Ecosyste.ms: Papers

10.1186/gb-2013-14-12-r141

Obligate mutualism within a host drives the extreme specialization of a fig wasp genome
Cited by: 79
Author(s): Jin‐Hua Xiao, Zhen Yue, Ling-Yi Jia, Xinhua Yang, Lihua Niu, Zhuo Wang, Peng Zhang, Bao‐Fa Sun, Shunmin He, Zi Li, Tuanlin Xiong, Xintian Wen, Haifeng Gu, Bo Wang, John H. Werren, Robert W. Murphy, David A. Wheeler, Li‐Ming Niu, Guang-Chang Ma, Ting Tang, Sheng‐Nan Bian, Ningxin Wang, Caiqiong Yang, Nan Wang, Yanlong Fu, Wenzhu Li, Soojin V. Yi, Xingyu Yang, Qing Zhou, Changxin Lu, Chunyan Xu, Li He, Lili Yu, Ming Chen, Yawen Zheng, Shaowei Wang, Shuang Zhao, Yanhong Li, Yangyang Yu, Xiaoju Qian, Yuchen Cai, Lianle Bian, Shu Zhang, Junyi Wang, Ye Yin, Hui Xiao, Guan-Hong Wang, Hui Yu, Wei-Jian Wu, James M. Cook, Jun Wang, Dawei Huang
Software Mentions: 4
Published: almost 12 years ago

10.1038/srep12615

Decrease of mRNA Editing after Spinal Cord Injury is Caused by Down-regulation of ADAR2 that is Triggered by Inflammatory Response
Cited by: 27
Author(s): Antonio Fabio Di Narzo, Alexey Kozlenkov, Yongchao Ge, Bin Zhang, Leo Sanelli, Zacnicte May, Yanqing Li, Karim Fouad, Christopher P. Cardozo, Eugene V. Koonin, David J. Bennett, Stella Dracheva
Software Mentions: 4
Published: over 9 years ago

10.1038/sdata.2018.305

The sequence and de novo assembly of hog deer genome
Cited by: 7
Author(s): Wei Wang, Yan Huang, Shiyi Chen, Zhenzhen Li, Jun Yi, Lili Niu, Jia-Po Deng, Weigang Chen, Yunfeng Pu, Xianbo Jia, Yu Qu, Ang Chen, Yan Zhong, Xiaoxi Yu, Shuai Pang, Wanlong Huang, Yue Han, Guangjian Liu, Jianqiu Yu
Software Mentions: 4
Published: almost 6 years ago

10.1371/journal.pone.0145257

Comparative Transcriptome Analysis of the Pacific Oyster Crassostrea gigas Characterized by Shell Colors: Identification of Genetic Bases Potentially Involved in Pigmentation
Cited by: 73
Author(s): Dandan Feng, Qi Li, Hong Yu, Xuelin Zhao, Lingfeng Kong
Software Mentions: 4
Published: almost 9 years ago

10.1186/gb-2013-14-12-r146

Lsh regulates LTR retrotransposon repression independently of Dnmt3b function
Cited by: 53
Author(s): Donncha S. Dunican, Hazel A Cruickshanks, Masako Suzuki, Colin A. Semple, Tracey Davey, Robert J. Arceci, John M. Greally, Ian R. Adams, Richard R. Meehan
Software Mentions: 4
Published: almost 12 years ago

10.1126/sciadv.abg5982

Single-cell analyses unravel cell type–specific responses to a vitamin D analog in prostatic precancerous lesions
Cited by: 9
Author(s): Mohamed A. Abu el Maaty, Élise Grelet, Céline Keime, Anna‐Isavella Rerra, Justine Gantzer, C. Emprou, Julie Terzic, Régis Lutzing, Jean‐Marc Bornert, Gilles Laverny, Daniel Metzger
Software Mentions: 4
Published: over 3 years ago

10.1093/bioinformatics/btu749

M3D: a kernel-based test for spatially correlated changes in methylation profiles
Cited by: 27
Author(s): Tom Mayo, Gabriele Schweikert, Guido Sanguinetti
Software Mentions: 4
Published: about 10 years ago

10.1371/journal.pone.0115842

Identifying Glioblastoma Gene Networks Based on Hypergeometric Test Analysis
Cited by: 14
Author(s): Vasileios Stathias, Chiara Pastori, Tess Z. Griffin, Ricardo J. Komotar, Jennifer Clarke, Ming Zhang, Nagi G. Ayad
Software Mentions: 4
Published: almost 10 years ago

10.1186/s13059-014-0536-6

TNFα signalling primes chromatin for NF-κB binding and induces rapid and widespread nucleosome repositioning
Cited by: 41
Author(s): Sarah D. Diermeier, Petros Kolovos, Leonhard Heizinger, Uwe Schwartz, Theodore Georgomanolis, Anne Zirkel, Gero Wedemann, Frank Grosveld, Tobias Knoch, Rainer Merkl, Peter R. Cook, Gernot Längst, Argyris Papantonis
Software Mentions: 4
Published: almost 10 years ago

10.1371/journal.pone.0093846

The SLE Transcriptome Exhibits Evidence of Chronic Endotoxin Exposure and Has Widespread Dysregulation of Non-Coding and Coding RNAs
Cited by: 104
Author(s): Lei Shi, Zhe Zhang, Angela M Yu, Wei Wang, Zhi Wei, Ehtisham Akhter, Kelly Maurer, Patrícia Costa-Reis, Li Song, Michelle Petri, Kathleen E. Sullivan
Software Mentions: 4
Published: over 10 years ago

10.1186/s13059-015-0590-8

Field pathogenomics reveals the emergence of a diverse wheat yellow rust population
Cited by: 175
Author(s): Amelia Hubbard, Clare M. Lewis, Kentaro Yoshida, Ricardo H. Ramírez-González, C. de Vallavieille‐Pope, Jane Thomas, Sophien Kamoun, R. A. Bayles, Cristóbal Uauy, Diane G. O. Saunders
Software Mentions: 4
Published: over 9 years ago

10.1186/s13059-015-0671-8

An integrative analysis of post-translational histone modifications in the marine diatom Phaeodactylum tricornutum
Cited by: 76
Author(s): Alaguraj Veluchamy, Achal Rastogi, Xin Lin, Bérangère Lombard, Omer Murik, Y. Thomas, Florent Dingli, Máximo Rivarola, Sandra Ott, Xinyue Liu, Yan Sun, Pablo D. Rabinowicz, James S. McCarthy, Andrew E. Allen, Damarys Loew, Chris Bowler, Leïla Tirichine
Software Mentions: 4
Published: over 9 years ago

10.1038/s41438-020-00432-8

Transcriptional regulation of bark freezing tolerance in apple (Malus domestica Borkh.)
Cited by: 9
Author(s): Yin Liang, Shanshan Wang, Chang Zhao, Xinwei Ma, Yiyong Zhao, Jing Shao, Yuebo Li, Honglian Li, Song Hong‐wei, Hong Mā, Hao Li, Bingbing Zhang, Liangsheng Zhang
Software Mentions: 4
Published: almost 4 years ago

10.1038/s41422-018-0066-y

Single-cell RNA-seq reveals the diversity of trophoblast subtypes and patterns of differentiation in the human placenta
Cited by: 242
Author(s): Yawei Liu, Xiaoying Fan, Rui Wang, Xiaoyin Lu, Yan-Li Dang, Huiying Wang, Haiyan Lin, Cheng Zhu, Hao Ge, James C. Cross, Hongmei Wang
Software Mentions: 4
Published: over 6 years ago

10.1016/j.heliyon.2020.e03493

Efficient differentiation and purification of human induced pluripotent stem cell-derived endothelial progenitor cells and expansion with the use of inhibitors of ROCK, TGF-β, and GSK3β
Cited by: 9
Author(s): Hiromasa Aoki, Misaki Yamashita, Tadahiro Hashita, Koichi Ogami, Shin‐ichi Hoshino, Takahiro Iwao, Tamihide Matsunaga
Software Mentions: 4
Published: over 4 years ago

10.1101/mcs.a002444

Resistance-promoting effects of ependymoma treatment revealed through genomic analysis of multiple recurrences in a single patient
Cited by: 15
Author(s): Christopher A. Miller, Sonika Dahiya, Tiandao Li, Robert S. Fulton, Matthew D. Smyth, Gavin P. Dunn, Joshua B. Rubin, Elaine R. Mardis
Software Mentions: 4
Published: almost 7 years ago

10.1038/s41438-020-00416-8

Identification of key gene networks controlling organic acid and sugar metabolism during watermelon fruit development by integrating metabolic phenotypes and gene expression profiles
Cited by: 66
Author(s): Muhammad Umer, Luqman Bin Safdar, Haileslassie Gebremeskel, Shengjie Zhao, Pingli Yuan, Huiling Zhu, Mohamed Omar Kaseb, Muhammad Anees, Xingrong Lu, Nan He, Chengsheng Gong, Wenge Liu
Software Mentions: 4
Published: almost 4 years ago

10.1038/s41438-021-00531-0

Whole-genome resequencing of Osmanthus fragrans provides insights into flower color evolution
Cited by: 28
Author(s): Chen Hong-guo, Xiangling Zeng, Jie Yang, Xuan Cai, Yumin Shi, Rencheng Zheng, Zhenqi Wang, Junyi Liu, Xiao Su Yi, Siwei Xiao, Qiang Fu, Jingjing Zou, Caiyun Wang
Software Mentions: 4
Published: over 3 years ago

10.3390/insects9040185

Differential Gene Expression in Red Imported Fire Ant (Solenopsis invicta) (Hymenoptera: Formicidae) Larval and Pupal Stages
Cited by: 11
Author(s): Margaret L. Allen, Joshua H. Rhoades, Michael E. Sparks, Michael J. Grodowitz
Software Mentions: 4
Published: almost 6 years ago

10.3390/cells9071745

Ribosomal Protein uL11 as a Regulator of Metabolic Circuits Related to Aging and Cell Cycle
Cited by: 7
Author(s): Mateusz Mołoń, Eliza Molestak, Monika Kula-Maximenko, Przemysław Grela, Marek Tchórzewski
Software Mentions: 4
Published: over 4 years ago

10.1038/s41438-018-0073-7

Tomato DCL2b is required for the biosynthesis of 22-nt small RNAs, the resulting secondary siRNAs, and the host defense against ToMV
Cited by: 39
Author(s): Tian Wang, Zhiqi Deng, Xi Zhang, Hongzheng Wang, Yu Wang, Xiuying Liu, Songyu Liu, Feng Xu, Tao Li, Daqi Fu, Beiwei Zhu, Yunbo Luo, Hongliang Zhu
Software Mentions: 4
Published: about 6 years ago

10.3390/plants10040669

Integrative Analysis of Gene Expression and miRNAs Reveal Biological Pathways Associated with Bud Paradormancy and Endodormancy in Grapevine
Cited by: 4
Author(s): Shuchi Smita, Michael Robben, Anup Deuja, Monica Accerbi, Pamela J. Green, Senthil Subramanian, Anne Fennell
Software Mentions: 4
Published: over 3 years ago

10.1111/imb.12688

Jekyll or Hyde? The genome (and more) of <i>Nesidiocoris tenuis</i>, a zoophytophagous predatory bug that is both a biological control agent and a pest
Cited by: 11
Author(s): Kim Ferguson, Sako Visser, Martina Dalíková, Irena Provazníková, Alberto Urbaneja, František Marec, John H. Werren, Bas J. Zwaan, Bart A. Pannebakker, Eveline C. Verhulst
Software Mentions: 4
Published: almost 4 years ago

10.1186/s13068-018-1060-9

Deciphering lignocellulose deconstruction by the white rot fungus Irpex lacteus based on genomic and transcriptomic analyses
Cited by: 33
Author(s): Xing Qin, Xiaoyun Su, Huiying Luo, Rui Ma, Bin Yao, Fuying Ma
Software Mentions: 4
Published: over 6 years ago

10.1172/jci.insight.142980

Treating ICB-resistant glioma with anti-CD40 and mitotic spindle checkpoint controller BAL101553 (lisavanbulin)
Cited by: 5
Author(s): Vassilis Genoud, Felipe I Espinoza, Eliana Marinari, Viviane Rochemont, Pierre‐Yves Dietrich, Paul M.J. McSheehy, Felix Bachmann, Heidi A. Lane, Paul R Walker
Software Mentions: 4
Published: about 3 years ago

10.3389/fgene.2014.00312

Gene expression responses of threespine stickleback to salinity: implications for salt-sensitive hypertension
Cited by: 33
Author(s): Gang Wang, Ence Yang, Kerri J. Smith, Yong Zeng, Guoli Ji, Richard E. Connon, Nann A. Fangue, James J. Cai
Software Mentions: 4
Published: about 10 years ago

10.1371/journal.pone.0151697

Comparative RNA-Seq Analysis Reveals That Regulatory Network of Maize Root Development Controls the Expression of Genes in Response to N Stress
Cited by: 19
Author(s): Xiujing He, Hui Ma, Xing Zhao, Shujun Nie, Yuhua Li, Zhiming Zhang, Yaou Shen, Qi Chen, Yanli Lu, Hai Long, Shufeng Zhou, Shibin Gao, Guangtang Pan, Hung-Ching Lin
Software Mentions: 4
Published: over 8 years ago

10.1186/2049-1891-3-8

Current status and future perspectives for sequencing livestock genomes
Cited by: 40
Author(s): Yongsheng Bai, Maureen A. Sartor, James D. Cavalcoli
Software Mentions: 4
Published: over 12 years ago

10.1016/j.stem.2019.09.008

Sphingolipid Modulation Activates Proteostasis Programs to Govern Human Hematopoietic Stem Cell Self-Renewal
Cited by: 71
Author(s): Stephanie Z. Xie, Laura García‐Prat, Véronique Voisin, Raffaele Ferrari, Olga I. Gan, Elvin Wagenblast, Kerstin B. Kaufmann, Andy G.X. Zeng, Shin‐ichiro Takayanagi, Ishita Patel, Esther K. Lee, Joseph Jargstorf, Gareth D. Holmes, Guy Romm, Kristele Pan, Michelle Shoong, Aditi Vedi, Chiara Luberto, Mark D. Minden, Gary D. Bader, Elisa Laurenti, John E. Dick
Software Mentions: 4
Published: about 5 years ago

10.3389/fgene.2020.00736

DNA N6-Methyladenine Modification in Wild and Cultivated Soybeans Reveals Different Patterns in Nucleus and Cytoplasm
Cited by: 13
Author(s): Di Yuan, Jian-Feng Xing, Meiwei Luan, Kai-Kai Ji, Jun Guo, Shuang Xie, Yuanming Zhang
Software Mentions: 4
Published: over 4 years ago

10.1186/s40104-021-00626-7

NORHA, a novel follicular atresia-related lncRNA, promotes porcine granulosa cell apoptosis via the miR-183-96-182 cluster and FoxO1 axis
Cited by: 16
Author(s): Yao Wang, Zengxiang Pan, Xiaohong Du, Jinbi Zhang, Honglin Liu, Qifa Li
Software Mentions: 4
Published: about 3 years ago

10.1038/s41422-020-0378-6

Comparative analysis of cell lineage differentiation during hepatogenesis in humans and mice at the single-cell transcriptome level
Cited by: 49
Author(s): Xin Wang, Li Yang, Yanchun Wang, Ziran Xu, Yang Feng, Jing Zhang, Yi Wang, Cheng‐Ran Xu
Software Mentions: 4
Published: over 4 years ago

10.1016/j.stem.2017.03.003

H3K4 Methylation-Dependent Memory of Somatic Cell Identity Inhibits Reprogramming and Development of Nuclear Transfer Embryos
Cited by: 85
Author(s): Eva Hörmanseder, Angela Simeone, George E. Allen, Charles R. Bradshaw, Magdalena Figlmüller, J. B. Gurdon, Jérôme Jullien
Software Mentions: 4
Published: over 7 years ago

10.1007/s11105-017-1032-4

Drought-Tolerant Brassica rapa Shows Rapid Expression of Gene Networks for General Stress Responses and Programmed Cell Death Under Simulated Drought Stress
Cited by: 25
Author(s): Yi Guo, Birgit Samans, Sheng Chen, Kidist B. Kibret, Sarah Hatzig, Neil C. Turner, Matthew N. Nelson, Wallace Cowling, Rod J. Snowdon
Software Mentions: 4
Published: over 7 years ago

10.1038/s42003-021-02089-y

Regulation of mammalian 3D genome organization and histone H3K9 dimethylation by H3K9 methyltransferases
Cited by: 10
Author(s): Kei Fukuda, Chikako Shimura, Hisashi Miura, Akie Tanigawa, Takehiro Suzuki, Naoshi Dohmae, Ichiro Hiratani, Yoichi Shinkai
Software Mentions: 4
Published: over 3 years ago

10.1093/gigascience/giaa036

Chromosome-level reference genome of the jellyfish Rhopilema esculentum
Cited by: 16
Author(s): Yunfeng Li, Lei Gao, Yongjia Pan, Meilin Tian, Yulong Li, Chongbo He, Ying Dong, Yamin Sun, Zunchun Zhou
Software Mentions: 4
Published: over 4 years ago

10.1186/s13068-020-01774-0

Integrating GWAS, linkage mapping and gene expression analyses reveals the genetic control of growth period traits in rapeseed (Brassica napus L.)
Cited by: 17
Author(s): Tengyue Wang, Lijuan Wei, Jia Wang, Ling Xie, Yang Yang Li, Shuyao Ran, Lanyang Ren, Kun Lu, Jiana Li, Michael P. Timko, Liezhao Liu
Software Mentions: 4
Published: over 4 years ago

10.1371/journal.pone.0166104

Piphillin: Improved Prediction of Metagenomic Content by Direct Inference from Human Microbiomes
Cited by: 249
Author(s): Shoko Iwai, Thomas Weinmaier, Brian L. Schmidt, Donna G. Albertson, Neil J. Poloso, Karim Dabbagh, Todd Z. DeSantis
Software Mentions: 4
Published: about 8 years ago

10.1172/jci.insight.143289

LncRNA DRAIR is downregulated in diabetic monocytes and modulates inflammatory phenotype via epigenetic mechanisms
Cited by: 15
Author(s): Marpadga A. Reddy, Vishnu Amaram, Sadhan Das, Vinay Singh Tanwar, Rituparna Ganguly, Mei Wang, Linda Lanting, Lingxiao Zhang, Maryam Abdollahi, Zhuo Chen, Xiwei Wu, Sridevi Devaraj, Rama Natarajan
Software Mentions: 4
Published: over 3 years ago

10.3390/cells9122593

Induced Pluripotent Stem Cells to Understand Mucopolysaccharidosis. I: Demonstration of a Migration Defect in Neural Precursors
Cited by: 3
Author(s): Silvin Lito, Adama Sidibé, Sten Ilmjärv, Patricie Burda, Matthias R. Baumgartner, Bernhard Wehrle-Haller, Karl‐Heinz Krause, Antoine Marteyn
Software Mentions: 4
Published: almost 4 years ago

10.3390/cells7110205

The Heterochromatin Landscape in Migrating Cells and the Importance of H3K27me3 for Associated Transcriptome Alterations
Cited by: 25
Author(s): Tamar Segal, Mali Salmon‐Divon, Gabi Gerlitz
Software Mentions: 4
Published: about 6 years ago

10.1111/tpj.14299

Hybrid sequencing reveals insight into heat sensing and signaling of bread wheat
Cited by: 46
Author(s): Xiaoming Wang, Siyuan Chen, Song Xue, Danni Liu, Peng Zhao, Yunze Lu, Yanbing Cheng, Zhenshan Liu, Xiaojun Nie, Weining Song, Qixin Sun, Shengbao Xu, Chuang Ma
Software Mentions: 4
Published: over 5 years ago

10.1186/s13059-014-0410-6

Corset: enabling differential gene expression analysis for de novoassembled transcriptomes
Cited by: 278
Author(s): N. Davidson, Alicia Oshlack
Software Mentions: 4
Published: over 10 years ago

10.1186/s13059-014-0513-0

TET1 regulates hypoxia-induced epithelial-mesenchymal transition by acting as a co-activator
Cited by: 120
Author(s): Ya-Ping Tsai, Hsiao-Fan Chen, Sung-Yuan Chen, Wei‐Chung Cheng, Hsei‐Wei Wang, Zih-Jie Shen, Chun-Xiao Song, Shan-Yuan Teng, Chuan He, Kou-Juey Wu
Software Mentions: 4
Published: almost 10 years ago

10.3389/fgene.2019.00306

Chromatin State-Based Analysis of Epigenetic H3K4me3 Marks of Arabidopsis in Response to Dark Stress
Cited by: 13
Author(s): Hengyu Yan, Yue Liu, Kang Zhang, Jakyoung Song, Wenying Xu, Zhen Su
Software Mentions: 4
Published: over 5 years ago

10.1186/gb-2013-14-4-r31

Quartz-Seq: a highly reproducible and sensitive single-cell RNA sequencing method, reveals non-genetic gene-expression heterogeneity
Cited by: 368
Author(s): Yohei Sasagawa, Itoshi Nikaido, Tetsutaro Hayashi, Hiroki Danno, Kenichiro D. Uno, Takeshi Imai, Hiroki R. Ueda
Software Mentions: 4
Published: over 11 years ago

10.1186/gb-2013-14-11-r131

Chromatin signatures at transcriptional start sites separate two equally populated yet distinct classes of intergenic long noncoding RNAs
Cited by: 162
Author(s): Ana C. Marques, Jim R. Hughes, Bryony Graham, Monika S. Kowalczyk, Douglas R. Higgs, Chris P. Ponting
Software Mentions: 4
Published: almost 12 years ago

10.1038/bcj.2017.71

Alternative splicing discriminates molecular subtypes and has prognostic impact in diffuse large B-cell lymphoma
Cited by: 13
Author(s): Suvi‐Katri Leivonen, M.-R. Taskinen, Alejandra Cervera, Marja‐Liisa Karjalainen‐Lindsberg, Jan Delabie, Harald Holte, Rainer Lehtonen, Sampsa Hautaniemi, Sirpa Leppä
Software Mentions: 4
Published: about 7 years ago

10.1126/sciadv.abf7346

Functional coordination of BET family proteins underlies altered transcription associated with memory impairment in fragile X syndrome
Cited by: 4
Author(s): Seung Kyoon Kim, Xihui Liu, Jong-Min Park, Dahun Um, Gokhul Kilaru, Cheng Ming Chiang, Min-Hee Kang, Kimberly M. Huber, Keunsoo Kang, Tae Kyung Kim
Software Mentions: 4
Published: over 3 years ago

10.1111/jcmm.15569

LIX1 regulates YAP activity and controls gastrointestinal cancer cell plasticity
Cited by: 8
Author(s): Amandine Guérin, Delphine Martire, Eva Trenquier, Tom Lesluyes, Sébastien Sagnol, Marine Pratlong, Elise Lefebvre, Frédéric Chibon, Pascal de Santa Barbara, Sandrine Faure
Software Mentions: 4
Published: over 4 years ago

10.3390/insects11050323

Transcriptome Analysis of the Oriental Fruit Fly Bactrocera dorsalis Early Embryos
Cited by: 2
Author(s): Wei Peng, Shu-Ning Yu, Alfred M. Handler, H. Zhang
Software Mentions: 4
Published: over 4 years ago

10.1016/j.celrep.2020.107748

Chromatin Priming Renders T Cell Tolerance-Associated Genes Sensitive to Activation below the Signaling Threshold for Immune Response Genes
Cited by: 20
Author(s): Sarah L Bevington, Sky T. H. Ng, Graham J. Britton, Peter Keane, David C. Wraith, Peter N. Cockerill
Software Mentions: 4
Published: over 4 years ago

10.1371/journal.pone.0225658

Highly multiplexed quantitative PCR-based platform for evaluation of chicken immune responses
Cited by: 15
Author(s): Dominika Borowska, Richard Kuo, Richard Bailey, Kellie Watson, Pete Kaiser, Lonneke Vervelde, Mark P. Stevens
Software Mentions: 4
Published: almost 5 years ago

10.1111/jcmm.14163

LncRNA-mRNA competing endogenous RNA network depicts transcriptional regulation in ischaemia reperfusion injury
Cited by: 19
Author(s): Hongying Liu, Dan-Ping Xu, Xin Zhong, Dongsheng Xu, Geng Chen, Junbo Ge, Hua Li
Software Mentions: 4
Published: almost 6 years ago

10.1186/gb-2014-15-2-r34

A multi-split mapping algorithm for circular RNA, splicing, trans-splicing and fusion detection
Cited by: 230
Author(s): Steve Hoffmann, Christian Otto, Gero Doose, Andrea Tanzer, David Langenberger, Sabina Christ, Manfred Kunz, Lesca M. Holdt, Daniel Teupser, Jörg Hackermüller, Peter F. Stadler
Software Mentions: 4
Published: almost 11 years ago

10.1371/journal.pbio.1001126

Sex Chromosome-Specific Regulation in the Drosophila Male Germline But Little Evidence for Chromosomal Dosage Compensation or Meiotic Inactivation
Cited by: 123
Author(s): Colin D. Meiklejohn, Emily L. Landeen, Jodi M. Cook, Sarah B. Kingan, Daven C. Presgraves
Software Mentions: 4
Published: over 13 years ago

10.1038/sdata.2018.255

Combined RNA-seq and RAT-seq mapping of long noncoding RNAs in pluripotent reprogramming
Cited by: 16
Author(s): Zhonghua Du, Lin Jia, Yichen Wang, Cong Wang, Wei Xue, Jingcheng Chen, Yanbo Zhu, Dehai Yu, Lei Zhou, Naifei Chen, Shilin Zhang, Ilkay Celik, Ferhat Ay, Sujun Gao, Songling Zhang, Wei Li, Andrew R. Hoffman, Jiuwei Cui
Software Mentions: 4
Published: about 6 years ago

10.1016/j.celrep.2018.11.032

Cooperative Transcription Factor Induction Mediates Hemogenic Reprogramming
Cited by: 27
Author(s): Andreia Gomes, Ilia Kurochkin, Betty Chang, Michael G. Daniel, Kenneth Law, Namita Satija, Alexander Lachmann, Zichen Wang, Lino Ferreira, Avi Ma’ayan, Benjamin Chen, Dmitri Papatsenko, Ihor R. Lemischka, Kateri Moore, Carlos Filipe Pereira
Software Mentions: 4
Published: almost 6 years ago

10.3389/fgene.2017.00052

Evolinc: A Tool for the Identification and Evolutionary Comparison of Long Intergenic Non-coding RNAs
Cited by: 25
Author(s): Andrew D. L. Nelson, Upendra Kumar Devisetty, Kyle Palos, Asher Haug-Baltzell, Eric Lyons, Mark A. Beilstein
Software Mentions: 4
Published: over 7 years ago

10.1016/j.celrep.2019.11.093

Dysregulation of RNA Splicing in Tauopathies
Cited by: 49
Author(s): Daniel J. Apicco, Cheng Zhang, Brandon F. Maziuk, Lulu Jiang, Heather Ballance, Samantha Boudeau, Choong Yong Ung, Hu Li, Benjamin Wolozin
Software Mentions: 4
Published: almost 5 years ago

10.1371/journal.pbio.3000382

LATS1/2 suppress NFκB and aberrant EMT initiation to permit pancreatic progenitor differentiation
Cited by: 19
Author(s): Caitlin M. Braitsch, D. Berfin Azizoglu, Yadanar Htike, Haley R. Barlow, Ulrike Schnell, Christopher Chaney, Thomas J. Carroll, Ben Z. Stanger, Ondine Cleaver
Software Mentions: 4
Published: over 5 years ago

10.1186/gb-2014-15-1-r7

RIP-seq analysis of eukaryotic Sm proteins identifies three major categories of Sm-containing ribonucleoproteins
Cited by: 32
Author(s): Zhipeng Lu, Xiaojun Guan, Casey A. Schmidt, A. Gregory Matera
Software Mentions: 4
Published: almost 11 years ago

10.1016/j.celrep.2018.07.026

Fine-Tuning Mybl2 Is Required for Proper Mesenchymal-to-Epithelial Transition during Somatic Reprogramming
Cited by: 16
Author(s): Carl Ward, Giacomo Volpe, Pierre Cauchy, Anetta Ptasińska, Ruba Almaghrabi, Daniel Blakemore, Monica Nafria, Doris Kestner, Jon Frampton, George J. Murphy, Yosef Buganim, Keisuke Kaji, Paloma García
Software Mentions: 4
Published: over 6 years ago

10.3389/fgene.2021.645443

Global Transcriptome and Weighted Gene Co-expression Network Analyses of Growth-Stage-Specific Drought Stress Responses in Maize
Cited by: 21
Author(s): Songtao Liu, Tinashe Zenda, Anyi Dong, Yatong Yang, Nan Wang, Huijun Duan
Software Mentions: 4
Published: almost 4 years ago

10.3389/fgene.2020.599292

Hybrid Incompatibilities and Transgressive Gene Expression Between Two Closely Related Subspecies of Drosophila
Cited by: 10
Author(s): Alwyn C. Go, Alberto Civetta
Software Mentions: 4
Published: almost 4 years ago

10.3389/fimmu.2019.00479

Second Case of HOIP Deficiency Expands Clinical Features and Defines Inflammatory Transcriptome Regulated by LUBAC
Cited by: 50
Author(s): Hirotsugu Oda, David B. Beck, Hye Sun Kuehn, Natalia Sampaio Moura, Patrycja Hoffmann, Maria Ibarra, Jennifer Stoddard, Wanxia Li Tsai, Gustavo Gutierrez-Cruz, Massimo Gadina, Sergio D. Rosenzweig, Daniel L. Kastner, Luigi D. Notarangelo, Ivona Aksentijevich
Software Mentions: 4
Published: over 5 years ago

10.1186/gb-2013-14-3-r28

The western painted turtle genome, a model for the evolution of extreme physiological adaptations in a slowly evolving lineage
Cited by: 272
Author(s): H. Bradley Shaffer, Patrick Minx, Daniel E. Warren, Andrew M. Shedlock, Robert C. Thomson, Nicole Valenzuela, John Abramyan, Chris T. Amemiya, Daleen Badenhorst, Kyle K. Biggar, Glen M. Borchert, Christopher W. Botka, Rachel M. Bowden, Edward L. Braun, Anne M. Bronikowski, Benoit G. Bruneau, Leslie T. Buck, Blanche Capel, Todd A. Castoe, Michael Czerwinski, Kim D. Delehaunty, Scott V. Edwards, Catrina C. Fronick, Matthew K. Fujita, Lucinda A. Fulton, Tina Graves, Edward Green, Wilfried Haerty, Ramkumar Hariharan, Omar Hernández, LaDeana W. Hillier, Alisha K. Holloway, Daniel E. Janes, Fredric J. Janzen, Cyriac Kandoth, Lesheng Kong, A. P. Jason de Koning, Yang Li, Robert Literman, Suzanne E. McGaugh, Lindsey Mork, Michelle O’Laughlin, Ryan T. Paitz, David D. Pollock, Chris P. Ponting, S. Radhakrishnan, Brian J. Raney, Joy M. Richman, John St. John, Tonia S. Schwartz, Arun Sethuraman, Phillip Q. Spinks, Kenneth B. Storey, Nay Thane, Tomáš Vinař, Laura M. Zimmerman, Wesley C. Warren, Elaine R. Mardis, Richard K. Wilson
Software Mentions: 4
Published: almost 12 years ago

10.3389/fgene.2017.00175

Smooth, an hnRNP-L Homolog, Might Decrease Mitochondrial Metabolism by Post-Transcriptional Regulation of Isocitrate Dehydrogenase (Idh) and Other Metabolic Genes in the Sub-Acute Phase of Traumatic Brain Injury
Cited by: 21
Author(s): Arko Sen, Katherine Gurdziel, Jenney Liu, Qian Wen, Oluwademi O Nuga, Rayanne B. Burl, Maik Hüttemann, Roger Piqué-Regi, Douglas M. Ruden
Software Mentions: 4
Published: about 7 years ago

10.3389/fgene.2019.00917

Nuclear Lamin B1 Interactions With Chromatin During the Circadian Cycle Are Uncoupled From Periodic Gene Expression
Cited by: 19
Author(s): Annaël Brunet, Frida Forsberg, Qiong Fan, Thomas Sæther, Philippe Collas
Software Mentions: 4
Published: about 5 years ago

10.1038/srep22398

Gene dysregulation is restored in the Parkinson’s disease MPTP neurotoxic mice model upon treatment of the therapeutic drug CuII(atsm)
Cited by: 12
Author(s): Lesley Cheng, Camelia Quek, Lin W. Hung, Robyn A. Sharples, Nicki A. Sherratt, Kevin J. Barnham, Andrew F. Hill
Software Mentions: 4
Published: over 8 years ago

10.1186/s13148-019-0690-5

ARID1A facilitates KRAS signaling-regulated enhancer activity in an AP1-dependent manner in colorectal cancer cells
Cited by: 34
Author(s): Madhobi Sen, Xin Wang, Feda H. Hamdan, Jacobe Rapp, Jessica Eggert, Robyn Laura Kosinsky, Florian Wegwitz, Ana P. Kutschat, Fereshteh Younesi, Jochen Gaedcke, Marian Grade, Elisabeth Heßmann, Argyris Papantonis, Philipp Ströbel, Steven A. Johnsen
Software Mentions: 4
Published: over 5 years ago

10.1111/cmi.12397

The co‐transcriptome of uropathogenic<scp><i>E</i></scp><i>scherichia coli</i>‐infected mouse macrophages reveals new insights into host–pathogen interactions
Cited by: 62
Author(s): Charalampos Harris Mavromatis, Nilesh J. Bokil, Makrina Totsika, Asha Kakkanat, Kolja Schaale, Carlo Vittorio Cannistraci, Tae Woo Ryu, Scott A. Beatson, Glen C. Ulett, Mark A. Schembri, Matthew J. Sweet, Timothy Ravasi
Software Mentions: 4
Published: almost 10 years ago

10.1016/j.cmet.2020.09.001

Bone Marrow Mesenchymal Stem Cells Support Acute Myeloid Leukemia Bioenergetics and Enhance Antioxidant Defense and Escape from Chemotherapy
Cited by: 107
Author(s): Dorian Forte, María García-Fernández, Abel Sánchez-Aguilera, Vaia Stavropoulou, Claire Fielding, Daniel Martín-Pérez, Juan Antonio López, Ana S. H. Costa, Laura Tronci, Efterpi Nikitopoulou, M. Barber, Paolo Gallipoli, Ludovica Marando, Carlos L.F. de Castillejo, Alexandar Tzankov, Sabine Dietmann, Michèle Cavo, Lucia Catani, Antonio Curti, Jesús Vázquez, Christian Frezza, Brian J. P. Huntly, Juerg Schwaller, Simón Méndez-Ferrer
Software Mentions: 4
Published: about 4 years ago

10.1038/s41438-021-00471-9

The genome of Magnolia biondii Pamp. provides insights into the evolution of Magnoliales and biosynthesis of terpenoids
Cited by: 27
Author(s): Shanshan Dong, Min Liu, Yang Liu, Fei Chen, Ting Yang, Lu Chen, Xingtan Zhang, Xing Guo, Dongming Fang, Linzhou Li, Tian Deng, Zhen Yao, Xiaoan Lang, Yiqing Gong, Ernest Wu, Yaling Wang, Yamei Shen, Xun Gong, Huan Liu, Shouzhou Zhang
Software Mentions: 4
Published: over 3 years ago

10.1111/pbi.12520

Genome‐wide dissection of AP2/ERF and HSP90 gene families in five legumes and expression profiles in chickpea and pigeonpea
Cited by: 89
Author(s): Gaurav Agarwal, Vanika Garg, Himabindu Kudapa, Dadakhalandar Doddamani, Lekha T. Pazhamala, Aamir W. Khan, Mahendar Thudi, Suk-Ha Lee, Rajeev K. Varshney
Software Mentions: 4
Published: almost 9 years ago

10.1038/srep24375

RNA-seq analysis for detecting quantitative trait-associated genes
Cited by: 33
Author(s): Minseok Seo, Kwondo Kim, Joon Yoon, Jin Young Jeong, Hyun-Jeong Lee, Seoae Cho, Heebal Kim
Software Mentions: 4
Published: over 8 years ago

10.3389/fgene.2014.00329

A comparison of control samples for ChIP-seq of histone modifications
Cited by: 24
Author(s): Christoffer Flensburg, Sarah Kinkel, Andrew Keniry, Marnie E. Blewitt, Alicia Oshlack
Software Mentions: 4
Published: about 10 years ago

10.1038/srep15041

DDX3Y gene rescue of a Y chromosome AZFa deletion restores germ cell formation and transcriptional programs
Cited by: 57
Author(s): Cyril Ramathal, Benjamin Angulo, Meena Sukhwani, Jun Cui, Jens Durruthy-Durruthy, Fang Fang, Paula Schanes, Paul J. Turek, Kyle E. Orwig, Renee A. Reijo Pera
Software Mentions: 4
Published: about 9 years ago

10.1093/bioinformatics/btx143

The RNASeq-er API—a gateway to systematically updated analysis of public RNA-seq data
Cited by: 26
Author(s): Robert Petryszak, Nuno A. Fonseca, Anja Füllgrabe, Laura Huerta, Maria Keays, Y. Amy Tang, Alvis Brāzma
Software Mentions: 4
Published: over 7 years ago

10.3390/genes12020203

Characterization of Breed Specific Differences in Spermatozoal Transcriptomes of Sheep in Australia
Cited by: 8
Author(s): Marnie J. Hodge, Sara de las Heras‐Saldana, Sally J. Rindfleish, Cyril Stephen, Sameer D. Pant
Software Mentions: 4
Published: almost 4 years ago

10.1371/journal.pone.0120385

Genetic and Molecular Characterization of Submergence Response Identifies Subtol6 as a Major Submergence Tolerance Locus in Maize
Cited by: 58
Author(s): Malachy T. Campbell, Christopher A. Proctor, Yongchao Dou, Aaron J. Schmitz, Piyaporn Phansak, Greg R. Kruger, Chi Zhang, Harkamal Walia
Software Mentions: 4
Published: over 9 years ago

10.1038/s41598-017-18205-0

Tissue Tropism in Host Transcriptional Response to Members of the Bovine Respiratory Disease Complex
Cited by: 26
Author(s): Susanta K. Behura, P. C. Tizioto, JaeWoo Kim, Natália Vinhal Grupioni, Christopher M. Seabury, Robert D. Schnabel, Laurel J. Gershwin, Alison L. Van Eenennaam, Rachel L. Toaff-Rosenstein, Holly L. Neibergs, Luciana Correia de Almeida Regitano, Jeremy F. Taylor
Software Mentions: 4
Published: almost 7 years ago

10.1038/celldisc.2015.45

Mapping gene regulatory circuitry of Pax6 during neurogenesis
Cited by: 56
Author(s): Sudhir Thakurela, Neha Tiwari, Sandra Schick, Angela Garding, Robert Ivánek, Benedikt Berninger, Vijay Tiwari
Software Mentions: 4
Published: almost 9 years ago

10.1371/journal.pone.0102398

JAGuaR: Junction Alignments to Genome for RNA-Seq Reads
Cited by: 51
Author(s): Yaron S.N. Butterfield, Maayan Kreitzman, Nina Thiessen, Richard Corbett, Yisu Li, Johnson Pang, P. Yussanne, Steven J.M. Jones, İnanç Birol
Software Mentions: 4
Published: over 10 years ago

10.1038/s41598-018-25998-1

FACS-Seq analysis of Pax3-derived cells identifies non-myogenic lineages in the embryonic forelimb
Cited by: 8
Author(s): Arun Singh, Cheng-Chi Chang, Hsiao-Yen Ma, Stephen A. Ramsey, Theresa M. Filtz, Chrissa Kioussi
Software Mentions: 4
Published: over 6 years ago

10.3390/genes11030345

Arabidopsis thaliana MLK3, a Plant-Specific Casein Kinase 1, Negatively Regulates Flowering and Phosphorylates Histone H3 In Vitro
Cited by: 12
Author(s): Junmei Kang, Huiting Cui, Shangang Jia, Wenwen Liu, Renjie Yu, Zhihai Wu, Zhen Wang
Software Mentions: 4
Published: over 4 years ago

10.1111/rssc.12213

A Bayesian Model Selection Approach for Identifying Differentially Expressed Transcripts from RNA Sequencing Data
Cited by: 5
Author(s): Panagiotis Papastamoulis, Magnus Rattray
Software Mentions: 4
Published: almost 8 years ago

10.1371/journal.pone.0181061

Comparative transcriptome analysis of flower heterosis in two soybean F1 hybrids by RNA-seq
Cited by: 22
Author(s): Chunbao Zhang, Chunjing Lin, Fuyou Fu, Xiaofang Zhong, Bao Peng, Hao Yan, Jingyong Zhang, Weilong Zhang, Pengnian Wang, Xiaoyang Ding, Wei Zhang, Limei Zhao
Software Mentions: 4
Published: over 7 years ago

10.3390/jpm9020018

Aligning the Aligners: Comparison of RNA Sequencing Data Alignment and Gene Expression Quantification Tools for Clinical Breast Cancer Research
Cited by: 12
Author(s): Isaac Raplee, Alexei V. Evsikov, Caralina Marín de Evsikova
Software Mentions: 4
Published: over 5 years ago

10.3390/ijms22020574

The Resistance of Narrow-Leafed Lupin to Diaporthe toxica Is Based on the Rapid Activation of Defense Response Genes
Cited by: 7
Author(s): Michał Książkiewicz, Sandra Rychel-Bielska, Piotr Plewiński, Maria Nuc, Witold Irzykowski, M. Jędryczka, Paweł Krajewski
Software Mentions: 4
Published: almost 4 years ago

10.3390/genes9120574

A Two-Cohort RNA-seq Study Reveals Changes in Endometrial and Blood miRNome in Fertile and Infertile Women
Cited by: 25
Author(s): Kadri Rekker, Signe Altmäe, Marina Suhorutshenko, Maire Peters, Juan F. Martínez-Blanch, Francisco M. Codoñer, Felipe Vilella, Carlos Simón, Andres Salumets, Agne Velthut-Meikas
Software Mentions: 4
Published: almost 6 years ago

10.1155/2018/3028290

Stress-Adaptive Responses Associated with High-Level Carbapenem Resistance in KPC-ProducingKlebsiella pneumoniae
Cited by: 4
Author(s): Sheila Adams‐Sapper, Adam Gayoso, Lee W. Riley
Software Mentions: 4
Published: almost 7 years ago

10.1371/journal.pntd.0001409

A Deep Sequencing Approach to Comparatively Analyze the Transcriptome of Lifecycle Stages of the Filarial Worm, Brugia malayi
Cited by: 86
Author(s): Young Jun Choi, Elodie Ghedin, Matthew Berriman, Jacqueline A. McQuillan, Nancy Holroyd, George F. Mayhew, Bruce M. Christensen, Michelle L. Michalski
Software Mentions: 4
Published: almost 13 years ago

10.1371/journal.pone.0141225

A catalogue of novel bovine long noncoding RNA across 18 tissues
Cited by: 76
Author(s): Lambros T. Koufariotis, Yi‐Ping Phoebe Chen, Amanda J. Chamberlain, Christy Vander Jagt, Ben J. Hayes
Software Mentions: 4
Published: about 9 years ago

10.3390/ijms21061910

NR2F2 Orphan Nuclear Receptor is Involved in Estrogen Receptor Alpha-Mediated Transcriptional Regulation in Luminal A Breast Cancer Cells
Cited by: 8
Author(s): Edina Erdős, Bálint László Bálint
Software Mentions: 4
Published: over 4 years ago

10.3389/fpls.2020.574982

Metabolic, Enzymatic Activity, and Transcriptomic Analysis Reveals the Mechanism Underlying the Lack of Characteristic Floral Scent in Apricot Mei Varieties
Cited by: 6
Author(s): Fei Bao, Tengxun Zhang, Anqi Ding, Aiqin Ding, Weiru Yang, Jia Wang, Tangren Cheng, Qixiang Zhang
Software Mentions: 4
Published: about 4 years ago

10.1093/bioinformatics/bty125

AltHapAlignR: improved accuracy of RNA-seq analyses through the use of alternative haplotypes
Cited by: 28
Author(s): Wanseon Lee, Katharine Plant, Peter Humburg, Julian C. Knight
Software Mentions: 4
Published: over 6 years ago

10.3390/ijms19113687

Hierarchical Clustering of DNA k-mer Counts in RNAseq Fastq Files Identifies Sample Heterogeneities
Cited by: 5
Author(s): Wolfgang Kaisers, Holger Schwender, Heiner Schaal
Software Mentions: 4
Published: about 6 years ago

10.3390/ijms21093129

Bisphenol A Exposure in utero Disrupts Hypothalamic Gene Expression Particularly Genes Suspected in Autism Spectrum Disorders and Neuron and Hormone Signaling
Cited by: 18
Author(s): Anne De Piante Henriksen, Alejandro Andrade, Erin P. Harris, Emilie F. Rissman, Jennifer T. Wolstenholme
Software Mentions: 4
Published: over 4 years ago

10.1038/s41598-018-31072-7

Transcriptional shifts account for divergent resource allocation in feed efficient broiler chickens
Cited by: 12
Author(s): Henry Reyer, Barbara U. Metzler‐Zebeli, Nares Trakooljul, Michael Oster, Eduard Muráni, Siriluck Ponsuksili, Frieder Hadlich, Klaus Wimmers
Software Mentions: 4
Published: about 6 years ago