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: about 5 years ago

10.1371/journal.pone.0195747

UXT is required for spermatogenesis in mice
Cited by: 5
Author(s): Eric D. Schafler, Phillip A. Thomas, Susan Ha, Yu Wang, Keria Bermudez-Hernandez, Zuojian Tang, David Fenyö, Margarita Vigodner, Susan K. Logan
Software Mentions: 4
Published: over 7 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: almost 11 years ago

10.1371/journal.pone.0095875

The DNA Methylome and Transcriptome of Different Brain Regions in Schizophrenia and Bipolar Disorder
Cited by: 70
Author(s): Yun Xiao, Cynthia Camarillo, Yanyan Ping, Tania Bedard Arana, Hongying Zhao, Peter M. Thompson, Chaohan Xu, Bai-Horng Su, Huihui Fan, Javier Ordoñez, Li Wang, Chunxiang Mao, Yunpeng Zhang, Dianne A. Cruz, Michael Escamilla, Xia Li, Xu Chun
Software Mentions: 4
Published: about 11 years ago

10.1038/s42003-020-01516-w

miR-379 deletion ameliorates features of diabetic kidney disease by enhancing adaptive mitophagy via FIS1
Cited by: 17
Author(s): Mitsuo Kato, Maryam Abdollahi, Ragadeepthi Tunduguru, Walter Tsark, Zhuo Chen, Xiwei Wu, Jinhui Wang, Zhen Bouman Chen, Feng‐Mao Lin, Linda Lanting, Mei Wang, Janice M. Huss, Patrick T. Fueger, David C. Chan, Rama Natarajan
Software Mentions: 4
Published: over 4 years ago

10.3389/fpls.2017.01430

Transcriptomic Analysis Reveals Candidate Genes for Female Sterility in Pomegranate Flowers
Cited by: 32
Author(s): Lina Chen, Jie Zhang, Haoxian Li, Juan Niu, Hui Xue, Beibei Liu, Qi Wang, Xiang Luo, Fuhong Zhang, Dan Zhao, Shangyin Cao
Software Mentions: 4
Published: almost 8 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: over 5 years ago

10.3389/fpls.2015.00718

A novel workflow correlating RNA-seq data to Phythophthora infestans resistance levels in wild Solanum species and potato clones
Cited by: 20
Author(s): Itziar Frades, Kibrom B. Abreha, Estelle Proux‐Wéra, Åsa Lankinen, Erik Andréasson, Erik Alexandersson
Software Mentions: 4
Published: almost 10 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: almost 5 years ago

10.1186/s13059-015-0746-6

Comparative genomics of Steinernema reveals deeply conserved gene regulatory networks
Cited by: 74
Author(s): Adler R. Dillman, Marissa Macchietto, Camille F. Porter, Alicia K. Rogers, Brian A. Williams, Igor Antoshechkin, Ming Min Lee, Z. Goodwin, Xiaojun Lu, Edwin E. Lewis, Heidi Goodrich-Blair, S. Patricia Stock, Byron J. Adams, Paul W. Sternberg, A Mortazavi
Software Mentions: 4
Published: almost 10 years ago

10.1371/journal.pone.0150002

CG Methylation Covaries with Differential Gene Expression between Leaf and Floral Bud Tissues of Brachypodium distachyon
Cited by: 23
Author(s): Kyria Roessler, Shohei Takuno, Brandon S. Gaut
Software Mentions: 4
Published: over 9 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: almost 9 years ago

10.1186/1752-0509-7-S5-S1

Co-expression network analysis identifies Spleen Tyrosine Kinase (SYK) as a candidate oncogenic driver in a subset of small-cell lung cancer
Cited by: 68
Author(s): Akshata R. Udyavar, Megan D. Hoeksema, Jonathan E. Clark, Yong Zou, Zuojian Tang, Zhiguo Li, Ming Li, Heidi Chen, Alexander Statnikov, Yu Shyr, Daniel C. Liebler, John K. Field, Rosana Eisenberg, Lourdes Estrada, Pierre P. Massion, Vito Quaranta
Software Mentions: 4
Published: over 11 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: almost 8 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: 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: over 11 years ago

10.1186/s13059-015-0825-8

Loss of function of myosin chaperones triggers Hsf1-mediated transcriptional response in skeletal muscle cells
Cited by: 26
Author(s): Christelle Etard, Olivier Armant, Urmas Roostalu, Victor Gourain, Marco Ferg, Uwe Strähle
Software Mentions: 4
Published: over 9 years ago

10.3389/fpls.2019.00603

Analysis of Key Genes Involved in Potato Anthocyanin Biosynthesis Based on Genomics and Transcriptomics Data
Cited by: 13
Author(s): Nie Tengkun, Dongdong Wang, Xiaoyan Ma, Yue Chen, Qin Chen
Software Mentions: 4
Published: about 6 years ago

10.3389/fpls.2018.00005

Abiotic Stresses Modulate Landscape of Poplar Transcriptome via Alternative Splicing, Differential Intron Retention, and Isoform Ratio Switching
Cited by: 84
Author(s): Sergei A. Filichkin, Michael Hamilton, Palitha Dharmawardhana, Sunil Kumar Singh, Christopher Sullivan, Asa Ben‐Hur, Anireddy S. N. Reddy, Pankaj Jaiswal
Software Mentions: 4
Published: over 7 years ago

10.3389/fpls.2020.00551

Glycosyltransferase-Like RSE1 Negatively Regulates Leaf Senescence Through Salicylic Acid Signaling in Arabidopsis
Cited by: 8
Author(s): Seulbee Lee, Myung‐Hee Kim, Jae Ho Lee, Jieun Jeon, June M. Kwak, Yun Ju Kim
Software Mentions: 4
Published: about 5 years ago

10.1534/g3.119.400152

Early Developmental Stress Affects Subsequent Gene Expression Response to an Acute Stress in Atlantic Salmon: An Approach for Creating Robust Fish for Aquaculture?
Cited by: 23
Author(s): Nick Robinson, Hanne Johnsen, Hooman K. Moghadam, Øivind Andersen, Helge Tveiten
Software Mentions: 4
Published: about 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: over 7 years ago

10.3389/fpls.2021.664250

New Insights Into Lignification via Network and Multi-Omics Analyses of Arogenate Dehydratase Knock-Out Mutants in Arabidopsis thaliana
Cited by: 1
Author(s): Kim Hixson, Joaquim V. Marques, Jason P. Wendler, Jason McDermott, Karl K. Weitz, Therese RW Clauss, Matthew E. Monroe, Ronald J. Moore, Joseph N. Brown, Mary Lipton, Callum J. Bell, Ljiljana Paša‐Tolić, Laurence Davin, Norman Lewis
Software Mentions: 4
Published: about 4 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: about 8 years ago

10.7554/eLife.36998

Downregulation of ribosome biogenesis during early forebrain development
Cited by: 63
Author(s): Kevin F. Chau, Morgan L. Shannon, Ryann M. Fame, Erin Fonseca, Hillary Mullan, Matthew B. Johnson, Anoop K. Sendamarai, Mark W. Springel, Laurent Beaugerie, Maria K. Lehtinen
Software Mentions: 4
Published: about 7 years ago

10.1016/j.cell.2018.07.001

Heteromeric RNP Assembly at LINEs Controls Lineage-Specific RNA Processing
Cited by: 110
Author(s): Jan Attig, Antonella Federico, Clare Gooding, Anob M. Chakrabarti, Aarti Singh, Nejc Haberman, Julian A. Zagalak, Warren Emmett, Christopher W. Smith, Nicholas M. Luscombe, Jernej Ule
Software Mentions: 4
Published: almost 7 years ago

10.1186/s12870-017-1108-1

Maize RNA PolIV affects the expression of genes with nearby TE insertions and has a genome-wide repressive impact on transcription
Cited by: 17
Author(s): Cristian Forestan, Silvia Farinati, Riccardo Aiese Cigliano, Alice Lunardon, Walter Sanseverino, Serena Varotto
Software Mentions: 4
Published: almost 8 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 6 years ago

10.7554/eLife.46566

The transcription factor odd-paired regulates temporal identity in transit-amplifying neural progenitors via an incoherent feed-forward loop
Cited by: 29
Author(s): Merve Deniz Abdusselamoglu, Elif Eroğlu, Thomas R Burkard, Juergen A. Knoblich
Software Mentions: 4
Published: about 6 years ago

10.7554/eLife.00170

Dual functions of TAF7L in adipocyte differentiation
Cited by: 39
Author(s): Haiying Zhou, Tommy Kaplan, Yan Li, Ivan Grubisic, Zhengjian Zhang, P. Jeremy Wang, Michael B. Eisen, Robert Tjian
Software Mentions: 4
Published: over 12 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: over 8 years ago

10.1186/s12870-017-0996-4

Stress-responsive pathways and small RNA changes distinguish variable developmental phenotypes caused by MSH1 loss
Cited by: 24
Author(s): Mon Ray Shao, Sunil Kumar Kenchanmane Raju, John D. Laurie, Robersy Sánchez, Sally A. Mackenzie
Software Mentions: 4
Published: over 8 years ago

10.3389/fpls.2017.00184

Analysis of Plant Pan-Genomes and Transcriptomes with GET_HOMOLOGUES-EST, a Clustering Solution for Sequences of the Same Species
Cited by: 60
Author(s): Bruno Contreras‐Moreira, Carlos Pérez Cantalapiedra, María Jesús García-Pereira, Sean P. Gordon, John P. Vogel, Ernesto Igartua, Ana M. Casas, Pablo Vinuesa
Software Mentions: 4
Published: over 8 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: over 4 years ago

10.7554/eLife.22039

Mapping cell type-specific transcriptional enhancers using high affinity, lineage-specific Ep300 bioChIP-seq
Cited by: 48
Author(s): Pingzhu Zhou, Fei Gu, Lina Zhang, Brynn N. Akerberg, Qing Ma, Kai Li, Aibin He, Zhiqiang Lin, Sean Stevens, Bin Zhou, William T. Pu
Software Mentions: 4
Published: over 8 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: over 8 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: about 7 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: about 5 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: about 5 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: almost 7 years ago

10.1186/s12864-020-6564-6

Transcriptome analysis of fungicide-responsive gene expression profiles in two Penicillium italicum strains with different response to the sterol demethylation inhibitor (DMI) fungicide prochloraz
Cited by: 15
Author(s): Tingfu Zhang, Qing Cao, Na Li, De Li Liu, Yongze Yuan
Software Mentions: 4
Published: over 5 years ago

10.1186/s12864-021-07710-2

Whole-genome resequencing provides insights into the population structure and domestication signatures of ducks in eastern China
Cited by: 11
Author(s): Peishi Feng, Tao Zeng, Hua Yang, Guohong Chen, Junzheng Du, Li Chen, Junda Shen, Zhenrong Tao, Ping Wang, Lin Yang, Lizhi Liu
Software Mentions: 4
Published: about 4 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: over 5 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: over 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: about 5 years ago

10.1186/s12859-015-0795-6

TOGGLE: toolbox for generic NGS analyses
Cited by: 20
Author(s): Cécile Monat, Christine Tranchant‐Dubreuil, Ayité Kougbeadjo, Cédric Farcy, Enrique Ortega-Abboud, Souhila Amanzougarene, Sébastien Ravel, Mawussé Agbessi, Julie Orjuela, Marilyne Summo, François Sabot
Software Mentions: 4
Published: over 9 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: over 4 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: about 6 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: over 7 years ago

10.1186/s12863-018-0608-9

RNA-seq analysis of lncRNA-controlled developmental gene expression during puberty in goat &amp; rat
Cited by: 21
Author(s): Xiaoxiao Gao, Jing Ye, Chen Yang, Lei Luo, Ya Liu, Jianping Ding, Yunhai Zhang, Yinghui Ling, Weiping Huang, Xiaorong Zhang, Kaifa Zhang, Xiumei Li, Jie Zhou, Fugui Fang, Zubing Cao
Software Mentions: 4
Published: over 7 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: about 7 years ago

10.1186/s12864-015-2270-1

Comprehensive evaluation of AmpliSeq transcriptome, a novel targeted whole transcriptome RNA sequencing methodology for global gene expression analysis
Cited by: 66
Author(s): Wenli Li, Amy Turner, Praful Aggarwal, Andrea Matter, Erin Storvick, Donna K. Arnett, Ulrich Broeckel
Software Mentions: 4
Published: over 9 years ago

10.1186/s12859-015-0859-7

Effects of Mecp2 loss of function in embryonic cortical neurons: a bioinformatics strategy to sort out non-neuronal cells variability from transcriptome profiling
Cited by: 9
Author(s): Marcella Vacca, Kumar Parijat Tripathi, Luisa Speranza, Riccardo Aiese Cigliano, Francesco Scalabrì, Federico Marracino, Michele Madonna, Walter Sanseverino, Carla Perrone-Capano, Mario Rosario Guarracino, Maurizio D’Esposito
Software Mentions: 4
Published: over 9 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: over 5 years ago

10.1186/s12864-018-5115-x

Genome-wide identification and differentially expression analysis of lncRNAs in tilapia
Cited by: 19
Author(s): Bi Jun Li, Dan Jiang, Zhijun Meng, Yong Zhang, Zong Xian Zhu, Haoran Lin, Jun Xia
Software Mentions: 4
Published: almost 7 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: over 6 years ago

10.1186/1471-2105-12-323

RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome
Cited by: 14,016
Author(s): Bo Li, Colin N. Dewey
Software Mentions: 4
Published: almost 14 years ago

10.1186/1471-2164-15-1081

Adaptive genomic structural variation in the grape powdery mildew pathogen, Erysiphe necator
Cited by: 137
Author(s): Laura M. Jones, Summaira Riaz, Abraham Morales‐Cruz, Katherine C. H. Amrine, Brianna McGuire, W. D. Gubler, Michael Walker, Dario Cantu
Software Mentions: 4
Published: over 10 years ago

10.1186/s12862-017-0902-6

Transcriptomic insights into the genetic basis of mammalian limb diversity
Cited by: 19
Author(s): Jennifer Maier, Marcelo Rivas‐Astroza, Jenny Deng, Anna Dowling, Paige Oboikovitz, Xiaoyi Cao, Richard R. Behringer, Chris J. Cretekos, John J. Rasweiler, Sheng Zhong, Karen E. Sears
Software Mentions: 4
Published: over 8 years ago

10.1186/s12864-019-5832-9

A survey of transcriptome complexity using PacBio single-molecule real-time analysis combined with Illumina RNA sequencing for a better understanding of ricinoleic acid biosynthesis in Ricinus communis
Cited by: 23
Author(s): Lijun Wang, Xiaoling Jiang, Lei Wang, Wei Wang, Chunling Fu, Xin Yan, Xinxin Geng
Software Mentions: 4
Published: about 6 years ago

10.1186/s12864-016-3442-3

Comparative transcriptome analysis of two contrasting watermelon genotypes during fruit development and ripening
Cited by: 65
Author(s): Qianglong Zhu, Shi Liu, Zhu Zhang, Sikandar Amanullah, Angela R. Davis, Feishi Luan
Software Mentions: 4
Published: over 8 years ago

10.1186/s12859-017-1816-4

mmquant: how to count multi-mapping reads?
Cited by: 29
Author(s): Matthias Zytnicki
Software Mentions: 4
Published: almost 8 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: about 8 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: over 10 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: over 6 years ago

10.1016/j.ccell.2018.04.004

Molecular, Pathological, Radiological, and Immune Profiling of Non-brainstem Pediatric High-Grade Glioma from the HERBY Phase II Randomized Trial
Cited by: 136
Author(s): Alan Mackay, Anna Burford, Valeria Molinari, David Jones, Elisa Izquierdo, Jurriaan Brouwer‐Visser, Felice Giangaspero, Christine Haberler, Torsten Pietsch, Thomas S. Jacques, Dominique Figarella‐Branger, Daniel Rodriguez, Paul S. Morgan, Pichai Raman, Angela J. Waanders, Adam Resnick, Maura Massimino, Maria Luisa Garré, Smith Hw, David Capper, Stefan M. Pfister, Thomas Würdinger, Rachel Tam, Josep Garcia, Meghna Das Thakur, Gilles Vassal, Jacques Grill, Tim Jaspan, Pascale Varlet, Chris Jones
Software Mentions: 4
Published: about 7 years ago

10.1016/j.ajhg.2018.04.011

Landscape of Conditional eQTL in Dorsolateral Prefrontal Cortex and Co-localization with Schizophrenia GWAS
Cited by: 118
Author(s): Amanda Dobbyn, Laura Huckins, James Boocock, Laura Sloofman, Benjamin S. Glicksberg, Claudia Giambartolomei, Gabriel E. Hoffman, Thanneer M. Perumal, Kiran Girdhar, Yan Jiang, Towfique Raj, Douglas M. Ruderfer, Robin Kramer, Dalila Pinto, Schahram Akbarian, Panos Roussos, Enrico Domenici, Bernie Devlin, Pamela Sklar, Eli A. Stahl, Solveig K. Sieberts
Software Mentions: 4
Published: about 7 years ago

10.1186/s12864-019-5775-1

Translation of upstream open reading frames in a model of neuronal differentiation
Cited by: 25
Author(s): Caitlin M. Rodriguez, Sang-Young Chun, Ryan E. Mills, Peter K. Todd
Software Mentions: 4
Published: about 6 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: over 9 years ago

10.1186/s12859-017-1897-0

Identification of streptococcal small RNAs that are putative targets of RNase III through bioinformatics analysis of RNA sequencing data
Cited by: 6
Author(s): Ethan Rath, Stephanie Pitman, Kyu Hong Cho, Yongsheng Bai
Software Mentions: 4
Published: over 7 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: over 4 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 7 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: about 5 years ago

10.1093/bib/bby121

Homeolog expression quantification methods for allopolyploids
Cited by: 24
Author(s): Tony Kuo, Masaomi Hatakeyama, Toshiaki Tameshige, Kentaro Shimizu, Jun Sese
Software Mentions: 4
Published: over 6 years ago

10.1186/1471-2105-14-S7-S10

NGS-Trex: Next Generation Sequencing Transcriptome profile explorer
Cited by: 13
Author(s): Ilenia Boria, Lara Boatti, Graziano Pesole, Flavio Mignone
Software Mentions: 4
Published: over 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: almost 7 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: almost 8 years ago

10.1186/s12935-019-0953-4

Effect of hyperoside on cervical cancer cells and transcriptome analysis of differentially expressed genes
Cited by: 22
Author(s): Guo Wei, Hui Yu, Lu Zhang, Xiuwei Chen, Yunduo Liu, Yaoxian Wang, Yunyan Zhang
Software Mentions: 4
Published: almost 6 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: almost 10 years ago

10.1016/j.molcel.2019.04.002

Functional Landscape of PCGF Proteins Reveals Both RING1A/B-Dependent-and RING1A/B-Independent-Specific Activities
Cited by: 116
Author(s): Andrea Scelfo, Daniel Fernández-Pérez, Simone Tamburri, Marika Zanotti, Elisa Lavarone, Monica Soldi, Tiziana Bonaldi, Karin Johanna Ferrari, Diego Pasini
Software Mentions: 4
Published: about 6 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: about 4 years ago

10.1371/journal.pone.0243911

The pharmacodynamic and differential gene expression analysis of PPAR α/δ agonist GFT505 in CDAHFD-induced NASH model
Cited by: 12
Author(s): Linfu Liu, Chuang Liu, Menglong Zhao, Qianru Zhang, Ying Lu, Ping Liu, Hua Yang, Jinliang Yang, Xiaoxin Chen, Yuqin Yao
Software Mentions: 4
Published: over 4 years ago

10.1186/s12864-016-3345-3

TRPM2 SNP genotype previously associated with susceptibility to Rhodococcus equi pneumonia in Quarter Horse foals displays differential gene expression identified using RNA-Seq
Cited by: 6
Author(s): Cole M. McQueen, Canaan Whitfield-Cargile, Kranti Konganti, Glenn P. Blodgett, Scott V. Dindot, Noah D. Cohen
Software Mentions: 4
Published: over 8 years ago

10.1371/journal.pone.0228933

Transcriptomic analysis to elucidate the response of honeybees (Hymenoptera: Apidae) to amitraz treatment
Cited by: 5
Author(s): Ye Liang, Peng Liu, Tengfei Shi, Wang AnRan, Yujie Zhu, Lai Li, Linsheng Yu
Software Mentions: 4
Published: over 5 years ago

10.1186/s12864-015-1624-z

Distinctive expansion of gene families associated with plant cell wall degradation, secondary metabolism, and nutrient uptake in the genomes of grapevine trunk pathogens
Cited by: 132
Author(s): Abraham Morales‐Cruz, Katherine C. H. Amrine, Bárbara Blanco-Ulate, Daniel P. Lawrence, Renaud Travadon, Philippe E. Rolshausen, Kendra Baumgartner, Dario Cantu
Software Mentions: 4
Published: about 10 years ago

10.1186/s12864-020-6613-1

Genome-wide analysis reveals molecular convergence underlying domestication in 7 bird and mammals
Cited by: 11
Author(s): Yali Hou, Furong Qi, Xue Bai, Tong Ren, Xu Shen, Qing Chu, Xiquan Zhang, Xuemei Lu
Software Mentions: 4
Published: over 5 years ago

10.15252/msb.20188591

Widespread inter‐individual gene expression variability in <i>Arabidopsis thaliana</i>
Cited by: 48
Author(s): Sandra Cortijo, Zeynep Gökçe Gayretli Aydın, Sebastian E. Ahnert, James Locke
Software Mentions: 4
Published: over 6 years ago

10.1371/journal.pone.0216679

Seasonal adaptations of the hypothalamo-neurohypophyseal system of the dromedary camel
Cited by: 8
Author(s): Fatma Zohra Djazouli Alim, Elena V. Romanova, Yea Ling Tay, Ahmad Yamin bin Abdul Rahman, Kok‐Gan Chan, Kar‐Wai Hong, Mark F. Rogers, Bruce R. Southey, Michael Greenwood, André Souza Mecawi, Mohammad Rais Mustafa, Nicole Mahy, Colin Campbell, José Antunes‐Rodrigues, Jonathan V. Sweedler, David Murphy, Charles C.T. Hindmarch
Software Mentions: 4
Published: about 6 years ago

10.1186/s12864-021-07679-y

Global investigation of estrogen-responsive genes regulating lipid metabolism in the liver of laying hens
Cited by: 14
Author(s): Jingyao Ren, Weihua Tian, Keren Jiang, Zhang Wang, Dandan Wang, Zhuanjian Li, Fengbin Yan, Yanbin Wang, Yadong Tian, Kepeng Ou, Hongjun Wang, Xiangtao Kang, Hong Li, Xiaojun Liu
Software Mentions: 4
Published: about 4 years ago

10.3390/vaccines5040037

Elucidating the Role of Host Long Non-Coding RNA during Viral Infection: Challenges and Paths Forward
Cited by: 8
Author(s): David J. Lemler, Hayden Brochu, Fang Yang, Erin Harrell, Xinxia Peng
Software Mentions: 4
Published: almost 8 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 7 years ago

10.18632/aging.102034

A large-scale CRISPR screen and identification of essential genes in cellular senescence bypass
Cited by: 5
Author(s): Xuehui Li, Lei Wei, Qiongye Dong, Liyang Liu, Michael Q. Zhang, Zhen Xie, Xiaowo Wang
Software Mentions: 4
Published: about 6 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: over 4 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: about 10 years ago

10.1186/s12864-016-2896-7

Read-Split-Run: an improved bioinformatics pipeline for identification of genome-wide non-canonical spliced regions using RNA-Seq data
Cited by: 8
Author(s): Yongsheng Bai, Jeff Kinne, Brandon Donham, Feng Jiang, Lizhong Ding, Justin Hassler, Randal J. Kaufman
Software Mentions: 4
Published: almost 9 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: over 10 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: over 12 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: almost 5 years ago

10.1155/2013/340620

State-of-the-Art Fusion-Finder Algorithms Sensitivity and Specificity
Cited by: 79
Author(s): Matteo Carrara, Marco Beccuti, Fulvio Lazzarato, Federica Cavallo, Francesca Cordero, Susanna Donatelli, Raffaele Calogero
Software Mentions: 4
Published: over 12 years ago

10.1371/journal.pone.0210672

Identification of new regulators through transcriptome analysis that regulate anthocyanin biosynthesis in apple leaves at low temperatures
Cited by: 28
Author(s): Tingting Song, Keting Li, Ting Wu, Yi Wang, Xinzhong Zhang, Xuefeng Xu, Yuncong Yao, Zhenhai Han
Software Mentions: 4
Published: over 6 years ago