pypi: bowtie | Projects | Ecosyste.ms: Papers

10.1371/journal.pone.0182528

Using local chromatin structure to improve CRISPR/Cas9 efficiency in zebrafish
Cited by: 29
Author(s): Yunru Chen, Shiyang Zeng, Ruikun Hu, Xiangxiu Wang, Wenyan Huang, Jiangfang Liu, Luying Wang, Guifen Liu, Ying Cao, Yong Zhang
Software Mentions: 3
Published: over 7 years ago

10.1186/1746-4811-8-12

Targeted parallel sequencing of large genetically-defined genomic regions for identifying mutations in Arabidopsis
Cited by: 18
Author(s): Kun-Hsiang Liu, Matthew McCormack, Jenq-Yunn Sheen
Software Mentions: 3
Published: almost 13 years ago

10.7554/eLife.39842

Environmentally-induced epigenetic conversion of a piRNA cluster
Cited by: 23
Author(s): Karine Casier, Valérie Delmarre, Nathalie Gueguen, Catherine Hermant, Elise Viodé, Chantal Vaury, Stéphane Ronsseray, Emilie Brasset, Laure Teysset, Antoine Boivin
Software Mentions: 3
Published: over 5 years ago

10.1186/s12864-016-3164-6

Q-nexus: a comprehensive and efficient analysis pipeline designed for ChIP-nexus
Cited by: 12
Author(s): Peter J. Hansen, Jochen Hecht, Jonas Ibn-Salem, Benjamin S. Menkuec, Sebastian Roskosch, Mathias Truss, Peter N. Robinson
Software Mentions: 3
Published: about 8 years ago

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

10.3390/plants9091080

Transcriptome-Wide N6-Methyladenosine (m6A) Methylome Profiling of Heat Stress in Pak-choi (Brassica rapa ssp. chinensis)
Cited by: 30
Author(s): Gaofeng Liu, Jin Wang, Xilin Hou
Software Mentions: 3
Published: over 4 years ago

10.3390/v7072788

Ultra Deep Sequencing of a Baculovirus Population Reveals Widespread Genomic Variations
Cited by: 58
Author(s): Aurélien Chateigner, Annie Bézier, Carole Labrousse, Davy Jiolle, Valérie Barbe, Elisabeth A. Herniou
Software Mentions: 3
Published: over 9 years ago

10.1007/s11626-017-0140-7

Relevant principal factors affecting the reproducibility of insect primary culture
Cited by: 2
Author(s): Naoya Ogata, Kikuo Iwabuchi
Software Mentions: 3
Published: over 7 years ago

10.1016/j.ijpara.2020.06.002

Extracellular vesicles from Heligmosomoides bakeri and Trichuris muris contain distinct microRNA families and small RNAs that could underpin different functions in the host
Cited by: 15
Author(s): Ruby White, Sujai Kumar, Wang Ngai Chow, E. Graeme Robertson, Kelly S. Hayes, Richard K. Grencis, María A. Duque-Correa, Amy H. Buck
Software Mentions: 3
Published: over 4 years ago

10.1371/journal.pbio.2002039

Dual role of starvation signaling in promoting growth and recovery
Cited by: 17
Author(s): Yonat Gurvich, Dena Leshkowitz, Naama Barkai
Software Mentions: 3
Published: almost 7 years ago

10.1186/s12864-015-1445-0

Genome-wide co-occupancy of AML1-ETO and N-CoR defines the t(8;21) AML signature in leukemic cells
Cited by: 28
Author(s): Daniel J. Trombly, Troy W. Whitfield, Srivatsan Padmanabhan, Jonathan A. R. Gordon, Jane B. Lian, André J. van Wijnen, Sayyed K. Zaidi, Janet L. Stein
Software Mentions: 3
Published: over 9 years ago

10.1080/21505594.2020.1797274

Transcriptional remodeling during metacyclogenesis in Trypanosoma cruzi I
Cited by: 11
Author(s): Lissa Cruz-Saavedra, Gustavo Adolfo Calderón Vallejo, Felipe Guhl, Louisa A. Messenger, Juan David Ramírez
Software Mentions: 3
Published: over 4 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

10.1186/s12985-021-01569-1

Molecular-genetic characterization of human parvovirus B19 prevalent in Kerala State, India
Cited by: 4
Author(s): Seetha Dayakar, Heera Pillai, Sai Ravi Chandra Nori, Sanu Ghosh Kalpathodi, Vineetha P. Thulasi, Radhakrishnan R. Nair
Software Mentions: 3
Published: over 3 years ago

10.1093/hmg/ddaa053

DUX4 expressing immortalized FSHD lymphoblastoid cells express genes elevated in FSHD muscle biopsies, correlating with the early stages of inflammation
Cited by: 16
Author(s): Christopher R. S. Banerji, Maryna Panamarova, Peter S. Zammit
Software Mentions: 3
Published: over 4 years ago

10.1016/j.ijpddr.2018.03.006

The anti-fecundity effect of 5-azacytidine (5-AzaC) on Schistosoma mansoni is linked to dis-regulated transcription, translation and stem cell activities
Cited by: 18
Author(s): Kathrin K. Geyer, Sabrina E. Munshi, Martin Vickers, Michael Squance, Toby Wilkinson, Daniel Berrar, Cristian Chaparro, Martin Swain, Karl F. Hoffmann
Software Mentions: 3
Published: over 6 years ago

10.1128/mBio.01053-20

FEDS: a Novel Fluorescence-Based High-Throughput Method for Measuring DNA Supercoiling In Vivo
Cited by: 3
Author(s): Alexandre Duprey, Eduardo A. Groisman
Software Mentions: 3
Published: about 4 years ago

10.1128/mSystems.00046-17

Total Lipopolysaccharide from the Human Gut Microbiome Silences Toll-Like Receptor Signaling
Cited by: 179
Author(s): Eva d’Hennezel, Sahar Abubucker, Leon O. Murphy, Thomas W. Cullen
Software Mentions: 3
Published: almost 7 years ago

10.1128/mBio.02047-18

Nucleotide Resolution Comparison of Transcription of Human Cytomegalovirus and Host Genomes Reveals Universal Use of RNA Polymerase II Elongation Control Driven by Dissimilar Core Promoter Elements
Cited by: 25
Author(s): Mrutyunjaya Parida, Kyle A. Nilson, Ming Li, Christopher B. Ball, Harrison A. Fuchs, Christine Lawson, Donal S. Luse, Jeffery L. Meier, David H. Price
Software Mentions: 3
Published: over 5 years ago

10.1371/journal.pcbi.1007543

Automated minute scale RNA-seq of pluripotent stem cell differentiation reveals early divergence of human and mouse gene expression kinetics
Cited by: 6
Author(s): Christopher Barry, Matthew T. Schmitz, Cara Argus, Jennifer M. Bolin, Mitchell D. Probasco, Ning Leng, Bret Duffin, John Steill, Scott Swanson, Brian E. McIntosh, Ron Stewart, Christina Kendziorski, James A. Thomson, Rhonda Bacher
Software Mentions: 3
Published: almost 5 years ago

10.1128/mBio.01950-18

Cicada Endosymbionts Have tRNAs That Are Correctly Processed Despite Having Genomes That Do Not Encode All of the tRNA Processing Machinery
Cited by: 8
Author(s): James T. Van Leuven, Meng Mao, Denghui Xing, Gordon M. Bennett, John P. McCutcheon
Software Mentions: 3
Published: over 5 years ago

10.1038/tp.2016.181

Impaired GABA synthesis, uptake and release are associated with depression-like behaviors induced by chronic mild stress
Cited by: 110
Author(s): Kewei Ma, Aidong Xu, Sheng Cui, Sun Mr, Xue Yc, Wang Jh
Software Mentions: 3
Published: about 8 years ago

10.1038/s41398-019-0538-y

Temporal dynamics of miRNAs in human DLPFC and its association with miRNA dysregulation in schizophrenia
Cited by: 24
Author(s): Zhonghua Hu, Shaojian Gao, Daniel M. Lindberg, Debabrata Panja, Yoshi Wakabayashi, Keshen Li, Joel E. Kleinman, Jun Zhu, Zheng Li
Software Mentions: 3
Published: over 5 years ago

10.3390/toxins12050290

AFB1 Induced Transcriptional Regulation Related to Apoptosis and Lipid Metabolism in Liver of Chicken
Cited by: 27
Author(s): Xueqin Liu, Suchismita Mishra, Tao Wang, Zhongxian Xu, Xiaoling Zhao, Yan Wang, Huadong Yin, Xiaolan Fan, Bo Zeng, Mingyao Yang, Dapeng Yang, Qingyong Ni, Yan Li, Mingwang Zhang, Qing Zhu, Feng Chen, Diyan Li
Software Mentions: 3
Published: over 4 years ago

10.1186/s13567-015-0153-8

Genomic analysis of host – Peste des petits ruminants vaccine viral transcriptome uncovers transcription factors modulating immune regulatory pathways
Cited by: 40
Author(s): Siddappa Manjunath, Girish Kumar, Bishnu Prasad Mishra, Bina Mishra, Aditya Prasad Sahoo, Chaitanya G. Joshi, Ashok Kumar Tiwari, Kaushal Kishor Rajak, Sarath Chandra Janga
Software Mentions: 3
Published: over 9 years ago

10.1186/1471-2164-15-808

De novo transcriptome of Ischnura elegans provides insights into sensory biology, colour and vision genes
Cited by: 47
Author(s): Pallavi Chauhan, Bengt Hansson, Ken Kraaijeveld, Peter de Knijff, Erik I. Svensson, Maren Wellenreuther
Software Mentions: 3
Published: almost 11 years ago

10.1186/s12915-014-0079-z

Checkpoint-independent scaling of the Saccharomyces cerevisiaeDNA replication program
Cited by: 11
Author(s): Ariel Gispan, Miri Carmi, Naama Barkai
Software Mentions: 3
Published: about 10 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.pcbi.1001138

deFuse: An Algorithm for Gene Fusion Discovery in Tumor RNA-Seq Data
Cited by: 495
Author(s): Andrew McPherson, Fereydoun Hormozdiari, Abdalnasser Zayed, Ryan Giuliany, Gavin Ha, Mark Sun, Malachi Griffith, Alireza Heravi Moussavi, Janine Senz, Nataliya Melnyk, Marina Pacheco, Marco A. Marra, Martin Hirst, Torsten O. Nielsen, S. Cenk Şahinalp, David G. Huntsman, Sohrab P. Shah
Software Mentions: 3
Published: over 13 years ago

10.1186/1471-2164-13-50

Genome-wide landscape of liver X receptor chromatin binding and gene regulation in human macrophages
Cited by: 68
Author(s): Petri Pehkonen, Lynn Welter-Stahl, Janine Diwo, Jussi Ryynänen, Anke Wienecke-Baldacchino, Sami Heikkinen, Eckardt Treuter, Knut R. Steffensen, Carsten Carlberg
Software Mentions: 3
Published: almost 13 years ago

10.15252/msb.20188462

Enzyme promiscuity shapes adaptation to novel growth substrates
Cited by: 47
Author(s): Gabriela I. Guzmán, Troy E. Sandberg, Ryan A. LaCroix, Ákos Nyerges, Henrietta Papp, Markus de Raad, Zachary A. King, Ying Hefner, Trent Northen, Richard A. Notebaart, Csaba Pál, Bernhard Palsson, Balázs Papp, Adam M. Feist
Software Mentions: 3
Published: over 5 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

10.1002/1878-0261.12608

Comparative analysis of TTF‐1 binding DNA regions in small‐cell lung cancer and non‐small‐cell lung cancer
Cited by: 19
Author(s): Satoshi Hokari, Yusuke Tamura, Atsushi Kaneda, Akihiro Katsura, Masato Morikawa, Fumihiko Murai, Shogo Ehata, Sadami Tsutsumi, Yuichi Ishikawa, Hiroyuki Aburatani, Toshiaki Kikuchi, Kohei Miyazono, Daizo Koinuma
Software Mentions: 3
Published: almost 5 years ago

10.1186/s12864-016-2539-z

A novel enrichment strategy reveals unprecedented number of novel transcription start sites at single base resolution in a model prokaryote and the gut microbiome
Cited by: 117
Author(s): Laurence Ettwiller, John A. Buswell, Erbay Yigit, Ira Schildkraut
Software Mentions: 3
Published: over 8 years ago

10.1186/1751-0473-8-6

RECOT: a tool for the coordinate transformation of next-generation sequencing reads for comparative genomics and transcriptomics
Cited by: 1
Author(s): Izawa Akiko, Jun Sese
Software Mentions: 3
Published: over 11 years ago

10.1016/j.molmet.2021.101231

Adhesion receptor ADGRG2/GPR64 is in the GI-tract selectively expressed in mature intestinal tuft cells
Cited by: 9
Author(s): Kaare V. Grunddal, Sarah Tonack, Kristoffer L. Egerod, Jonatan J Thompson, Natalia Petersen, Maja S. Engelstoft, Constance Vagne, Céline Keime, Gérard Gradwohl, Stefan Offermanns, Thue W. Schwartz
Software Mentions: 3
Published: about 3 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

10.1186/1471-2164-14-648

Combining in silico prediction and ribosome profiling in a genome-wide search for novel putatively coding sORFs
Cited by: 80
Author(s): Jeroen Crappé, Wim Van Criekinge, Geert Trooskens, Eisuke Hayakawa, Walter Luyten, Geert Baggerman, Gerben Menschaert
Software Mentions: 3
Published: almost 12 years ago

10.1242/jcs.252767

N1-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.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

10.1093/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

10.1016/j.molcel.2020.01.008

Localized Inhibition of Protein Phosphatase 1 by NUAK1 Promotes Spliceosome Activity and Reveals a MYC-Sensitive Feedback Control of Transcription
Cited by: 33
Author(s): Giacomo Cossa, Isabelle Roeschert, Florian Prinz, Apoorva Baluapuri, Raphael Silveira Vidal, Christina Schülein-Völk, Yun-Chien Chang, Carsten P. Ade, Guido Mastrobuoni, Cyrille Girard, Amit Kumar, Lars Wortmann, Susanne Walz, Reinhard Lührmann, Stefan Kempa, Bernhard Küster, Elmar Wolf, Dominik Mumberg, Martin Eilers
Software Mentions: 3
Published: over 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

10.1093/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

10.7554/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

10.1007/s11033-018-4247-z

HIRA directly targets the enhancers of selected cardiac transcription factors during in vitro differentiation of mouse embryonic stem cells
Cited by: 4
Author(s): Rasha N.M. Saleh, Daniel Dilg, Abla Ahmed Abou Zeid, Doaa Hashad, Peter Scambler, Ariane Chapgier
Software Mentions: 3
Published: over 6 years ago

10.1371/journal.pone.0140077

GATA1 and PU.1 Bind to Ribosomal Protein Genes in Erythroid Cells: Implications for Ribosomopathies
Cited by: 14
Author(s): Elsa P. Amanatiadou, Giorgio L. Papadopoulos, John Strouboulis, Ioannis S. Vizirianakis
Software Mentions: 3
Published: about 9 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

10.1371/journal.pone.0016344

Genomewide Analyses Define Different Modes of Transcriptional Regulation by Peroxisome Proliferator-Activated Receptor-β/δ (PPARβ/δ)
Cited by: 76
Author(s): Till Adhikary, Kerstin Kaddatz, Florian Finkernagel, Anne Schönbauer, Wolfgang Meißner, Maren Scharfe, Michael Jarek, Helmut Blöcker, Sabine Müller‐Brüsselbach, Rolf Müller
Software Mentions: 3
Published: almost 14 years ago

10.1371/journal.pone.0100864

Novel Bioinformatics Method for Identification of Genome-Wide Non-Canonical Spliced Regions Using RNA-Seq Data
Cited by: 10
Author(s): Yongsheng Bai, Justin Hassler, Ahdad Ziyar, Hui Li, Zachary C. Wright, Rajasree Menon, Gilbert S. Omenn, James D. Cavalcoli, Randal J. Kaufman, Maureen A. Sartor
Software Mentions: 3
Published: over 10 years ago

10.1186/s13100-017-0086-z

Considerations and complications of mapping small RNA high-throughput data to transposable elements
Cited by: 9
Author(s): Alexandros Bousios, Brandon S. Gaut, Nikos Darzentas
Software Mentions: 3
Published: almost 8 years ago

10.1186/s13100-019-0192-1

Tools and best practices for retrotransposon analysis using high-throughput sequencing data
Cited by: 51
Author(s): Aurélie Teissandier, Nicolas Servant, Emmanuel Barillot, Déborah Bourc’his
Software Mentions: 3
Published: almost 5 years ago

10.1371/journal.pgen.1007224

SOX2 regulates common and specific stem cell features in the CNS and endoderm derived organs
Cited by: 44
Author(s): Daniel W. Hagey, Susanne Klum, Idha Kurtsdotter, Cécile Zaouter, Danijal Topcic, Olov Andersson, Maria Bergsland, Jonas Muhr
Software Mentions: 3
Published: almost 7 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

10.1371/journal.pone.0131787

Quantitative Analysis of MicroRNAs in Vaccinia virus Infection Reveals Diversity in Their Susceptibility to Modification and Suppression
Cited by: 5
Author(s): Amy H. Buck, Alasdair Ivens, Katrina Gordon, Nicky Craig, Alexandre Houzelle, Alice Roche, Neil Turnbull, Philippa M. Beard
Software Mentions: 3
Published: over 9 years ago

10.1186/s13059-021-02409-9

Evolution of mouse circadian enhancers from transposable elements
Cited by: 29
Author(s): Julius Judd, Hayley Sanderson, Cédric Feschotte
Software Mentions: 3
Published: over 3 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

10.1186/s12864-017-3623-8

Comparative transcriptome analyses of flower development in four species of Achimenes (Gesneriaceae)
Cited by: 28
Author(s): Wade R. Roberts, Eric H. Roalson
Software Mentions: 3
Published: over 7 years ago

10.1371/journal.pone.0231738

mmannot: How to improve small–RNA annotation?
Cited by: 1
Author(s): Matthias Zytnicki, Christine Gaspin
Software Mentions: 3
Published: over 4 years ago

10.1371/journal.pone.0193527

Circulating miRNAs, isomiRs and small RNA clusters in human plasma and breast milk
Cited by: 48
Author(s): Mercedes Rubio, Mariona Bustamante, Carles Hernandez‐Ferrer, Dietmar Fernández‐Orth, Lorena Pantano, Yaris Sarria, Maria Riera Piqué-Borràs, Kilian Vellvé, Sílvia Agramunt, Ramón Carreras, Xavier Estivill, Juan R. González, Alfredo Mayor
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

10.1371/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

10.1186/2049-2618-2-25

The dynamics of a family’s gut microbiota reveal variations on a theme
Cited by: 86
Author(s): Patrick D. Schloss, Kathryn Iverson, Joseph F. Petrosino, Sarah J Schloss
Software Mentions: 3
Published: over 10 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

10.1371/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

10.1371/journal.pone.0089755

Tissue-Specific Expression and Regulatory Networks of Pig MicroRNAome
Cited by: 20
Author(s): Paolo Martini, Gabriele Sales, Mattia Brugiolo, Alessandro Gandaglia, Filippo Naso, Cristiano De Pittà, Michele Spina, Gino Gerosa, Francesco Chemello, Chiara Romualdi, Stefano Cagnin, Gerolamo Lanfranchi
Software Mentions: 3
Published: over 10 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.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.pgen.1009438

Toxic Y chromosome: Increased repeat expression and age-associated heterochromatin loss in male Drosophila with a young Y chromosome
Cited by: 18
Author(s): Alison H. Nguyen, Doris Bachtrog
Software Mentions: 3
Published: over 3 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

10.1371/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

10.1186/1471-2407-14-880

Deep Sequencing the microRNA profile in rhabdomyosarcoma reveals down-regulation of miR-378 family members
Cited by: 55
Author(s): Francesca Megiorni, Samantha Cialfi, Heather P. McDowell, Armando Felsani, Simona Camero, Alessandro Guffanti, Barry Pizer, Aldo Clerico, Alessandra De Grazia, Antonio Pizzuti, Anna Moles, Carlo Dominici
Software Mentions: 3
Published: almost 10 years ago

10.1371/journal.pgen.1009689

The native cistrome and sequence motif families of the maize ear
Cited by: 13
Author(s): Savannah D Savadel, Thomas Hartwig, Zachary M. Turpin, Daniel Vera, Pei-Yau Lung, Xin Sui, Max Blank, Wolf B. Frommer, Jane A Dennis, Jinfeng Zhang, Hank W. Bass
Software Mentions: 3
Published: over 3 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

10.1186/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/s12859-016-1326-9

Genome-wide functional analysis using the barcode sequence alignment and statistical analysis (Barcas) tool
Cited by: 9
Author(s): Jihyeob Mun, Donguk Kim, Kwang Lae Hoe, Seon‐Young Kim
Software Mentions: 3
Published: almost 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

10.1371/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

10.1111/1751-7915.12328

Understanding butanol tolerance and assimilation in <scp> P </scp> seudomonas putida <scp>BIRD</scp> ‐1: an integrated omics approach
Cited by: 34
Author(s): María del Sol Cuenca, Amalia Roca, Carlos Molina‐Santiago, Estrella Duque, Jean Armengaud, María Gómez–García, Juan L. Ramos
Software Mentions: 3
Published: almost 9 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

10.1371/journal.pgen.1004143

DNA Sequence Explains Seemingly Disordered Methylation Levels in Partially Methylated Domains of Mammalian Genomes
Cited by: 62
Author(s): Dimos Gaidatzis, Lukas Burger, Rabih Murr, Anita Lerch, Sophie Dessus-Babus, Dirk Schübeler, Michael Stadler
Software Mentions: 3
Published: almost 11 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

10.1186/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

10.1186/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

10.1371/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

10.1371/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

10.1186/s12859-018-2593-4

An integrated package for bisulfite DNA methylation data analysis with Indel-sensitive mapping
Cited by: 44
Author(s): Qiangwei Zhou, Jing-Quan Lim, Wing-Kin Sung, Guoliang Li
Software Mentions: 3
Published: almost 6 years ago

10.1371/journal.pgen.1006628

Nucleotide pools dictate the identity and frequency of ribonucleotide incorporation in mitochondrial DNA
Cited by: 55
Author(s): Anders Berglund, Clara Navarrete, Martin K. M. Engqvist, Eike Hoberg, Zsolt Szilágyi, Robert W. Taylor, Claes M. Gustafsson, Maria Falkenberg, Anders R. Clausen
Software Mentions: 3
Published: almost 8 years ago

10.1371/journal.pgen.1002728

Target Gene Analysis by Microarrays and Chromatin Immunoprecipitation Identifies HEY Proteins as Highly Redundant bHLH Repressors
Cited by: 66
Author(s): Julia Heisig, D. F. Weber, Eva Englberger, Anja Winkler, Susanne Kneitz, Wing-Kin Sung, Elmar Wolf, Martin Eilers, Wei Chia-Lin, Manfred Gessler
Software Mentions: 3
Published: over 12 years ago

10.1186/gb-2011-12-5-r44

EMIRGE: reconstruction of full-length ribosomal genes from microbial community short read sequencing data
Cited by: 309
Author(s): Christopher S. Miller, Brett J. Baker, Brian C. Thomas, Steven W. Singer, Jillian F. Banfield
Software Mentions: 3
Published: over 13 years ago

10.1186/gb-2013-14-7-r72

A compact, in vivo screen of all 6-mers reveals drivers of tissue-specific expression and guides synthetic regulatory element design
Cited by: 18
Author(s): Robin P. Smith, Samantha J. Riesenfeld, Alisha K. Holloway, Qiang Li, Karl K. Murphy, Natalie M. Feliciano, Lorenzo Orecchia, Nir Oksenberg, Katherine S. Pollard, Nadav Ahituv
Software Mentions: 3
Published: almost 12 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

10.3390/genes8100237

Optimized mtDNA Control Region Primer Extension Capture Analysis for Forensically Relevant Samples and Highly Compromised mtDNA of Different Age and Origin
Cited by: 45
Author(s): Mayra Eduardoff, Catarina Xavier, Christina Strobl, Andrea Casas-Vargas, Walther Parson
Software Mentions: 3
Published: about 7 years ago

10.3390/genes10100795

Identification of Long Non-Coding RNA-Associated Competing Endogenous RNA Network in the Differentiation of Chicken Preadipocytes
Cited by: 21
Author(s): Lan Chen, Tao Zhang, Shanshan Zhang, Jen‐Wei Huang, Genxi Zhang, Kaizhou Xie, Jinyu Wang, Haiqing Wang, Guojun Dai
Software Mentions: 3
Published: about 5 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

10.26508/lsa.202000645

Integrin α3β1 in hair bulge stem cells modulates CCN2 expression and promotes skin tumorigenesis
Cited by: 5
Author(s): Veronika Ramovs, Ana Krotenberg Garcia, Ji‐Ying Song, Iris de Rink, Maaike Kreft, Roel Goldschmeding, Arnoud Sonnenberg
Software Mentions: 3
Published: over 4 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

10.26508/lsa.201900497

Sufficiency analysis of estrogen responsive enhancers using synthetic activators
Cited by: 10
Author(s): Matthew Ginley-Hidinger, Julia B. Carleton, Adriana C. Rodriguez, Kristofer C. Berrett, Jason Gertz
Software Mentions: 3
Published: about 5 years ago

10.1186/1471-2164-15-733

Integrating dilution-based sequencing and population genotypes for single individual haplotyping
Cited by: 1
Author(s): Hirotaka Matsumoto, Hisanori Kiryu
Software Mentions: 3
Published: almost 11 years ago

Projects: pypi: bowtie

Papers Mentioning bowtie 1,566