, Benjamin J. Frankfort
Software Mentions: 2
Published: almost 6 years ago

10.1038/s41598-020-57451-7

Identification, functional prediction, and key lncRNA verification of cold stress-related lncRNAs in rats liver
Cited by: 13
Author(s): Hong Ji, Chunyang Niu, Xuelong Zhan, Jing Xu, Shuai Lian, Bin Xu, Jiang Guo, Zhen Li, Huanmin Yang, Shize Li, Li Ma
Software Mentions: 2
Published: almost 5 years ago

10.1038/s41598-020-58167-4

Transcriptome analysis of potato shoots, roots and stolons under nitrogen stress
Cited by: 47
Author(s): Jagesh Kumar Tiwari, Tanuja Buckseth, Rasna Zinta, Aastha Saraswati, Rajesh Kumar Singh, Shashi Rawat, V. K. Dua, S. K. Chakrabarti
Software Mentions: 2
Published: almost 5 years ago

10.1038/s41598-020-69386-0

Combining transcriptomics and genetic linkage based information to identify candidate genes associated with Heterobasidion-resistance in Norway spruce
Cited by: 3
Author(s): Rajiv Chaudhary, Karl Lundén, Kerstin Dalman, Mukesh Dubey, Miguel Nemesio‐Gorriz, Bo Karlsson, Jan Stenlid, Malin Elfstrand
Software Mentions: 2
Published: over 4 years ago

10.1038/s41598-021-94544-3

The value of GATA6 immunohistochemistry and computer-assisted diagnosis to predict clinical outcome in advanced pancreatic cancer
Cited by: 11
Author(s): Kai Duan, Gun-Ho Jang, Robert C. Grant, Julie M. Wilson, Faiyaz Notta, Grainne M. O’Kane, Jennifer J. Knox, Steven Gallinger, Sandra E. Fischer
Software Mentions: 2
Published: over 3 years ago

Projects: pypi: cufflinks

Papers Mentioning cufflinks 415