Ecosyste.ms: Papers

10.1093/function/zqaa004

The Mechanism of High-Output Cardiac Hypertrophy Arising From Potassium Channel Gain-of-Function in Cantú Syndrome
Cited by: 17
Author(s): Conor McClenaghan, Yan Huang, Scot J. Matkovich, Attila Kovács, Carla J. Weinheimer, Ronald A. Perez, Thomas J. Broekelmann, Theresa Harter, Jin-Moo Lee, Marı́a S. Remedi, Colin G. Nichols
Software Mentions: 4
Published: almost 5 years ago

10.1534/g3.116.033308

Genomic, Transcriptomic, and Proteomic Analysis Provide Insights Into the Cold Adaptation Mechanism of the Obligate Psychrophilic Fungus <i>Mrakia psychrophila</i>
Cited by: 37
Author(s): Su Yao, Xianzhi Jiang, Wenping Wu, Manman Wang, Muhammad Imran Hamid, Meichun Xiang, Xingzhong Liu
Software Mentions: 4
Published: about 8 years ago

10.1534/g3.116.028324

Histone H1 Limits DNA Methylation in Neurospora crassa
Cited by: 18
Author(s): Michael Seymour, Lexiang Ji, Alex M. Santos, Masayuki Kamei, Takahiko Sasaki, Evelina Y. Basenko, Robert J. Schmitz, Xiaoyu Zhang, Zachary A. Lewis
Software Mentions: 4
Published: over 8 years ago

10.1371/journal.pone.0188264

Wnt co-receptors Lrp5 and Lrp6 differentially mediate Wnt3a signaling in osteoblasts
Cited by: 25
Author(s): Aimy Sebastian, Nicholas R. Hum, Deepa K. Murugesh, Sarah Hatsell, Aris N. Economides, Gabriela G. Loots
Software Mentions: 4
Published: almost 7 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

10.1534/g3.119.400777

<i>rmtA</i>-Dependent Transcriptome and Its Role in Secondary Metabolism, Environmental Stress, and Virulence in<i>Aspergillus flavus</i>
Cited by: 5
Author(s): Timothy Satterlee, Sarah Entwistle, Yanbin Yin, J. W. Cary, Matthew D. Lebar, Liliana Losada, Ana M. Calvo
Software Mentions: 4
Published: almost 5 years ago

10.1186/s12864-016-2950-5

The influence of trematode parasite burden on gene expression in a mammalian host
Cited by: 9
Author(s): Bhagya K. Wijayawardena, Dennis J. Minchella, J. Andrew DeWoody
Software Mentions: 4
Published: over 8 years ago

10.3390/genes7040013

Bioinformatics Analysis of MAPKKK Family Genes in Medicago truncatula
Cited by: 10
Author(s): Wei Li, Hanyun Xu, Ying Liu, Lili Song, Changhong Guo, Yongjun Shu
Software Mentions: 4
Published: over 8 years ago

10.1186/1755-8794-7-32

Conserved recurrent gene mutations correlate with pathway deregulation and clinical outcomes of lung adenocarcinoma in never-smokers
Cited by: 45
Author(s): Zhifu Sun, Liang Wang, Bruce W. Eckloff, Bo Deng, Yi Wang, Jason A. Wampfler, Jiseon Jang, Eric D. Wieben, Jin Jen, Ming You, Ping Yang
Software Mentions: 4
Published: over 10 years ago

10.1371/journal.pone.0114461

Inference of the Oxidative Stress Network in Anopheles stephensi upon Plasmodium Infection
Cited by: 10
Author(s): Jatin Shrinet, Umesh K. Nandal, T. Adak, Raj K. Bhatnagar, Sujatha Sunil
Software Mentions: 4
Published: almost 10 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

10.3389/fcimb.2017.00227

Transcriptomic Profiling of High-Density Giardia Foci Encysting in the Murine Proximal Intestine
Cited by: 32
Author(s): Jonathan K Pham, Christopher Nosala, Elaine P. Scott, Kristofer Nguyen, Kari D. Hagen, Hannah Starcevich, Scott C. Dawson
Software Mentions: 4
Published: over 7 years ago

10.1186/s12915-018-0569-5

Reduced PRC2 function alters male germline epigenetic programming and paternal inheritance
Cited by: 16
Author(s): Jessica M Stringer, Samuel C. Forster, Zhibo Qu, Lexie Prokopuk, Moira K O'Bryan, David K. Gardner, Stefan J. White, David L. Adelson, Patrick Western
Software Mentions: 4
Published: about 6 years ago

10.1186/s12864-021-07699-8

Chromosome-level genome assembly and manually-curated proteome of model necrotroph Parastagonospora nodorum Sn15 reveals a genome-wide trove of candidate effector homologs, and redundancy of virulence-related functions within an accessory chromosome
Cited by: 8
Author(s): Stefania Bertazzoni, Darcy A. B. Jones, H. Phan, Kar‐Chun Tan, James K. Hane
Software Mentions: 4
Published: over 3 years ago

10.3389/fcell.2021.591754

Scaffold-Mediated Developmental Effects on Human Induced Pluripotent Stem Cell-Derived Cardiomyocytes Are Preserved After External Support Removal
Cited by: 1
Author(s): Jun Li, Jong-Kook Lee, Keiko Miwa, Yuki Kuramoto, Kiyoshi Masuyama, Hideki Yasutake, Satoki Tomoyama, Hiroyuki Nakanishi, Yasushi Sakata
Software Mentions: 4
Published: almost 4 years ago

10.3389/fcell.2021.675438

Identification of Key Genes With Differential Correlations in Lung Adenocarcinoma
Cited by: 9
Author(s): You Zhou, Bin Xu, Yi Zhou, Jian Liu, Xiao Zheng, Yingting Liu, Hepu Deng, Ming Liu, Xiubao Ren, Jianchuan Xia, Xiangyin Kong, Tao Huang, Jingting Jiang
Software Mentions: 4
Published: over 3 years ago

10.1186/1471-2164-15-845

Identification and functional analysis of long non-coding RNAs in mouse cleavage stage embryonic development based on single cell transcriptome data
Cited by: 66
Author(s): Kunshan Zhang, Kefei Huang, Yuan Luo, Siguang Li
Software Mentions: 4
Published: about 10 years ago

10.1186/s12864-016-2618-1

Transcriptome analysis of highly purified mouse spermatogenic cell populations: gene expression signatures switch from meiotic-to postmeiotic-related processes at pachytene stage
Cited by: 107
Author(s): Irene da Cruz, Rosana Rodríguez-Casuriaga, Federico F. Santiñaque, Joaquina Farías, Gianni Curti, Carlos A. Capoano, Gustavo A. Folle, Ricardo Benavente, José Sotelo‐Silveira, Adriana Geisinger
Software Mentions: 4
Published: over 8 years ago

10.1371/journal.pone.0091918

RNA-Sequence Analysis of Primary Alveolar Macrophages after In Vitro Infection with Porcine Reproductive and Respiratory Syndrome Virus Strains of Differing Virulence
Cited by: 34
Author(s): Bouabid Badaoui, Teresa Rutigliano, Anna Anselmo, Merijn Vanhee, Hans Nauwynck, Elisabetta Giuffra, Sara Botti
Software Mentions: 4
Published: over 10 years ago

10.1186/s12915-019-0659-z

Biological and RNA regulatory function of MOV10 in mammalian germ cells
Cited by: 18
Author(s): Kaiqiang Fu, Suwen Tian, Huanhuan Tan, Caifeng Wang, Hanben Wang, Min Wang, Yuan‐Yuan Wang, Zhen Chen, Yanfeng Wang, Qiuling Yue, Qiushi Xu, Shuya Zhang, Haixin Li, Jie Xie, Mingyan Lin, Mengcheng Luo, Feng Chen, Lan Ye, Ke Zheng
Software Mentions: 4
Published: over 5 years ago

10.12688/f1000research.9037.2

SNPsplit: Allele-specific splitting of alignments between genomes with known SNP genotypes
Cited by: 74
Author(s): Felix Krueger, Simon Andrews
Software Mentions: 4
Published: over 8 years ago

10.3389/fcell.2021.715762

Probing Synergistic Targets by Natural Compounds for Hepatocellular Carcinoma
Cited by: 2
Author(s): Jian Gao, Zuojing Yin, Zhuanbin Wu, Zhonghua Sheng, Chao Ma, Rui Chen, Xiongwen Zhang, Kailin Tang, Jian Fei, Zhiwei Cao
Software Mentions: 4
Published: over 3 years ago

10.1186/s12864-018-4783-x

The genomic features of parasitism, Polyembryony and immune evasion in the endoparasitic wasp Macrocentrus cingulum
Cited by: 27
Author(s): Chuanlin Yin, Meizhen Li, Jian Hu, Kun Lang, Qiming Chen, Jinding Liu, Dan Guo, Kang He, Yipei Dong, Jiapeng Luo, Zhenkun Song, James R. Walters, Wenqing Zhang, Fĕi Li, Xue-Xin Chen
Software Mentions: 4
Published: over 6 years ago

10.1371/journal.pone.0081809

Next Generation Sequencing Analysis of Human Platelet PolyA+ mRNAs and rRNA-Depleted Total RNA
Cited by: 55
Author(s): Antheia Kissopoulou, Jon Jonasson, Tomas Lindahl, Abdimajid Osman
Software Mentions: 4
Published: almost 11 years ago

10.1186/s12864-017-4183-7

Transcriptome analyses reveal SR45 to be a neutral splicing regulator and a suppressor of innate immunity in Arabidopsis thaliana
Cited by: 49
Author(s): Xiaoning Zhang, Yi-Fei Shi, Jordan J. Powers, Niraj Gowda, Chong Zhang, Heba M. M. Ibrahim, Hannah B. Ball, Samuel Chen, Hua Lu, Stephen M. Mount
Software Mentions: 4
Published: about 7 years ago

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

10.12688/f1000research.15604.1

Androgen-dependent alternative mRNA isoform expression in prostate cancer cells
Cited by: 14
Author(s): Jennifer Munkley, Teresa Maia, Jesús Ibarluzea, Karen E. Livermore, Daniel Vodák, Ingrid Ehrmann, Katherine James, Prabhakar Rajan, Nuno L. Barbosa‐Morais, David Elliott
Software Mentions: 4
Published: over 6 years ago

10.3389/fcell.2020.602731

CircRNA hsa_circ_0008500 Acts as a miR-1301-3p Sponge to Promote Osteoblast Mineralization by Upregulating PADI4
Cited by: 11
Author(s): Qiaoli Zhai, Yi Zhao, Linping Wang, Yan Dai, Peiqing Zhao, Xinxin Xiang, Kui Liu, Wei Du, Wenxiu Tian, Baoye Yang, Tao Li, Lianqing Wang
Software Mentions: 4
Published: almost 4 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

10.1186/s12864-017-3929-6

Ethylene induces combinatorial effects of histone H3 acetylation in gene expression in Arabidopsis
Cited by: 42
Author(s): Likai Wang, Fan Zhang, Siddharth Rode, Kevin Chin, Eun Esther Ko, Jonghwan Kim, Vishwanath R. Iyer, Hong Qiao
Software Mentions: 4
Published: over 7 years ago

10.1371/journal.pone.0141910

Union Exon Based Approach for RNA-Seq Gene Quantification: To Be or Not to Be?
Cited by: 25
Author(s): Shanrong Zhao, Li Xi, Baohong Zhang
Software Mentions: 4
Published: about 9 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

10.1111/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/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

10.1186/s12864-021-07881-y

Comprehensive analysis of lncRNAs involved in skeletal muscle development in ZBED6-knockout Bama pigs
Cited by: 5
Author(s): Dandan Wang, Pu Yun, Yefang Li, Dengke Pan, Shengnan Wang, Wenjie Tian, Yuehui Ma, Lin Jiang
Software Mentions: 4
Published: over 3 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

10.1186/s13072-017-0153-1

Application of dual reading domains as novel reagents in chromatin biology reveals a new H3K9me3 and H3K36me2/3 bivalent chromatin state
Cited by: 25
Author(s): Rebekka Mauser, Goran Kungulovski, Corinna Keup, Richard Reinhardt, Albert Jeltsch
Software Mentions: 4
Published: about 7 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.pgen.1006959

Loss of the chromatin modifier Kdm2aa causes BrafV600E-independent spontaneous melanoma in zebrafish
Cited by: 12
Author(s): Catherine Scahill, Zsofia Digby, Ian Sealy, Sonia Wojciechowska, Richard White, John Collins, Derek L. Stemple, Till Bartke, Marie E. Mathers, E. Elizabeth Patton, Elisabeth M Busch-Nentwich
Software Mentions: 4
Published: over 7 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

10.1186/s13072-018-0186-0

Transient reduction of DNA methylation at the onset of meiosis in male mice
Cited by: 36
Author(s): Valeriya Gaysinskaya, Brendan Miller, Chiara De Luca, Godfried W. van der Heijden, Kasper D. Hansen, Alex Bortvin
Software Mentions: 4
Published: over 6 years ago

10.1371/journal.pgen.1003997

Comprehensive Analysis of Transcriptome Variation Uncovers Known and Novel Driver Events in T-Cell Acute Lymphoblastic Leukemia
Cited by: 110
Author(s): Zeynep Kalender Atak, Valentina Gianfelici, Gert Hulselmans, Kim De Keersmaecker, Arun George Devasia, Ellen Geerdens, Nele Mentens, Sabina Chiaretti, Kaat Durinck, Anne Uyttebroeck, Peter Vandenberghe, Iwona Włodarska, Jacqueline Cloos, Robin Foà, Franki Speleman, Jan Cools, Stein Aerts
Software Mentions: 4
Published: almost 11 years ago

10.3390/ani10010002

Atmospheric Ammonia Affects Myofiber Development and Lipid Metabolism in Growing Pig Muscle
Cited by: 10
Author(s): Shouwei Tang, Jingjing Xie, Sheng Zhang, Weida Wu, Bao Yi, Hongfu Zhang
Software Mentions: 4
Published: almost 5 years ago

10.1371/journal.pntd.0007743

Transcriptome of the parasitic flatworm Schistosoma mansoni during intra-mammalian development
Cited by: 19
Author(s): Arporn Wangwiwatsin, Anna V. Protasio, Shona Wilson, Christian Owusu, Nancy Holroyd, Mandy Sanders, Jacqueline A. Keane, Michael J. Doenhoff, Gabriel Rinaldi, Matthew Berriman
Software Mentions: 4
Published: over 4 years ago

10.1038/s41598-019-44266-4

Transcriptomics Analysis Reveals New Insights into the Roles of Notch1 Signaling on Macrophage Polarization
Cited by: 21
Author(s): Chetan P. Hans, Neekun Sharma, Sidharth Sen, Shuai Zeng, Rishabh Dev, Yuyong Jiang, Advitiya Mahajan, Trupti Joshi
Software Mentions: 4
Published: over 5 years ago

10.1038/s41598-019-49817-3

An integrated genome-wide multi-omics analysis of gene expression dynamics in the preimplantation mouse embryo
Cited by: 35
Author(s): Steffen Israel, Markus Ernst, Olympia E. Psathaki, Hannes C.A. Drexler, Ellen Casser, Yutaka Suzuki, Wojciech Makałowski, Michele Boiani, Georg Fuellen, Leila Taher
Software Mentions: 4
Published: about 5 years ago

10.1002/ece3.5965

Draft genome of the famous ornamental plant <i>Paeonia suffruticosa</i>
Cited by: 31
Author(s): Shuzuo Lv, Shu Cheng, Zhanying Wang, Shiming Li, Xin Jin, Lei Lan, Bing Yang, Kun Yu, Xiliang Ni, Ning Li, Xiaogai Hou, Gang Huang, Jie Wang, Yang Dong, Erqiang Wang, Jun Huang, Gengyun Zhang, Zhang Can-jun
Software Mentions: 4
Published: over 4 years ago

10.1186/s13072-018-0246-5

Dnmt1 is essential for egg production and embryo viability in the large milkweed bug, Oncopeltus fasciatus
Cited by: 54
Author(s): Adam J. Bewick, Zachary Sanchez, Elizabeth C. McKinney, Allen J. Moore, Patricia J. Moore, Robert J. Schmitz
Software Mentions: 4
Published: almost 6 years ago

10.1002/ece3.3976

Brain gene expression analyses in virgin and mated queens of fire ants reveal mating-independent and socially regulated changes
Cited by: 14
Author(s): Travis L. Calkins, Mei Er Chen, Arinder K. Arora, Chloë Hawkings, Cécilia Tamborindeguy, Patricia V. Pietrantonio
Software Mentions: 4
Published: over 6 years ago

10.1038/s41598-019-40897-9

Extensive epigenetic and transcriptomic variability between genetically identical human B-lymphoblastoid cells with implications in pharmacogenomics research
Cited by: 17
Author(s): Lilla Ozgyin, Attila Horváth, Zsuzsanna Hevessy, Bálint László Bálint
Software Mentions: 4
Published: over 5 years ago

10.1038/s41598-018-35086-z

RETRACTED ARTICLE: Non-coding RNAome of RPE cells under oxidative stress suggests unknown regulative aspects of Retinitis pigmentosa etiopathogenesis
Cited by: 16
Author(s): Luigi Donato, Concetta Scimone, Carmela Rinaldi, Rosalia D’Angelo, Antonina Sidoti
Software Mentions: 4
Published: about 6 years ago

10.1038/s41598-019-42570-7

Stage-specific transcriptome of Bursaphelenchus xylophilus reveals temporal regulation of effector genes and roles of the dauer-like stages in the lifecycle
Cited by: 22
Author(s): Shino Tanaka, Mehmet Dayı, Y. Maeda, Isheng Jason Tsai, Ryusei Tanaka, Mark W. Bligh, Yuko Takeuchi-Kaneko, Kenji Fukuda, Natsumi Kanzaki, Taisei Kikuchi
Software Mentions: 4
Published: over 5 years ago

10.1186/1471-2164-14-331

Differential transcript isoform usage pre- and post-zygotic genome activation in zebrafish
Cited by: 32
Author(s): Håvard Aanes, Oľga Østrup, Ingrid S. Andersen, Lars Fredrik Moen, Sinnakaruppan Mathavan, Philippe Collas, Peter Aleström
Software Mentions: 4
Published: over 11 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

10.1038/s41598-018-32904-2

Transcriptomics and co-expression networks reveal tissue-specific responses and regulatory hubs under mild and severe drought in papaya (Carica papaya L.)
Cited by: 33
Author(s): Samuel David Gamboa-Tuz, Alejandro Pereira-Santana, Jesús Alejandro Zamora‐Briseño, Enrique Castaño, Francisco Espadas-Gil, Jorge Tonatiuh Ayala-Sumuano, Miguel A. Keb-Llanes, Lorenzo Felipe Sánchez Teyer, Luis Carlos Rodríguez-Zapata
Software Mentions: 4
Published: about 6 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

10.1186/s12864-015-1767-y

Experimental validation of methods for differential gene expression analysis and sample pooling in RNA-seq
Cited by: 132
Author(s): Anto P. Rajkumar, Per Qvist, Ross Lazarus, Francesco Lescai, Jia Ju, Mette Nyegaard, Ole Mors, Anders D. Børglum, Qibin Li, Jane H. Christensen
Software Mentions: 4
Published: over 9 years ago

10.1038/s41598-018-24227-z

A new way of producing pediocin in Pediococcus acidilactici through intracellular stimulation by internalized inulin nanoparticles
Cited by: 19
Author(s): Whee-Soo Kim, Jun-Yeong Lee, Bijay Singh, Sushila Maharjan, Liang Hong, Sang-Mok Lee, Lianhua Cui, Ki-June Lee, Girak Kim, Cheol‐Heui Yun, Seoung-Hun Kang, Yun‐Jaie Choi, Chong‐Su Cho
Software Mentions: 4
Published: over 6 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

10.1186/s12859-017-1861-z

LSTrAP: efficiently combining RNA sequencing data into co-expression networks
Cited by: 33
Author(s): Sebastian Proost, Agnieszka Krawczyk
Software Mentions: 4
Published: about 7 years ago

10.1038/s41598-017-17337-7

Ensemble Modeling Approach Targeting Heterogeneous RNA-Seq data: Application to Melanoma Pseudogenes
Cited by: 2
Author(s): Enrico Capobianco, Camilo Valdes, Samanta Sarti, Zhijie Jiang, Laura Poliseno, Nicolas F. Tsinoremas
Software Mentions: 4
Published: almost 7 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

10.1002/advs.201903366

Transferrin Receptor 1 Regulates Thermogenic Capacity and Cell Fate in Brown/Beige Adipocytes
Cited by: 33
Author(s): Jin Li, Xiaohan Pan, Guihua Pan, Zijun Song, Yao He, Susu Zhang, Xueru Ye, Yang Xiang, Enjun Xie, Xinhui Wang, Xudong Mai, Xing Yin, Biyao Tang, Xuan Shu, Pengyu Chen, Xiaoshuang Dai, Ye Tian, Liheng Yao, Mulan Han, Guohuan Xu, Huijie Zhang, Jia Sun, Hong Chen, Fudi Wang, Junxia Min, Liwei Xie
Software Mentions: 4
Published: over 4 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

10.1038/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/s41598-018-27189-4

A Nasal Brush-based Classifier of Asthma Identified by Machine Learning Analysis of Nasal RNA Sequence Data
Cited by: 47
Author(s): Gaurav Pandey, O.P. Pandey, Angela Rogers, Mehmet Eren Ahsen, Gabriel E. Hoffman, Benjamin A. Raby, Scott T. Weiss, Eric E. Schadt, Supinda Bunyavanich
Software Mentions: 4
Published: over 6 years ago

10.1016/j.ydbio.2016.06.016

Developmentally regulated long non-coding RNAs in Xenopus tropicalis
Cited by: 17
Author(s): Elmira Forouzmand, Nick Owens, Ira L. Blitz, Kitt D. Paraiso, Mustafa K. Khokha, Michael J. Gilchrist, Xiaohui Xie, Ken W.Y. Cho
Software Mentions: 4
Published: over 7 years ago

10.1186/s12864-017-3675-9

Transcriptome analysis reveals potential mechanisms underlying differential heart development in fast- and slow-growing broilers under heat stress
Cited by: 23
Author(s): J. Zhang, Carl J. Schmidt, Susan J. Lamont
Software Mentions: 4
Published: over 7 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

10.3390/ani11041002

Differentially Expressed Gene Patterns in Ascarid-Infected Chickens of Higher- or Lower-Performing Genotypes
Cited by: 0
Author(s): Isabel Kilic, Manuel Stehr, Mark Hennies, C. C. Metges, Sören Franzenburg, Clemens Falker‐Gieske, Jens Tetens, Gürbüz Daş
Software Mentions: 4
Published: over 3 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

10.1186/s12864-017-4214-4

Metabolic differentiation of surface and invasive cells of yeast colony biofilms revealed by gene expression profiling
Cited by: 13
Author(s): Jana Maršíková, Derek Wilkinson, Otakar Hlaváček, Gregor D. Gilfillan, Alexandru Mizeranschi, Timothy R. Hughes, Markéta Begany, Stanislava Rešetárová, Libuše Váchová, Zdena Palková
Software Mentions: 4
Published: about 7 years ago

10.1093/database/baz053

CropCircDB: a comprehensive circular RNA resource for crops in response to abiotic stress
Cited by: 26
Author(s): Kai Wang, Chong Wang, Baohuan Guo, Kun Song, Chuanhong Shi, Xin Jiang, Keyi Wang, Yacong Tan, Lequn Wang, Lin Wang, Jiangjiao Li, Ying Liu, Yu-Dong Cai, Hongwei Zhao, Xiaoyong Sun
Software Mentions: 4
Published: almost 6 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/s12864-019-5734-x

A new reference genome for Sorghum bicolor reveals high levels of sequence similarity between sweet and grain genotypes: implications for the genetics of sugar metabolism
Cited by: 66
Author(s): Elizabeth A. Cooper, Zachary Brenton, Barry S. Flinn, Jerry Jenkins, Shengqiang Shu, Dave Flowers, Feng Luo, Yunsheng Wang, Penny Xia, Kerrie Barry, Chris Daum, Anna Lipzen, Yuko Yoshinaga, Jeremy Schmutz, Christopher Saski, Wilfred Vermerris, Stephen Kresovich
Software Mentions: 4
Published: over 5 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

10.1038/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.dib.2016.05.007

Whole transcriptome data analysis of zebrafish mutants affecting muscle development
Cited by: 7
Author(s): Olivier Armant, Victor Gourain, Christelle Etard, Uwe Strähle
Software Mentions: 4
Published: about 8 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

10.1111/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

10.1172/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

10.3390/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

10.1186/2049-1891-3-8

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

10.1111/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

10.1016/j.dib.2018.11.034

Differential gene expression analysis and SNP/InDel marker discovery in resistant wild Asparagus kiusianus and susceptible A. officinalis in response to Phomopsis asparagi infection
Cited by: 4
Author(s): Mostafa Abdelrahman, Mai Mitoma, Takao Ikeuchi, Motoyuki Mori, Kyoko Murakami, Yukio Ozaki, Masaru Matsumoto, Atsuko Uragami, Akira Kanno
Software Mentions: 4
Published: almost 6 years ago

10.3389/fmicb.2021.605095

Improvement of Free Fatty Acid Secretory Productivity in Aspergillus oryzae by Comprehensive Analysis on Time-Series Gene Expression
Cited by: 4
Author(s): Pui Shan Wong, Koichi Tamano, Sachiyo Aburatani
Software Mentions: 4
Published: over 3 years ago

10.18632/aging.101565

Identification and characterization of human ovary-derived circular RNAs and their potential roles in ovarian aging
Cited by: 38
Author(s): Hong-Cai Cai, Yamin Li, Huimin Li, Jean Damascene Niringiyumukiza, Mengdi Zhang, Li Chen, Gang Chen, Wenpei Xiang
Software Mentions: 4
Published: about 6 years ago

10.1186/s12864-017-4359-1

A next generation sequencing based approach to identify extracellular vesicle mediated mRNA transfers between cells
Cited by: 19
Author(s): Jialiang Yang, Jacob Hagen, Kalyani V. P. Guntur, Kimaada Allette, Sarah Schuyler, Jyoti Ranjan, Francesca Petralia, Stéphane Gesta, Robert Sebra, Milind Mahajan, Bin Zhang, Jun Zhu, Sander M. Houten, Andrew Kasarskis, Vivek K. Vishnudas, Viatcheslav R. Akmaev, Rangaprasad Sarangarajan, Niven R. Narain, Eric E. Schadt, Carmen Argmann, Zhidong Tu
Software Mentions: 4
Published: almost 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

10.1111/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

10.1038/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

10.1155/2018/3028290

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

10.1038/hortres.2017.5

Differential gene expression analysis of ‘Chili’ (Pyrus bretschneideri) fruit pericarp with two types of bagging treatments
Cited by: 22
Author(s): Yuling Wang, Xinfu Zhang, Ran Wang, Ying-Xin Bai, Chenglian Liu, Yuan Yang, Yingjie Yang, Shaolan Yang
Software Mentions: 3
Published: over 7 years ago

10.1038/s42003-019-0461-z

C/EBPβ-LIP induces cancer-type metabolic reprogramming by regulating the let-7/LIN28B circuit in mice
Cited by: 11
Author(s): Tobias Ackermann, Götz Hartleben, Christine Müller, Guido Mastrobuoni, Marco Groth, Britt A. Sterken, Mohamad Amr Zaini, Sameh A. Youssef, Hidde R. Zuidhof, Sara Russo Krauss, Gertrud Kortman, Gerald de Haan, Alain de Bruin, Zhao Qi Wang, Matthias Platzer, Stefan Kempa, Cornelis F. Calkhoven
Software Mentions: 3
Published: over 5 years ago

10.1038/s41438-019-0164-0

Draft genome sequence of cauliflower (Brassica oleracea L. var. botrytis) provides new insights into the C genome in Brassica species
Cited by: 46
Author(s): Sun DeLing, Chunguo Wang, Xiaoli Zhang, Wenlin Zhang, Hanmin Jiang, Xingwei Yao, Li‐Li Liu, Wen Zhang, Guobao Niu, Xiaozheng Shan
Software Mentions: 3
Published: over 5 years ago

10.1038/s42003-021-02412-7

From the first touch to biofilm establishment by the human pathogen Candida glabrata: a genome-wide to nanoscale view
Cited by: 7
Author(s): Mafalda Cavalheiro, Diana Pereira, Cécile Formosa-Dague, Carolina Leitão, Pedro Pais, Easter Ndlovu, Romeu Viana, Andreia I. Pimenta, Rui Santos, Azusa Takahashi‐Nakaguchi, Michiyo Okamoto, Mihaela Ola, Hiroji Chibana, Arsénio M. Fialho, Geraldine Butler, Étienne Dague, Miguel C. Teixeira
Software Mentions: 3
Published: over 3 years ago

10.1371/journal.pone.0190992

HAfTs are novel lncRNA transcripts from aflatoxin exposure
Cited by: 9
Author(s): B. Alex Merrick, Justin Chang, Dhiral Phadke, Meredith A. Bostrom, Ruchir Shah, Xinguo Wang, Oksana Gordon, Garron M. Wright
Software Mentions: 3
Published: almost 7 years ago

10.1038/s41438-020-0328-y

A chromosome-scale reference genome of Aquilegia oxysepala var. kansuensis
Cited by: 18
Author(s): Jinghe Xie, Haifeng Zhao, Kunpeng Li, Rui Zhang, Yanling Jiang, Meimei Wang, Xijie Guo, Ben Yu, Hongzhi Kong, Yuannian Jiao, Guiyun Xu
Software Mentions: 3
Published: over 4 years ago

10.1038/s41438-020-00449-z

A chromosome-level reference genome of non-heading Chinese cabbage [Brassica campestris (syn. Brassica rapa) ssp. chinensis]
Cited by: 41
Author(s): Ying Li, Gao-Feng Liu, Liming Ma, Tongkun Liu, Changwei Zhang, Dong Xiao, Hongkun Zheng, Fei Chen, Xilin Hou
Software Mentions: 3
Published: almost 4 years ago

10.1038/s41438-020-0238-z

MdMYB8 is associated with flavonol biosynthesis via the activation of the MdFLS promoter in the fruits of Malus crabapple
Cited by: 32
Author(s): Hua Li, Li Yu, Jiaxuan Yu, Ting Wu, Jie Zhang, Ji Tian
Software Mentions: 3
Published: almost 5 years ago