pypi: bowtie | Projects | Ecosyste.ms: Papers

10.1002/ece3.6688

Examining the molecular mechanisms contributing to the success of an invasive species across different ecosystems
Cited by: 0
Author(s): Sarah K. Lamar, Ian Beddows, Charlyn Partridge
Software Mentions: 3
Published: about 4 years ago

10.3389/fmicb.2020.02069

Transcriptomic Analysis and Functional Characterization Reveal the Duck Interferon Regulatory Factor 1 as an Important Restriction Factor in the Replication of Tembusu Virus
Cited by: 8
Author(s): Chengwei Xiang, Mei Huang, Tingting Xiong, Rong Fang, Linyu Li, Ding Xiang Liu, Rui Ai Chen
Software Mentions: 3
Published: about 4 years ago

10.7554/eLife.34870

OGT binds a conserved C-terminal domain of TET1 to regulate TET1 activity and function in development
Cited by: 44
Author(s): Joel Hrit, Leeanne Goodrich, Li Cheng, Bang-An Wang, Ji Nie, Xiaolong Cui, Elizabeth Allene Martin, Eric Simental, Jenna Fernandez, Monica Yun Liu, Joseph R. Nery, Rosa Castanon, Rahul M. Kohli, Natalia Tretyakova, Chuan He, Joseph R. Ecker, Mary Goll, Barbara Panning
Software Mentions: 3
Published: about 6 years ago

10.3389/fmicb.2020.00163

Synthesis, Regulation and Degradation of Carotenoids Under Low Level UV-B Radiation in the Filamentous Cyanobacterium Chlorogloeopsis fritschii PCC 6912
Cited by: 26
Author(s): Carole A. Llewellyn, Ruth L. Airs, Garry Farnham, Carolyn Greig
Software Mentions: 3
Published: almost 5 years ago

10.15252/embr.201947789

Dynamic expression of tRNA‐derived small RNAs define cellular states
Cited by: 89
Author(s): Srikar Krishna, Daniel Yim, Vairavan Lakshmanan, Varsha Tirumalai, Judice L.Y. Koh, Jung Eun Park, Jit Kong Cheong, Joo-Leng Low, Michelle Gek Liang Lim, Siu Kwan Sze, P. V. Shivaprasad, Akash Gulyani, Srikala Raghavan, Dasaradhi Palakodeti, Ramanuj DasGupta
Software Mentions: 2
Published: over 5 years ago

10.1093/database/bax074

Echinobase: an expanding resource for echinoderm genomic information
Cited by: 60
Author(s): Parul Kudtarkar, R. Andrew Cameron
Software Mentions: 2
Published: almost 8 years ago

10.1016/j.ydbio.2012.03.024

The transcriptional programme controlled by Runx1 during early embryonic blood development
Cited by: 41
Author(s): Yosuke Tanaka, Anagha Joshi, Nicola K. Wilson, Sarah Kinston, Shin‐Ichi Nishikawa, Berthold Göttgens
Software Mentions: 2
Published: over 12 years ago

10.1242/dev.136051

microRNA deep sequencing in two adult stem cell populations identifies miR-501 as novel regulator of myosin heavy chain during muscle regeneration
Cited by: 15
Author(s): Amir Mizbani, Edlira Luca, Elisabeth J. Rushing, Jan Krützfeldt
Software Mentions: 2
Published: almost 9 years ago

10.3390/diagnostics10090701

Sepsis Diagnostics: Intensive Care Scoring Systems Superior to MicroRNA Biomarker Testing
Cited by: 1
Author(s): Fabian Link, Knut Krohn, Anna-Maria Burgdorff, Annett Christel, Julia Schümann
Software Mentions: 2
Published: about 4 years ago

10.1038/emboj.2013.177

Identification of the missing pluripotency mediator downstream of leukaemia inhibitory factor
Cited by: 192
Author(s): Graziano Martello, Paul Bertone, Austin Smith
Software Mentions: 2
Published: over 11 years ago

10.15252/embj.201695323

<scp>GT</scp> ‐rich promoters can drive <scp>RNA</scp> pol <scp>II</scp> transcription and deposition of H2A.Z in African trypanosomes
Cited by: 65
Author(s): Carolin Wedel, Konrad U. Förstner, Ramona Derr, T. Nicolai Siegel
Software Mentions: 2
Published: over 7 years ago

10.15252/embj.201592532

Sororin actively maintains sister chromatid cohesion
Cited by: 84
Author(s): René Ladurner, Emanuel Kreidl, Miroslav P Ivanov, Heinz Ekker, Maria Helena Idarraga-Amado, Georg A. Busslinger, Gordana Wutz, David A. Cisneros, Jan‐Michael Peters
Software Mentions: 2
Published: over 8 years ago

10.15252/embj.2020107455

HASTY , the Arabidopsis EXPORTIN5 ortholog, regulates cell‐to‐cell and vascular microRNA movement
Cited by: 27
Author(s): Florian Brioudes, Florence Jay, Alexis Sarazin, Thomas Grentzinger, Emanuel A. Devers, Olivier Voinnet
Software Mentions: 2
Published: over 3 years ago

10.1080/22221751.2019.1637702

Comprehensive subspecies identification of 175 nontuberculous mycobacteria species based on 7547 genomic profiles
Cited by: 59
Author(s): Yuki Matsumoto, Takeshi Kinjo, Daisuke Motooka, Daijiro Nabeya, Nicolas Jung, Kohei Uechi, Toshihiro Horii, Tetsuya Iida, Jiro Fujita, Shota Nakamura
Software Mentions: 2
Published: almost 6 years ago

10.1186/1756-8935-8-8

DNase I hypersensitivity analysis of the mouse brain and retina identifies region-specific regulatory elements
Cited by: 57
Author(s): Matthew S. Wilken, Joseph A. Brzezinski, Anna La Torre, Kyle Siebenthall, Robert E. Thurman, Peter J. Sabo, Richard Sandstrom, Jeff Vierstra, Theresa K. Canfield, R. Scott Hansen, Michael A. Bender, J Stamatoyannopoulos, Thomas A. Reh
Software Mentions: 2
Published: over 9 years ago

10.1186/s13072-019-0290-9

Hyperinsulinemia promotes aberrant histone acetylation in triple-negative breast cancer
Cited by: 21
Author(s): Parijat Senapati, Hiroyuki Kato, Michael Lee, Amy Leung, Christine Thai, Angelica Sanchez, Emily J. Gallagher, Derek LeRoith, Victoria L. Seewaldt, David K. Ann, Dustin E. Schones
Software Mentions: 2
Published: over 5 years ago

10.1186/s13072-019-0313-6

Chromatin accessibility and transcription dynamics during in vitro astrocyte differentiation of Huntington’s Disease Monkey pluripotent stem cells
Cited by: 7
Author(s): Alexandra V. Goodnight, Isaac Kremsky, Sujittra Khampang, Younghun Jung, James M. Billingsley, Steven E. Bosinger, Victor G. Corcés, Anthony W.S. Chan
Software Mentions: 2
Published: about 5 years ago

10.1038/ejhg.2014.281

Huntington’s disease biomarker progression profile identified by transcriptome sequencing in peripheral blood
Cited by: 69
Author(s): Anastasios Mastrokolias, Yavuz Ariyürek, Jelle J. Goeman, Erik van Duijn, Raymund A.C. Roos, Roos C. van der Mast, Gert‐Jan B. van Ommen, Johan T. den Dunnen, Peter A C ‘t Hoen, Willeke M. C. van Roon‐Mom
Software Mentions: 2
Published: almost 10 years ago

10.1002/evl3.71

Convergent phenotypic evolution of the visual system via different molecular routes: How Neotropical cichlid fishes adapt to novel light environments
Cited by: 33
Author(s): Andreas Härer, Axel Meyer, Julián Torres‐Dowdall
Software Mentions: 2
Published: over 6 years ago

10.1038/s12276-019-0267-6

IRF1 is critical for the TNF-driven interferon response in rheumatoid fibroblast-like synoviocytes
Cited by: 39
Author(s): Michael Bonelli, K Dalwigk, Alexander Platzer, Isabel Olmos Calvo, Silvia Hayer, Birgit Niederreiter, Johannes Holinka, Florian Sevelda, Thomas Pap, Günter Steiner, Giulio Superti‐Furga, Josef S Smolen, Hans P. Kiener, Thomas Karonitsch
Software Mentions: 2
Published: over 5 years ago

10.1096/fj.201801638R

NF‐κB p65 dimerization and DNA‐binding is important for inflammatory gene expression
Cited by: 26
Author(s): Tabea Riedlinger, Robert Liefke, Johanna Meier-Soelch, Liane Jurida, Andrea Nist, Thorsten Stiewe, Michael Kracht, M. Lienhard Schmitz
Software Mentions: 2
Published: almost 6 years ago

10.1002/2211-5463.12377

Micro RNA profiling during directed differentiation of cortical interneurons from human‐induced pluripotent stem cells
Cited by: 9
Author(s): Jiajie Tu, Dandan Cao, Li Lü, Hoi‐Hung Cheung, Wai‐Yee Chan
Software Mentions: 2
Published: almost 7 years ago

10.3389/fnbeh.2015.00255

Differentially expressed genes linked to natural variation in long-term memory formation in Cotesia parasitic wasps
Cited by: 7
Author(s): Joke J.F.A. van Vugt, Katja M. Hoedjes, H.C. van de Geest, Elio W. G. M. Schijlen, Louise E. M. Vet, Hans M. Smid
Software Mentions: 2
Published: about 9 years ago

10.3389/fcell.2020.568116

Systematic Analysis of tRNA-Derived Small RNAs Discloses New Therapeutic Targets of Caloric Restriction in Myocardial Ischemic Rats
Cited by: 17
Author(s): Wenjing Liu, Yang Liu, Zhaohai Pan, Xin Zhang, Yao Jun Qin, Xiaojie Chen, Minjing Li, Xiaoyu Chen, Qiusheng Zheng, Xiaona Liu, Defang Li
Software Mentions: 2
Published: about 4 years ago

10.3389/fcimb.2020.625576

Phylogeography of Human and Animal Coxiella burnetii Strains: Genetic Fingerprinting of Q Fever in Belgium
Cited by: 12
Author(s): Sara Tomaiuolo, Samira Boarbi, Tiziano Fancello, Patrick P. Michel, Damien Desqueper, Fabien Grégoire, Jozefien Callens, David Frétin, Bert Devriendt, Eric Cox, Marcella Mori
Software Mentions: 2
Published: over 3 years ago

10.3389/fcimb.2021.673966

In Vivo and In Vitro Genome-Wide Profiling of RNA Secondary Structures Reveals Key Regulatory Features in Plasmodium falciparum
Cited by: 4
Author(s): Yanwei Qi, Yuhong Zhang, Guixing Zheng, Bingxia Chen, Mengxin Zhang, Jian Li, Tao Peng, Jun Huang, Xinhua Wang
Software Mentions: 2
Published: over 3 years ago

10.3389/fcimb.2021.555072

Microbiota Detection Patterns Correlate With Presence and Severity of Barrett’s Esophagus
Cited by: 4
Author(s): Ikenna Okereke, Aaron L. Miller, Daniel C. Jupiter, Catherine Hamilton, Gabriel Reep, Timothy Krill, Clark R. Andersen, Richard B. Pyles
Software Mentions: 2
Published: over 3 years ago

10.3389/fcimb.2019.00123

Genomic and Epidemiological Evidence of a Dominant Panton-Valentine Leucocidin-Positive Methicillin Resistant Staphylococcus aureus Lineage in Sri Lanka and Presence Among Isolates From the United Kingdom and Australia
Cited by: 8
Author(s): Sharla M. McTavish, Sarah J Snow, Ellie C Cook, Bruno Pichon, Sarah Coleman, Geoffrey W. Coombs, Stanley Pang, César A. Arias, Lorena Díaz, Emma Boldock, Sue Davies, M. Udukala, Angela Kearns, Sisira Siribaddana, Thushan I. de Silva
Software Mentions: 2
Published: over 5 years ago

10.3389/fncel.2017.00003

Deep Sequencing of the Human Retinae Reveals the Expression of Odorant Receptors
Cited by: 17
Author(s): Nikolina Jovancevic, Kirsten A. Wunderlich, Claudia Haering, Caroline Flegel, Désirée Maßberg, Markus Weinrich, Lea Weber, Lars Tebbe, Anselm Kampik, Günter Gisselmann, Uwe Wolfrum, Hanns Hatt, Lian Gelis
Software Mentions: 2
Published: almost 8 years ago

10.3389/fncel.2017.00348

Adaptive Changes in the Vestibular System of Land Snail to a 30-Day Spaceflight and Readaptation on Return to Earth
Cited by: 7
Author(s): Nikolay Aseyev, Aliya Vinarskaya, Matvey Roshchin, Tatiana Korshunova, Aleksey Malyshev, Alena B. Zuzina, Victor N. Ierusalimsky, M. S. Lemak, И. С. Захаров, Novikov Ia, P. M. Kolosov, Е. А. Чеснокова, С. А. Волкова, Artem S. Kasianov, Л. А. Урошлев, Yekaterina Popova, Richard D. Boyle, P. M. Balaban
Software Mentions: 2
Published: about 7 years ago

10.3389/fendo.2018.00611

Tissue-Based Mapping of the Fathead Minnow (Pimephales promelas) Transcriptome and Proteome
Cited by: 5
Author(s): Candice M. Lavelle, L. Cody Smith, Joseph H. Bisesi, Fahong Yu, Cecilia Silva-Sanchez, David Moraga-Amador, A. Buerger, Natàlia García-Reyero, Tara Sabo‐Attwood, Nancy D. Denslow
Software Mentions: 2
Published: about 6 years ago

10.3389/fendo.2019.00739

Circulating miRNA Expression Profiling in Primary Aldosteronism
Cited by: 20
Author(s): Ábel Decmann, G Nyírő, Ottó Darvasi, Péter István Turai, Irina Bancos, Ravinder Kaur, Raffaele Pezzani, Maurizio Iacobone, Ivana Kraljević, Darko Kaštelan, Mirko Parasiliti-Caprino, Mauro Maccario, Nina Nirschl, Daniel A. Heinrich, Martín Reincke, Attila Patócs, Péter Igaz
Software Mentions: 2
Published: about 5 years ago

10.3389/fgene.2019.00531

RNA-Seq Revealed Novel Non-proliferative Retinopathy Specific Circulating MiRNAs in T2DM Patients
Cited by: 24
Author(s): Zimeng Li, Ying Dong, Chang He, Xingchen Pan, Dianyuan Liu, Jianli Yang, Liankun Sun, Peng Chen, Qing Wang
Software Mentions: 2
Published: over 5 years ago

10.3389/fgene.2019.00296

Mining Magnaporthe oryzae sRNAs With Potential Transboundary Regulation of Rice Genes Associated With Growth and Defense Through Expression Profile Analysis of the Pathogen-Infected Rice
Cited by: 7
Author(s): Hao Zhang, Sifei Liu, Haowu Chang, Mengping Zhan, Qing‐Ming Qin, Borui Zhang, Zhi Li, Yuanning Liu
Software Mentions: 2
Published: over 5 years ago

10.3389/fgene.2021.634635

Research on the Mechanism of Soybean Resistance to Phytophthora Infection Using Machine Learning Methods
Cited by: 5
Author(s): Junxia Chi, Shizeng Song, Hao Zhang, Yuanning Liu, Hengyi Zhao, Liyan Dong
Software Mentions: 2
Published: almost 4 years ago

10.3389/fgene.2021.660366

UMIc: A Preprocessing Method for UMI Deduplication and Reads Correction
Cited by: 4
Author(s): Maria Tsagiopoulou, Μαρία Μανιού, Nikolaos Pechlivanis, Anastasis Togkousidis, Michaela Kotrová, Tobias Hutzenlaub, Ilias Kappas, Anastasia Chatzidimitriou, Fotis Psomopoulos
Software Mentions: 2
Published: over 3 years ago

10.3389/fgene.2020.00375

Identifying Candida albicans Gene Networks Involved in Pathogenicity
Cited by: 4
Author(s): Graham H. Thomas, Judith M. Bain, Susan Budge, Alistair J. P. Brown, Ryan M. Ames
Software Mentions: 2
Published: over 4 years ago

10.3389/fgene.2021.602528

Transcriptome and Comparative Chloroplast Genome Analysis of Vincetoxicum versicolor: Insights Into Molecular Evolution and Phylogenetic Implication
Cited by: 10
Author(s): Xiaolei Yu, Wenxiu Wang, Hongxia Yang, Xiaoying Zhang, Dan Wang, Xiaoxuan Tian
Software Mentions: 2
Published: over 3 years ago

10.3389/fgene.2019.01183

Transcriptome Analysis Identifies Candidate Genes and Pathways Associated With Feed Efficiency in Hu Sheep
Cited by: 25
Author(s): Deyin Zhang, Xiaoxue Zhang, Fadi Li, Chong Li, Yongfu La, Futao Mo, Guoze Li, Yukun Zhang, Xiaolong Li, Qizhi Song, Yuan Zhao, Weimin Wang
Software Mentions: 2
Published: about 5 years ago

10.3389/fgene.2019.00957

Review, Evaluation, and Directions for Gene-Targeted Assembly for Ecological Analyses of Metagenomes
Cited by: 7
Author(s): Jiarong Guo, John F. Quensen, Yanni Sun, Qiong Wang, C. Titus Brown, James R. Cole, James M. Tiedje
Software Mentions: 2
Published: about 5 years ago

10.3389/fgene.2021.695178

Changthangi Pashmina Goat Genome: Sequencing, Assembly, and Annotation
Cited by: 0
Author(s): Basharat Ahmad Bhat, Nazir Ahmad Ganai, Ashutosh Singh, Rakeeb Ahmad Mir, Syed Mudasir Ahmad, Sajad Majeed Zargar, Firdose Ahmad Malik
Software Mentions: 2
Published: over 3 years ago

10.3389/fgene.2019.00105

Using Pan RNA-Seq Analysis to Reveal the Ubiquitous Existence of 5′ and 3′ End Small RNAs
Cited by: 14
Author(s): Xiao Xu, Haishuo Ji, Xiufeng Jin, Zhi Cheng, Xuemei Yao, Yanqiang Liu, Qiang Zhao, Tao Zhang, Jishou Ruan, Wenjun Bu, Ze Chen, Shan Gao
Software Mentions: 2
Published: almost 6 years ago

10.3389/fimmu.2020.00027

Computational Prediction and Validation of Tumor-Associated Neoantigens
Cited by: 72
Author(s): Vladimir Roudko, Benjamin Greenbaum, Nina Bhardwaj
Software Mentions: 2
Published: almost 5 years ago

10.3389/fmicb.2017.00126

Exo-miRExplorer: A Comprehensive Resource for Exploring and Comparatively Analyzing Exogenous MicroRNAs
Cited by: 5
Author(s): Ling‐Ling Zheng, Kai-Wen Deng, An-Cheng Deng, Jie Wu, Jianhua Yang, Zhao‐Rong Lun, Liang‐Hu Qu
Software Mentions: 2
Published: almost 8 years ago

10.3389/fmicb.2021.683481

Bacteriomic Analyses of Asian Citrus Psyllid and Citrus Samples Infected With “Candidatus Liberibacter asiaticus” in Southern California and Huanglongbing Management Implications
Cited by: 4
Author(s): Jiaquan Huang, Zhigang Dai, Zheng Zhang, Priscila A da Silvia, Lucita Kumagai, Qijun Xiang, Jianchi Chen, Xiaoling Deng
Software Mentions: 2
Published: over 3 years ago

10.1186/s40064-016-2902-1

Comparative profiling of differentially expressed microRNAs between the follicular and luteal phases ovaries of goats
Cited by: 10
Author(s): Long Zhu, Tao Chen, Menghua Sui, Chunyang Han, Fugui Fang, Yuehui Ma, Mingxing Chu, Xiaorong Zhang, Cuiyan Liu, Yinghui Ling
Software Mentions: 2
Published: over 8 years ago

10.1016/j.stemcr.2016.11.014

Cytosine-5 RNA Methylation Regulates Neural Stem Cell Differentiation and Motility
Cited by: 118
Author(s): Joana V. Flores, Lucía Cordero-Espinoza, Feride Oeztuerk-Winder, Amanda Andersson-Rolf, Tommaso Selmi, Sandra Blanco, Jignesh Tailor, Sabine Dietmann, Michaela Frye
Software Mentions: 2
Published: almost 8 years ago

10.1186/s13287-015-0116-z

Human bone marrow- and adipose-mesenchymal stem cells secrete exosomes enriched in distinctive miRNA and tRNA species
Cited by: 559
Author(s): S. Rubina Baglio, Koos Rooijers, Danijela Koppers-Lalić, Frederik J. Verweij, M Pérez Lanzón, Nicoletta Zini, B.A. Naaijkens, Francesca Perut, Hans W.M. Niessen, Nicola Baldini, D. Michiel Pegtel
Software Mentions: 2
Published: over 9 years ago

10.7150/thno.43577

Exercise protects proliferative muscle satellite cells against exhaustion via the Igfbp7-Akt-mTOR axis
Cited by: 24
Author(s): Zhe Chen, Lei Li, Weiru Wu, Zhilong Liu, Yongxiu Huang, Li Yang, Qing Luo, Jieping Chen, Yu Hou, Guanbin Song
Software Mentions: 2
Published: almost 5 years ago

10.3390/toxins12010041

Aberrant Expressional Profiling of Known MicroRNAs in the Liver of Silver Carp (Hypophthalmichthys molitrix) Following Microcystin-LR Exposure Based on samllRNA Sequencing
Cited by: 6
Author(s): Yiyi Feng, Xi Chen, Jing Ma, Bangjun Zhang, Xiaoyü Li
Software Mentions: 2
Published: almost 5 years ago

10.1101/2020.11.16.385278

High resolution profiling of pathways of escape for SARS-CoV-2 spike-binding antibodies
Cited by: 8
Author(s): Meghan Garrett, Jared Galloway, Helen Y. Chu, Hannah L. Itell, Caitlin I. Stoddard, Caitlin R Wolf, Jennifer K. Logue, Dylan McDonald, F. A. Matsen, Julie Overbaugh
Software Mentions: 2
Published: about 4 years ago

10.1128/mBio.02027-20

Survey of Early-Diverging Lineages of Fungi Reveals Abundant and Diverse Mycoviruses
Cited by: 32
Author(s): Jillian M. Myers, Anne E. Bonds, Rebecca A. Clemons, Natasha Thapa, D. Rabern Simmons, Derreck Carter-House, Jericho Ortañez, P. Liu, Alejandro Miralles-Durán, Alessandro Desirò, Joyce E. Longcore, Gregory Bonito, Jason E. Stajich, J. W. Spatafora, Ying Chang, Luis M. Corrochano, Andrii P. Gryganskyi, Igor V. Grigoriev, Timothy Y. James
Software Mentions: 2
Published: about 4 years ago

10.1128/mBio.03649-20

Whole-Genome Transformation Promotes tRNA Anticodon Suppressor Mutations under Stress
Cited by: 2
Author(s): Quinten Deparis, Jorge Duitama, María R. Foulquié-Moreno, Johan M. Thevelein
Software Mentions: 2
Published: over 3 years ago

10.1128/mSphere.00855-20

Structured RNA Contaminants in Bacterial Ribo-Seq
Cited by: 15
Author(s): Brayon J. Fremin, Ami S. Bhatt
Software Mentions: 2
Published: about 4 years ago

10.1128/mSystems.00673-19

Selection Is a Significant Driver of Gene Gain and Loss in the Pangenome of the Bacterial Genus Sulfurovum in Geographically Distinct Deep-Sea Hydrothermal Vents
Cited by: 33
Author(s): Alief Moulana, R. Anderson, Caroline S. Fortunato, Julie A. Huber
Software Mentions: 2
Published: over 4 years ago

10.1128/mSystems.01078-20

Complementary Roles of Wood-Inhabiting Fungi and Bacteria Facilitate Deadwood Decomposition
Cited by: 61
Author(s): Vojtěch Tláskal, Vendula Brabcová, Tomáš Větrovský, Mayuko Jomura, Rubén López-Mondéjar, Lummy Maria Oliveira Monteiro, J. Saraiva, Zander Rainier Human, Tomáš Cajthaml, Ulisses Nunes da Rocha, Petr Baldrián
Software Mentions: 2
Published: over 3 years ago

10.1128/mSystems.00704-21

Identification and Differentiation of Pseudomonas Species in Field Samples Using an rpoD Amplicon Sequencing Methodology
Cited by: 9
Author(s): Jonas Greve Lauritsen, Morten Lindqvist Hansen, Pernille Kjersgaard Bech, Lars Jelsbak, Lone Gram, Mikael Lenz Strube
Software Mentions: 2
Published: about 3 years ago

10.1093/hmg/ddy405

Dynamic transcriptomic analysis reveals suppression of PGC1α/ERRα drives perturbed myogenesis in facioscapulohumeral muscular dystrophy
Cited by: 46
Author(s): Christopher R. S. Banerji, Maryna Panamarova, Johanna Prüller, Nicolas Figeac, Husam Hebaishi, Efthymios Fidanis, Alka Saxena, Julian Contet, Sabrina Sacconi, Simone Severini, Peter S. Zammit
Software Mentions: 2
Published: almost 6 years ago

10.1155/2015/527054

Genome-Wide Identification of Genes Probably Relevant to the Uniqueness of Tea Plant (Camellia sinensis) and Its Cultivars
Cited by: 2
Author(s): Yan Wei, Jing Wang, Youxiang Zhou, Mingming Zhao, Yan Gong, Hua Ding, Lijun Peng, HU Ding-jin
Software Mentions: 2
Published: almost 10 years ago

10.1038/s41388-018-0530-7

Acetylation of AGO2 promotes cancer progression by increasing oncogenic miR-19b biogenesis
Cited by: 50
Author(s): Hailong Zhang, Yanli Wang, Jinzhuo Dou, Yanmin Guo, Jianfeng He, Lian Li, Xiaojia Liu, Ran Chen, Rong Deng, Jian Huang, Ruiyu Xie, Xian Zhao, Jianxiu Yu
Software Mentions: 2
Published: about 6 years ago

10.1038/s41389-020-0205-4

Post-transcriptional regulation of BRG1 by FIRΔexon2 in gastric cancer
Cited by: 9
Author(s): Guzhanuer Ailiken, Kazuo Kïtamura, Tyuji Hoshino, Mamoru Satoh, Nobuko Tanaka, Toshinari Minamoto, Bahityar Rahmutulla, Sohei Kobayashi, Masayuki Kano, Tomoaki Tanaka, Atsushi Kaneda, Fumio Nomura, Hisahiro Matsubara, Hiroshi Matsushita
Software Mentions: 2
Published: almost 5 years ago

10.3892/or.2019.7300

In�vivo effects of mutant RHOA on tumor formation in an orthotopic inoculation model
Cited by: 2
Author(s): Takashi Nishizawa, Kiyotaka Nakano, Etsuko Fujii, Daisuke Komura, Yoshie Kuroiwa, Chisako Ishimaru, Makoto Monnai, Hiroyuki Aburatani, Shumpei Ishikawa, Masami Suzuki
Software Mentions: 2
Published: about 5 years ago

10.7554/eLife.48725

Tyr1 phosphorylation promotes phosphorylation of Ser2 on the C-terminal domain of eukaryotic RNA polymerase II by P-TEFb
Cited by: 21
Author(s): Joshua E. Mayfield, Seema Irani, Edwin E. Escobar, Zhao Zhang, Nathaniel T. Burkholder, Michelle Robinson, M. Rachel Mehaffey, Sarah N. Sipe, Weiwei Yang, Nicholas Adrian Prescott, Karan R. Kathuria, Zhijie Liu, Jennifer S. Brodbelt, Yan Zhang
Software Mentions: 2
Published: over 5 years ago

10.7554/eLife.06205

In vivo targeting of de novo DNA methylation by histone modifications in yeast and mouse
Cited by: 142
Author(s): Marco Morselli, William A. Pastor, Barbara Montanini, Kevin Nee, Roberto Ferrari, Kai Fu, Giancarlo Bonora, Liudmilla Rubbi, Amander T. Clark, Simone Ottonello, Steven E. Jacobsen, Matteo Pellegrini
Software Mentions: 2
Published: over 9 years ago

10.7554/eLife.29938

Msn2/4 regulate expression of glycolytic enzymes and control transition from quiescence to growth
Cited by: 47
Author(s): Zheng Kuang, Sudarshan Pinglay, Hongkai Ji, Jef D. Boeke
Software Mentions: 2
Published: about 7 years ago

10.7554/eLife.06722

Quality control of transcription start site selection by nonsense-mediated-mRNA decay
Cited by: 105
Author(s): Christophe Malabat, Frank Feuerbach, Laurence Ma, Cosmin Saveanu, Alain Jacquier
Software Mentions: 2
Published: over 9 years ago

10.7554/eLife.09003

A gene-expression screen identifies a non-toxic sumoylation inhibitor that mimics SUMO-less human LRH-1 in liver
Cited by: 32
Author(s): Miyuki Suzawa, Diego A. Miranda, Karmela A Ramos, Kenny K-H Ang, Emily J. Faivre, Christopher G. Wilson, Laura Caboni, Michelle R. Arkin, Yeong-Sang Kim, Robert J. Fletterick, Aaron A. Diaz, John S. Schneekloth, Holly A. Ingraham
Software Mentions: 2
Published: almost 9 years ago

10.7554/eLife.52212

MS-275, a class 1 histone deacetylase inhibitor augments glucagon-like peptide-1 receptor agonism to improve glycemic control and reduce obesity in diet-induced obese mice
Cited by: 9
Author(s): Shilpak Dilip Bele, Shravan Babu Girada, Arnab Ray, Abhishek Gupta, Srinivas Oruganti, Phanithi Prakash Babu, Rahul Sr Rayalla, Shashi Vardhan Kalivendi, Ahamed Ibrahim, Vishwajeet Puri, Venkateswar Adalla, Madhumohan R. Katika, Richard D. DiMarchi, Prasenjit Mitra
Software Mentions: 2
Published: almost 4 years ago

10.7554/eLife.21615

TGF-β reduces DNA ds-break repair mechanisms to heighten genetic diversity and adaptability of CD44+/CD24− cancer cells
Cited by: 33
Author(s): Debjani Pal, Anja Pertot, Nitin H. Shirole, Zhan Yao, Naishitha Anaparthy, Tyler Garvin, Hilary Cox, Kenneth Chang, Fred Rollins, Jude Kendall, Leyla Edwards, Vijay A Singh, Gary C. Stone, Michael C. Schatz, James Hicks, Gregory J. Hannon, Raffaella Sordella
Software Mentions: 2
Published: almost 8 years ago

10.7554/eLife.18270

MYC activation and BCL2L11 silencing by a tumour virus through the large-scale reconfiguration of enhancer-promoter hubs
Cited by: 74
Author(s): C. David Wood, Hildegonda Veenstra, Sarika Khasnis, Andrea Gunnell, Helen Webb, Claire Shannon-Lowe, Simon Andrews, Cameron S. Osborne, Michelle J. West
Software Mentions: 2
Published: over 8 years ago

10.7554/eLife.67236

High-resolution, genome-wide mapping of positive supercoiling in chromosomes
Cited by: 27
Author(s): Monica S. Guo, Ryo Kawamura, Megan L Littlehale, John F. Marko, Michael T. Laub
Software Mentions: 2
Published: over 3 years ago

10.7554/eLife.06068

Release of human cytomegalovirus from latency by a KAP1/TRIM28 phosphorylation switch
Cited by: 85
Author(s): Benjamin Rauwel, Suk Min Jang, Marco Cassano, Adamandia Kapopoulou, Isabelle Barde, Didier Trono
Software Mentions: 2
Published: over 9 years ago

10.7554/eLife.57858

Functional interrogation of HOXA9 regulome in MLLr leukemia via reporter-based CRISPR/Cas9 screen
Cited by: 21
Author(s): Hao Zhang, Yang Zhang, Xinyue Zhou, Shaela Wright, Judith Hyle, Lianzhong Zhao, Jie An, Xujie Zhao, Ying Shao, Beisi Xu, Hyeong-Min Lee, Taosheng Chen, Yang Zhou, Xiang Chen, Rui Lu, Chunliang Li
Software Mentions: 2
Published: about 4 years ago

10.7554/eLife.62994

The Arabidopsis active demethylase ROS1 cis-regulates defence genes by erasing DNA methylation at promoter-regulatory regions
Cited by: 54
Author(s): Thierry Halter, Jingyu Wang, Delase Amesefe, Emmanuelle Lastrucci, Magali Charvin, Meenu Singla Rastogi, Lionel Navarro
Software Mentions: 2
Published: almost 4 years ago

10.7554/eLife.33361

G9a regulates temporal preimplantation developmental program and lineage segregation in blastocyst
Cited by: 27
Author(s): J. Ż̷ylicz, Maud Borensztein, Frederick C K Wong, Yun Huang, Caroline Lee, Sabine Dietmann, M. Azim Surani
Software Mentions: 2
Published: over 6 years ago

10.7554/eLife.11275

Comparative analysis of viral RNA signatures on different RIG-I-like receptors
Cited by: 79
Author(s): Raul Y. Sanchez David, Chantal Combredet, Odile Sismeiro, Marie‐Agnès Dillies, Bernd Jagla, Jean‐Yves Coppée, Marie Mura, Mathilde Guerbois Galla, Philippe Desprès, Frédéric Tangy, Anastassia V. Komarova
Software Mentions: 2
Published: over 8 years ago

10.7554/eLife.17548

Co-transcriptional R-loops are the main cause of estrogen-induced DNA damage
Cited by: 208
Author(s): Caroline Townsend Stork, M Bocek, Madzia P Crossley, Julie Sollier, Lionel A. Sanz, Frédéric Chédin, Tomek Swigut, Karlene A. Cimprich
Software Mentions: 2
Published: about 8 years ago

10.7554/eLife.09571

Chromatin dynamics and the role of G9a in gene regulation and enhancer silencing during early mouse development
Cited by: 95
Author(s): J. Ż̷ylicz, Sabine Dietmann, Ufuk Günesdogan, Jim Hackett, Delphine Cougot, Caroline Lee, M. Azim Surani
Software Mentions: 2
Published: about 9 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

10.1016/j.ajhg.2017.01.011

Decreased STARD10 Expression Is Associated with Defective Insulin Secretion in Humans and Mice
Cited by: 61
Author(s): Gaëlle Carrat, Ming Hu, Marie‐Sophie Nguyen‐Tu, Pauline Chabosseau, Kyle J. Gaulton, Martijn van de Bunt, Afshan Siddiq, Mario Falchi, Matthias Thurner, Mickaël Canouil, François Pattou, Isabelle Leclerc, Timothy J. Pullen, Matthew Cane, Priyanka Prabhala, William W. Greenwald, Anke Schulte, Piero Marchetti, Mark Ibberson, Patrick E. MacDonald, Jocelyn E. Manning Fox, Anna L. Gloyn, Philippe Froguel, Michele Solimena, Mark I. McCarthy, Guy A. Rutter
Software Mentions: 2
Published: almost 8 years ago

10.1111/age.12992

Identification and characterization of miRNAs during early pregnancy in domestic sheep
Cited by: 6
Author(s): Kisun Pokharel, Jaana Peippo, Menghua Li, Juha Kantanen
Software Mentions: 2
Published: over 4 years ago

10.1186/s12859-017-1601-4

QuickMIRSeq: a pipeline for quick and accurate quantification of both known miRNAs and isomiRs by jointly processing multiple samples from microRNA sequencing
Cited by: 34
Author(s): Shanrong Zhao, William Gordon, Sarah Du, Chi Zhang, Wen He, Li Xi, Sachin Mathur, Michael Agostino, Theresa Paradis, David von Schack, Michael S. Vincent, Baohong Zhang
Software Mentions: 2
Published: over 7 years ago

10.1186/1471-2105-12-S14-S2

Optimizing de novo transcriptome assembly from short-read RNA-Seq data: a comparative study
Cited by: 417
Author(s): Qiongyi Zhao, Yi Wang, Yawei Kong, Da Luo, Xuan Li, Pei Hao
Software Mentions: 2
Published: almost 13 years ago

10.1186/s12859-017-1873-8

riboviz: analysis and visualization of ribosome profiling datasets
Cited by: 35
Author(s): Oana Carja, Tongji Xing, Eric Wallace, Joshua B. Plotkin, Premal Shah
Software Mentions: 2
Published: about 7 years ago

10.1186/s12859-017-1548-5

Manananggal - a novel viewer for alternative splicing events
Cited by: 7
Author(s): Matthias Barann, Ralf Zimmer, Fabian Birzele
Software Mentions: 2
Published: almost 8 years ago

10.1186/1471-2105-11-514

Data structures and compression algorithms for high-throughput sequencing technologies
Cited by: 45
Author(s): Kenneth Daily, Paul Rigor, Scott Christley, Xiaohui Xie, Pierre Baldi
Software Mentions: 2
Published: about 14 years ago

10.1186/s12859-015-0704-z

EMSAR: estimation of transcript abundance from RNA-seq data by mappability-based segmentation and reclustering
Cited by: 18
Author(s): Mi Kyung Lee, Chae Hwa Seo, B. Alver, Sanghyuk Lee, Peter J. Park
Software Mentions: 2
Published: about 9 years ago

10.1186/s12859-018-2570-y

Stepwise large genome assembly approach: a case of Siberian larch (Larix sibirica Ledeb)
Cited by: 38
Author(s): Dmitry A. Kuzmin, Sergey Feranchuk, Vadim V. Sharov, Alexander N. Cybin, Stepan V. Makolov, Yuliya A. Putintseva, Н. В. Орешкова, Konstantin V. Krutovsky
Software Mentions: 2
Published: almost 6 years ago

10.1186/s12859-021-04004-y

HOME-BIO (sHOtgun MEtagenomic analysis of BIOlogical entities): a specific and comprehensive pipeline for metagenomic shotgun sequencing data analysis
Cited by: 7
Author(s): Carlo Ferravante, Domenico Memoli, Domenico Palumbo, Paolo Ciaramella, Antonio Di Loria, Ylenia D’Agostino, Giovanni Nassa, Francesca Rizzo, Roberta Tarallo, Alessandro Weisz, Giorgio Giurato
Software Mentions: 2
Published: over 3 years ago

10.1186/s12915-020-00926-w

miR-31-5p regulates cold acclimation of the wood-boring beetle Monochamus alternatus via ascaroside signaling
Cited by: 26
Author(s): Bin Zhang, Lilin Zhao, Jing Ning, Jacob D. Wickham, Huanfang Tian, Xiaoming Zhang, Meiling Yang, Xiangming Wang, Sun Jian
Software Mentions: 2
Published: almost 4 years ago

10.1186/1471-213X-14-15

Integrated proteomic and transcriptomic analysis of the Aedes aegyptieggshell
Cited by: 58
Author(s): Osvaldo Marinotti, Tuan Ngo, Bianca Burini Kojin, Shao‐Pei Chou, Brian D. Nguyen, Jennifer Juhn, Rebeca Carballar-Lejarazú, Pedro N. Marinotti, Xiaofang Jiang, Marika F. Walter, Zhijian Tu, Paul D. Gershon, Anthony A. James
Software Mentions: 2
Published: over 10 years ago

10.1186/s12861-015-0089-2

MiR-21 is required for efficient kidney regeneration in fish
Cited by: 27
Author(s): Beate Hoppe, Stefan Pietsch, Martin Franke, Sven Engel, Marco Groth, Matthias Platzer, Christoph Englert
Software Mentions: 2
Published: about 9 years ago

10.1186/s12862-016-0844-4

Genetic mechanisms of bone digestion and nutrient absorption in the bone-eating worm Osedax japonicus inferred from transcriptome and gene expression analyses
Cited by: 19
Author(s): Norio Miyamoto, Masa‐aki Yoshida, Hisao Koga, Yoshihiro Fujiwara
Software Mentions: 2
Published: almost 8 years ago

10.1186/s12864-016-3271-4

Identification and characterization of microRNAs in Humulus lupulus using high-throughput sequencing and their response to Citrus bark cracking viroid (CBCVd) infection
Cited by: 25
Author(s): Ajay Kumar Mishra, G Duraisamy, J. Matoušek, Sebastjan Radišek, Branka Javornik, Jernej Jakše
Software Mentions: 2
Published: about 8 years ago

10.1186/s12864-020-07318-y

Unbiased RNA-Seq-driven identification and validation of reference genes for quantitative RT-PCR analyses of pooled cancer exosomes
Cited by: 17
Author(s): Yanjun Dai, Yumeng Cao, Jens Köhler, Aiping Lu, Shaohua Xu, Haiyun Wang
Software Mentions: 2
Published: almost 4 years ago

10.1186/s12864-015-1442-3

Transcriptome characterization of three wild Chinese Vitis uncovers a large number of distinct disease related genes
Cited by: 20
Author(s): Chen Jiao, Min Gao, Xiping Wang, Zhangjun Fei
Software Mentions: 2
Published: over 9 years ago

10.1186/1471-2164-14-415

Global transcriptome profiles of Camellia sinensis during cold acclimation
Cited by: 239
Author(s): Xinchao Wang, Qiongyi Zhao, Chun-Lei Ma, Zong Hong Zhang, Hongli Cao, Yawei Kong, Chuan Yue, Xinyuan Hao, Liang Chen, Jianqiang Ma, Jiye Jin, Xuan Li, Yajun Yang
Software Mentions: 2
Published: over 11 years ago

10.1186/s12864-015-2011-5

The Perchlorate Reduction Genomic Island: Mechanisms and Pathways of Evolution by Horizontal Gene Transfer
Cited by: 30
Author(s): Ryan A. Melnyk, John D. Coates
Software Mentions: 2
Published: about 9 years ago

10.1186/1471-2164-15-98

A genomic perspective to assessing quality of mass-reared SIT flies used in Mediterranean fruit fly (Ceratitis capitata) eradication in California
Cited by: 31
Author(s): Bernarda Calla, Brian E. Hall, Shaobin Hou, Scott M. Geib
Software Mentions: 2
Published: almost 11 years ago

10.1186/s12864-020-06906-2

Precise annotation of tick mitochondrial genomes reveals multiple copy number variation of short tandem repeats and one transposon-like element
Cited by: 16
Author(s): Ze Chen, Yibo Xuan, Guangcai Liang, Xiaolong Yang, Zhou Yu, Stephen C. Barker, Samuel Kelava, Wenjun Bu, Jingze Liu, Shan Gao
Software Mentions: 2
Published: over 4 years ago

Projects: pypi: bowtie

Papers Mentioning bowtie 1,566