10.3389/fonc.2021.669270

A Comprehensive RNA Study to Identify circRNA and miRNA Biomarkers for Docetaxel Resistance in Breast Cancer
Cited by: 11
Author(s): Peide Huang, Fengyu Li, Zongchao Mo, Chunyu Geng, Wen Fang, Chunyan Zhang, Jia Guo, Song Wu, Lin Li, Nils Brünner, Jan Stenvang
Software Mentions: 3
Published: over 5 years ago

10.1038/s41598-019-53802-1

Oral microbiome diversity in chimpanzees from Gombe National Park
Cited by: 14
Author(s): Andrew T. Ozga, Ian C. Gilby, Rebecca Nockerts, Michael L. Wilson, Anne E. Pusey, Anne C. Stone
Software Mentions: 3
Published: almost 7 years ago

10.1371/journal.pone.0242194

Identification of potential target genes and crucial pathways in small cell lung cancer based on bioinformatic strategy and human samples
Cited by: 6
Author(s): Xiuwen Chen, Li Wang, Xiaomin Su, Senyuan Luo, Xianbin Tang, Yugang Huang
Software Mentions: 3
Published: almost 6 years ago

10.1186/s12951-021-01047-4

An atherosclerotic plaque-targeted single-chain antibody for MR/NIR-II imaging of atherosclerosis and anti-atherosclerosis therapy
Cited by: 15
Author(s): Liwei Zhang, Sheng Xue, Feng Ren, Si-Yang Huang, Ruizhi Zhou, Yu Wang, Chunxiao Zhou, Zhen Li
Software Mentions: 3
Published: about 5 years ago

10.1038/s41598-018-37792-0

Diversified secondary metabolite biosynthesis gene repertoire revealed in symbiotic dinoflagellates
Cited by: 20
Author(s): Girish Beedessee, Kanako Hisata, Michael C. Roy, Frances M. Van Dolah, Noriyuki Satoh, Eiichi Shoguchi
Software Mentions: 3
Published: over 7 years ago

10.1038/s41598-018-36059-y

Genome-Wide Transcriptome Landscape of Embryonic Brain-Derived Neural Stem Cells Exposed to Alcohol with Strain-Specific Cross-Examination in BL6 and CD1 Mice
Cited by: 22
Author(s): Wayne Xu, Vichithra R. B. Liyanage, Aaron MacAulay, Romina D. Levy, Kyle Curtis, Carl O. Olson, Robby M. Zachariah, Shayan Amiri, Marjorie Buist, Geoffrey Hicks, James R. Davie, Mojgan Rastegar
Software Mentions: 3
Published: over 7 years ago

10.1371/journal.pbio.2003769

Extreme genome diversity in the hyper-prevalent parasitic eukaryote Blastocystis
Cited by: 88
Author(s): Eleni Gentekaki, Bruce A. Curtis, Courtney W. Stairs, Vladimír Klimeš, Marek Eliáš, Dayana E. Salas‐Leiva, Emily K. Herman, Laura Eme, María Cecilia Arias, Bernard Henrissat, Frédérique Hilliou, Mary J. Klute, Hiroshi Suga, Shehre-Banoo Malik, Arthur W. Pightling, Martin Kolísko, Richard A. Rachubinski, Alexander Schlacht, Darren M. Soanes, Anastasios D. Tsaousis, John M. Archibald, Steven Ball, Joel B. Dacks, C. Graham Clark, Mark van der Giezen, Andrew J. Roger
Software Mentions: 3
Published: about 9 years ago

10.1038/s41598-018-31770-2

Characterisation and functional predictions of canine long non-coding RNAs
Cited by: 24
Author(s): Céline Le Béguec, Valentin Wucher, Laëtitia Lagoutte, Édouard Cadieu, Nadine Botherel, Benoît. Hédan, Clotilde De Brito, Anne-Sophie Guillory, Catherine André, Thomas Derrien, Christophe Hitte
Software Mentions: 3
Published: about 8 years ago

10.1111/pbi.12940

Chromosome‐based survey sequencing reveals the genome organization of wild wheat progenitor <i>Triticum dicoccoides</i>
Cited by: 27
Author(s): Bala Anı Akpınar, Sezgi Biyiklioglu, Burcu Alptekin, M. Havránková, Jan Vrána, Jaroslav Doležel, Assaf Distelfeld, Pilar Hernández, Hikmet Budak
Software Mentions: 3
Published: over 8 years ago

10.1038/s41598-018-30583-7

The landscape of the A-to-I RNA editome from 462 human genomes
Cited by: 14
Author(s): Zhangyi Ouyang, Chao Ren, Feng Liu, Gaole An, Xiaochen Bo, Wenjie Shu
Software Mentions: 3
Published: about 8 years ago

10.3390/plants10091874

Analysis of PRX Gene Family and Its Function on Cell Lignification in Pears (Pyrus bretschneideri)
Cited by: 3
Author(s): Zhihua Xie, Weikang Rui, Yazhou Yuan, Xiaofei Song, Xing Liu, Xin Gong, Jianping Bao, Shaoling Zhang, Khanizadeh Shahrokh, Shutian Tao
Software Mentions: 3
Published: about 5 years ago

10.1038/s41598-018-33744-w

Genome-wide identification of AP2/ERF superfamily genes and their expression during fruit ripening of Chinese jujube
Cited by: 42
Author(s): Zhijun Zhong, Xingang Li
Software Mentions: 3
Published: almost 8 years ago

10.1038/s41598-018-23334-1

Genome-wide identification, putative functionality and interactions between lncRNAs and miRNAs in Brassica species
Cited by: 32
Author(s): Jinfang Zhang, Lijuan Wei, Jun Jiang, Annaliese S. Mason, Haojie Li, Cheng Cui, Linna Chai, Beibei Zheng, Yongqing Zhu, Qing Xia, Long Jiang, Donghui Fu
Software Mentions: 3
Published: over 8 years ago

10.1038/s41598-018-21560-1

Transcriptomic signature of drought response in pearl millet (Pennisetum glaucum (L.) and development of web-genomic resources
Cited by: 40
Author(s): Sarika Jaiswal, Tushar J. Antala, M. K. Mandavia, Meenu Chopra, Rahul Singh Jasrotia, R. S. Tomar, Jashminkumar Kheni, U. B. Angadi, Mir Asif Iquebal, B. A. Golakia, Anil Rai, Dinesh Kumar
Software Mentions: 3
Published: over 8 years ago

10.1038/s41598-017-17484-x

Comparative analysis of the genomes of Stylophora pistillata and Acropora digitifera provides evidence for extensive differences between species of corals
Cited by: 109
Author(s): Christian Cr Voolstra, Yong Li, Yi Jin Liew, Sebastian Baumgarten, Didier Zoccola, Jean‐François Flot, Sylvie Tambutté, Denis Allemand, Manuel Aranda
Software Mentions: 3
Published: almost 9 years ago

10.3389/fpls.2021.668623

The Wild Sugarcane and Sorghum Kinomes: Insights Into Expansion, Diversification, and Expression Patterns
Cited by: 16
Author(s): Alexandre Hild Aono, Ricardo José Gonzaga Pimenta, Ana Letycia Basso Garcia, Fernando Henrique Correr, Guilherme Kenichi Hosaka, Marishani Marin Carrasco, Cláudio Benício Cardoso-Silva, Melina Cristina Mancini, Danilo Augusto Sforça, Lucas Borges dos Santos, James Shiniti Nagai, Luciana Rossini Pinto, Marcos Guimarães de Andrade Landell, Monalisa Sampaio Carneiro, Thiago Willian Almeida Balsalobre, Marcos G. Quiles, Welison Andrade Pereira, Gabriel Rodrigues Alves Margarido, Anete Pereira de Souza
Software Mentions: 3
Published: over 5 years ago

10.1038/s41598-018-20862-8

Variation in Raw Milk Microbiota Throughout 12 Months and the Impact of Weather Conditions
Cited by: 79
Author(s): Nan Li, Yuezhu Wang, Chunping You, Jianke Ren, Chen Wan-yi, Huajun Zheng, Zhenmin Liu
Software Mentions: 3
Published: over 8 years ago

10.1371/journal.pone.0118528

A Cell-Based Systems Biology Assessment of Human Blood to Monitor Immune Responses after Influenza Vaccination
Cited by: 73
Author(s): Kristen L. Hoek, Parimal Samir, Leigh M. Howard, Xinnan Niu, Nripesh Prasad, Allison C. Galassie, Qi Liu, Tara M. Allos, Kyle A. Floyd, Yan Guo, Yu Shyr, Shawn Levy, Sebastian Joyce, Kathryn M. Edwards, Andrew J. Link
Software Mentions: 3
Published: over 11 years ago

10.3389/fpls.2018.01332

Genome-Wide Identification, Characterization, and Expression Profiling of the Legume BZR Transcription Factor Gene Family
Cited by: 28
Author(s): Yueying Li, Liangliang He, Jing Li, Jianghua Chen, Changning Liu
Software Mentions: 3
Published: about 8 years ago

10.3389/fmicb.2018.01763

Comprehensive Insights Into Composition, Metabolic Potentials, and Interactions Among Archaeal, Bacterial, and Viral Assemblages in Meromictic Lake Shunet in Siberia
Cited by: 11
Author(s): Yuting Wu, Cheng‐Yu Yang, Pei‐Wen Chiang, Chwan-Lu Tseng, Hsiu‐Hui Chiu, Isaam Saeed, Bayanmunkh Baatar, D. Yu. Rogozin, Saman K. Halgamuge, А. Г. Дегерменджи, Sen‐Lin Tang
Software Mentions: 3
Published: about 8 years ago

10.7717/peerj.740

First genomic insights into members of a candidate bacterial phylum responsible for wastewater bulking
Cited by: 97
Author(s): Yuji Sekiguchi, Akiko Ohashi, Donovan H. Parks, Toshihiro Yamauchi, Gene W. Tyson, Philip Hugenholtz
Software Mentions: 3
Published: over 11 years ago

10.3389/fmicb.2016.00941

Diversity and Distribution of Prokaryotes within a Shallow-Water Pockmark Field
Cited by: 23
Author(s): Donato Giovannelli, Giuseppe d’Errico, Federica Fiorentino, Daniele Fattorini, Francesco Regoli, Lorenzo Angeletti, Tatjana Bakran‐Petricioli, Costantino Vetriani, Mustafa Yücel, Marco Taviani, Elena Manini
Software Mentions: 3
Published: over 10 years ago

10.1038/s41598-018-28299-9

Identification of Biomarkers Based on Differentially Expressed Genes in Papillary Thyroid Carcinoma
Cited by: 38
Author(s): Jun Han, Meijun Chen, Yihan Wang, Boxuan Gong, Tianwei Zhuang, Lingyu Liang, Hong Qiao
Software Mentions: 3
Published: over 8 years ago

10.3389/fonc.2021.591893

Screening and Identification of Key Biomarkers of Gastric Cancer: Three Genes Jointly Predict Gastric Cancer
Cited by: 3
Author(s): Mengjie Shan, Ling‐Bing Meng, Peng Guo, Yuanmeng Zhang, Dexian Kong, Ya-Bin Liu
Software Mentions: 3
Published: about 5 years ago

10.1371/journal.pone.0192499

Active BRAF-V600E is the key player in generation of a sessile serrated polyp-specific DNA methylation profile
Cited by: 16
Author(s): Somaye Dehghanizadeh, Vahid Khoddami, Timothy Mosbruger, Saher Sue Hammoud, Kornelia Edes, Therese S. Berry, Michelle W. Done, Wade S. Samowitz, James A. DiSario, Daniel G. Luba, Randall W. Burt, David A. Jones
Software Mentions: 3
Published: over 8 years ago

10.1186/gb-2014-15-2-r39

Genome sequencing of the high oil crop sesame provides insight into oil biosynthesis
Cited by: 226
Author(s): Linhai Wang, Shanlin Yu, Chaobo Tong, Yingzhong Zhao, Yan Liu, Chi Song, Yanxin Zhang, Xudong Zhang, Ying Wang, Wei Hua, Donghua Li, Dan Li, Fang Li, Jingyin Yu, Chunyan Xu, Xuelian Han, Shunmou Huang, Shuaishuai Tai, Junyi Wang, Xun Xu, Yingrui Li, Liu S, Rajeev K. Varshney, Jun Wang, Xiurong Zhang
Software Mentions: 3
Published: almost 13 years ago

10.1371/journal.pone.0218938

Genome-wide comparative analysis of RNA-binding Glycine-rich protein family genes between Gossypium arboreum and Gossypium raimondii
Cited by: 11
Author(s): Yang Wei, Min Yu, Changsong Zou, Changming Lu, Daoqian Yu, Hongyan Cheng, Pengfei Jiang, Feng Xu, Youping Zhang, Qiaolian Wang, Hong Zhang, Guoli Song, Zhuqing Zhou
Software Mentions: 3
Published: over 7 years ago

10.1093/gigascience/giaa148

Chromosome-level reference genome of the European wasp spider<i>Argiope bruennichi</i>: a resource for studies on range expansion and evolutionary adaptation
Cited by: 29
Author(s): Monica M. Sheffer, Anica Hoppe, Henrik Krehenwinkel, Gabriele Uhl, Andreas W. Kuß, Lars Riff Jensen, C. J. Jensen, Rosemary G. Gillespie, Katharina J. Hoff, Stefan Prost
Software Mentions: 3
Published: almost 6 years ago

10.1186/s13059-015-0837-4

Genomic legacy of the African cheetah, Acinonyx jubatus
Cited by: 159
Author(s): Pavel Dobrynin, Shi Ping Liu, Gaik Tamazian, Zijun Xiong, Andrey A. Yurchenko, Ksenia Krasheninnikova, Sergei Kliver, Anne Schmidt‐Küntzel, Klaus‐Peter Koepfli, Warren E. Johnson, Lukas F. K. Kuderna, Raquel García-Pérez, Marc de Manuel, Ricardo Godinez, Aleksey Komissarov, Alex Makunin, Vladimir Brukhin, Wei‐Lin Qiu, Long Zhang, Fang Li, Jine Yi, Carlos A. Driscoll, Agostinho Antunes, Tarás K. Oleksyk, Eduardo Eizirik, Polina L. Perelman, Melody E. Roelke, David E. Wildt, Mark Diekhans, Tomàs Marquès‐Bonet, Laurie Marker, Jong Bhak, Jun Wang, Guojie Zhang, Stephen J. O’Brien
Software Mentions: 3
Published: almost 11 years ago

10.1371/journal.pone.0130198

Chronic Insulin Exposure Induces ER Stress and Lipid Body Accumulation in Mast Cells at the Expense of Their Secretory Degranulation Response
Cited by: 10
Author(s): William E. Greineisen, Kristina Maaetoft-Udsen, Mark Speck, Januaria M. Balajadia, Lori M. N. Shimoda, Carl Sung, Helen Turner
Software Mentions: 3
Published: about 11 years ago

10.3389/fmicb.2019.01325

Cultivation and Transcriptional Analysis of a Canonical Nitrospira Under Stable Growth Conditions
Cited by: 29
Author(s): Aniela B. Mundinger, Christopher E. Lawson, Mike S. M. Jetten, Hanna Koch, Sebastian Lücker
Software Mentions: 3
Published: over 7 years ago

10.1186/s13073-015-0127-5

Ploidy-Seq: inferring mutational chronology by sequencing polyploid tumor subpopulations
Cited by: 6
Author(s): Ankit Malhotra, Yong Wang, Jill Waters, Ken Chen, Funda Meric‐Bernstam, Ira M. Hall, Nicholas E. Navin
Software Mentions: 3
Published: almost 12 years ago

10.3389/fmicb.2021.660002

Whole-Genome Analysis of Mycobacterium avium subsp. paratuberculosis IS900Insertions Reveals Strain Type-Specific Modalities
Cited by: 6
Author(s): Cyril Condé, Marian Price-Carter, Thierry Cochard, Maxime Branger, Karen Stevenson, Richard J. Whittington, John P. Bannantine, Franck Biet
Software Mentions: 3
Published: over 5 years ago

10.1093/gbe/evt189

The Complex Intron Landscape and Massive Intron Invasion in a Picoeukaryote Provides Insights into Intron Evolution
Cited by: 27
Author(s): Bram Verhelst, Yves Van de Peer, Pierre Rouzé
Software Mentions: 3
Published: almost 13 years ago

10.1093/gbe/evz048

A High-Quality Grapevine Downy Mildew Genome Assembly Reveals Rapidly Evolving and Lineage-Specific Putative Host Adaptation Genes
Cited by: 40
Author(s): Yann Dussert, Isabelle D. Mazet, Carole Couture, Jérôme Gouzy, Marie-Christine Piron, Claire Kuchly, Olivier Bouchez, Claude Rispe, Pere Mestre, François Delmotte
Software Mentions: 3
Published: over 7 years ago

10.3389/fmicb.2017.01448

PacBio But Not Illumina Technology Can Achieve Fast, Accurate and Complete Closure of the High GC, Complex Burkholderia pseudomallei Two-Chromosome Genome
Cited by: 33
Author(s): Jade L. L. Teng, Man Lung Yeung, Elaine Chan, Lilong Jia, Chi Ho Lin, Yi Huang, Herman Tse, Samson S. Y. Wong, Pak C. Sham, Susanna K. P. Lau, Patrick C. Y. Woo
Software Mentions: 3
Published: about 9 years ago

10.3389/fmicb.2020.00082

Comparative Genomic Analysis of a Novel Strain of Taiwan Hot-Spring Cyanobacterium Thermosynechococcus sp. CL-1
Cited by: 25
Author(s): Yen I. Cheng, Li-Dek Chou, Yi Fang Chiu, Hsin Ta Hsueh, Chih Horng Kuo, Hsiu-An Chu
Software Mentions: 3
Published: over 6 years ago

10.7717/peerj.8359

A novel computational approach to the silencing of <i>Sugarcane Bacilliform Guadeloupe A Virus</i> determines potential host-derived MicroRNAs in sugarcane (<i>Saccharum officinarum</i> L.)
Cited by: 10
Author(s): Fakiha Ashraf, Muhammad Aleem Ashraf, Xiaowen Hu, Shuzhen Zhang
Software Mentions: 3
Published: over 6 years ago

10.1371/journal.pone.0125964

Genome-Wide Distribution, Organisation and Functional Characterization of Disease Resistance and Defence Response Genes across Rice Species
Cited by: 34
Author(s): S. P. Singh, Suresh Chand, Nagendra Singh, Tilak Raj Sharma
Software Mentions: 3
Published: over 11 years ago

10.1016/j.gpb.2018.06.002

5-Hydroxymethylome in Circulating Cell-free DNA as A Potential Biomarker for Non-small-cell Lung Cancer
Cited by: 51
Author(s): Ji Zhang, Xiao Han, Chun-Chun Gao, Yurong Xing, Qi Zheng, Ruijuan Liu, Yueqin Wang, Xiaojian Zhang, Ying Yang, Xiangnan Li, Bao‐Fa Sun, Xin Tian
Software Mentions: 3
Published: over 8 years ago

10.1186/s13059-018-1552-8

Comparative genomics reveals the distinct evolutionary trajectories of the robust and complex coral lineages
Cited by: 56
Author(s): Hua Ying, Ira Cooke, Susanne Sprungala, Weiwen Wang, David C. Hayward, Yurong Tang, Gavin A. Huttley, Eldon E. Ball, Sylvain Forêt, David J. Miller
Software Mentions: 3
Published: almost 8 years ago

10.7717/peerj.1310

Expression of temperature-sensitive ion channel TRPM8 in sperm cells correlates with vertebrate evolution
Cited by: 25
Author(s): Rakesh Kumar Majhi, S. K. Saha, Ashutosh Kumar, Arijit Ghosh, Nirlipta Swain, Luna Goswami, Pratyush P. Mohapatra, Apratim Maity, Vivek Kumar Sahoo, Abhishek Kumar, Chandan Goswami
Software Mentions: 3
Published: almost 11 years ago

10.1016/j.gpb.2018.10.004

C: Consensus Cancer Driver Gene Caller
Cited by: 2
Author(s): Chenyu Zhu, Chi Zhou, Yun-Qin Chen, Albert Yuh-Jer Shen, Zong-Ming Guo, Zhaoyi Yang, Xiangyun Ye, Shen Qu, Jia Wei, Qi Liu
Software Mentions: 3
Published: over 7 years ago

10.3389/fmicb.2020.01142

Underlying Mechanism of Wild Radix pseudostellariae in Tolerance to Disease Under the Natural Forest Cover
Cited by: 10
Author(s): Hongmiao Wu, Jinshen Xia, Xianjin Qin, Huiming Wu, Shengkai Zhang, Yanlin Zhao, Christopher Rensing, Wenxiong Lin
Software Mentions: 3
Published: over 6 years ago

10.3389/fmicb.2018.02668

Ancestrality and Mosaicism of Giant Viruses Supporting the Definition of the Fourth TRUC of Microbes
Cited by: 41
Author(s): Philippe Colson, Anthony Levasseur, Bernard La Scola, Vikas Sharma, Arshan Nasir, Pierre Pontarotti, Gustavo Caetano‐Anollés, Didier Raoult
Software Mentions: 3
Published: almost 8 years ago

10.3389/fmicb.2019.01446

Pan-Genomic and Polymorphic Driven Prediction of Antibiotic Resistance in Elizabethkingia
Cited by: 13
Author(s): Bryan Naidenov, Alexander Lim, Karyn Willyerd, Nathanial Torres, William L. Johnson, Hong Jin Hwang, Peter R. Hoyt, John E. Gustafson, Charles Chen
Software Mentions: 3
Published: over 7 years ago

10.3389/fmicb.2019.00805

Prevalence of Antibiotic and Heavy Metal Resistance Determinants and Virulence-Related Genetic Elements in Plasmids of Staphylococcus aureus
Cited by: 23
Author(s): Michał Bukowski, Rafał Piwowarczyk, Anna Mądry, Rafal Zagorski-Przybylo, Marcin Hydzik, Benedykt Władyka
Software Mentions: 3
Published: over 7 years ago

10.1186/gb-2012-13-8-r74

Gene functionalities and genome structure in Bathycoccus prasinos reflect cellular specializations at the base of the green lineage
Cited by: 139
Author(s): Hervé Moreau, Bram Verhelst, Arnaud Couloux, Évelyne Derelle, Stéphane Rombauts, Nigel Grimsley, Michiel Van Bel, Julie Poulain, Michaël Katinka, Martin F. Hohmann‐Marriott, Gwenaël Piganeau, Pierre Rouzé, Corinne Da Silva, Patrick Wincker, Yves Van de Peer, Klaas Vandepoele
Software Mentions: 3
Published: almost 15 years ago

10.1186/s13059-019-1631-5

Genomic introgression through interspecific hybridization counteracts genetic bottleneck during soybean domestication
Cited by: 37
Author(s): Xutong Wang, Liyang Chen, Jianxin Ma
Software Mentions: 3
Published: over 7 years ago

10.1093/gbe/evaa063

An Annotated Chromosome-Level Reference Genome of the Red-Eared Slider Turtle (Trachemys scripta elegans)
Cited by: 23
Author(s): W. Brian Simison, James F. Parham, Theodore J. Papenfuss, Athena Lam, James Henderson
Software Mentions: 3
Published: over 6 years ago

10.1093/gigascience/giy044

Whole-genome de novo sequencing reveals unique genes that contributed to the adaptive evolution of the Mikado pheasant
Cited by: 9
Author(s): Chien‐Yueh Lee, Ping-Han Hsieh, Li-Mei Chiang, Amrita Chattopadhyay, Kuanyi Li, Yi-Fang Lee, Tzu-Pin Lu, Liang‐Chuan Lai, Eric S. Lin, Hsinyu Lee, Shih‐Torng Ding, Mong‐Hsun Tsai, Chien‐Yu Chen, Eric Y. Chuang
Software Mentions: 3
Published: over 8 years ago

10.1186/s13099-016-0084-6

Genome sequence of Escherichia coli NCCP15653, a group D strain isolated from a diarrhea patient
Cited by: 2
Author(s): Min Jung Kwak, Myoung Soo Kim, Soon Kyeong Kwon, Seung Hak Cho, Jihyun F. Kim
Software Mentions: 3
Published: over 10 years ago

10.3389/fmicb.2020.01930

New Plasmodium vivax Genomes From the China-Myanmar Border
Cited by: 5
Author(s): Awtum Brashear, Adam C Huckaby, Qi Fan, Luke J Dillard, Yubing Hu, Yuling Li, Yan Zhao, Zenglei Wang, Yaming Cao, Jun Miao, Jennifer L. Guler, Liwang Cui
Software Mentions: 3
Published: about 6 years ago

10.3389/fmicb.2021.682356

Comparative Transcriptome and Endophytic Bacterial Community Analysis of Morchella conica SH
Cited by: 3
Author(s): Bei Lü, Guo Wu, Yu Sun, Liang S. Zhang, Xiao Wu, Wei Jiang, Peng Li, Yan Huang, Jin B. Wang, Yong Zhao, Hua Liu, Li Song, Qin Mo, Ai H. Pan, Yan Yang, Xuan Long, Wei Cui, Chao Zhang, Xu Wang, Xue Tang
Software Mentions: 3
Published: about 5 years ago

10.3389/fpls.2020.00176

Performance of Mapping Approaches for Whole-Genome Bisulfite Sequencing Data in Crop Plants
Cited by: 14
Author(s): Claudius Grehl, M. Wagner, Ioana Lemnian, Bruno Glaser, Ivo Große
Software Mentions: 3
Published: over 6 years ago

10.1038/s41438-020-0269-5

A high-quality genome provides insights into the new taxonomic status and genomic characteristics of Cladopus chinensis (Podostemaceae)
Cited by: 9
Author(s): Ting Xue, Xinqing Zheng, Duo Chen, Limin Liang, Nan Chen, Zhen Huang, Wenfang Fan, Jiannan Chen, Chengsong Wan, Shuai Chen, Jinmao Zhu, Binghua Chen, Xingtan Zhang, Youqiang Chen
Software Mentions: 3
Published: over 6 years ago

10.1093/gigascience/giab020

A chromosome-level genome assembly for the Pacific oyster <i>Crassostrea gigas</i>
Cited by: 70
Author(s): Carolina Peñaloza, Alejandro P. Gutiérrez, Lél Eöry, Shan Wang, Ximing Guo, Alan Archibald, Tim P. Bean, Ross D. Houston
Software Mentions: 3
Published: over 5 years ago

10.1371/journal.pone.0184119

Discovery of numerous novel small genes in the intergenic regions of the Escherichia coli O157:H7 Sakai genome
Cited by: 25
Author(s): Sarah M. Hücker, Zachary Ardern, Tatyana Goldberg, Andrea Schafferhans, Michael Bernhofer, Gisle Vestergaard, Chase W. Nelson, Michael Schloter, Burkhard Rost, Siegfried Scherer, Klaus Neuhaus
Software Mentions: 3
Published: about 9 years ago

10.3389/fpls.2019.00918

A High-Density Linkage Map of the Forage Grass Eragrostis curvula and Localization of the Diplospory Locus
Cited by: 10
Author(s): Diego Zappacosta, Jimena Gallardo, José Luís Carballo, M Meier, Juan Manuel Rodrigo, Cristian Gallo, Juan Pablo Selva, Juliana Stein, Juan Pablo Amelio Ortiz, Emidio Albertini, Viviana Echenique
Software Mentions: 3
Published: over 7 years ago

10.3389/fpls.2019.01514

Genome-Wide Comparisons of Mutations Induced by Carbon-Ion Beam and Gamma-Rays Irradiation in Rice via Resequencing Multiple Mutants
Cited by: 23
Author(s): Gangyi Yang, Wenlong Luo, Jian Zhang, Xian-cheng Yan, Yuguo Du, Libin Zhou, Wenjian Li, Hui Wang, Zhiqiang Chen, Tao Guo
Software Mentions: 3
Published: almost 7 years ago

10.3389/fpls.2016.01186

Origination, Expansion, Evolutionary Trajectory, and Expression Bias of AP2/ERF Superfamily in Brassica napus
Cited by: 31
Author(s): Xiaoming Song, Jinpeng Wang, Xiao Ma, Yuxian Li, Tianyu Lei, Li Wang, Weina Ge, Di Guo, Zhenyi Wang, Chunjin Li, Zhao Jian-jun, Xiyin Wang
Software Mentions: 3
Published: about 10 years ago

10.3389/fpls.2021.640163

A 598-bp InDel Variation in the Promoter Region of Bna.SOC1.A05 Is Predominantly Present in Winter Type Rapeseeds
Cited by: 1
Author(s): Sarah Matar, Siegbert Melzer
Software Mentions: 3
Published: over 5 years ago

10.1038/s41598-017-17203-6

Genome-wide analysis of SSR and ILP markers in trees: diversity profiling, alternate distribution, and applications in duplication
Cited by: 15
Author(s): Xinnian Xia, Lin Lin Luan, Gengsheng Qin, Yu Li, Zhi Wei Wang, Wan Chen Dong, Youjian Song, Yongli Qiao, Xian Sheng Zhang, Long Yang
Software Mentions: 3
Published: almost 9 years ago

10.3389/fpls.2018.00771

Molecular Profiling of Pierce’s Disease Outlines the Response Circuitry of Vitis vinifera to Xylella fastidiosa Infection
Cited by: 28
Author(s): Paulo A. Zaini, Rafael Nascimento, Hossein Gouran, Dario Cantu, Sandeep Chakraborty, My L. Phu, Luíz Ricardo Goulart, Abhaya M. Dandekar
Software Mentions: 3
Published: over 8 years ago

10.1038/s41598-019-39286-z

Comprehensive identification of the full-length transcripts and alternative splicing related to the secondary metabolism pathways in the tea plant (Camellia sinensis)
Cited by: 41
Author(s): Dahe Qiao, Chun Yang, Juan Chen, Yan Guo, Yán Li, Suzhen Niu, Kemei Cao, Zhengwu Chen
Software Mentions: 3
Published: over 7 years ago

10.1038/s41598-018-22237-5

Gene expression models based on a reference laboratory strain are poor predictors of Mycobacterium tuberculosis complex transcriptional diversity
Cited by: 13
Author(s): Álvaro Chiner‐Oms, Fernando Gónzález-Candelas, Iñaki Comas
Software Mentions: 3
Published: over 8 years ago

10.3389/fpls.2020.545042

Molecular Evolution and Expansion of the KUP Family in the Allopolyploid Cotton Species Gossypium hirsutum and Gossypium barbadense
Cited by: 3
Author(s): Kai Fan, Zhijun Mao, Jiaxin Zheng, Yunrui Chen, Zhaowei Li, Weiwei Lin, Yongqiang Zhang, Jinwen Huang, Wenxiong Lin
Software Mentions: 3
Published: about 6 years ago

10.3389/fpls.2016.01857

Identification and Network-Enabled Characterization of Auxin Response Factor Genes in Medicago truncatula
Cited by: 10
Author(s): David J. Burks, Rajeev K. Azad
Software Mentions: 3
Published: almost 10 years ago

10.3389/fpls.2014.00789

Genome-wide analysis and expression profiling suggest diverse roles of GH3 genes during development and abiotic stress responses in legumes
Cited by: 38
Author(s): Vikash Singh, Mukesh Jain, Rohini Garg
Software Mentions: 3
Published: over 11 years ago

10.3389/fimmu.2017.01063

Gut REG3γ-Associated Lactobacillus Induces Anti-inflammatory Macrophages to Maintain Adipose Tissue Homeostasis
Cited by: 16
Author(s): Yugang Huang, Houbao Qi, Zhiqian Zhang, Enlin Wang, Huan Yun, Hui Yan, Xiaomin Su, Yingquan Liu, Zenzen Tang, Yuan Gao, Wencong Shang, Zhou Jiang, Tianze Wang, Yongzhe Che, Yuan Zhang, Rongcun Yang
Software Mentions: 3
Published: about 9 years ago

10.1523/ENEURO.0205-16.2016

Graph Theoretic and Motif Analyses of the Hippocampal Neuron Type Potential Connectome
Cited by: 24
Author(s): Colin Rees, Diek W. Wheeler, D. R. Hamilton, Charise M. White, Alexander O. Komendantov, Giorgio A. Ascoli
Software Mentions: 3
Published: almost 10 years ago

10.3389/fpls.2021.721253

Genome-Wide Identification, Evolution, and Expression Analysis of LBD Transcription Factor Family in Bread Wheat (Triticum aestivum L.)
Cited by: 12
Author(s): Zhenyu Wang, Ruoyu Zhang, Yue Cheng, Pengzheng Lei, Weining Song, Wenbin Zheng, Xiaojun Nie
Software Mentions: 3
Published: about 5 years ago

10.3389/fpls.2015.01247

Genome-Wide Analysis of the AP2/ERF Superfamily Genes and their Responses to Abiotic Stress in Medicago truncatula
Cited by: 84
Author(s): Yongjun Shu, Ying Liu, Jun Zhang, Lili Song, Changhong Guo
Software Mentions: 3
Published: over 10 years ago

10.1128/JVI.02083-19

Bottleneck Size-Dependent Changes in the Genetic Diversity and Specific Growth Rate of a Rotavirus A Strain
Cited by: 11
Author(s): Syun suke Kadoya, Syun-ichi Urayama, Takuro Nunoura, Miho Hirai, Yoshihiro Takaki, Masaaki Kitajima, Toyoko Nakagomi, Osamu Nakagomi, Satoshi Okabe, Osamu Nishimura, Daisuke Sano
Software Mentions: 3
Published: over 6 years ago

10.18632/oncotarget.26225

Transcriptomic and genomic profiling of early-stage ovarian carcinomas associated with histotype and overall survival
Cited by: 10
Author(s): Hanna Engqvist, Toshima Z. Parris, Elisabeth Werner Rönnerman, Elin Söderberg, Jana Biermann, Claudia Mateoiu, Karin Sundfeldt, Anikó Kovács, Per Karlsson, Khalil Helou
Software Mentions: 3
Published: about 8 years ago

10.1002/path.4230

Distinct evolutionary trajectories of primary high‐grade serous ovarian cancers revealed through spatial mutational profiling
Cited by: 351
Author(s): Ali Bashashati, Gavin Ha, Alicia A. Tone, Jiarui Ding, Leah M Prentice, Andrew Roth, Jamie Rosner, Karey Shumansky, Steve E. Kalloger, Janine Senz, Winnie Yang, Melissa K. McConechy, Nataliya Melnyk, Michael S. Anglesio, Margaret Luk, Kane Tse, Thomas Zeng, Richard A. Moore, Yongjun Zhao, Marco A. Marra, Blake Gilks, Stephen Yip, David G. Huntsman, Jessica N. McAlpine, Sohrab P. Shah
Software Mentions: 3
Published: about 13 years ago

10.3389/fgene.2021.713224

Genome-Wide Identification and Expression Analysis of Metal Tolerance Protein Gene Family in Medicago truncatula Under a Broad Range of Heavy Metal Stress
Cited by: 18
Author(s): Ahmed H. El-Sappah, Rania G. Elbaiomy, Ahmed S. Elrys, Yu Wang, Yumin Zhu, Qiulan Huang, Yan Ke, Xingbo Zhao, Yun Li, Khaled A. El‐Tarabily, Jia Li
Software Mentions: 3
Published: about 5 years ago

10.1186/s12967-021-02845-y

Identification of an immune classification for cervical cancer and integrative analysis of multiomics data
Cited by: 7
Author(s): Xintong Lyu, Guang Li, Qiao Qiao
Software Mentions: 3
Published: over 5 years ago

10.1371/journal.pone.0088229

Comparative Variation within the Genome of Campylobacter jejuni NCTC 11168 in Human and Murine Hosts
Cited by: 29
Author(s): Dallas Thomas, Abdul G. Lone, L. Brent Selinger, Eduardo N. Taboada, Richard R. E. Uwiera, D. Wade Abbott, G. Douglas Inglis
Software Mentions: 3
Published: over 12 years ago

10.3390/ijms22169002

Insights into the Host Specificity of a New Oomycete Root Pathogen, Pythium brassicum P1: Whole Genome Sequencing and Comparative Analysis Reveals Contracted Regulation of Metabolism, Protein Families, and Distinct Pathogenicity Repertoire
Cited by: 2
Author(s): Mojtaba Mohammadi, Eric A. Smith, M. E. Stanghellini, Rakesh Kaundal
Software Mentions: 3
Published: about 5 years ago

10.3389/fonc.2018.00183

Genome-Wide Analysis of Interchromosomal Interaction Probabilities Reveals Chained Translocations and Overrepresentation of Translocation Breakpoints in Genes in a Cutaneous T-Cell Lymphoma Cell Line
Cited by: 8
Author(s): Anne Steininger, Grit Ebert, B Becker, Chalid Assaf, Markus Möbs, Christian A. Schmidt, Piotr Grabarczyk, Lars Riff Jensen, Grzegorz K. Przybylski, Matthias Port, Andreas W. Kuß, Reinhard Ullmann
Software Mentions: 3
Published: over 8 years ago

10.1080/20002297.2020.1773067

A case study of salivary microbiome in smokers and non-smokers in Hungary: analysis by shotgun metagenome sequencing
Cited by: 14
Author(s): Roland Wirth, Gergely Maróti, Róbert Mihók, Donát Simon-Fiala, Márk Antal, Bernadett Pap, Anett Demcsák, János Minárovits, Kornél L. Kovács
Software Mentions: 3
Published: almost 7 years ago

10.3390/ijms22094919

Genome-Wide Identification and Expression Profiling of the WOX Gene Family in Citrus sinensis and Functional Analysis of a CsWUS Member
Cited by: 9
Author(s): Faiza Shafique Khan, Ren‐Fang Zeng, Zhi-Meng Gan, Jin‐Zhi Zhang, Chun-Gen Hu
Software Mentions: 3
Published: over 5 years ago

10.3390/ijms22094326

Delineating the Tnt1 Insertion Landscape of the Model Legume Medicago truncatula cv. R108 at the Hi-C Resolution Using a Chromosome-Length Genome Assembly
Cited by: 10
Author(s): Parwinder Kaur, Christopher Lui, Olga Dudchenko, Raja Sekhar Nandety, Bhavna Hurgobin, Melanie Pham, E Aiden, Jiangqi Wen, Kirankumar S. Mysore
Software Mentions: 3
Published: over 5 years ago

10.3390/ijms22147401

Analysis of Immune Associated Co-Expression Networks Reveals Immune-Related Long Non-Coding RNAs during MI in the Presence and Absence of HDC
Cited by: 2
Author(s): Zhiwei Zhang, Saidan Ding, Xiangdong Yang, Junbo Ge
Software Mentions: 3
Published: over 5 years ago

10.18632/oncotarget.13937

Conditionally reprogrammed normal and primary tumor prostate epithelial cells: a novel patient-derived cell model for studies of human prostate cancer
Cited by: 50
Author(s): Olga Timofeeva, Nancy Palechor-Ceron, Guanglei Li, Hang Yuan, Ewa Krawczyk, Xiaogang Zhong, Geng Li, Geeta Upadhyay, Aleksandra Dakić, Songtao Yu, Shuang Fang, Sujata Maiti Choudhury, Xueping Zhang, Andrew Ju, Myeong-Seon Lee, Dong Han, Youngmi Ji, Yong Hou, Yun‐Ling Zheng, Chris Albanese, Johng S. Rhim, Richard Schlegel, Anatoly Dritschilo, Xuefeng Li
Software Mentions: 3
Published: almost 10 years ago

10.3389/fgene.2014.00319

Bioremediation in marine ecosystems: a computational study combining ecological modeling and flux balance analysis
Cited by: 11
Author(s): Marianna Taffi, Nicola Paoletti, Claudio Angione, Sandra Pucciarelli, Mauro Marini, Píetro Lió
Software Mentions: 3
Published: about 12 years ago

10.3389/fnins.2017.00358

Altered Functional Connectivity Following an Inflammatory White Matter Injury in the Newborn Rat: A High Spatial and Temporal Resolution Intrinsic Optical Imaging Study
Cited by: 7
Author(s): Edgar Guevara, Wyston C. Pierre, Camille Tessier, Luis Akakpo, Irène Londono, Frédéric Lesage, Gregory A. Lodygensky
Software Mentions: 3
Published: over 9 years ago

10.3390/ijms21238934

Identification and Characterization of PLATZ Transcription Factors in Wheat
Cited by: 20
Author(s): Yuxin Fu, Mengping Cheng, Maolian Li, Xiaojiang Guo, Yongrui Wu, Jirui Wang
Software Mentions: 3
Published: almost 6 years ago

10.1111/tpj.14538

Transposons played a major role in the diversification between the closely related almond and peach genomes: results from the almond genome sequence
Cited by: 82
Author(s): Tyler Alioto, Konstantinos G. Alexiou, Amélie Bardil, Fabio Barteri, Raúl Castanera, Fernando Cruz, Amit Dhingra, Henri Duval, Angel V. Fernández i Martí, Leonor Frías, Beatriz Galán, José Luis Garcı́a, Werner Howad, Jèssica Gómez‐Garrido, Marta Gut, Irene Julca, Jordi Morata, Pere Puigdomènech, Paolo Ribeca, María José Rubio Cabetas, Anna Vlasova, M. Wirthensohn, Jordi García-Más, Toni Gabaldón, Josep M. Casacuberta, Pere Arús
Software Mentions: 3
Published: almost 7 years ago

10.3390/ijms21103660

Genome-Wide Dissection of the CRF Gene Family in Brassica napus Indicates that BnaCRF8s Specifically Regulate Root Architecture and Phosphate Homeostasis against Phosphate Fluctuation in Plants
Cited by: 7
Author(s): Sheliang Wang, Hao Zhang, Lei Shi, Fangsen Xu, Guangda Ding
Software Mentions: 3
Published: over 6 years ago

10.3390/ijms22042060

Long-Read Sequencing Improves the Detection of Structural Variations Impacting Complex Non-Coding Elements of the Genome
Cited by: 13
Author(s): Ghausia Begum, Ammar Albanna, Asma Bankapur, Nasna Nassir, Richa Tambi, Bakhrom K. Berdiev, Hosneara Akter, Noushad Karuvantevida, Barbara Kellam, Deena Alhashmi, Wilson W L Sung, Bhooma Thiruvahindrapuram, Alawi A. Alsheikh‐Ali, Stephen W. Scherer, Mohammed Uddin
Software Mentions: 3
Published: over 5 years ago

10.3390/ijms20184593

Identification and Expression Analysis of GRAS Transcription Factors to Elucidate Candidate Genes Related to Stolons, Fruit Ripening and Abiotic Stresses in Woodland Strawberry (Fragaria vesca)
Cited by: 16
Author(s): Hong Chen, Huihui Li, Xiaoyan Lu, Longzheng Chen, Jing Liu, Hongmiao Wu
Software Mentions: 3
Published: about 7 years ago

10.3390/s20123362

The Role of Dactylis Glomerata and Diesel Oil in the Formation of Microbiome and Soil Enzyme Activity
Cited by: 13
Author(s): Agata Borowik, Jadwiga Wyszkowska, M. Kucharski, J. Kucharski
Software Mentions: 3
Published: over 6 years ago

10.1038/s41598-021-88029-6

Transcriptomic analysis to infer key molecular players involved during host response to NDV challenge in Gallus gallus (Leghorn &amp; Fayoumi)
Cited by: 4
Author(s): Venkata Krishna Vanamamalai, Priyanka Garg, Gautham Kolluri, Ravi Kumar Gandham, Itishree Jali, Shailesh Sharma
Software Mentions: 3
Published: over 5 years ago

10.3389/fninf.2018.00052

BRANT: A Versatile and Extendable Resting-State fMRI Toolkit
Cited by: 49
Author(s): Kaibin Xu, Yong Liu, Yafeng Zhan, Jiaji Ren, Tianzi Jiang
Software Mentions: 3
Published: about 8 years ago

10.1038/s41598-021-89146-y

Macrosynteny analysis between Lentinula edodes and Lentinula novae-zelandiae reveals signals of domestication in Lentinula edodes
Cited by: 3
Author(s): Chris Smith
Software Mentions: 3
Published: over 5 years ago

10.3390/ijms21020483

Subchromosome-Scale Nuclear and Complete Mitochondrial Genome Characteristics of Morchella crassipes
Cited by: 25
Author(s): Wei Liu, Yingli Cai, Qianqian Zhang, Shu Fang, Lianfu Chen, Xiaolong Ma, Yinbing Bian
Software Mentions: 3
Published: over 6 years ago

10.3389/fneur.2020.00184

Identification of Co-expressed Genes Between Atrial Fibrillation and Stroke
Cited by: 13
Author(s): Yanfei Zhang, Ling‐Bing Meng, Meng-lei Hao, Jiao Yang, Tong Zou
Software Mentions: 3
Published: over 6 years ago

10.3389/fmicb.2017.01009

Comparative Genome Analysis Provides Insights into Both the Lifestyle of Acidithiobacillus ferrivorans Strain CF27 and the Chimeric Nature of the Iron-Oxidizing Acidithiobacilli Genomes
Cited by: 8
Author(s): Tam Tran, Sophie Mangenot, Ghislaine Magdelenat, Emilie Payen, Zoé Rouy, Hassiba Belahbib, Barry M. Grail, D. Barrie Johnson, Violaine Bonnefoy, Emmanuel Talla
Software Mentions: 3
Published: over 9 years ago