pypi: bowtie | Projects | Ecosyste.ms: Papers

10.1186/1471-2164-14-273

Six novel Y chromosome genes in Anophelesmosquitoes discovered by independently sequencing males and females
Cited by: 105
Author(s): Andrew Brantley Hall, Yumin Qi, Vladimir A. Timoshevskiy, Maria V. Sharakhova, Igor V. Sharakhov, Zhijian Tu
Software Mentions: 2
Published: over 11 years ago

10.1186/s12864-015-1456-x

Distinguishing low frequency mutations from RT-PCR and sequence errors in viral deep sequencing data
Cited by: 48
Author(s): Richard Orton, Caroline F. Wright, Marco J. Morelli, David J. King, David Paton, Donald P. King, Daniel T. Haydon
Software Mentions: 2
Published: over 9 years ago

10.1186/1471-2164-14-704

Integrating microRNA and mRNA expression profiling in Symbiodinium microadriaticum, a dinoflagellate symbiont of reef-building corals
Cited by: 92
Author(s): Sebastian Baumgarten, Till Bayer, Manuel Aranda, Yi Jin Liew, Adrian R. Carr, Gos Micklem, Christian R. Voolstra
Software Mentions: 2
Published: about 11 years ago

10.1186/s12864-020-6730-x

Construction of a high-density genetic map and mapping of growth related QTLs in the grass carp (Ctenopharyngodon idellus)
Cited by: 18
Author(s): Xiaoli Huang, Yanxin Jiang, Wanting Zhang, Yingyin Cheng, Yaping Wang, Xiaocui Ma, You Duan, L. Xia, Yaxin Chen, Nan Wu, Minjun Shi, Xiao-Qin Xia
Software Mentions: 2
Published: over 4 years ago

10.1186/s12864-015-1577-2

Neural transcriptome reveals molecular mechanisms for temporal control of vocalization across multiple timescales
Cited by: 29
Author(s): Ni Feng, Daniel J. Fergus, Andrew H. Bass
Software Mentions: 2
Published: over 9 years ago

10.1186/s12864-017-3570-4

Leaf transcriptome analysis of a subtropical evergreen broadleaf plant, wild oil-tea camellia (Camellia oleifera), revealing candidate genes for cold acclimation
Cited by: 41
Author(s): Jiaming Chen, Xiaoqiang Yang, Xiaomao Huang, Shi-Hua Duan, Chengnian Long, Jiakuan Chen, Jun Rong
Software Mentions: 2
Published: over 7 years ago

10.1186/s12864-015-2147-3

Combined metabolome and transcriptome profiling provides new insights into diterpene biosynthesis in S. pomifera glandular trichomes
Cited by: 38
Author(s): Fotini A. Trikka, Alexandros K. Nikolaidis, Codruţa Ignea, Aphrodite Tsaballa, Leto‐Aikaterini Tziveleka, Efstathia Iοannou, Vassilios Roussis, Eleni A. Stea, Dragana Božić, Anagnostis Argiriou, Angelos K. Kanellis, Sotirios C. Kampranis, Antonios M. Makris
Software Mentions: 2
Published: about 9 years ago

10.1186/s12864-015-1965-7

Deep sequencing shows microRNA involvement in bovine mammary gland adaptation to diets supplemented with linseed oil or safflower oil
Cited by: 56
Author(s): Ran Li, Frédéric Beaudoin, Adolf A. Ammah, Nathalie Bissonnette, C. Benchaar, Xin Zhao, Chuzhao Lei, Eveline M. Ibeagha‐Awemu
Software Mentions: 2
Published: about 9 years ago

10.1186/s12864-017-3549-1

Effect of light and prey availability on gene expression of the mixotrophic chrysophyte, Ochromonas sp.
Cited by: 25
Author(s): Alle A. Y. Lie, Zhenfeng Liu, Ramón Terrado, Avery O. Tatters, Karla B. Heidelberg, David A. Caron
Software Mentions: 2
Published: almost 8 years ago

10.1186/s12864-019-5521-8

Identification and profiling of narrow-leafed lupin (Lupinus angustifolius) microRNAs during seed development
Cited by: 16
Author(s): Kathleen D. DeBoer, Su Melser, Jana Sperschneider, Lars G. Kamphuis, Gagan Garg, Lingling Gao, Karen M. Frick, Karam B. Singh
Software Mentions: 2
Published: almost 6 years ago

10.1186/s12864-018-4932-2

RNA-seq assistant: machine learning based methods to identify more transcriptional regulated genes
Cited by: 36
Author(s): Likai Wang, Yanpeng Xi, Sibum Sung, Hong Qiao
Software Mentions: 2
Published: over 6 years ago

10.1186/s12864-015-1253-6

Transcriptome analysis of northern elephant seal (Mirounga angustirostris) muscle tissue provides a novel molecular resource and physiological insights
Cited by: 27
Author(s): Jane Khudyakov, Likit Preeyanon, Cory D. Champagne, Rudy M. Ortiz, Daniel E. Crocker
Software Mentions: 2
Published: almost 10 years ago

10.1186/s12864-016-2514-8

Small RNA and PARE sequencing in flower bud reveal the involvement of sRNAs in endodormancy release of Japanese pear (Pyrus pyrifolia 'Kosui')
Cited by: 21
Author(s): Songling Bai, Takanori Saito, Akiko Ito, Phạm Anh Tuấn, Ying Xu, Yuanwen Teng, Takaya Moriguchi
Software Mentions: 2
Published: over 8 years ago

10.1186/1471-2164-16-S13-S6

Comparison of American mink embryonic stem and induced pluripotent stem cell transcriptomes
Cited by: 24
Author(s): А. Г. Мензоров, N. M. Matveeva, Marios Nektarios Markakis, Veniamin Fishman, K. Christensen, А. А. Хабарова, Inna E. Pristyazhnyuk, Elena A. Kizilova, Susanna Cirera, Razvan Anistoroaei, O. L. Serov
Software Mentions: 2
Published: almost 9 years ago

10.1186/s12864-015-1492-6

Histone modifications induced by MDV infection at early cytolytic and latency phases
Cited by: 13
Author(s): Apratim Mitra, Juan Luo, Yanghua He, Yue Gu, Huanmin Zhang, Keji Zhao, Kairong Cui, Jiuzhou Song
Software Mentions: 2
Published: over 9 years ago

10.1186/s12864-018-4533-0

Histone modification profiling in breast cancer cell lines highlights commonalities and differences among subtypes
Cited by: 56
Author(s): Yuanxin Xi, Jiejun Shi, Wenqian Li, Kaori Tanaka, Kendra L. Allton, Dana Richardson, Jing Li, Hector L. Franco, Anusha Nagari, Venkat S. Malladi, Luis Della Coletta, Melissa S. Simper, Khandan Keyomarsi, Jianjun Shen, Mark T. Bedford, Xiaobing Shi, Michelle C. Barton, W. Lee Kraus, Wei Li, Sharon Y.R. Dent
Software Mentions: 2
Published: almost 7 years ago

10.1186/s12864-015-1251-8

Deep RNA sequencing reveals a high frequency of alternative splicing events in the fungus Trichoderma longibrachiatum
Cited by: 33
Author(s): Bin-Bin Xie, Dan Li, Wenhao Shi, Qi‐Long Qin, Xiaowei Wang, Jin-Cheng Rong, Caiyun Sun, Feng Huang, Xiying Zhang, Xiaowei Dong, Xiu-Lan Chen, Biao Zhou, Yuzhong Zhang, Xiao‐Yan Song
Software Mentions: 2
Published: almost 10 years ago

10.1186/s12864-018-4463-x

The aquatic animals’ transcriptome resource for comparative functional analysis
Cited by: 4
Author(s): Chih‐Hung Chou, Hsi‐Yuan Huang, Wei‐Chih Huang, Sheng Da Hsu, Chung-Der Hsiao, Chia-Yu Liu, Yu-Hung Chen, Yuchen Liu, Wei Huang, Meng-Lin Lee, Yi‐Chang Chen, Hsien-Da Huang
Software Mentions: 2
Published: over 6 years ago

10.1186/1471-2164-15-1042

Role of chromatin and transcriptional co-regulators in mediating p63-genome interactions in keratinocytes
Cited by: 36
Author(s): Isha Sethi, Satrajit Sinha, Michael Buck
Software Mentions: 2
Published: almost 10 years ago

10.1186/s12864-016-3360-4

Dhurrin metabolism in the developing grain of Sorghum bicolor (L.) Moench investigated by metabolite profiling and novel clustering analyses of time-resolved transcriptomic data
Cited by: 51
Author(s): Lasse Nielsen, Peter Stuart, Martina Pičmanová, Simon Rasmussen, Carl Erik Olsen, Jesper Harholt, Birger Lindberg Møller, Nanna Bjarnholt
Software Mentions: 2
Published: almost 8 years ago

10.1186/1471-2164-15-190

Immunomic, genomic and transcriptomic characterization of CT26 colorectal carcinoma
Cited by: 263
Author(s): John C. Castle, Martin Löewer, Sebastian Boegel, Jos de Graaf, Christian Bender, Arbel D. Tadmor, Valesca Boisguérin, Thomas Bukur, Patrick Sorn, Claudia Paret, Mustafa Diken, Sebastian Kreiter, Özlem Türeci, Uğur Şahin
Software Mentions: 2
Published: almost 11 years ago

10.1186/1471-2164-15-20

Sex specific expression and distribution of small RNAs in papaya
Cited by: 21
Author(s): Rishi Aryal, Guru Jagadeeswaran, Yun Zheng, Qingyi Yu, Ramanjulu Sunkar, Ray Ming
Software Mentions: 2
Published: almost 11 years ago

10.1186/1471-2164-14-703

Large-scale polymorphism discovery in macaque G-protein coupled receptors
Cited by: 6
Author(s): Dharmendra B. Goswami, Lisa M. Ogawa, Joshua Ward, Gregory M. Miller, Eric J. Vallender
Software Mentions: 2
Published: about 11 years ago

10.1186/s12864-017-3963-4

Genome-wide identification of soybean microRNA responsive to soybean cyst nematodes infection by deep sequencing
Cited by: 48
Author(s): Bin Tian, Shichen Wang, T. C. Todd, Charles D. Johnson, Guiliang Tang, Harold N. Trick
Software Mentions: 2
Published: over 7 years ago

10.1186/1471-2164-15-1186

A hyper-dynamic nature of bivalent promoter states underlies coordinated developmental gene expression modules
Cited by: 11
Author(s): Akshay Shah, Anja R. Oldenburg, Philippe Collas
Software Mentions: 2
Published: almost 10 years ago

10.1186/s12864-015-1355-1

Learning-induced gene expression in the heads of two Nasonia species that differ in long-term memory formation
Cited by: 17
Author(s): Katja M. Hoedjes, Hans M. Smid, Elio Schijlen, Louise E. M. Vet, Joke J.F.A. van Vugt
Software Mentions: 2
Published: over 9 years ago

10.1186/1471-2164-13-480

Genome-wide association between DNA methylation and alternative splicing in an invertebrate
Cited by: 142
Author(s): Kevin Flores, Florian Wolschin, Jason J. Corneveaux, April N. Allen, Matthew J. Huentelman, Gro V. Amdam
Software Mentions: 2
Published: almost 13 years ago

10.1186/s12879-016-1737-2

Whole genome sequencing reveals mycobacterial microevolution among concurrent isolates from sputum and blood in HIV infected TB patients
Cited by: 7
Author(s): Willy Ssengooba, Bouke C. de Jong, Moses Joloba, Frank Cobelens, Conor J. Meehan
Software Mentions: 2
Published: over 8 years ago

10.1186/s12920-016-0220-7

Immunoseq: the identification of functionally relevant variants through targeted capture and sequencing of active regulatory regions in human immune cells
Cited by: 24
Author(s): Andréanne Morin, Tony Kwan, Bing Ge, Louis Létourneau, Masashi Ban, Karolina Tandre, Maxime Caron, Johanna K. Sandling, Jonas Carlsson, Guillaume Bourque, Catherine Laprise, Alexandre Montpetit, Ann‐Christine Syvänen, Lars Rönnblom, Stephen Sawcer, Mark Lathrop, Tomi Pastinen
Software Mentions: 2
Published: about 8 years ago

10.1186/1471-2180-13-302

Comparison of the Legionella pneumophila population structure as determined by sequence-based typing and whole genome sequencing
Cited by: 43
Author(s): Anthony Underwood, Garan Jones, M. Mentasti, Norman K. Fry, Timothy G. Harrison
Software Mentions: 2
Published: almost 12 years ago

10.1186/s12867-018-0110-y

Positive cofactor 4 (PC4) contributes to the regulation of replication-dependent canonical histone gene expression
Cited by: 2
Author(s): Aleksandra Brzęk, Marlena Cichocka, Jakub Dolata, Wojciech Juzwa, Daniel Schümperli, Katarzyna Dorota Raczyńska
Software Mentions: 2
Published: over 6 years ago

10.1186/s12870-018-1438-7

Rice stripe virus-derived siRNAs play different regulatory roles in rice and in the insect vector Laodelphax striatellus
Cited by: 32
Author(s): Meiling Yang, Zhongtian Xu, Wan Zhao, Qing Liu, Qiong Li, Lu Lu, Renyi Liu, Xiaoming Zhang, Feng Cui
Software Mentions: 2
Published: about 6 years ago

10.1186/1471-2229-13-229

Four distinct types of dehydration stress memory genes in Arabidopsis thaliana
Cited by: 191
Author(s): Yong Ding, Ning Liu, Laëtitia Virlouvet, Jean-Jack M. Riethoven, Michael Fromm, Zoya Avramova
Software Mentions: 2
Published: almost 11 years ago

10.1186/s12870-021-02957-z

Comparative physiological and full-length transcriptome analyses reveal the molecular mechanism of melatonin-mediated salt tolerance in okra (Abelmoschus esculentus L.)
Cited by: 22
Author(s): Yihua Zhan, Tingting Wu, Xuan Zhao, Zhanqi Wang, Yue Chen
Software Mentions: 2
Published: over 3 years ago

10.1186/s12870-016-0770-z

Identification of miRNAs and their targets through high-throughput sequencing and degradome analysis in male and female Asparagus officinalis
Cited by: 31
Author(s): Jingli Chen, Yi Zheng, Qin Li, Yan Wang, Lifei Chen, Yanjun He, Zhangjun Fei, Gang Lü
Software Mentions: 2
Published: over 8 years ago

10.1186/s12870-020-2286-9

Genome-wide analysis of long non-coding RNAs (lncRNAs) in two contrasting rapeseed (Brassica napus L.) genotypes subjected to drought stress and re-watering
Cited by: 27
Author(s): Xiaoyu Tan, Li Su, Liyong Hu, Chunlei Zhang
Software Mentions: 2
Published: almost 5 years ago

10.1186/s12870-015-0549-7

Transposable elements, mRNA expression level and strand-specificity of small RNAs are associated with non-additive inheritance of gene expression in hybrid plants
Cited by: 12
Author(s): Qing Li, Ying Li, Stephen P. Moose, Matthew E. Hudson
Software Mentions: 2
Published: over 9 years ago

10.1186/1471-2229-12-177

Divergent patterns of endogenous small RNA populations from seed and vegetative tissues of Glycine max
Cited by: 34
Author(s): Gracia Zabala, Edhilvia J. Campos, Kranthi Varala, Sean Bloomfield, Sarah I. Jones, Hlaing Win, Jigyasa H. Tuteja, Bernarda Calla, Steven J. Clough, Matthew E. Hudson, Lila O. Vodkin
Software Mentions: 2
Published: about 12 years ago

10.1186/s12870-016-0724-5

Exogenous auxin regulates multi-metabolic network and embryo development, controlling seed secondary dormancy and germination in Nicotiana tabacum L.
Cited by: 17
Author(s): Zhenhua Li, Jie Zhang, Yiling Liu, Jiehong Zhao, Junjie Fu, Xueliang Ren, Guoying Wang, Jianhua Wang
Software Mentions: 2
Published: almost 9 years ago

10.1186/1471-2229-14-45

Assembly and analysis of a male sterile rubber tree mitochondrial genome reveals DNA rearrangement events and a novel transcript
Cited by: 41
Author(s): Jeremy R. Shearman, Duangjai Sangsrakru, Panthita Ruang-areerate, Chutima Sonthirod, Pichahpuk Uthaipaisanwong, Thippawan Yoocha, Supannee Poopear, Kanikar Theerawattanasuk, Somvong Tragoonrung, Sithichoke Tangphatsornruang
Software Mentions: 2
Published: almost 11 years ago

10.1186/s12870-019-1637-x

Characterization of the mitochondrial genome of the MAX1 type of cytoplasmic male-sterile sunflower
Cited by: 18
Author(s): Maksim Makarenko, А. В. Усатов, Tatiana V. Tatarinova, Kirill Azarin, Maria D. Logacheva, В. А. Гаврилова, Renate Horn
Software Mentions: 2
Published: almost 6 years ago

10.1093/bioinformatics/btv071

Reference-based compression of short-read sequences using path encoding
Cited by: 48
Author(s): Carl Kingsford, Rob Patro
Software Mentions: 2
Published: almost 10 years ago

10.1093/bioinformatics/btu781

QuasR: quantification and annotation of short reads in R
Cited by: 241
Author(s): Dimos Gaidatzis, Anita Lerch, Florian Hahne, Michael Stadler
Software Mentions: 2
Published: almost 10 years ago

10.3390/biology8020047

Identification and Characterization of microRNAs and Their Predicted Functions in Biomineralization in the Pearl Oyster (Pinctada fucata)
Cited by: 12
Author(s): Songqian Huang, Yūki Ichikawa, Kazutoshi Yoshitake, Shigeharu Kinoshita, Yoji Igarashi, Fumito Omori, Kaoru Maeyama, Kiyohito Nagai, Shugo Watabe, Shuichi Asakawa
Software Mentions: 2
Published: over 5 years ago

10.1155/2014/529271

RNA-Seq Identifies Key Reproductive Gene Expression Alterations in Response to Cadmium Exposure
Cited by: 16
Author(s): Hanyang Hu, Xing Lü, Xiang Cen, Xiaohua Chen, Feng Li, Shan Zhong
Software Mentions: 2
Published: almost 11 years ago

10.3390/biomedicines9020142

Novel Ex Vivo Model to Examine the Mechanism and Relationship of Esophageal Microbiota and Disease
Cited by: 4
Author(s): Samuel Cass, Catherine Hamilton, Aaron L. Miller, Daniel C. Jupiter, Kamil Khanipov, Adam L. Booth, Richard B. Pyles, Timothy Krill, Gabriel Reep, Ikenna Okereke
Software Mentions: 2
Published: almost 4 years ago

10.1186/s13058-019-1130-3

The lncRNA MIR2052HG regulates ERα levels and aromatase inhibitor resistance through LMTK3 by recruiting EGR1
Cited by: 33
Author(s): Junmei Cairns, James N. Ingle, Krishna R. Kalari, Lois E. Shepherd, Michiaki Kubo, Matthew P. Goetz, Richard M. Weinshilboum, Liewei Wang
Software Mentions: 2
Published: over 5 years ago

10.26508/lsa.201800117

CARM1 methylates MED12 to regulate its RNA-binding ability
Cited by: 39
Author(s): Donghang Cheng, Vidyasiri Vemulapalli, Yue Lu, Jianjun Shen, Sakae Aoyagi, Christopher J. Fry, Yanzhong Yang, Charles E. Foulds, Fabio Stossi, Lindsey S. Treviño, Michael A. Mancini, Bert W. O’Malley, Cheryl L. Walker, Thomas G. Boyer, Mark T. Bedford
Software Mentions: 2
Published: about 6 years ago

10.1186/s12944-016-0190-y

Fish oil alleviated high-fat diet–induced non-alcoholic fatty liver disease via regulating hepatic lipids metabolism and metaflammation: a transcriptomic study
Cited by: 60
Author(s): Fahu Yuan, Hualin Wang, Yu Tian, Qi Li, Lei He, Na Li, Zhiguo Liu
Software Mentions: 2
Published: almost 9 years ago

10.3390/md15070213

Genome Sequences of Marine Shrimp Exopalaemon carinicauda Holthuis Provide Insights into Genome Size Evolution of Caridea
Cited by: 44
Author(s): Jianbo Yuan, Yi Gao, Xiaojun Zhang, Jiankai Wei, Xianhui Qin, Fuhua Li, Jianhai Xiang
Software Mentions: 2
Published: over 7 years ago

10.1097/MD.0000000000022964

Long non-coding RNAs expression profile and functional analysis of acute ischemic stroke
Cited by: 7
Author(s): Jia Li, Miao Hao, Ben Yang, Tianji Shi, Yingyu Zhang, Jun Feng, Jiajun Chen
Software Mentions: 2
Published: almost 4 years ago

10.1111/1751-7915.12556

Comparison of biofilm formation and motility processes in arsenic‐resistant Thiomonas spp. strains revealed divergent response to arsenite
Cited by: 11
Author(s): Julien Farasin, Sandrine Koechler, Hugo Varet, Julien Deschamps, Marie‐Agnès Dillies, Caroline Proux, Mathieu Erhardt, Aline Huber, Bernd Jagla, Romain Briandet, Jean‐Yves Coppée, Florence Arsène-Ploetze
Software Mentions: 2
Published: almost 8 years ago

10.1186/s40168-020-00837-6

Gut bacterial ClpB-like gene function is associated with decreased body weight and a characteristic microbiota profile
Cited by: 44
Author(s): María Arnoriaga-Rodríguez, Jordi Mayneris‐Perxachs, Aurelijus Burokas, Vicente Pérez‐Brocal, Andrés Moya, Manuel Portero-Otı́n, Wifredo Ricart, Rafaël Maldonado, José Manuel Fernández‐Real
Software Mentions: 2
Published: over 4 years ago

10.3390/microorganisms9061142

Molecular Analysis of East African Lumpy Skin Disease Viruses Reveals a Mixed Isolate with Features of Both Vaccine and Field Isolates
Cited by: 10
Author(s): Tesfaye Rufael, Melaku Sombo, Jacqueline Kasiiti Lichoti, Tajelser Adam, Yang Liu, Yazeed Abd Elraouf, Reingard Grabherr, Tirumala Bharani Kumar Settypalli, Francisco J. Berguido, Angelika Loitsch, Mesfin Sahle, Giovanni Cattoli, Adama Diallo, Charles Euloge Lamien
Software Mentions: 2
Published: over 3 years ago

10.3390/microorganisms8111759

Response of Coral Reef Dinoflagellates to Nanoplastics under Experimental Conditions Suggests Downregulation of Cellular Metabolism
Cited by: 24
Author(s): Christina Ripken, Konstantin Khalturin, Eiichi Shoguchi
Software Mentions: 2
Published: about 4 years ago

10.1080/23802359.2018.1464412

The complete chloroplast genome of Sisymbrium irio
Cited by: 2
Author(s): Takahiro Kawanabe, Hiroaki Nukii, Hazuka Y. Furihata, Takanori Yoshida, Akira Kawabe
Software Mentions: 2
Published: over 6 years ago

10.1186/2040-2392-4-3

MeCP2 modulates gene expression pathways in astrocytes
Cited by: 74
Author(s): Dag H. Yasui, Huichun Xu, Keith W. Dunaway, Janine M. LaSalle, Lee‐Way Jin, Izumi Maezawa
Software Mentions: 2
Published: almost 12 years ago

10.1093/molbev/msx123

Genomic Signature of Kin Selection in an Ant with Obligately Sterile Workers
Cited by: 47
Author(s): Michael Warner, Alexander S. Mikheyev, Timothy A. Linksvayer
Software Mentions: 2
Published: over 7 years ago

10.1186/1476-4598-12-131

The long non-coding RNA ERIC is regulated by E2F and modulates the cellular response to DNA damage
Cited by: 63
Author(s): Orit Feldstein, Tal Nizri, Tirza Doniger, Jasmine Jacob, Gideon Rechavi, Doron Ginsberg
Software Mentions: 2
Published: about 11 years ago

10.3390/molecules24091774

A Novel G-Quadruplex Binding Protein in Yeast—Slx9
Cited by: 16
Author(s): Silvia Götz, Satyaprakash Pandey, Sabrina Bartsch, Stefan Juranek, Katrin Paeschke
Software Mentions: 2
Published: over 5 years ago

10.3390/molecules25194466

Polyunsaturated Fatty Acids of Both the Omega-3 and the Omega-6 Family Abrogate the Cytokine-Induced Upregulation of miR-29a-3p by Endothelial Cells
Cited by: 5
Author(s): Daniel Maucher, Birte Schmidt, Kevin Kuhlmann, Julia Schümann
Software Mentions: 2
Published: about 4 years ago

10.1002/1878-0261.12357

Role of hepatoma‐derived growth factor in promoting de novo lipogenesis and tumorigenesis in hepatocellular carcinoma
Cited by: 25
Author(s): Xuejie Min, Jun Wen, Li Zhao, Kaiying Wang, Qingli Li, Gang Huang, Jianjun Li, Xiaoping Zhao
Software Mentions: 2
Published: over 6 years ago

10.1111/mpp.12761

DCL-suppressedNicotiana benthamianaplants: valuable tools in research and biotechnology
Cited by: 16
Author(s): Κωνσταντίνα Κατσαρού, Eleni Mitta, Eirini Bardani, Anastasis Oulas, Elena Dadami, Kriton Kalantidis
Software Mentions: 2
Published: almost 6 years ago

10.15252/msb.20145172

Cell cycle population effects in perturbation studies
Cited by: 103
Author(s): Eoghan O’Duibhir, Philip Lijnzaad, Joris J. Benschop, Tineke L. Lenstra, Dik van Leenen, Marian J. A. Groot Koerkamp, Thanasis Margaritis, Mariël Brok, Patrick Kemmeren, Frank C. P. Holstege
Software Mentions: 2
Published: over 10 years ago

10.15252/msb.202110302

Spurious regulatory connections dictate the expression‐fitness landscape of translation factors
Cited by: 6
Author(s): Jean-Benoît Lalanne, Darren J. Parker, Gene-Wei Li
Software Mentions: 2
Published: over 3 years ago

10.1186/s13567-021-00892-3

Exosomal miRNA profiling from H5N1 avian influenza virus-infected chickens
Cited by: 15
Author(s): Yeong Ho Hong, Anh Duc Truong, Jiae Lee, Thi Hao Vu, Sooyeon Lee, Ki-Duk Song, Hyun S. Lillehoj
Software Mentions: 2
Published: over 3 years ago

10.1186/1743-422X-10-169

Comparative analysis of the genome sequences and replication profiles of chikungunya virus isolates within the East, Central and South African (ECSA) lineage
Cited by: 38
Author(s): Karen Caiyun Chen, Yiu‐Wing Kam, Raymond Pin Tzer Lin, Mary Mah-Lee Ng, Lisa F. P. Ng, Justin Jang Hann Chu
Software Mentions: 2
Published: over 11 years ago

10.1186/s12985-015-0332-2

Identification of Hop stunt viroid infecting Citrus limon in China using small RNAs deep sequencing approach
Cited by: 12
Author(s): Xiu Su, Shuai Fu, Yajuan Qian, Yi Xu, Xueping Zhou
Software Mentions: 2
Published: over 9 years ago

10.3390/v5041042

Interpreting the Epstein-Barr Virus (EBV) Epigenome Using High-Throughput Data
Cited by: 43
Author(s): Aaron Arvey, Italo Tempera, Paul M. Lieberman
Software Mentions: 2
Published: over 11 years ago

10.1186/s13071-020-04253-5

In vitro shared transcriptomic responses of Aedes aegypti to arboviral infections: example of dengue and Rift Valley fever viruses
Cited by: 8
Author(s): Séverine Licciardi, Étienne Loire, Éric Cardinale, Marie Gislard, Emeric Dubois, Catherine Cêtre-Sossah
Software Mentions: 2
Published: over 4 years ago

10.1186/s13071-020-04047-9

Genome-wide analysis of differentially expressed profiles of mRNAs, lncRNAs and circRNAs in chickens during Eimeria necatrix infection
Cited by: 11
Author(s): Xian-Cheng Fan, Ting-Li Liu, Yi Wang, Xuemei Wu, Yuxin Wang, Lai Peng, Jun-Ke Song, Guang‐Hui Zhao
Software Mentions: 2
Published: over 4 years ago

10.7717/peerj.10796

Evaluation of key miRNAs during early pregnancy in Kazakh horse using RNA sequencing
Cited by: 2
Author(s): Lingling Liu, Chao Fang, YinZe Sun, Wujun Liu
Software Mentions: 2
Published: over 3 years ago

10.7717/peerj.4816

An improved primer set and amplification protocol with increased specificity and sensitivity targeting the Symbiodinium ITS2 region
Cited by: 68
Author(s): Benjamin C. C. Hume, Maren Ziegler, Julie Poulain, Xavier Pochon, Sarah Romac, Émilie Boissin, Colomban de Vargas, Serge Planes, Patrick Wincker, Christian R. Voolstra
Software Mentions: 2
Published: over 6 years ago

10.7717/peerj.10704

Genome-wide miRNA expression profiling in potato (Solanum tuberosum L.) reveals TOR-dependent post-transcriptional gene regulatory networks in diverse metabolic pathway
Cited by: 5
Author(s): Kexuan Deng, Huan Yin, Fei Xiong, Li Feng, Pan Dong, Maozhi Ren
Software Mentions: 2
Published: almost 4 years ago

10.7717/peerj.11812

Co-expression network and comparative transcriptome analysis for fiber initiation and elongation reveal genetic differences in two lines from upland cotton CCRI70 RIL population
Cited by: 8
Author(s): Xiao Jiang, Liqiang Fan, Pengtao Li, Xianyan Zou, Zhen Zhang, Senmiao Fan, Jǔwǔ Gōng, Yǒulù Yuán, Hǎihóng Shāng
Software Mentions: 2
Published: over 3 years ago

10.7717/peerj.3249

The genetics of venom ontogeny in the eastern diamondback rattlesnake (Crotalus adamanteus)
Cited by: 36
Author(s): Darin R. Rokyta, Mark J. Margres, Micaiah J. Ward, Elda E. Sánchez
Software Mentions: 2
Published: over 7 years ago

10.7717/peerj.4537

Flavonoid biosynthesis controls fiber color in naturally colored cotton
Cited by: 20
Author(s): Haifeng Liu, Cheng Luo, Song Wu, Haitao Shen, Guoliang Li, Zhigang He, Wen-Gang Chen, Yanyan Cao, Fang Huang, Shouwu Tang, Hong Pan, Enfeng Zhao, Jianbo Zhu, Dajun He, Shaoming Wang, Guang-Ying Huo, Hailiang Liu
Software Mentions: 2
Published: over 6 years ago

10.1186/s13007-015-0087-1

Improved DNase-seq protocol facilitates high resolution mapping of DNase I hypersensitive sites in roots in Arabidopsis thaliana
Cited by: 21
Author(s): Jason S. Cumbie, Sergei A. Filichkin, Molly Megraw
Software Mentions: 2
Published: about 9 years ago

10.1186/s13007-018-0381-9

Regulatory chromatin landscape in Arabidopsis thaliana roots uncovered by coupling INTACT and ATAC-seq
Cited by: 32
Author(s): Miriam Tannenbaum, Avital Sarusi-Portuguez, Ronen Krispil, Michal Schwartz, Olga Loza, Jennifer I. C. Benichou, Assaf Mosquna, Ofir Hakim
Software Mentions: 2
Published: almost 6 years ago

10.1186/s13007-016-0139-1

Development of a universal and simplified ddRAD library preparation approach for SNP discovery and genotyping in angiosperm plants
Cited by: 63
Author(s): Guoqian Yang, Yunmei Chen, Jinpeng Wang, Cen Guo, Lei Zhao, Xiaoyan Wang, Ying Guo, Li Li, Li D, Zhenhua Guo
Software Mentions: 2
Published: over 8 years ago

10.1007/s11103-013-0106-4

Diversity in the complexity of phosphate starvation transcriptomes among rice cultivars based on RNA-Seq profiles
Cited by: 45
Author(s): Youko Oono, Yoshihiro Kawahara, Takayuki Yazawa, Hajime Kanamori, Masato Kuramata, Harumi Yamagata, Satomi Hosokawa, Hiroshi Minami, Shinya Ishikawa, Jianzhong Wu, Baltazar A. Antonio, Hirokazu Handa, Takeshi Itoh, Takashi Matsumoto
Software Mentions: 2
Published: over 11 years ago

10.3390/plants9070912

Inhibitory Mechanism of Trichoderma virens ZT05 on Rhizoctonia solani
Cited by: 29
Author(s): Saiyaremu Halifu, Xun Deng, Xiaoshuang Song, Ruiqing Song, Liang Xu
Software Mentions: 2
Published: over 4 years ago

10.1371/journal.pbio.3000297

Cytosine-5 RNA methylation links protein synthesis to cell metabolism
Cited by: 79
Author(s): Nikoletta A. Gkatza, Cecilia Castro, R Harvey, MM Heiss, Martyna Popis, Sandra Blanco, Susanne Bornelöv, Abdulrahim A. Sajini, Joseph G. Gleeson, Julian L. Griffin, James A. West, Stefanie Kellner, Anne E. Willis, Sabine Dietmann, Michaela Frye
Software Mentions: 2
Published: over 5 years ago

10.1371/journal.pbio.3000636

Millipede genomes reveal unique adaptations during myriapod evolution
Cited by: 15
Author(s): Zhe Qu, Wenyan Nong, Wai Lok So, Tom Barton-Owen, Yiqian Li, Thomas Leung, Chade Li, Tobias Baril, Hon Kit Wong, Thomas Swale, Ting‐Fung Chan, Alexander Hayward, Sai-Ming Ngai, Jerome H.L. Hui
Software Mentions: 2
Published: about 4 years ago

10.1371/journal.pbio.1002316

Bromodomain Proteins Contribute to Maintenance of Bloodstream Form Stage Identity in the African Trypanosome
Cited by: 53
Author(s): Danae Schulz, Monica R. Mugnier, Eda Margaret Paulsen, Hee Sook Kim, Chun Wa Chung, David F. Tough, Inmaculada Rioja, Rab K. Prinjha, F. Nina Papavasiliou, Erik Debler
Software Mentions: 2
Published: almost 9 years ago

10.1371/journal.pbio.1000371

Most “Dark Matter” Transcripts Are Associated With Known Genes
Cited by: 384
Author(s): Harm van Bakel, Corey Nislow, Benjamin J. Blencowe, Timothy R. Hughes
Software Mentions: 2
Published: over 14 years ago

10.1371/journal.pbio.2001069

Transcriptional regulatory logic of the diurnal cycle in the mouse liver
Cited by: 65
Author(s): Jonathan Sobel, Irina Krier, Teemu Andersin, Sunil K. Raghav, Donatella Canella, Federica Gilardi, Alexandra Styliani Kalantzi, Guillaume Rey, Benjamin D. Weger, Frédéric Gachon, Matteo Dal Peraro, Nouria Hernandez, Ueli Schibler, Bart Deplancke, Félix Naef
Software Mentions: 2
Published: over 7 years ago

10.1371/journal.pcbi.1006030

4Cin: A computational pipeline for 3D genome modeling and virtual Hi-C analyses from 4C data
Cited by: 9
Author(s): Ibai Irastorza-Azcárate, Rafael D. Acemel, Juan J. Tena, Ignacio Maeso, José Luis Gómez-Skármeta, Damien P. Devos
Software Mentions: 2
Published: over 6 years ago

10.1371/journal.pgen.1003461

The Histone Demethylase Jarid1b Ensures Faithful Mouse Development by Protecting Developmental Genes from Aberrant H3K4me3
Cited by: 109
Author(s): Mareike Albert, Sandra U. Schmitz, Susanne M. Kooistra, Martina Malatesta, Cristina Morales Torres, Jens C. Rekling, Jens Vilstrup Johansen, Iratxe Abarrategui, Kristian Helin
Software Mentions: 2
Published: over 11 years ago

10.1371/journal.pgen.1008916

Trappc9 deficiency causes parent-of-origin dependent microcephaly and obesity
Cited by: 17
Author(s): Zhengzheng S. Liang, Irène Cimino, Binnaz Yalcin, Narayanan Raghupathy, Valerie E. Vancollie, Ximena Ibarra-Soria, Helen V. Firth, Debra Rimmington, I. Sadaf Farooqi, Christopher J. Lelliott, Steven C. Munger, Stephen O’Rahilly, Anne C. Ferguson‐Smith, Anthony P. Coll, Darren W. Logan
Software Mentions: 2
Published: about 4 years ago

10.1371/journal.pgen.1006348

Metatranscriptomic Study of Common and Host-Specific Patterns of Gene Expression between Pines and Their Symbiotic Ectomycorrhizal Fungi in the Genus Suillus
Cited by: 50
Author(s): Hui‐Ling Liao, Yuan Chen, Rytas Vilgalys
Software Mentions: 2
Published: about 8 years ago

10.1371/journal.pgen.1008397

Chromatin dynamics enable transcriptional rhythms in the cnidarian Nematostella vectensis
Cited by: 9
Author(s): Eviatar Weizman, Miriam Tannenbaum, Ann M. Tarrant, Ofir Hakim, Oren Levy
Software Mentions: 2
Published: about 5 years ago

10.1371/journal.pgen.1002736

The NSL Complex Regulates Housekeeping Genes in Drosophila
Cited by: 82
Author(s): Kin Chung Lam, Friederike Mühlpfordt, Juan M. Vaquerizas, Sunil Jayaramaiah Raja, Heribert Holz, Nicholas M. Luscombe, Thomas Manke, Asifa Akhtar
Software Mentions: 2
Published: over 12 years ago

10.1371/journal.pgen.1006861

Splicing stimulates siRNA formation at Drosophila DNA double-strand breaks
Cited by: 16
Author(s): Karin Merk, Marco Breinig, Romy Böttcher, Stefan Krebs, Helmut Blum, Michael Boutros, Klaus Förstemann
Software Mentions: 2
Published: over 7 years ago

10.1371/journal.pgen.1002646

Sequence-Specific Targeting of Dosage Compensation in Drosophila Favors an Active Chromatin Context
Cited by: 53
Author(s): Artyom A. Alekseyenko, Joshua W. K. Ho, Shouyong Peng, Marnie E. Gelbart, Michael Y. Tolstorukov, Annette Plachetka, Peter V. Kharchenko, Youngsook L. Jung, Andrey A. Gorchakov, Erica Larschan, Tingting Gu, Aki Minoda, Nicole C. Riddle, Yuri B. Schwartz, Sarah C. R. Elgin, Gary H. Karpen, Vincenzo Pirrotta, Mitzi I. Kuroda, Peter J. Park
Software Mentions: 2
Published: over 12 years ago

10.1371/journal.pgen.1004153

A Cohesin-Independent Role for NIPBL at Promoters Provides Insights in CdLS
Cited by: 122
Author(s): Jessica Zuin, Vedran Franke, Wilfred F. J. van IJcken, Antoine A.J. van der Sloot, Ian D. Krantz, Michael I.J.A. van der Reijden, Ryuichiro Nakato, Boris Lenhard, Kerstin S. Wendt
Software Mentions: 2
Published: almost 11 years ago

10.1371/journal.pgen.1008291

Monitoring the interplay between transposable element families and DNA methylation in maize
Cited by: 49
Author(s): Jaclyn M. Noshay, Sarah N. Anderson, Peng Zhou, Lexiang Ji, William A. Ricci, Zefu Lu, Michelle C. Stitzer, Peter A. Crisp, Candice N. Hirsch, Xiaoyu Zhang, Robert J. Schmitz, Nathan M. Springer
Software Mentions: 2
Published: about 5 years ago

10.1371/journal.pgen.1004090

Defining NELF-E RNA Binding in HIV-1 and Promoter-Proximal Pause Regions
Cited by: 55
Author(s): John M. Pagano, Ho Young Kwak, Colin T. Waters, Rebekka O. Sprouse, Brian S. White, Abdullah Ozer, Kylan Szeto, David Shalloway, Harold G. Craighead, John T. Lis
Software Mentions: 2
Published: almost 11 years ago

10.1371/journal.pgen.1004211

An Epigenetic Signature in Peripheral Blood Associated with the Haplotype on 17q21.31, a Risk Factor for Neurodegenerative Tauopathy
Cited by: 65
Author(s): Yun Li, Jason Chen, Renee L. Sears, Fuying Gao, Eric Klein, Anna Karydas, Michael D. Geschwind, Howard J. Rosen, Adam L. Boxer, Weilong Guo, Matteo Pellegrini, Steve Horvath, Bruce L. Miller, Daniel H. Geschwind, Giovanni Coppola
Software Mentions: 2
Published: over 10 years ago

10.1371/journal.pgen.1004850

A Multi-Megabase Copy Number Gain Causes Maternal Transmission Ratio Distortion on Mouse Chromosome 2
Cited by: 76
Author(s): John P. Didion, Andrew P. Morgan, Amelia M.-F. Clayshulte, Rachel McMullan, Liran Yadgary, Petko M. Petkov, Timothy A. Bell, Daniel M. Gatti, James J. Crowley, Kunjie Hua, David L. Aylor, Ling Bai, Mark Calaway, Elissa J. Chesler, John E. French, Thomas Geiger, Terry J. Gooch, Theodore Garland, Alison H. Harrill, Kent W. Hunter, Leonard McMillan, Matt Holt, Darla R. Miller, Deborah A. O’Brien, Kenneth Paigen, Wei Pan, Lucy B. Rowe, Ginger D. Shaw, Petr Šimeček, Patrick F. Sullivan, Karen L. Svenson, George M. Weinstock, David W. Threadgill, Daniel Pomp, Gary A. Churchill, Fernando P Pardo Manuel De Villena
Software Mentions: 2
Published: almost 10 years ago

Projects: pypi: bowtie

Papers Mentioning bowtie 1,566