Ecosyste.ms: Papers

An open API service providing mapping between scientific papers and software projects that are mentioned in them.
All mentions data is based on the CZI Software Mentions dataset.

Projects: pypi: bowtie

https://packages.ecosyste.ms/registries/pypi.org/packages/bowtie

Interactive Dashboard Toolkit.
43 versions
Latest release: about 6 years ago
1 dependent package
221 downloads last month

Papers Mentioning bowtie 1,566

10.7554/eLife.41927
Nuclear genetic regulation of the human mitochondrial transcriptome
Cited by: 50
Author(s): Ali At, Lena Boehme, Guillermo Carbajosa, Vlad C. Seitan, Kerrin S. Small, Alan Hodgkinson
Software Mentions: 3
Published: almost 6 years ago
10.7554/eLife.02407
Genome-wide dynamics of Pol II elongation and its interplay with promoter proximal pausing, chromatin, and exons
Cited by: 464
Author(s): Iris Jonkers, Ho Young Kwak, John T. Lis
Software Mentions: 3
Published: over 10 years ago
10.7554/eLife.00808
Condensin controls recruitment of RNA polymerase II to achieve nematode X-chromosome dosage compensation
Cited by: 159
Author(s): William S. Kruesi, Leighton J. Core, Colin T. Waters, John T. Lis, Barbara J Meyer
Software Mentions: 3
Published: over 11 years ago
10.7554/eLife.36144
TALE factors use two distinct functional modes to control an essential zebrafish gene expression program
Cited by: 21
Author(s): Franck Ladam, William Stanney, Ian J. Donaldson, Ozge Yildiz, Nicoletta Bobola, Charles G. Sagerström
Software Mentions: 3
Published: over 6 years ago
10.7554/eLife.14295
Activation of GCN2 kinase by ribosome stalling links translation elongation with translation initiation
Cited by: 125
Author(s): Ryuta Ishimura, Gábor Nagy, Iván Dotú, Jeffrey H. Chuang, Susan L. Ackerman
Software Mentions: 3
Published: over 8 years ago
10.7554/eLife.35989
Systematic perturbation of retroviral LTRs reveals widespread long-range effects on human gene regulation
Cited by: 129
Author(s): Daniel Fuentes, Tomek Swigut, Joanna Wysocka
Software Mentions: 3
Published: over 6 years ago
10.7554/eLife.29494
Alternative RNA splicing in the endothelium mediated in part by Rbfox2 regulates the arterial response to low flow
Cited by: 23
Author(s): Patrick A. Murphy, Vincent Butty, Paul L. Boutz, Shahinoor Begum, Amy Kimble, Phillip A. Sharp, Christopher B. Burge, Richard O. Hynes
Software Mentions: 3
Published: almost 7 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
10.7554/eLife.01439
Coordinated genomic control of ciliogenesis and cell movement by RFX2
Cited by: 115
Author(s): Mei I. Chung, Taejoon Kwon, Fan Tu, Eric Brooks, Ritu Gupta, Matthew D. Meyer, Julie C. Baker, Edward M. Marcotte, John B. Wallingford
Software Mentions: 3
Published: almost 11 years ago
10.7554/eLife.32341
CATaDa reveals global remodelling of chromatin accessibility during stem cell differentiation in vivo
Cited by: 60
Author(s): Gabriel Aughey, Alicia Estacio-Gómez, Jamie Thomson, Hang Yin, Tony D. Southall
Software Mentions: 3
Published: over 6 years ago
10.7554/eLife.18290
Tet2 and Tet3 cooperate with B-lineage transcription factors to regulate DNA modification and chromatin accessibility
Cited by: 109
Author(s): Chan-Wang Jerry Lio, Jiayuan Zhang, Edahí González-Avalos, Patrick G. Hogan, Xing Chang, Anjana Rao
Software Mentions: 3
Published: about 8 years ago
10.7554/eLife.27596
Maturation of selected human mitochondrial tRNAs requires deadenylation
Cited by: 68
Author(s): Sarah F Pearce, Joanna Rorbach, Lindsey Van Haute, Aaron R. D’Souza, Pedro Rebelo-Guiomar, Christopher A. Powell, Ian Brierley, Andrew E. Firth, Michal Minczuk
Software Mentions: 3
Published: over 7 years ago
10.7554/eLife.26845
Unfolded protein response transducer IRE1-mediated signaling independent of XBP1 mRNA splicing is not required for growth and development of medaka fish
Cited by: 34
Author(s): Tokiro Ishikawa, Makoto Kashima, Atsushi J. Nagano, Tomoko Ishikawa-Fujiwara, Yasuhiro Kamei, Tomoki Todo, Kazutoshi Mori
Software Mentions: 3
Published: about 7 years ago
10.7554/eLife.71611
A nascent polypeptide sequence modulates DnaA translation elongation in response to nutrient availability
Cited by: 3
Author(s): Michèle Felletti, Cédric Romilly, E. Gerhart H. Wagner, Kristina Jonas
Software Mentions: 3
Published: about 3 years ago
10.7554/eLife.00011
Nascent-Seq reveals novel features of mouse circadian transcriptional regulation
Cited by: 273
Author(s): Jérôme S. Menet, Joseph Rodriguez, Katharine C. Abruzzi, Michael Rosbash
Software Mentions: 3
Published: about 12 years ago
10.7554/eLife.21964
DNA methylation directs genomic localization of Mbd2 and Mbd3 in embryonic stem cells
Cited by: 25
Author(s): Sarah J. Hainer, Kurtis N. McCannell, Jun Yu, Ly-Sha Ee, Lihua Julie Zhu, Oliver J. Rando, Thomas G. Fazzio
Software Mentions: 3
Published: about 8 years ago
10.7554/eLife.49314
Kinetics of cytokine receptor trafficking determine signaling and functional selectivity
Cited by: 31
Author(s): Jonathan Martínez-Fábregas, Stephan Wilmes, Luopin Wang, Maximillian Hafer, Elizabeth Pöhler, Juliane Lokau, Christoph Garbers, Adeline Cozzani, Paul K. Fyfe, Jacob Piehler, Majid Kazemian, Suman Mitra, Ignacio Moraga
Software Mentions: 3
Published: almost 5 years ago
10.3390/ijms21218252
Aging Induces Profound Changes in sncRNA in Rat Sperm and These Changes Are Modified by Perinatal Exposure to Environmental Flame Retardant
Cited by: 9
Author(s): Alexander Suvorov, J. Richard Pilsner, В. А. Наумов, Victoria Shtratnikova, Anna Zheludkevich, Evgeny S. Gerasimov, Maria D. Logacheva, Oleg Sergeyev
Software Mentions: 3
Published: about 4 years ago
10.3389/fcvm.2018.00159
Transcriptional Profiling of Hypoxia-Regulated Non-coding RNAs in Human Primary Endothelial Cells
Cited by: 22
Author(s): Pierre R. Moreau, Tiit Örd, Nicholas Downes, Henri Niskanen, Maria Bouvy-Liivrand, Einari Aavik, Seppo Ylä‐Herttuala, Minna U. Kaikkonen
Software Mentions: 3
Published: about 6 years ago
10.3389/fcell.2021.697947
Coordinated Expressional Landscape of the Human Placental miRNome and Transcriptome
Cited by: 14
Author(s): Rain Inno, Triin Kikas, Kristiina Lillepea, Maris Laan
Software Mentions: 3
Published: over 3 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 4 years ago
10.1371/journal.pone.0096105
Patterns of Genome-Wide VDR Locations
Cited by: 112
Author(s): Pauli Tuoresmäki, Sami Vaïsänen, Antonio Neme, Sami Heikkinen, Carsten Carlberg
Software Mentions: 3
Published: over 10 years ago
10.1371/journal.pone.0067788
LOcating Non-Unique matched Tags (LONUT) to Improve the Detection of the Enriched Regions for ChIP-seq Data
Cited by: 11
Author(s): Rui Wang, Hang Kai Hsu, Adam Blattler, Yisong Wang, Xun Lan, Yao Wang, Pei Yin Hsu, Yu Wei Leu, Tim H.M. Huang, Peggy J. Farnham, Victor X. Jin
Software Mentions: 3
Published: over 11 years ago
10.1371/journal.pone.0226905
Identification and characterization of miRNAs involved in cold acclimation of zebrafish ZF4 cells
Cited by: 9
Author(s): Xiangqin Ji, Penglei Jiang, Juntao Luo, Mengjia Li, Yajing Bai, Junfang Zhang, Bingshe Han
Software Mentions: 3
Published: almost 5 years ago
10.1371/journal.pone.0094270
Improved Annotation of 3′ Untranslated Regions and Complex Loci by Combination of Strand-Specific Direct RNA Sequencing, RNA-Seq and ESTs
Cited by: 27
Author(s): Nicholas J. Schurch, Christian Callebaut, Alexander Sherstnev, Junfang Song, Céline Duc, Kate G. Storey, Whi McLean, Sara J. Brown, Gordon G. Simpson, Geoffrey J. Barton
Software Mentions: 3
Published: over 10 years ago
10.1186/s13059-020-02256-0
Disome-seq reveals widespread ribosome collisions that promote cotranslational protein folding
Cited by: 55
Author(s): Taolan Zhao, Yanming Chen, Yü Liu, Jia Wang, Siyu Chen, Ning Gao, Wenfeng Qian
Software Mentions: 3
Published: almost 4 years ago
10.3389/fgene.2021.686851
RESIC: A Tool for Comprehensive Adenosine to Inosine RNA Editing Site Identification and Classification
Cited by: 4
Author(s): Dean Light, Roni Haas, Mahmoud Yazbak, Tal Elfand, Tal Blau, Ayelet T. Lamm
Software Mentions: 3
Published: over 3 years ago
10.3389/fgene.2019.01268
Epigenetic and Transcriptomic Characterization of Pure Adipocyte Fractions From Obese Pigs Identifies Candidate Pathways Controlling Metabolism
Cited by: 10
Author(s): Mette Juul Jacobsen, Jakob Hull Havgaard, Christian Anthon, Caroline M. Junker Mentzel, Susanna Cirera, Poula Maltha Krogh, Sachin Pundhir, Peter Karlskov-Mortensen, Camilla S. Bruun, Philippe Lesnik, Maryse Guérin, Jan Gorodkin, Claus B. Jørgensen, Merete Fredholm, Romain Barrès
Software Mentions: 3
Published: almost 5 years ago
10.1371/journal.pone.0151522
Genome-Wide Analysis and Characterization of Aux/IAA Family Genes in Brassica rapa
Cited by: 25
Author(s): Paul Pavlidis, Vignesh Dhandapani, Jana Jeevan Rameneni, Xiaonan Li, Ganesan Sivanandhan, Su Ryun Choi, Wenxing Pang, Subin Im, Yong Pyo Lim
Software Mentions: 3
Published: over 8 years ago
10.1186/s13059-020-02142-9
RNA G-quadruplex structures exist and function in vivo in plants
Cited by: 63
Author(s): Xiaofei Yang, Jitender Cheema, Yueying Zhang, Huiyong Deng, Susan Duncan, Mubarak Ishaq Umar, Jieyu Zhao, Qi Liu, Xiaofeng Cao, Chun Kit Kwok, Yiliang Ding
Software Mentions: 3
Published: about 4 years ago
10.3390/ijms20225734
A Single Synonymous Variant (c.354G>A [p.P118P]) in ADAMTS13 Confers Enhanced Specific Activity
Cited by: 23
Author(s): Ryan Hunt, Gaya Hettiarachchi, Upendra Katneni, Nancy Hernandez, David D. Holcomb, Jacob Kames, Redab Alnifaidy, Brian C. Lin, Nobuko Hamasaki-Katagiri, Aaron Wesley, Tal Kafri, Christina Morris, Laura Bouché, Maria Panico, Tal Schiller, Juan C. Ibla, Haim Bar, Amra Ismail, Howard R. Morris, Anton A. Komar
Software Mentions: 3
Published: about 5 years ago
10.3389/fgene.2014.00031
Multi-genome alignment for quality control and contamination screening of next-generation sequencing data
Cited by: 21
Author(s): James Hadfield, Matthew Eldridge
Software Mentions: 3
Published: almost 11 years ago
10.3389/fgene.2014.00150
Characterization of HPV DNA methylation of contiguous CpG sites by bisulfite treatment and massively parallel sequencing—the FRAGMENT approach
Cited by: 8
Author(s): Chang Sun, Thomas McAndrew, Benjamin Smith, Zigui Chen, Marina Frimer, Robert D. Burk
Software Mentions: 3
Published: over 10 years ago
10.3389/fgene.2019.01356
The Sole Mycobacterium smegmatis MazF Toxin Targets tRNALys to Impart Highly Selective, Codon-Dependent Proteome Reprogramming
Cited by: 7
Author(s): Valdir C. Barth, Nancy A. Woychik
Software Mentions: 3
Published: almost 5 years ago
10.3389/fgene.2019.00431
Analyses of a Panel of Transcripts Identified From a Small Sample Size and Construction of RNA Networks in Hepatocellular Carcinoma
Cited by: 13
Author(s): Sheng Zhang, Xiaolin Wang, Ge‐Liang Xu, Shengfang Ge, Chen Liang
Software Mentions: 3
Published: over 5 years ago
10.3389/fgene.2020.590672
Integrative Epigenomic Analysis of Transcriptional Regulation of Human CircRNAs
Cited by: 3
Author(s): Xuecang Li, Zhidong Tang, Li Peng, Yanyu Li, Fengcui Qian, Jian Zhao, Ling-Wen Ding, Xiaojuan Du, Meng Li, Jian Zhang, Xuefeng Bai, Jiang Zhu, Chenchen Feng, Qiuyu Wang, Jian Pan, Chunquan Li
Software Mentions: 3
Published: almost 4 years ago
10.1186/s13059-020-02036-w
Protection from DNA re-methylation by transcription factors in primordial germ cells and pre-implantation embryos can explain trans-generational epigenetic inheritance
Cited by: 38
Author(s): Isaac Kremsky, Victor G. Corcés
Software Mentions: 3
Published: over 4 years ago
10.1523/ENEURO.0416-18.2019
Identification of Immediate Early Genes in the Nervous System of Snail<i>Helix lucorum</i>
Cited by: 7
Author(s): Chuan Xu, Qian Li, Olga Efimova, Xi Jiang, Marina Petrova, Aliya Vinarskaya, P. M. Kolosov, Nikolay Aseyev, Kira Koshkareva, Victor N. Ierusalimsky, P. M. Balaban, Philipp Khaitovich
Software Mentions: 3
Published: over 5 years ago
10.18632/oncotarget.27406
Characterization of unique <i>PMEPA1</i> gene splice variants (isoforms <i>d</i> and <i>e</i>) from RNA Seq profiling provides novel insights into prognostic evaluation of prostate cancer
Cited by: 7
Author(s): Shashwat Sharad, Allissa Dillman, Zsófia Sztupinszki, Zoltán Szállási, Inger L. Rosner, Jennifer Cullen, Shiv Srivastava, Alagarsamy Srinivasan, Hua Li
Software Mentions: 3
Published: almost 5 years ago
10.3389/fgene.2020.00594
Comparison of Normalization Methods for Analysis of TempO-Seq Targeted RNA Sequencing Data
Cited by: 11
Author(s): Pierre R. Bushel, Stephen S. G. Ferguson, Sreenivasa Ramaiahgari, Richard S. Paules, Scott S. Auerbach
Software Mentions: 3
Published: over 4 years ago
10.18632/oncotarget.23614
The mutational landscape of <i>MYCN</i>, <i>Lin28b</i> and <i>ALK</i><i>F1174L</i> driven murine neuroblastoma mimics human disease
Cited by: 6
Author(s): Bram De Wilde, Anneleen Beckers, Sven Lindner, Kristina Althoff, Katleen De Preter, Pauline Depuydt, Pieter Mestdagh, Tom Sante, Steve Lefever, Falk Hertwig, Zhiyu Peng, Leming Shi, Sangkyun Lee, Elien Vandermarliere, Lennart Martens, Björn Menten, Alexander Schramm, Matthias Fischer, Johannes H. Schulte, Jo Vandesompele, Frank Speleman
Software Mentions: 3
Published: almost 7 years ago
10.3389/fgene.2015.00188
Emerging applications of read profiles towards the functional annotation of the genome
Cited by: 9
Author(s): Sachin Pundhir, Panayiota Poirazi, Jan Gorodkin
Software Mentions: 3
Published: over 9 years ago
10.3389/fgene.2020.00133
Comparison of Adult Testis and Ovary MicroRNA Expression Profiles in Reeves’ Pond Turtles (Mauremys reevesii) With Temperature-Dependent Sex Determination
Cited by: 6
Author(s): Lei Xiong, Mengli Yang, Kai Zheng, Ziming Wang, Shengli Gu, Jiucui Tong, Jianjun Li, Nadar Ali Shah, Liuwang Nie
Software Mentions: 3
Published: over 4 years ago
10.3390/ijms19113354
Transcriptome Profiles Reveal the Crucial Roles of Auxin and Cytokinin in the “Shoot Branching” of Cremastra appendiculata
Cited by: 13
Author(s): Xiang Lv, Mingsheng Zhang, Xiaolan Li, Ye RuiHua, Xiaohong Wang
Software Mentions: 3
Published: about 6 years ago
10.3389/fmicb.2018.01739
The Culture Environment Influences Both Gene Regulation and Phenotypic Heterogeneity in Escherichia coli
Cited by: 37
Author(s): Ashley Smith, Agnieszka Kaczmar, Rosemary A. Bamford, Christopher Smith, Simona Frustaci, Andrea Kovacs-Simon, Paul O’Neill, Karen Moore, Konrad Paszkiewicz, Richard W. Titball, Stefano Pagliara
Software Mentions: 3
Published: over 6 years ago
10.1186/s13059-019-1726-z
Codon usage optimization in pluripotent embryonic stem cells
Cited by: 37
Author(s): Susanne Bornelöv, Tommaso Selmi, Sophia Flad, Sabine Dietmann, Michaela Frye
Software Mentions: 3
Published: over 5 years ago
10.1186/s13059-018-1598-7
Analysis of 3D genomic interactions identifies candidate host genes that transposable elements potentially regulate
Cited by: 38
Author(s): Ramya Raviram, Pedro P. Rocha, Vincent Luo, Emily Swanzey, Emily R. Miraldi, Edward B. Chuong, Cédric Feschotte, Richard Bonneau, Jane A. Skok
Software Mentions: 3
Published: almost 6 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
10.1186/s13059-018-1553-7
Holo-Seq: single-cell sequencing of holo-transcriptome
Cited by: 26
Author(s): Zhengyun Xiao, Cheng Guo, Jiao Yang, Ci Pan, Ran Li, Danmei Jia, Jing Zhu, Chao Wu, Min Zheng, Junling Jia
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
10.1186/s13059-016-1059-0
Widespread natural variation of DNA methylation within angiosperms
Cited by: 398
Author(s): Chad E. Niederhuth, Adam J. Bewick, Lexiang Ji, Magdy S. Alabady, Kyung Do Kim, Qing Li, Nicholas A. Rohr, Aditi Rambani, John M. Burke, Joshua A. Udall, Chiedozie Egesi, Jeremy Schmutz, Jane Grimwood, Scott A. Jackson, Nathan M. Springer, Robert J. Schmitz
Software Mentions: 3
Published: about 8 years ago
10.1186/s13059-017-1173-7
Functional variation in allelic methylomes underscores a strong genetic contribution and reveals novel epigenetic alterations in the human epigenome
Cited by: 70
Author(s): Warren A. Cheung, Xiaojian Shao, Andréanne Morin, Valérie Siroux, Tony Kwan, Bing Ge, Dylan Aïssi, Lu Chen, Louella Vasquez, Fiona Allum, Frédéric Guénard, Emmanuelle Bouzigon, Simon Maguire, Elodie Boulier, Adriana Redensek, Stephen Watt, Avik Datta, Laura Clarke, Paul Flicek, Daniel Mead, Dirk S. Paul, Stephan Beck, Guillaume Bourque, Mark Lathrop, André Tchernof, Marie‐Claude Vohl, Florence Demenais, Isabelle Pin, Kate Downes, Hendrick G. Stunnenberg, Nicole Soranzo, Tomi Pastinen, Elin Grundberg
Software Mentions: 3
Published: over 7 years ago
10.1186/s13059-017-1186-2
Epigenetic aging signatures in mice livers are slowed by dwarfism, calorie restriction and rapamycin treatment
Cited by: 232
Author(s): Tina Wang, Brian Tsui, Jason F. Kreisberg, Neil Robertson, Andrew M. Gross, Michael Yu, Hannah Carter, Holly M. Brown–Borg, Peter D. Adams, Trey Ideker
Software Mentions: 3
Published: over 7 years ago
10.1186/s13059-018-1464-7
DNMT3A and TET1 cooperate to regulate promoter epigenetic landscapes in mouse embryonic stem cells
Cited by: 109
Author(s): Tianpeng Gu, Xueqiu Lin, Shay Cullen, Min Luo, Mira Jeong, Marcos R.H. Estécio, Jianjun Shen, Swanand Hardikar, Deqiang Sun, Jianzhong Su, Danielle Rux, Anna Guzman, Minjung Lee, Lei Qi, Jiajia Chen, Michael Kyba, Yun Huang, Taiping Chen, Wei Li, Margaret A. Goodell
Software Mentions: 3
Published: over 6 years ago
10.1371/journal.pone.0142262
High-Throughput Profiling of Caenorhabditis elegans Starvation-Responsive microRNAs
Cited by: 16
Author(s): Laura García-Segura, Cei Abreu‐Goodger, Armando Hernández-Mendoza, Tzvetanka D. Dinkova, Luis Padilla-Noriega, Martha Elva Pérez-Andrade, Juan Miranda-Ríos
Software Mentions: 3
Published: about 9 years ago
10.1371/journal.pone.0150591
Analysis of the Phialocephala subalpina Transcriptome during Colonization of Its Host Plant Picea abies
Cited by: 11
Author(s): Vanessa Reininger, Markus Schlegel
Software Mentions: 3
Published: over 8 years ago
10.1371/journal.pone.0041645
Deep Sequencing-Based Transcriptome Analysis of Chicken Spleen in Response to Avian Pathogenic Escherichia coli (APEC) Infection
Cited by: 36
Author(s): Qinghua Nie, Erin Sandford, Xiquan Zhang, Lisa K. Nolan, Susan J. Lamont
Software Mentions: 3
Published: over 12 years ago
10.18632/oncotarget.21694
Unique expression signatures of circular RNAs in response to DNA tumor virus SV40 infection
Cited by: 19
Author(s): Jiandong Shi, Ningzhu Hu, Jianfang Li, Zong Yuan Zeng, Ling Mo, Jing Sun, Man‐Li C. Wu, Yunzhang Hu
Software Mentions: 3
Published: about 7 years ago
10.1371/journal.pone.0226707
High expression of olfactomedin-4 is correlated with chemoresistance and poor prognosis in pancreatic cancer
Cited by: 15
Author(s): Ryotaro Ohkuma, Erica Yada, Shumpei Ishikawa, Daisuke Komura, Hidenobu Ishizaki, Koji Tamada, Yutaro Kubota, Kazuyuki Hamada, Hiroo Ishida, Yuya Hirasawa, Hirotsugu Ariizumi, Etsuko Satoh, Midori Shida, Makoto Watanabe, Rie Onoue, Kiyohiro Ando, Junji Tsurutani, Kiyoshi Yoshimura, Takehiko Yokobori, Tetsuro Sasada, Takeshi Aoki, Masahiko Murakami, Tomoko Norose, Nobuyuki Ohike, Masafumi Takimoto, Masahiko Izumizaki, Shinichi Kobayashi, Takuya Tsunoda, Satoshi Wada
Software Mentions: 3
Published: almost 5 years ago
10.1186/s12977-017-0378-x
Modulation of the functional association between the HIV-1 intasome and the nucleosome by histone amino-terminal tails
Cited by: 14
Author(s): Mohamed Salah Benleulmi, Julien Matysiak, Xavier Robert, Csaba Miskey, Eric Mauro, Delphine Lapaillerie, Paul Lesbats, Stéphane Chaignepain, Daniel R. Henríquez, Christina Calmels, Oyindamola Oladosu, Eloïse Thierry, Óscar León, Marc Lavigne, Marie‐Line Andréola, Olivier Delelis, Zoltán Ivics, Marc Ruff, Patrice Gouet, Vincent Parissi
Software Mentions: 3
Published: almost 7 years ago
10.1371/journal.pone.0129396
Transcriptional Slippage and RNA Editing Increase the Diversity of Transcripts in Chloroplasts: Insight from Deep Sequencing of Vigna radiata Genome and Transcriptome
Cited by: 26
Author(s): Ching-Ping Lin, Chih‐Yuan Ko, Ching-I Kuo, Mao-Sen Liu, Roland Schafleitner, Long-Fang Oliver Chen
Software Mentions: 3
Published: over 9 years ago
10.18632/oncotarget.12888
Dysregulated expression of microRNAs and mRNAs in pulmonary artery remodeling in ascites syndrome in broiler chickens
Cited by: 23
Author(s): Ping Liu, Fei Yang, Zhuang Yu, Qingyang Xiao, Cao H, Caiying Zhang, Tiancheng Wang, Huayuan Lin, Xiaoquan Guo, Guoliang Hu
Software Mentions: 3
Published: about 8 years ago
10.1371/journal.pone.0077490
Transcriptional Reprogramming of CD11b+Esamhi Dendritic Cell Identity and Function by Loss of Runx3
Cited by: 29
Author(s): Joseph Dicken, Alexander Mildner, Dena Leshkowitz, Ivo P. Touw, Shay Hantisteanu, Steffen Jung, Yoram Groner
Software Mentions: 3
Published: about 11 years ago
10.1371/journal.pone.0233394
Gene expression regulation by the Chromodomain helicase DNA-binding protein 9 (CHD9) chromatin remodeler is dispensable for murine development
Cited by: 11
Author(s): Andrej Alendar, Jan-Paul Lambooij, Rajith Bhaskaran, Cesare Lancini, Ji‐Ying Song, H. van Vugt, Michiel Snoek, Anton Berns
Software Mentions: 3
Published: over 4 years ago
10.1098/rspb.2020.3169
Conservation and turnover of miRNAs and their highly complementary targets in early branching animals
Cited by: 5
Author(s): Daniela Praher, Bob Zimmermann, Rohit Dnyansagar, David J. Miller, Aurélie Moya, Vengamanaidu Modepalli, Arie Fridrich, Daniel Sher, Lene Friis-Møller, Per Sundberg, Sylvain Forêt, Regan Ashby, Yehu Moran, Ulrich Technau
Software Mentions: 3
Published: over 3 years ago
10.1371/journal.pone.0162402
Comprehensive Transcriptome Analyses of the Fructose-Fed Syrian Golden Hamster Liver Provides Novel Insights into Lipid Metabolism
Cited by: 8
Author(s): Ziyang Li, Chaoliang Xiong, Suo Mo, Haiying Tian, Mengqian Yu, Tingting Mao, Qian Chen, Huai‐Rong Luo, Quan-Zhen Li, Jianxin Lü, Yi Zhao, Wei Li
Software Mentions: 3
Published: about 8 years ago
10.1371/journal.pone.0083723
Function of GATA Factors in the Adult Mouse Liver
Cited by: 39
Author(s): Rena Zheng, Boris Rebolledo‐Jaramillo, Yiwei Zong, Liqing Wang, Pierre Russo, Wayne W. Hancock, Ben Z. Stanger, Ross C. Hardison, Gerd A. Blobel
Software Mentions: 3
Published: almost 11 years ago
10.1371/journal.ppat.1008660
Identification of oncolytic vaccinia restriction factors in canine high-grade mammary tumor cells using single-cell transcriptomics
Cited by: 3
Author(s): Béatrice Cambien, Kévin Lebrigand, Alberto Baeri, Nicolas Nottet, Catherine Compin, Audrey Lamit, Olivier Ferraris, Christophe N. Peyrefitte, Virginie Magnone, Jérôme Henriques, Laure‐Emmanuelle Zaragosi, Sophie Giorgetti‐Peraldi, Fréd́eric Bost, Marine Gautier-Isola, Roger Rezzonico, Pascal Barbry, Robert Barthel, Bernard Mari, Georges Vassaux
Software Mentions: 3
Published: about 4 years ago
10.1371/journal.ppat.1008402
Human cytomegalovirus IE2 drives transcription initiation from a select subset of late infection viral promoters by host RNA polymerase II
Cited by: 30
Author(s): Ming Li, Christopher B. Ball, Geoffrey S Collins, Qiaolin Hu, Donal S. Luse, David H. Price, Jeffery L. Meier
Software Mentions: 3
Published: over 4 years ago
10.1371/journal.pone.0211430
Role of CsrA in stress responses and metabolism important for Salmonella virulence revealed by integrated transcriptomics
Cited by: 36
Author(s): Anastasia H. Potts, Yinping Guo, Brian M. M. Ahmer, Tony Romeo
Software Mentions: 3
Published: almost 6 years ago
10.1371/journal.pone.0094646
Post-Translational Decrease in Respiratory Chain Proteins in the Polg Mutator Mouse Brain
Cited by: 12
Author(s): David N. Hauser, Allissa Dillman, Jinhui Ding, Li Yan, Mark Cookson
Software Mentions: 3
Published: over 10 years ago
10.1523/JNEUROSCI.2836-16.2016
LHX2 Interacts with the NuRD Complex and Regulates Cortical Neuron Subtype Determinants<i>Fezf2</i>and<i>Sox11</i>
Cited by: 52
Author(s): Bhavana Muralidharan, Zeba Khatri, Upasana Maheshwari, Rupesh Gupta, Basabdatta Roy, Saurabh J. Pradhan, Krishanpal Karmodiya, Hari Padmanabhan, Ashwin S. Shetty, Chinthapalli Balaji, Ullas Kolthur‐Seetharam, Jeffrey D. Macklis, Sanjeev Galande, Shubha Tole
Software Mentions: 3
Published: almost 8 years ago
10.1242/jcs.252767
<i>N</i>1-acetylspermidine is a determinant of hair follicle stem cell fate
Cited by: 11
Author(s): Kira Allmeroth, Christine S. Kim, Andrea Annibal, Andromachi Pouikli, Janis Koester, Maxime Derisbourg, Carlos Andrés Chacón‐Martínez, Christian Latza, Adam Antebi, Peter Tessarz, Sara A. Wickström, Martin S. Denzel
Software Mentions: 3
Published: over 3 years ago
10.1371/journal.pone.0233044
Runx3 prevents spontaneous colitis by directing the differentiation of anti-inflammatory mononuclear phagocytes
Cited by: 13
Author(s): Shay Hantisteanu, Yosef Dicken, Varda Negreanu, Dalia Goldenberg, Ori Brenner, Dena Leshkowitz, Joseph Lotem, Ditsa Levanon, Yoram Groner
Software Mentions: 3
Published: over 4 years ago
10.1371/journal.pone.0195003
Improved methods of DNA extraction from human spermatozoa that mitigate experimentally-induced oxidative DNA damage
Cited by: 5
Author(s): Miguel J Xavier, Brett Nixon, Shaun D. Roman, R. John Aitken
Software Mentions: 3
Published: over 6 years ago
10.1371/journal.pone.0113800
ViVar: A Comprehensive Platform for the Analysis and Visualization of Structural Genomic Variation
Cited by: 44
Author(s): Tom Sante, Sarah Vergult, Pieter-Jan Volders, Wigard P. Kloosterman, Geert Trooskens, Katleen De Preter, Annelies Dheedene, Franki Speleman, Tim De Meyer, Björn Menten
Software Mentions: 3
Published: almost 10 years ago
10.1371/journal.pone.0062547
p63 Attenuates Epithelial to Mesenchymal Potential in an Experimental Prostate Cell Model
Cited by: 29
Author(s): Jan Roger Olsen, Anne Margrete Øyan, Kari Rostad, Margrete R. Hellem, Jie Liu, Lisha Li, David Micklem, Hallvard Haugen, James B. Lorens, Varda Rotter, Xisong Ke, Biaoyang Lin, Karl‐Henning Kalland
Software Mentions: 3
Published: over 11 years ago
10.1093/gigascience/giy095
Draft genome assembly of the invasive cane toad, Rhinella marina
Cited by: 56
Author(s): Richard J. Edwards, Daniel Enosi Tuipulotu, Timothy G. Amos, Denis O’Meally, Mark F. Richardson, Tonia Russell, Marcelo Vallinoto, Miguel Carneiro, Nuno Ferrand, Marc R. Wilkins, Fernando Sequeira, Lee A. Rollins, Edward C. Holmes, Richard Shine
Software Mentions: 3
Published: over 6 years ago
10.1093/gigascience/giy074
Long-read sequencing and de novo genome assembly of Ammopiptanthus nanus, a desert shrub
Cited by: 18
Author(s): Fei Gao, Xue Wang, Xuming Li, Mingyue Xu, Huayun Li, Merhaba Abla, Han Sun, Shanjun Wei, Jinchao Feng, Yijun Zhou
Software Mentions: 3
Published: over 6 years ago
10.1371/journal.pone.0237087
Sequencing and assembly of the Egyptian buffalo genome
Cited by: 10
Author(s): Dina A. El-Khishin, Amr Ageez, Mohamed E. Saad, Amr Ibrahim, Moustafa Shokrof, L. Hassan, Mohamed Abouelhoda
Software Mentions: 3
Published: over 4 years ago
10.1093/database/baab053
OUP accepted manuscript
Cited by: 3
Author(s): Yi-Wei Lee, Ming Chen, I‐Fang Chung, Ting‐Yu Chang
Software Mentions: 3
Published: almost 4 years ago
10.1186/s13073-015-0180-0
The oxidative demethylase ALKBH3 marks hyperactive gene promoters in human cancer cells
Cited by: 14
Author(s): Robert Liefke, Indra M. Windhof-Jaidhauser, Jochen Gaedcke, Gabriela Salinas-Riester, Feizhen Wu, Michael Ghadimi, Sebastian Dango
Software Mentions: 3
Published: over 9 years ago
10.1371/journal.pone.0210273
Identification of whole blood mRNA and microRNA biomarkers of tissue damage and immune function resulting from amphetamine exposure or heat stroke in adult male rats
Cited by: 6
Author(s): Luísa Camacho, Camila S. Silva, Joseph P. Hanig, Robert P. Schleimer, Nysia I. George, John F. Bowyer
Software Mentions: 3
Published: almost 6 years ago
10.1186/s13073-015-0168-9
Widespread intron retention diversifies most cancer transcriptomes
Cited by: 254
Author(s): Heidi Dvinge, Robert K. Bradley
Software Mentions: 3
Published: over 9 years ago
10.1016/j.devcel.2017.05.021
Distinct Roles of RNA Helicases MVH and TDRD9 in PIWI Slicing-Triggered Mammalian piRNA Biogenesis and Function
Cited by: 60
Author(s): Joanna M. Wenda, David Homolka, Zhaolin Yang, Pietro Spinelli, Ravi Sachidanandam, Radha Raman Pandey, Ramesh S. Pillai
Software Mentions: 3
Published: over 7 years ago
10.1371/journal.pone.0076276
Differential Expression of Tomato Spotted Wilt Virus-Derived Viral Small RNAs in Infected Commercial and Experimental Host Plants
Cited by: 56
Author(s): Neena Mitter, Vikas Koundal, Sarah Williams, H. R. Pappu
Software Mentions: 3
Published: about 11 years ago
10.1186/s13073-015-0167-x
JAFFA: High sensitivity transcriptome-focused fusion gene detection
Cited by: 130
Author(s): N. Davidson, Ian J. Majewski, Alicia Oshlack
Software Mentions: 3
Published: over 9 years ago
10.1016/j.ebiom.2016.06.048
Premalignant SOX2 overexpression in the fallopian tubes of ovarian cancer patients: Discovery and validation studies
Cited by: 33
Author(s): Karin Hellner, Fabrizio Miranda, Donatien Fotso Chedom, Sandra Herrero-González, Daniel M. Hayden, Rick Tearle, Mara Artibani, Mohammad KaramiNejadRanjbar, Ruth M. Williams, Kezia Gaitskell, Samar Elorbany, Ruoyan Xu, Alexandros Laios, Petronela Buiga, Karim Ahmed, Sunanda Dhar, Rebecca Yu Zhang, Leticia Campo, Kevin A. Myers, M. Luz Lozano, Maria Ruiz‐Miró, Sònia Gatius, Alba Mota, Gema Moreno‐Bueno, Xavier Matías‐Guiu, Javier Benı́tez, Lorna Witty, Gil McVean, Simon J. Leedham, Ian Tomlinson, Radoje Drmanac, Jean‐Baptiste Cazier, Robert J. Klein, Kevin Dunne, Robert C. Bast, Stephen Kennedy, A. Bassim Hassan, Stefano Lise, María José García, Brock A. Peters, Christopher Yau, Tatjana Sauka‐Spengler, Ahmed A. Ahmed
Software Mentions: 3
Published: over 8 years ago
10.3390/ijms22147414
An Integrative Study of Aortic mRNA/miRNA Longitudinal Changes in Long-Term LVAD Support
Cited by: 1
Author(s): Dana Dlouhá, Peter Ivák, Ivan Netuka, Sarka Benesova, Z. Tučanová, Jaroslav A. Hubacek
Software Mentions: 3
Published: over 3 years ago
10.15252/embj.2018100788
The Nucleosome Remodelling and Deacetylation complex suppresses transcriptional noise during lineage commitment
Cited by: 41
Author(s): Thomas Burgold, M. Barber, Susan L. Kloet, Julie Cramard, Sarah Gharbi, Robin Floyd, Masaki Kinoshita, Markus Ralser, Michiel Vermeulen, Nicola Reynolds, Sabine Dietmann, Brian Hendrich
Software Mentions: 3
Published: over 5 years ago
10.1371/journal.pone.0085648
RNA Polymerase III Transcriptomes in Human Embryonic Stem Cells and Induced Pluripotent Stem Cells, and Relationships with Pluripotency Transcription Factors
Cited by: 32
Author(s): Ravi Alla, Bradley R. Cairns
Software Mentions: 3
Published: almost 11 years ago
10.15252/emmm.202114150
Long‐lived macrophage reprogramming drives spike protein‐mediated inflammasome activation in COVID‐19
Cited by: 83
Author(s): Sebastian J. Theobald, Alexander Simonis, Theodoros Georgomanolis, Christoph Kreer, Matthias Zehner, Hannah S. Eisfeld, Marie‐Christine Albert, Jason Chhen, Susanne Motameny, Florian Erger, Julia Fischer, Jakob J Malin, Jessica Gräb, Sandra Winter, Andromachi Pouikli, Friederike S. David, Boris Böll, Philipp Köehler, Kanika Vanshylla, Henning Gruell, Isabelle Suárez, Michael Hallek, Gerd Fätkenheuer, Norma Jung, Oliver A. Cornely, Clara Lehmann, Peter Tessarz, Janine Altmüller, Peter Nürnberg, Hamid Kashkar, Florian Klein, Manuel Koch, Jan Rybniker
Software Mentions: 3
Published: over 3 years ago
10.1002/ece3.5991
New genome assembly of the barn owl (<i>Tyto alba alba</i>)
Cited by: 8
Author(s): Anne‐Lyse Ducrest, Samuel Neuenschwander, Emanuel Schmid‐Siegert, Marco Pagni, Clément Train, David Dylus, Yannis Nevers, Alex Warwick Vesztrocy, Luis M. San‐Jose, Mélanie Dupasquier, Christophe Dessimoz, Ioannis Xénarios, Alexandre Roulin, Jérôme Goudet
Software Mentions: 3
Published: almost 5 years ago
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
10.1080/22221751.2020.1821581
mRNA and miRNA profiling of Zika virus-infected human umbilical cord mesenchymal stem cells identifies miR-142-5p as an antiviral factor
Cited by: 23
Author(s): Rak Kyun Seong, Jae Kwan Lee, Geum Joon Cho, Mukesh Kumar, Ok Sarah Shin
Software Mentions: 3
Published: almost 5 years ago
10.1186/s13072-017-0123-7
Comprehensive evaluation of genome-wide 5-hydroxymethylcytosine profiling approaches in human DNA
Cited by: 64
Author(s): Ksenia Skvortsova, Elena Zotenko, Phuc-Loi Luu, Cathryn M. Gould, Shalima S. Nair, Susan J. Clark, Clare Stirzaker
Software Mentions: 3
Published: over 7 years ago
10.1186/s13072-015-0004-x
DNA demethylation by 5-aza-2′-deoxycytidine is imprinted, targeted to euchromatin, and has limited transcriptional consequences
Cited by: 37
Author(s): María Paz Ramos, N. Ari Wijetunga, Andrew McLellan, Masako Suzuki, John M. Greally
Software Mentions: 3
Published: over 9 years ago
10.1371/journal.pone.0151105
Transcriptome Profiling of Two Asparagus Bean (Vigna unguiculata subsp. sesquipedalis) Cultivars Differing in Chilling Tolerance under Cold Stress
Cited by: 23
Author(s): Haidong Tan, Haitao Huang, Manman Tie, Yi Tang, Yunsong Lai, Huanxiu Li
Software Mentions: 3
Published: over 8 years ago
10.1155/2021/6029237
Tianma Formula Alleviates Dementia via ACER2-Mediated Sphingolipid Signaling Pathway Involving Aβ
Cited by: 1
Author(s): Haochang Lin, Sha Wu, Zhiying Weng, Hongyan Wang, Rui Shi, Minglei Tian, Youlan Wang, Haiyan He, Yuchuan Wang, Xuan Li, Zhimin Jian, Fuqin Wei, Peng Wang, Liuyi Zhang, Yi Liu, Qiuzhe Guo, Chen Chen, Weimin Ye
Software Mentions: 3
Published: over 3 years ago
10.1186/s13059-021-02465-1
NucHMM: a method for quantitative modeling of nucleosome organization identifying functional nucleosome states distinctly associated with splicing potentiality
Cited by: 5
Author(s): Kun Fang, Tianbao Li, Yufei Huang, Victor X. Jin
Software Mentions: 3
Published: about 3 years ago