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 10 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: over 6 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: almost 6 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 6 years ago

10.1186/s13059-016-1088-8

Genome of the Asian longhorned beetle (Anoplophora glabripennis), a globally significant invasive species, reveals key functional and evolutionary innovations at the beetle–plant interface
Cited by: 214
Author(s): Duane D. McKenna, Erin D. Scully, Yannick Pauchet, Kelli Hoover, Roy Kirsch, Scott M. Geib, Robert F. Mitchell, Robert M. Waterhouse, Seung‐Joon Ahn, Deanna Arsala, Joshua B. Benoit, Heath Blackmon, Tiffany Bledsoe, Julia H. Bowsher, André Busch, Bernarda Calla, Hsu Chao, Anna K. Childers, Christopher P. Childers, Dave J. Clarke, Lorna Cohen, Jeffery P. Demuth, Huyen Dinh, Harshavardhan Doddapaneni, Amanda Dolan, Jian J. Duan, Shannon Dugan, Markus Friedrich, Karl M. Glastad, Michael A. D. Goodisman, Stéphanie Haddad, Yi Han, Daniel Hughes, Panagiotis Ioannidis, J. Spencer Johnston, Jeffery W. Jones, Leslie A. Kuhn, D. R. Lance, Chien Yueh Lee, Sandra L. Lee, Han Lin, Jeremy A. Lynch, Armin P. Moczek, Shwetha C. Murali, Donna M. Muzny, David R. Nelson, Subba Reddy Palli, Kristen A. Panfilio, Dan Pers, Monica F. Poelchau, Honghu Quan, Jiaxin Qu, Anandasankar Ray, Joseph P. Rinehart, Hugh M. Robertson, Richard L. Roehrdanz, Andrew J. Rosendale, Seunggwan Shin, Christian Silva, Alex S. Torson, Iris M. Vargas Jentzsch, John H. Werren, Kim C. Worley, George D. Yocum, Evgeny M. Zdobnov, Richard A. Gibbs, Stephen Richards
Software Mentions: 4
Published: almost 10 years ago

10.3389/fpls.2020.589005

Elucidation of the miR164c-Guided Gene/Protein Interaction Network Controlling Seed Vigor in Rice
Cited by: 5
Author(s): Kerui Huang, Shiqi Zhou, Kaimin Shen, Yan Zhou, Feng Wang, Xiaocheng Jiang
Software Mentions: 4
Published: almost 6 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: almost 7 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: about 7 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: almost 11 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 9 years ago

10.1186/s13059-016-1146-2

Chrom3D: three-dimensional genome modeling from Hi-C and nuclear lamin-genome contacts
Cited by: 148
Author(s): Jonas Paulsen, Monika Sekelja, Anja R. Oldenburg, Alice Barateau, Nolwenn Briand, Erwan Delbarre, Akshay Shah, Anita L. Sørensen, Corinne Vigouroux, Brigitte Buendia, Philippe Collas
Software Mentions: 4
Published: over 9 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 8 years ago

10.1186/s13059-016-0932-1

Single-cell analysis of long non-coding RNAs in the developing human neocortex
Cited by: 291
Author(s): Siyuan John Liu, Tomasz J. Nowakowski, Alex A. Pollen, Jan H. Lui, Max A. Horlbeck, Frank J. Attenello, Daniel He, Jonathan S. Weissman, Arnold R. Kriegstein, Aaron A. Diaz, Daniel A. Lim
Software Mentions: 4
Published: over 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 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 8 years ago

10.1093/gigascience/giy049

Population genomic data reveal genes related to important traits of quail
Cited by: 23
Author(s): Yan Wu, Yaolei Zhang, Zhuocheng Hou, Guangyi Fan, Jinsong Pi, Shuai Sun, Chen Jiang, Huaqiao Liu, Xiao Du, Jie Shen, Gang Hu, Wenbin Chen, Angelo Pan, Yin PingPing, Xiaoli Chen, Yuejin Pu, Zhonghu He, Zhen-Hua Liang, Jianbo Jian, Hao Zhang, Bin Wu, Jing Sun, Jianwei Chen, Hu Tao, Ting Yang, Hong‐Wei Xiao, Huan Yang, Chuanwei Zheng, Mingzhou Bai, Xiaodong Fang, David W. Burt, Wen Wang, Qingyi Li, Xun Xu, Chengfeng Li, Huanming Yang, Jian Wang, Ning Yang, Xin Liu, Junzheng Du
Software Mentions: 4
Published: over 8 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 7 years ago

10.1186/s13742-015-0046-9

RNA-Seq analysis and annotation of a draft blueberry genome assembly identifies candidate genes involved in fruit ripening, biosynthesis of bioactive compounds, and stage-specific alternative splicing
Cited by: 118
Author(s): Vikas Gupta, April D Estrada, Ivory C. Blakley, Robert W. Reid, Ketan Patel, Mason D. Meyer, Stig Uggerhøj Andersen, Allan Brown, Mary Ann Lila, Ann E. Loraine
Software Mentions: 4
Published: over 11 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: over 5 years ago

10.3389/fpls.2016.01924

Transcriptome Analysis Reveals Candidate Genes Involved in Gibberellin-Induced Fruit Setting in Triploid Loquat (Eriobotrya japonica)
Cited by: 25
Author(s): Shuang Jiang, Luo Jun, Fanjie Xu, Xueying Zhang
Software Mentions: 4
Published: over 9 years ago

10.1186/s13059-021-02444-6

Chromatin lncRNA Platr10 controls stem cell pluripotency by coordinating an intrachromosomal regulatory network
Cited by: 12
Author(s): Zhonghua Du, Wei Xue, Yichen Wang, Lin Jia, Shilin Zhang, Yudi Liu, Lei Zhou, Hui Li, Yang Wang, Cong Wang, Jingcheng Chen, Yajing Hao, Daniela Salgado Figueroa, Huiling Chen, Dan Li, Naifei Chen, Ilkay Celik, Yanbo Zhu, Zi Yan, Changhao Fu, Shanshan Liu, Benzheng Jiao, Zhuo Wang, Hui Zhang, Günhan Gülsoy, Jianjun Luo, Baoming Qin, Sujun Gao, Philipp Kapranov, Miguel A. Esteban, Songling Zhang, Wei Li, Ferhat Ay, Runsheng Chen, Andrew R. Hoffman, Jiuwei Cui, Ji-Fan Hu
Software Mentions: 4
Published: about 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: about 10 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 9 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 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 8 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 15 years ago

10.1186/s13059-019-1686-3

Whole genomes and transcriptomes reveal adaptation and domestication of pistachio
Cited by: 71
Author(s): Lin Zeng, Xiaolong Tu, He Dai, Fengming Han, LU Bing-she, Ming-Shan Wang, Hojjat Asadollahpour Nanaei, Ali Tajabadipour, Mehdi Mansouri, Xiaolong Li, Lili Ji, David M. Irwin, Zhou Hong, Min Liu, Hongkun Zheng, Ali Esmailizadeh, Dong‐Dong Wu
Software Mentions: 4
Published: over 7 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 5 years ago

10.1093/gigascience/giz136

Trochodendron aralioides, the first chromosome-level draft genome in Trochodendrales and a valuable resource for basal eudicot research
Cited by: 20
Author(s): Joeri S. Strijk, Damien Daniel Hinsinger, Fengping Zhang, Kaihua Cao
Software Mentions: 4
Published: almost 7 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: almost 8 years ago

10.1371/journal.pone.0191564

Study of formation of green eggshell color in ducks through global gene expression
Cited by: 4
Author(s): Fa Xu, Ang Li, Jing Lan, Yue Ming Wang, Mengmeng Yan, Sen Lian, Xu Wu
Software Mentions: 4
Published: over 8 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 9 years ago

10.1093/gbe/evy188

Genome Wide Identification of Mutational Hotspots in the Apicomplexan Parasite Neospora caninum and the Implications for Virulence
Cited by: 17
Author(s): Larissa Calarco, Joel Barratt, John Ellis
Software Mentions: 4
Published: about 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: about 9 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 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 5 years ago

10.1371/journal.pone.0192613

NetMiner-an ensemble pipeline for building genome-wide and high-quality gene co-expression network using massive-scale RNA-seq samples
Cited by: 17
Author(s): Hua Yu, Bingke Jiao, Lu Lu, Pengfei Wang, Shuangcheng Chen, Chengzhi Liang, Wei Liu
Software Mentions: 4
Published: over 8 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: about 12 years ago

10.1186/s13059-020-01973-w

Multiplexed capture of spatial configuration and temporal dynamics of locus-specific 3D chromatin by biotinylated dCas9
Cited by: 27
Author(s): Xin Liu, Yong Chen, Yuannyu Zhang, Nan Liu, Giovanni A. Botten, Hui Cao, Stuart H. Orkin, Michael Q. Zhang, Jian Xu
Software Mentions: 4
Published: over 6 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 9 years ago

10.1093/gigascience/giz112

Hybrid de novo genome assembly of Chinese chestnut (Castanea mollissima)
Cited by: 49
Author(s): Yu Xing, Yang Liu, Qing Zhang, Xinghua Nie, Yamin Sun, Zhiyong Zhang, Huchen Li, Kefeng Fang, Guangpeng Wang, Hongwen Huang, Ton Bisseling, Qingqin Cao, Ling Qin
Software Mentions: 4
Published: about 7 years ago

10.1186/s12943-018-0833-x

RNA-Seq profiling of circular RNAs in human laryngeal squamous cell carcinomas
Cited by: 57
Author(s): Cheng Hsien Lu, Xi Su, Amanda Y. Wang, Tao Yuan, Zhenxiao Wang, Chaoping Huang, Yuehua Qiao, Hongyi Hu, Liangfa Liu
Software Mentions: 4
Published: over 8 years ago

10.1186/1471-2164-15-218

Deciphering gamma-decalactone biosynthesis in strawberry fruit using a combination of genetic mapping, RNA-Seq and eQTL analyses
Cited by: 60
Author(s): José F. Sánchez-Sevilla, Eduardo Cruz-Rus, Victoriano Valpuesta, Miguel A. Botella, Iraida Amaya
Software Mentions: 4
Published: over 12 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 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: almost 8 years ago

10.1371/journal.pone.0227882

Comparison of the myometrial transcriptome from singleton and twin pregnancies by RNA-Seq
Cited by: 5
Author(s): Sarah Arrowsmith, Yongxiang Fang, Andrew Sharp
Software Mentions: 4
Published: over 6 years ago

10.1186/s12864-019-5895-7

Comparative physiology and transcriptome analysis allows for identification of lncRNAs imparting tolerance to drought stress in autotetraploid cassava
Cited by: 21
Author(s): Xiao Liang, Xianwen Shang, Sheng Cao, Xuewen Xie, Wendan Zeng, Lingyun Lu, Songbi Chen, Huabing Yan
Software Mentions: 4
Published: about 7 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: about 11 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: over 10 years ago

10.7554/eLife.08851

Maternal LSD1/KDM1A is an essential regulator of chromatin and transcription landscapes during zygotic genome activation
Cited by: 99
Author(s): Katia Ancelin, Laurène Syx, Maud Borensztein, Noémie Ranisavljevic, Ivaylo Vassilev, Luis Briseño-Roa, Tao Liu, Eric Metzger, Nicolas Servant, Emmanuel Barillot, Chongjian Chen, Roland Schüle, Edith Heard
Software Mentions: 4
Published: over 10 years ago

10.7554/eLife.02626

Multi-species, multi-transcription factor binding highlights conserved control of tissue-specific biological pathways
Cited by: 80
Author(s): Benoît Ballester, Alejandra Medina-Rivera, Dominic Schmidt, Mar Gonzàlez-Porta, Matthew Carlucci, Marc E. Rothenberg, Kyle Chessman, Aline Faure, Alister P. W. Funnell, Ângela Gonçalves, Claudia Kutter, Margus Lukk, Suraj Menon, William McLaren, Klara Stefflova, Stephen Watt, Matthew T. Weirauch, Merlin Crossley, John C. Marioni, Duncan T. Odom, Paul Flicek, Michael D. Wilson
Software Mentions: 4
Published: almost 12 years ago

10.3389/fcimb.2016.00193

Genome-Wide Transcriptional and Post-transcriptional Regulation of Innate Immune and Defense Responses of Bovine Mammary Gland to Staphylococcus aureus
Cited by: 41
Author(s): Lingzhao Fang, Yali Hou, Jinpeng An, Bingjie Li, Mengyuan Song, Xiao Wang, Peter Sørensen, Yichun Dong, Chao Liu, Yachun Wang, Huabin Zhu, Shengli Zhang, Ying Yu
Software Mentions: 4
Published: over 9 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 10 years ago

10.7554/eLife.41770

The novel lncRNA lnc-NR2F1 is pro-neurogenic and mutated in human neurodevelopmental disorders
Cited by: 51
Author(s): Cheen Euong Ang, Qing Ma, Orly L. Wapinski, Sheng Hua Fan, Ryan A. Flynn, Qian Yi Lee, Bradley P. Coe, Masahiro Onoguchi, Victor Hipolito Olmos, T. Brian, Lynn Dukes-Rimsky, Jin Xu, Koji Tanabe, Liang Jiang Wang, Ulrich Elling, Josef Penninger, Yang Zhao, Kun Qu, Evan E. Eichler, Anand Srivastava, Marius Wernig, Howard Y. Chang
Software Mentions: 4
Published: over 7 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 6 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 12 years ago

10.7554/eLife.27786

Translation repression via modulation of the cytoplasmic poly(A)-binding protein in the inflammatory response
Cited by: 29
Author(s): Xu Zhang, Xiaoli Chen, Qiuying Liu, Shaojie Zhang, Wenqian Hu
Software Mentions: 4
Published: about 9 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: over 10 years ago

10.1186/s12864-016-2482-z

Overlapping cell population expression profiling and regulatory inference in C. elegans
Cited by: 6
Author(s): Joshua T. Burdick, Travis Walton, Elicia Preston, Amanda L. Zacharias, Arjun Raj, John I. Murray
Software Mentions: 4
Published: over 10 years ago

10.3390/molecules21111431

Comparative Transcriptomic Analysis of Grape Berry in Response to Root Restriction during Developmental Stages
Cited by: 20
Author(s): Lu Feng, Qiong Lin, Di Wu, Shiping Wang, Dengliang Wang, Chongde Sun
Software Mentions: 4
Published: almost 10 years ago

10.7554/eLife.19893

The MBD7 complex promotes expression of methylated transgenes without significantly altering their methylation status
Cited by: 16
Author(s): Dongming Li, Ana Marie S. Palanca, So Youn Won, Lei Gao, Ying Feng, Ajay A. Vashisht, Li Liu, Yuanyuan Zhao, Xigang Liu, Xiuyun Wu, Shaofang Li, Brandon H. Le, Yun Ju Kim, Guodong Yang, Shengben Li, Jinyuan Liu, James A. Wohlschlegel, Hongwei Guo, Beixin Mo, Xuemei Chen, Julie A. Law
Software Mentions: 4
Published: over 9 years ago

10.7554/eLife.49501

Single cell analysis reveals immune cell–adipocyte crosstalk regulating the transcription of thermogenic adipocytes
Cited by: 103
Author(s): Prashant Rajbhandari, Douglas Arneson, Sydney K Hart, In Sook Ahn, Graciel Diamante, Leonardo D. Santos, Nima Zaghari, An‐Chieh Feng, Brandon J. Thomas, Laurent Vergnes, Stephen D. Lee, Abha K. Rajbhandari, Karen Reue, Stephen T. Smale, Xia Yang, Peter Tontonoz
Software Mentions: 4
Published: almost 7 years ago

10.7554/eLife.63556

Deficient spermiogenesis in mice lacking Rlim
Cited by: 7
Author(s): Feng Wang, María Gracia Gervasi, Ana Bošković, Fengyun Sun, Vera D. Rinaldi, Jun Yu, Mary C. Wallingford, Darya A Tourzani, Jesse Mager, Lihua Julie Zhu, Oliver J. Rando, Pablo E. Visconti, Lara Strittmatter, Ingolf Bach
Software Mentions: 4
Published: over 5 years ago

10.7554/eLife.21697

Loss of Dnmt3a and Dnmt3b does not affect epidermal homeostasis but promotes squamous transformation through PPAR-γ
Cited by: 43
Author(s): Lorenzo Rinaldi, Alexandra Avgustinova, Mercé Martı́n, Debayan Datta, Guiomar Solanas, Neus Prats, Salvador Aznar Benitah
Software Mentions: 4
Published: over 9 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 7 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: about 10 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 7 years ago

10.1186/s13072-016-0070-8

Changes of 5-hydroxymethylcytosine distribution during myeloid and lymphoid differentiation of CD34+ cells
Cited by: 18
Author(s): Xavier Tekpli, Alfonso Urbanucci, Adnan Hashim, Cathrine Broberg Vågbø, Robert Lyle, Marianne Kristiansen Kringen, Anne Cathrine Staff, Ingunn Dybedal, Ian G. Mills, Arne Klungland, Judith Staerk
Software Mentions: 4
Published: over 10 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 7 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: almost 9 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 8 years ago

10.1186/s13024-018-0303-3

Inhibition of monocyte-like cell extravasation protects from neurodegeneration in DBA/2J glaucoma
Cited by: 44
Author(s): Pete A. Williams, Catherine E. Braine, Krishnakumar Kizhatil, Nicole E. Foxworth, Nicholas G. Tolman, Jeffrey M. Harder, R. Scott, Gregory L. Sousa, Alyssa Panitch, Gareth R. Howell, Simon W. M. John
Software Mentions: 4
Published: over 7 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 7 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 7 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 10 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 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 8 years ago

10.1371/journal.pone.0246443

Unraveling the chaotic genomic landscape of primary and metastatic canine appendicular osteosarcoma with current sequencing technologies and bioinformatic approaches
Cited by: 4
Author(s): Shirley Chu, Zachary L. Skidmore, Jason Kunisaki, Jason Walker, Malachi Griffith, Obi L. Griffith, Jeffrey N. Bryan
Software Mentions: 4
Published: over 5 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 5 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: over 5 years ago

10.1016/j.molmet.2020.101078

Wnt/β-catenin signaling regulates adipose tissue lipogenesis and adipocyte-specific loss is rigorously defended by neighboring stromal-vascular cells
Cited by: 44
Author(s): Devika P. Bagchi, Akira Nishii, Ziru Li, Jennifer B. DelProposto, Callie A.S. Corsa, Hiroyuki Mori, Julie Hardij, Brian S. Learman, Carey N. Lumeng, Ormond A. MacDougald
Software Mentions: 4
Published: almost 6 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 12 years ago

10.12688/f1000research.22400.2

Ribosome profiling of HEK293T cells overexpressing codon optimized coagulation factor IX
Cited by: 1
Author(s): Aikaterini Alexaki, Jacob Kames, Gaya Hettiarachchi, John C. Athey, Upendra Katneni, Ryan Hunt, Nobuko Hamasaki-Katagiri, David D. Holcomb, Michael DiCuccio, Haim Bar, Anton A. Komar, Chava Kimchi-Sarfaty
Software Mentions: 4
Published: almost 6 years ago

10.1186/s13072-017-0142-4

Activation of the alpha-globin gene expression correlates with dramatic upregulation of nearby non-globin genes and changes in local and large-scale chromatin spatial structure
Cited by: 18
Author(s): Sergey V. Ulianov, Aleksandra A. Galitsyna, Ilya M. Flyamer, Arkadiy K. Golov, Ekaterina E. Khrameeva, Maxim Imakaev, Nezar Abdennur, Mikhail S. Gelfand, А. В. Гаврилов, Sergey V. Razin
Software Mentions: 4
Published: about 9 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: about 8 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 8 years ago

10.1186/s13059-018-1551-9

Alternative polyadenylation factors link cell cycle to migration
Cited by: 21
Author(s): Mithun Mitra, Elizabeth L. Johnson, Vinay Swamy, Lois E Nersesian, David C. Corney, David G. Robinson, Daniel Taylor, Aaron M. Ambrus, David Jelínek, Wei Wang, Sandra Batista, Hilary A. Coller
Software Mentions: 4
Published: almost 8 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: about 10 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: almost 10 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: almost 8 years ago

10.1371/journal.pone.0147221

Comprehensive Annotation of the Parastagonospora nodorum Reference Genome Using Next-Generation Genomics, Transcriptomics and Proteogenomics
Cited by: 36
Author(s): Robert A. Syme, Kar‐Chun Tan, James K. Hane, Kejal N Dodhia, Thomas Stoll, Marcus L. Hastie, Eiko Furuki, Simon R. Ellwood, Angela H. Williams, Yew‐Foon Tan, Alison C. Testa, Jeffrey J. Gorman, Richard P. Oliver
Software Mentions: 4
Published: over 10 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 11 years ago

10.1371/journal.pone.0148039

Reduced CYFIP1 in Human Neural Progenitors Results in Dysregulation of Schizophrenia and Epilepsy Gene Networks
Cited by: 27
Author(s): Rebecca A. Nebel, Dejian Zhao, Erika Pedrosa, Jill Kirschen, Herbert M. Lachman, Deyou Zheng, Brett S. Abrahams
Software Mentions: 3
Published: over 10 years ago

10.1038/srep23219

Identification of genes for controlling swine adipose deposition by integrating transcriptome, whole-genome resequencing, and quantitative trait loci data
Cited by: 42
Author(s): Kai Xing, Feng Zhu, Lichao Zhai, ShaoKang Chen, Zhen Tan, Yangyang Sun, Zhuocheng Hou, ChuDuan Wang
Software Mentions: 3
Published: over 10 years ago

10.1371/journal.pone.0079118

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

10.3389/fcell.2021.655201

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

10.1038/srep20837

Differential Expression of Genes and DNA Methylation associated with Prenatal Protein Undernutrition by Albumen Removal in an avian model
Cited by: 15
Author(s): Els Willems, Carlos Guerrero-Bosagna, Eddy Decuypere, Steven Janssens, Johan Buyse, Nadine Buys, Per Jensen, Nadia Everaert
Software Mentions: 3
Published: over 10 years ago

10.1111/pbi.13007

A <i>Ma10</i> gene encoding P‐type <scp>ATP</scp>ase is involved in fruit organic acid accumulation in apple
Cited by: 54
Author(s): Baiquan Ma, Liao Liao, Ting Fang, Qian Peng, Collins Ogutu, Hui Zhou, Fengwang Ma, Yuepeng Han
Software Mentions: 3
Published: almost 8 years ago

10.3389/fcvm.2018.00030

Postnatal and Adult Aortic Heart Valves Have Distinctive Transcriptional Profiles Associated With Valve Tissue Growth and Maintenance Respectively
Cited by: 10
Author(s): Emily Nordquist, Stephanie LaHaye, Casey Nagel, Joy Lincoln
Software Mentions: 3
Published: over 8 years ago

10.1038/srep17978

Identifying transcription start sites and active enhancer elements using BruUV-seq
Cited by: 26
Author(s): Brian Magnuson, Artur Veloso, Killeen S. Kirkconnell, Leonardo Carmo de Andrade Lima, Michelle T. Paulsen, Emily A. Ljungman, Karan Bedi, J.K. Prasad, Thomas E. Wilson, Mats Ljungman
Software Mentions: 3
Published: almost 11 years ago