pypi: bowtie | Projects | Ecosyste.ms: Papers

10.3390/cells9081776

A Transposon Story: From TE Content to TE Dynamic Invasion of Drosophila Genomes Using the Single-Molecule Sequencing Technology from Oxford Nanopore
Cited by: 22
Author(s): Mourdas Mohamed, Nguyet Thi-Minh Dang, Yuki Ogyama, Nelly Burlet, Bruno Mugat, Matthieu Boulesteix, Vincent Mérel, Philippe Veber, Judit Salces-Ortiz, Dany Séverac, Alain Pélisson, Cristina Vieira, François Sabot, Marie Fablet, Séverine Chambeyron
Software Mentions: 4
Published: about 6 years ago

10.1186/s13148-015-0086-0

Coordinated epigenetic remodelling of transcriptional networks occurs during early breast carcinogenesis
Cited by: 26
Author(s): Warwick J. Locke, Elena Zotenko, Clare Stirzaker, Mark D. Robinson, Rebecca A. Hinshelwood, Andrew Stone, Roger R. Reddel, Lily I. Huschtscha, Susan J. Clark
Software Mentions: 4
Published: over 11 years ago

10.1016/j.stem.2020.07.019

Naive Pluripotent Stem Cells Exhibit Phenotypic Variability that Is Driven by Genetic Variation
Cited by: 36
Author(s): Daniel Ortmann, Stephanie Brown, Anne Czechanski, Selcan Aydin, Daniele Muraro, Yuanhua Huang, Rute Tomaz, Anna Osnato, Giovanni Canu, Brandon T Wesley, Daniel A. Skelly, Oliver Stegle, Tae-Young Choi, Gary A. Churchill, Christopher L. Baker, Peter J. Rugg‐Gunn, Steven C. Munger, Laura G. Reinholdt, Ludovic Vallier
Software Mentions: 4
Published: about 6 years ago

10.1186/s13148-018-0576-y

Epigenomic profiling of archived FFPE tissues by enhanced PAT-ChIP (EPAT-ChIP) technology
Cited by: 14
Author(s): Stefano Amatori, Giuseppe Persico, Claudio Paolicelli, Roman Hillje, Nora Sahnane, Francesco Corini, Daniela Furlan, Lucilla Luzi, Saverio Minucci, Marco Giorgio, Pier Giuseppe Pelicci, Mirco Fanelli
Software Mentions: 4
Published: almost 8 years ago

10.7554/eLife.19406

Modeling susceptibility to drug-induced long QT with a panel of subject-specific induced pluripotent stem cells
Cited by: 79
Author(s): Francesca Stillitano, Jens Hansen, Chi-Wing Kong, Ioannis Karakikes, Christian Funck‐Brentano, Lin Geng, Stuart A. Scott, Stephan Reynier, Wu Ma, Yannick Valogne, Carole Desseaux, Joe‐Elie Salem, Dorota Jeziorowska, Noël Zahr, Ronald Li, Ravi Iyengar, Roger J. Hajjar, Jean‐Sébastien Hulot
Software Mentions: 4
Published: over 9 years ago

10.7554/eLife.60987

Adaptive evolution of an essential telomere protein restricts telomeric retrotransposons
Cited by: 9
Author(s): Bastien Saint-Leandre, Courtney J. Christopher, Mia T. Levine
Software Mentions: 4
Published: almost 6 years ago

10.7554/eLife.20023

Nematophagous fungus Arthrobotrys oligospora mimics olfactory cues of sex and food to lure its nematode prey
Cited by: 68
Author(s): Yu-Ting Hsueh, Matthew R. Gronquist, Erich M. Schwarz, Ravi D. Nath, Ching-Han Lee, Shalha Gharib, Frank C. Schroeder, Paul W. Sternberg
Software Mentions: 4
Published: almost 10 years ago

10.7554/eLife.21221

Pharmacological targeting of the transcription factor SOX18 delays breast cancer in mice
Cited by: 45
Author(s): Jeroen Overman, Frank Fontaine, Mehdi Moustaqil, Deepak Mittal, Emma Sierecki, Natalia Sacilotto, Johannes Zuegg, Avril A. B. Robertson, Kelly A. Holmes, Angela A. Salim, Sreeman K. Mamidyala, Mark S. Butler, Ashley Robinson, Emmanuelle Lesieur, Wayne A. Johnston, Kirill Alexandrov, Brian L. Black, Benjamin M. Hogan, Sarah De Val, Robert J. Capon, Jason S. Carroll, Timothy L. Bailey, Peter Koopman, Ralf Jauch, Mark J. Smyth, Matthew A. Cooper, Yann Gambin, Mathias François
Software Mentions: 4
Published: over 9 years ago

10.7717/peerj.2056

SigmoID: a user-friendly tool for improving bacterial genome annotation through analysis of transcription control signals
Cited by: 9
Author(s): Yevgeny Nikolaichik, Aliaksandr U. Damienikan
Software Mentions: 4
Published: over 10 years ago

10.1371/journal.pgen.1008466

Paralog buffering contributes to the variable essentiality of genes in cancer cell lines
Cited by: 59
Author(s): Barbara De Kegel, Colm J. Ryan
Software Mentions: 4
Published: almost 7 years ago

10.3389/fcimb.2016.00193

Genome-Wide Transcriptional and Post-transcriptional Regulation of Innate Immune and Defense Responses of Bovine Mammary Gland to Staphylococcus aureus
Cited by: 41
Author(s): Lingzhao Fang, Yali Hou, Jinpeng An, Bingjie Li, Mengyuan Song, Xiao Wang, Peter Sørensen, Yichun Dong, Chao Liu, Yachun Wang, Huabin Zhu, Shengli Zhang, Ying Yu
Software Mentions: 4
Published: almost 10 years ago

10.7554/eLife.31437

The formation of the light-sensing compartment of cone photoreceptors coincides with a transcriptional switch
Cited by: 29
Author(s): Janine M Daum, Özkan Keles, Sjoerd J.B. Holwerda, Hubertus Kohler, Filippo M. Rijli, Michael Stadler, Botond Roska
Software Mentions: 4
Published: almost 9 years ago

10.7554/eLife.34613

Transcriptional profiling reveals extraordinary diversity among skeletal muscle tissues
Cited by: 93
Author(s): Erin E. Terry, Xiping Zhang, Christy Hoffmann, Laura D. Hughes, Scott A. Lewis, Jiajia Li, Marianne Wallace, Lance A. Riley, Collin M Douglas, Miguel A. Gutiérrez-Monreal, Nicholas F. Lahens, Ming Gong, Francisco H. Andrade, Karyn A. Esser, Michael Hughes
Software Mentions: 4
Published: over 8 years ago

10.1186/s13048-021-00802-3

Small RNA sequencing reveals distinct nuclear microRNAs in pig granulosa cells during ovarian follicle growth
Cited by: 7
Author(s): Derek Toms, Bo Pan, Yinshan Bai, Julang Li
Software Mentions: 4
Published: over 5 years ago

10.7554/eLife.15477

Increasing Notch signaling antagonizes PRC2-mediated silencing to promote reprograming of germ cells into neurons
Cited by: 31
Author(s): Stefanie Seelk, Irene Adrian‐Kalchhauser, Balázs Hargitai, Martina Hajdůšková, Silvia Gutnik, Baris Tursun, Rafal Ciosk
Software Mentions: 4
Published: about 10 years ago

10.7554/eLife.47891

Epimutations are associated with CHROMOMETHYLASE 3-induced de novo DNA methylation
Cited by: 54
Author(s): Jered M. Wendte, Yinwen Zhang, Lexiang Ji, Xiulin Shi, Rashmi R. Hazarika, Yadollah Shahryary, Frank Johannes, Robert J. Schmitz
Software Mentions: 4
Published: about 7 years ago

10.1128/mSystems.00980-20

Elucidation of Regulatory Modes for Five Two-Component Systems in Escherichia coli Reveals Novel Relationships
Cited by: 22
Author(s): Kumari Sonal Choudhary, Julia A. Kleinmanns, Katherine Decker, Anand V. Sastry, Ye Gao, Richard Szubin, Yara Seif, Bernhard Ø. Palsson
Software Mentions: 4
Published: almost 6 years ago

10.1186/1471-2105-12-75

AnyExpress: Integrated toolkit for analysis of cross-platform gene expression data using a fast interval matching algorithm
Cited by: 16
Author(s): Jihoon Kim, Kiltesh Patel, Hyunchul Jung, Winston Patrick Kuo, Lucila Ohno-Machado
Software Mentions: 4
Published: over 15 years ago

10.1016/j.celrep.2020.107928

Diversification of DNA-Binding Specificity by Permissive and Specificity-Switching Mutations in the ParB/Noc Protein Family
Cited by: 17
Author(s): Adam S. B. Jalal, Ngat T. Tran, Clare E. M. Stevenson, Elliot W. Chan, Rebecca Lo, Xiao Tan, Agnes Noy, David M. Lawson, Tung B. K. Le
Software Mentions: 4
Published: over 6 years ago

10.3390/pathogens8040183

Whole Transcriptome Analyses Reveal Differential mRNA and microRNA Expression Profiles in Primary Human Dermal Fibroblasts Infected with Clinical or Vaccine Strains of Varicella Zoster Virus
Cited by: 12
Author(s): Soo Jin Oh, Soo Yeon Lim, Mee Hyun Song, Jinhee Ahn, Chan Hee Lee, Ok Sarah Shin
Software Mentions: 4
Published: about 7 years ago

10.1186/1471-2164-14-266

Characterization of differential transcript abundance through time during Nematostella vectensis development
Cited by: 73
Author(s): Rebecca R. Helm, Stefan Siebert, Sarah Tulin, Joel Smith, Casey W. Dunn
Software Mentions: 4
Published: almost 14 years ago

10.1128/mBio.02262-18

Genomic Analyses of Acute Flaccid Myelitis Cases among a Cluster in Arizona Provide Further Evidence of Enterovirus D68 Role
Cited by: 13
Author(s): Jolene R. Bowers, Michael Valentine, Veronica Harrison, Viacheslav Y. Fofanov, John D. Gillece, Josie Delisle, Bethany K. Patton, James M. Schupp, Krystal Sheridan, Darrin Lemmer, Scott Ostdiek, Harlori K. Bains, Jennifer Heim, Tammy Sylvester, Siru Prasai, Melissa Kretschmer, Nicole Fowle, Kenneth Komatsu, Shane Brady, Susan Robinson, Kathryn Fitzpatrick, Gholamabbas Amin Ostovar, Eric Alsop, Elizabeth Hutchins, Kendall Jensen, Paul Keim, David M. Engelthaler
Software Mentions: 4
Published: over 7 years ago

10.1038/s41421-018-0027-0

Gas41 links histone acetylation to H2A.Z deposition and maintenance of embryonic stem cell identity
Cited by: 38
Author(s): Chih Chao Hsu, Dan Zhao, Jiejun Shi, Danni Peng, Haipeng Guan, Yuanyuan Li, Yaling Huang, Hong Wen, Wei Li, Haitao Li, Xiaobing Shi
Software Mentions: 4
Published: over 8 years ago

10.3390/v10070388

Co-Infection Patterns in Individual Ixodes scapularis Ticks Reveal Associations between Viral, Eukaryotic and Bacterial Microorganisms
Cited by: 40
Author(s): Shaun T. Cross, Marylee Kapuscinski, Jacquelyn Perino, Bernadette L Maertens, James Weger-Lucarelli, Gregory D. Ebel, Mark D. Stenglein
Software Mentions: 4
Published: about 8 years ago

10.1128/mSystems.00284-18

Systems-Level Analysis of Oxygen Exposure in Zymomonas mobilis : Implications for Isoprenoid Production
Cited by: 22
Author(s): Julia Martien, Alexander S. Hebert, David Stevenson, Matthew Regner, Daven B. Khana, Joshua J. Coon, Daniel Amador‐Noguez
Software Mentions: 4
Published: over 7 years ago

10.7554/eLife.19893

The MBD7 complex promotes expression of methylated transgenes without significantly altering their methylation status
Cited by: 16
Author(s): Dongming Li, Ana Marie S. Palanca, So Youn Won, Lei Gao, Ying Feng, Ajay A. Vashisht, Li Liu, Yuanyuan Zhao, Xigang Liu, Xiuyun Wu, Shaofang Li, Brandon H. Le, Yun Ju Kim, Guodong Yang, Shengben Li, Jinyuan Liu, James A. Wohlschlegel, Hongwei Guo, Beixin Mo, Xuemei Chen, Julie A. Law
Software Mentions: 4
Published: over 9 years ago

10.1371/journal.ppat.1009644

Manipulation of the unfolded protein response: A pharmacological strategy against coronavirus infection
Cited by: 46
Author(s): Liliana Echavarría-Consuegra, G. M. W. Cook, Idoia Busnadiego, Charlotte Lefèvre, Sarah Keep, Katherine A. Brown, Nicole Doyle, Giulia Dowgier, Krzysztof Franaszek, Nathan Moore, Stuart G. Siddell, Erica Bickerton, Benjamin G. Hale, Andrew E. Firth, Ian Brierley, Nerea Irigoyen
Software Mentions: 4
Published: over 5 years ago

10.1093/ve/vey007

Easy and accurate reconstruction of whole HIV genomes from short-read sequence data with shiver
Cited by: 51
Author(s): Chris Wymant, François Blanquart, Tanya Golubchik, Astrid Gall, Margreet Bakker, Daniela Bezemer, Nicholas J. Croucher, Matthew Hall, Mariska Hillebregt, Swee Hoe Ong, Oliver Ratmann, Jan Albert, Norbert Bannert, Jacques Fellay, Katrien Fransen, Annabelle Gourlay, M Kate Grabowski, Barbara Gunsenheimer‐Bartmeyer, Huldrych F Günthard, Pia Kivelä, Roger D. Kouyos, Oliver Laeyendecker, Kirsi Liitsola, Laurence Meyer, Kholoud Porter, Matti Ristola, Ard van Sighem, Ben Berkhout, Marion Cornelissen, Paul Kellam, Peter Reiss, Christophe Fraser
Software Mentions: 4
Published: almost 9 years ago

10.1371/journal.pgen.1007473

RES complex is associated with intron definition and required for zebrafish early embryogenesis
Cited by: 23
Author(s): Juan Pablo Fernández, Miguel A. Moreno-Mateos, André Gohr, Liyun Miao, Shun Hang Chan, Manuel Irimia, Antonio J. Giráldez
Software Mentions: 4
Published: over 8 years ago

10.1371/journal.ppat.1009208

A multi-omics approach to Epstein-Barr virus immortalization of B-cells reveals EBNA1 chromatin pioneering activities targeting nucleotide metabolism
Cited by: 20
Author(s): Jason Lamontagne, Samantha S. Soldan, Chenhe Su, Andreas Wiedmer, Kyoung Jae Won, Fang Lü, Aaron R. Goldman, Jayamanna Wickramasinghe, Hsin‐Yao Tang, David W. Speicher, Louise C. Showe, Andrew V. Kossenkov, Paul M. Lieberman
Software Mentions: 4
Published: over 5 years ago

10.1080/15384101.2016.1261765

Genome-wide screen of cell-cycle regulators in normal and tumor cells identifies a differential response to nucleosome depletion
Cited by: 24
Author(s): Maria Sokolova, Mikko Turunen, Oliver Mortusewicz, Teemu Kivioja, Patrick Herr, Anna Vähärautio, Mikael Björklund, Minna Taipale, Thomas Helleday, Jussi Taipale
Software Mentions: 4
Published: almost 10 years ago

10.1007/s13238-017-0480-9

TDP-43 regulates cancer-associated microRNAs
Cited by: 28
Author(s): Xiaowei Chen, Zhen Fan, W Ambrose McGee, Mengmeng Chen, Ruirui Kong, Pushuai Wen, Tengfei Xiao, Xiaomin Chen, Jianghong Liu, Li Zhu, Runsheng Chen, Jane Y. Wu
Software Mentions: 4
Published: about 9 years ago

10.1371/journal.pone.0240885

Whole egg consumption increases gene expression within the glutathione pathway in the liver of Zucker Diabetic Fatty rats
Cited by: 2
Author(s): J. L. Webb, Amanda Bries, Brooke Vogel, Claudia Carrillo, Lily Harvison, Timothy A. Day, Michael J. Kimber, Rudy J. Valentine, Matthew J. Rowling, Stephanie Clark, Elizabeth McNeill, Kevin L. Schalinske
Software Mentions: 4
Published: almost 6 years ago

10.1186/s12985-016-0659-3

Derivation of chicken induced pluripotent stem cells tolerant to Newcastle disease virus-induced lysis through multiple rounds of infection
Cited by: 7
Author(s): Leonardo Susta, Ying He, Jessica M. Hutcheson, Yangqing Lu, Franklin D. West, Steven L. Stice, Ping Yu, Zaid Abdo, Claudio L. Afonso
Software Mentions: 4
Published: almost 10 years ago

10.1371/journal.ppat.1006302

Activated entomopathogenic nematode infective juveniles release lethal venom proteins
Cited by: 87
Author(s): Dihong Lu, Marissa Macchietto, Dennis Chang, Mirayana M. Barros, J. G. Baldwin, A Mortazavi, Adler R. Dillman
Software Mentions: 4
Published: over 9 years ago

10.1371/journal.pgen.1004642

Regulation of p53 and Rb Links the Alternative NF-κB Pathway to EZH2 Expression and Cell Senescence
Cited by: 80
Author(s): Alessio Iannetti, Adeline Ledoux, Susan J. Tudhope, Hélène Sellier, Bo Zhao, Sophia Mowla, Adam J. Moore, Holger Hummerich, Benjamin E. Gewurz, Simon Cockell, Parmjit Jat, Elaine Willmore, Neil D. Perkins
Software Mentions: 4
Published: about 12 years ago

10.1371/journal.pone.0067134

Global Identification of EVI1 Target Genes in Acute Myeloid Leukemia
Cited by: 57
Author(s): Carolyn Glass, Charles A. Wuertzer, Xiaohui Cui, Yingtao Bi, Ramana V. Davuluri, Ying Yi Xiao, Michael P. Wilson, Kristina M. Owens, Yi Zhang, Archibald S. Perkins
Software Mentions: 4
Published: over 13 years ago

10.1186/s12284-018-0211-8

Comparative analysis of the root transcriptomes of cultivated and wild rice varieties in response to Magnaporthe oryzae infection revealed both common and species-specific pathogen responses
Cited by: 27
Author(s): Lei Tian, Shaohua Shi, Fahad Nasir, Chunguang Chang, Weiqiang Li, Lam‐Son Phan Tran, Chunjie Tian
Software Mentions: 4
Published: over 8 years ago

10.7554/eLife.25607

lncRNA requirements for mouse acute myeloid leukemia and normal differentiation
Cited by: 47
Author(s): M. Joaquina Delás, Leah R. Sabin, Egor Dolzhenko, Simon Knott, Ester Munera Maravilla, Benjamin T. Jackson, Sophia A Wild, Tatjana Kovačević, Eva Maria Stork, Meng Zhou, Nicolas Erard, Emily Lee, David R. Kelley, Mareike Roth, Inês Barbosa, Johannes Zuber, John L. Rinn, Andrew D. Smith, Gregory J. Hannon
Software Mentions: 4
Published: about 9 years ago

10.15252/msb.20209569

Exploring the virulence gene interactome with <scp>CRISPR</scp> / <scp>dC</scp> as9 in the human malaria parasite
Cited by: 30
Author(s): Jessica M. Bryant, Sebastian Baumgarten, Florent Dingli, Damarys Loew, Ameya Sinha, Aurélie Claës, Peter R. Preiser, Peter C. Dedon, Artur Scherf
Software Mentions: 4
Published: about 6 years ago

10.1371/journal.pgen.1006828

p63 exerts spatio-temporal control of palatal epithelial cell fate to prevent cleft palate
Cited by: 34
Author(s): Rose Richardson, Karen S. Mitchell, Nigel L. Hammond, Maria Rosaria Mollo, Evelyn N. Kouwenhoven, Niki Wyatt, Ian J. Donaldson, Leo Zeef, Tim Burgis, Rognvald Blance, Simon J. van Heeringen, Hendrik G. Stunnenberg, Huiqing Zhou, Caterina Missero, Rose Anne Romano, Satrajit Sinha, Michael J. Dixon, Jill Dixon
Software Mentions: 4
Published: over 9 years ago

10.1371/journal.pone.0107259

Optimization of Extraction of Circulating RNAs from Plasma – Enabling Small RNA Sequencing
Cited by: 48
Author(s): Melanie Spornraft, Benedikt Kirchner, Bettina Haase, Vladimı́r Beneš, Michael W. Pfaffl, Irmgard Riedmaier
Software Mentions: 4
Published: about 12 years ago

10.15252/msb.20156505

A cell‐based model system links chromothripsis with hyperploidy
Cited by: 113
Author(s): Balca R. Mardin, Alexandros P. Drainas, Sebastian M. Waszak, Joachim Weischenfeldt, Mayumi Isokane, Adrian M. Stütz, Benjamin Raeder, Theocharis Efthymiopoulos, Christopher Buccitelli, Maia Segura-Wang, Paul A. Northcott, Stefan M. Pfister, Peter Lichter, Jan Ellenberg, Jan Korbel
Software Mentions: 4
Published: about 11 years ago

10.1371/journal.pgen.1002676

LINT, a Novel dL(3)mbt-Containing Complex, Represses Malignant Brain Tumour Signature Genes
Cited by: 30
Author(s): Karin Meier, Eve-Lyne Mathieu, Florian Finkernagel, L. Maximilian Reuter, Maren Scharfe, Gunther Doehlemann, Michael Jarek, Alexander Brehm
Software Mentions: 4
Published: over 14 years ago

10.1093/gbe/evaa094

piRNA and Transposon Dynamics in Drosophila: A Female Story
Cited by: 17
Author(s): Bastien Saint-Leandre, Pierre Capy, Aurélie Hua-Van, Jonathan Filée
Software Mentions: 4
Published: over 6 years ago

10.1371/journal.pgen.1007905

Tissue- and sex-specific small RNAomes reveal sex differences in response to the environment
Cited by: 21
Author(s): Alexandra Bezler, Fabian Braukmann, Sean M. West, Arthur Duplan, Raffaella Conconi, Frédéric Schütz, Pierre Gönczy, Fabio Piano, Kristin C. Gunsalus, Eric A. Miska, Laurent Keller
Software Mentions: 4
Published: over 7 years ago

10.1002/1878-0261.12503

HDAC7‐mediated control of tumour microenvironment maintains proliferative and stemness competence of human mammary epithelial cells
Cited by: 27
Author(s): Valentina Cutano, Eros Di Giorgio, Martina Minisini, Raffaella Picco, Emiliano Dalla, Claudio Brancolini
Software Mentions: 4
Published: over 7 years ago

10.1002/1878-0261.12478

Identification of tumor suppressor miRNAs by integrative miRNA and mRNA sequencing of matched tumor–normal samples in lung adenocarcinoma
Cited by: 38
Author(s): Namhee Yu, Seunghui Yong, Hong Kwan Kim, Yoon La Choi, Yeonjoo Jung, Doyeon Kim, Jihae Seo, Ye Eun Lee, Daehyun Baek, Jinseon Lee, Seungjae Lee, Jong Eun Lee, Jaesang Kim, Young Tae Kim, Sanghyuk Lee
Software Mentions: 4
Published: over 7 years ago

10.1186/s13059-021-02390-3

Transcription shapes DNA replication initiation to preserve genome integrity
Cited by: 17
Author(s): Yang Liu, Chen Ai, Tingting Gan, Jinchun Wu, Yongpeng Jiang, Xuhao Liu, Ru-Sen Lu, Ning Gao, Qing Li, Ji Xiong, Jiazhi Hu
Software Mentions: 4
Published: over 5 years ago

10.1007/s12035-021-02296-y

The Coding and Small Non-coding Hippocampal Synaptic RNAome
Cited by: 9
Author(s): Robert Epple, Dennis M. Krüger, Tea Berulava, Gerrit Brehm, Momchil Ninov, Rezaul Islam, Sarah Köster, André Fischer
Software Mentions: 4
Published: over 5 years ago

10.1371/journal.pgen.1009466

activin-2 is required for regeneration of polarity on the planarian anterior-posterior axis
Cited by: 13
Author(s): Jennifer Cloutier, Conor L. McMann, Isaac M. Oderberg, Peter W. Reddien
Software Mentions: 4
Published: over 5 years ago

10.1186/1471-2164-14-862

De novo characterization of the gene-rich transcriptomes of two color-polymorphic spiders, Theridion grallator and T. californicum (Araneae: Theridiidae), with special reference to pigment genes
Cited by: 51
Author(s): Peter J.P. Croucher, Michael S. Brewer, Christopher J. Winchell, Geoff Oxford, Rosemary G. Gillespie
Software Mentions: 4
Published: almost 14 years ago

10.1186/s12943-015-0358-5

Next-generation sequencing reveals novel differentially regulated mRNAs, lncRNAs, miRNAs, sdRNAs and a piRNA in pancreatic cancer
Cited by: 198
Author(s): Sören Müller, Susanne Raulefs, Philipp Bruns, Fabian Afonso-Grunz, Anne Plötner, Rolf Thermann, Carsten Jäger, Anna Melissa Schlitter, Bo Kong, Ivonne Regel, W. Kurt Roth, Björn Rotter, Klaus Hoffmeier, Günter Kahl, Ina Koch, Fabian J. Theis, Jörg Kleeff, Peter Winter, Christoph Michalski
Software Mentions: 4
Published: over 11 years ago

10.1371/journal.pgen.1008358

Multi-omics analysis identifies mitochondrial pathways associated with anxiety-related behavior
Cited by: 34
Author(s): R. Zuzanna Misiewicz, Stella Iurato, Natalia Kulesskaya, Laura Salminen, Luís Filipe Rodrigues, Giuseppina Maccarrone, Jade Martins, Darina Czamara, Mikaela Laine, Ewa Sokołowska, Kalevi Trontti, Christiane Rewerts, Božidar Novak, Naama Volk, Dong Ik Park, Eija Jokitalo, Lars Paulín, Petri Auvinen, Vootele Võikar, Alon Chen, Angelika Erhardt, Christoph W. Turck, Iiris Hovatta
Software Mentions: 4
Published: about 7 years ago

10.1371/journal.pgen.1006449

Genomic Characterization of Metformin Hepatic Response
Cited by: 38
Author(s): Marcelo R. Luizon, Walter L. Eckalbar, Yao Wang, Stacy L. Jones, Robin P. Smith, Laurance Megan, Lawrence Lin, Paul J. Gallins, Amy S. Etheridge, Fred A. Wright, Yifeng Zhou, Cliona Molony, Federico Innocenti, Sook Wah Yee, Kathleen M. Giacomini, Nadav Ahituv
Software Mentions: 4
Published: almost 10 years ago

10.1371/journal.pone.0128465

Connecting Anxiety and Genomic Copy Number Variation: A Genome-Wide Analysis in CD-1 Mice
Cited by: 6
Author(s): Julia Brenndörfer, André Altmann, Regina Widner-Andrä, Benno Pütz, Darina Czamara, Erik Tilch, Tony Kam‐Thong, Peter Weber, Monika Rex‐Haffner, Thomas Bettecken, Andrea Bultmann, Bertram Müller‐Myhsok, Elisabeth Binder, Rainer Landgraf, Ludwig Czibere
Software Mentions: 4
Published: over 11 years ago

10.1074/jbc.RA120.015896

YAP contributes to DNA methylation remodeling upon mouse embryonic stem cell differentiation
Cited by: 21
Author(s): Fabiana Passaro, Ilaria De Martino, Federico Zambelli, Giorgia Di Benedetto, Matteo Barbato, Anna Maria D’Erchia, Caterina Manzari, Graziano Pesole, Margherita Mutarelli, Davide Cacchiarelli, Dario Antonini, Silvia Parisi, Tommaso Russo
Software Mentions: 4
Published: almost 6 years ago

10.1093/molbev/msx144

Recent Sex Chromosome Divergence despite Ancient Dioecy in the Willow Salix viminalis
Cited by: 55
Author(s): Pascal Pucholt, Alison E. Wright, Lei Liu Conze, Judith E. Mank, Sofia Berlin
Software Mentions: 4
Published: over 9 years ago

10.1093/molbev/msab141

Rapid Parallel Adaptation to Anthropogenic Heavy Metal Pollution
Cited by: 14
Author(s): Alexander S. T. Papadopulos, Andrew J. Helmstetter, Owen G. Osborne, Aaron A. Comeault, Daniel P. Wood, Edward A. Straw, Laurence Mason, Michael F. Fay, Joe Parker, Luke T. Dunning, Andrew Foote, Rhian J. Smith, Jackie Lighten
Software Mentions: 4
Published: over 5 years ago

10.1007/s00401-021-02322-2

Altered oligodendroglia and astroglia in chronic traumatic encephalopathy
Cited by: 25
Author(s): Kevin Blake Chancellor, Sarah E. Chancellor, Joseph E. Duke-Cohan, Bertrand R. Huber, Thor D. Stein, Victor E. Alvarez, Benjamin W. Okaty, Susan M. Dymecki, Ann C. McKee
Software Mentions: 4
Published: over 5 years ago

10.1371/journal.pcbi.1008647

Independent component analysis recovers consistent regulatory signals from disparate datasets
Cited by: 24
Author(s): Anand V. Sastry, Alyssa Hu, David Heckmann, Saugat Poudel, Erol Kavvas, Bernhard Ø. Palsson
Software Mentions: 4
Published: over 5 years ago

10.1186/s12864-016-3227-8

Blood miRNomes and transcriptomes reveal novel longevity mechanisms in the long-lived bat, Myotis myotis
Cited by: 43
Author(s): Zixia Huang, David Jebb, Emma C. Teeling
Software Mentions: 4
Published: almost 10 years ago

10.1186/s13059-015-0742-x

Extensive identification and analysis of conserved small ORFs in animals
Cited by: 162
Author(s): Sebastian D. Mackowiak, Henrik Zauber, Chris Bielow, Denise Thiel, Kamila Kutz, Lorenzo Calviello, Guido Mastrobuoni, Nikolaus Rajewsky, Stefan Kempa, Matthias Selbach, Benedikt Obermayer
Software Mentions: 4
Published: about 11 years ago

10.1186/s13059-015-0746-6

Comparative genomics of Steinernema reveals deeply conserved gene regulatory networks
Cited by: 74
Author(s): Adler R. Dillman, Marissa Macchietto, Camille F. Porter, Alicia K. Rogers, Brian A. Williams, Igor Antoshechkin, Ming Min Lee, Z. Goodwin, Xiaojun Lu, Edwin E. Lewis, Heidi Goodrich-Blair, S. Patricia Stock, Byron J. Adams, Paul W. Sternberg, A Mortazavi
Software Mentions: 4
Published: about 11 years ago

10.1186/gb-2013-14-11-r131

Chromatin signatures at transcriptional start sites separate two equally populated yet distinct classes of intergenic long noncoding RNAs
Cited by: 162
Author(s): Ana C. Marques, Jim R. Hughes, Bryony Graham, Monika S. Kowalczyk, Douglas R. Higgs, Chris P. Ponting
Software Mentions: 4
Published: almost 14 years ago

10.1186/gb-2014-15-4-r57

Evidence for the biogenesis of more than 1,000 novel human microRNAs
Cited by: 214
Author(s): Marc R. Friedländer, Esther Lizano, Anna J.S. Houben, Daniela Bezdan, Mónica Báñez-Coronel, Grzegorz Kudla, Elisabet Mateu-Huertas, Birgit Kagerbauer, Justo González, Kevin C. Chen, Emily LeProust, Eulàlia Martı́, Xavier Estivill
Software Mentions: 4
Published: almost 13 years ago

10.1186/s13059-014-0410-6

Corset: enabling differential gene expression analysis for de novoassembled transcriptomes
Cited by: 278
Author(s): N. Davidson, Alicia Oshlack
Software Mentions: 4
Published: over 12 years ago

10.1371/journal.pgen.1008501

The MITF-SOX10 regulated long non-coding RNA DIRC3 is a melanoma tumour suppressor
Cited by: 51
Author(s): Elizabeth A. Coe, Jennifer Y. Tan, Michael Shapiro, Pakavarin Louphrasitthiphol, Andrew Bassett, Ana C. Marques, Colin R. Goding, Keith W. Vance
Software Mentions: 4
Published: almost 7 years ago

10.1186/gb-2014-15-2-r32

KDM5B focuses H3K4 methylation near promoters and enhancers during embryonic stem cell self-renewal and differentiation
Cited by: 112
Author(s): Benjamin L. Kidder, Gangqing Hu, Keji Zhao
Software Mentions: 4
Published: almost 13 years ago

10.1186/s13059-016-0882-7

Characterization of chromatin accessibility with a transposome hypersensitive sites sequencing (THS-seq) assay
Cited by: 50
Author(s): Brandon C. Sos, Ho-Lim Fung, Derek Gao, Trina Osothprarop, Amirali Kia, M.M. He, Kun Zhang
Software Mentions: 4
Published: over 10 years ago

10.1186/gb-2011-12-2-r16

Genomewide characterization of non-polyadenylated RNAs
Cited by: 358
Author(s): Li Yang, Michael O. Duff, Brenton R. Graveley, Gordon G. Carmichael, Lingling Chen
Software Mentions: 4
Published: almost 16 years ago

10.1186/s40168-018-0515-3

Breast cancer in postmenopausal women is associated with an altered gut metagenome
Cited by: 157
Author(s): Jia Zhu, Ming Liao, Ziting Yao, Wenying Liang, Qibin Li, Jianlun Liu, Huawei Yang, Yinan Ji, Wei Wei, Aihua Tan, Sai Liang, Yang Chen, Haisong Lin, Xinyuan Zhu, Shengzhu Huang, Jiarong Tian, Rongjiang Tang, Qiuyan Wang, Zengnan Mo
Software Mentions: 4
Published: about 8 years ago

10.1371/journal.pone.0242516

The small RNA locus map for Chlamydomonas reinhardtii
Cited by: 4
Author(s): Sebastian Müller, Nicholas E. Matthews, Adrián Vallí, David C. Baulcombe
Software Mentions: 4
Published: almost 6 years ago

10.1186/s12859-016-0969-x

MaGuS: a tool for quality assessment and scaffolding of genome assemblies with Whole Genome Profiling™ Data
Cited by: 11
Author(s): Mohammed‐Amin Madoui, Carole Dossat, Léo d'Agata, Jan van Oeveren, Edwin van der Vossen, Jean‐Marc Aury
Software Mentions: 4
Published: over 10 years ago

10.1186/gb-2011-12-8-r76

The head-regeneration transcriptome of the planarian Schmidtea mediterranea
Cited by: 110
Author(s): Thomas Sandmann, Matthias Christian Vogg, Suthira Owlarn, Michael Boutros, Kerstin Bartscherer
Software Mentions: 4
Published: almost 16 years ago

10.1186/s40168-018-0408-5

Integrated multi-omic analysis of host-microbiota interactions in acute oak decline
Cited by: 44
Author(s): Martin Broberg, James Doonan, Filip Mundt, Sandra Denman, James E. McDonald
Software Mentions: 4
Published: over 8 years ago

10.1038/s41380-020-0767-8

AP-1 controls the p11-dependent antidepressant response
Cited by: 25
Author(s): Revathy U. Chottekalapanda, Salina Kalik, Jodi Gresack, Alyssa Ayala, Melanie Gao, Wei Wang, Sarah J. Meller, Ammar Aly, Anne Schaefer, Paul Greengard
Software Mentions: 4
Published: over 6 years ago

10.1186/s12864-017-3929-6

Ethylene induces combinatorial effects of histone H3 acetylation in gene expression in Arabidopsis
Cited by: 42
Author(s): Likai Wang, Fan Zhang, Siddharth Rode, Kevin Chin, Eun Esther Ko, Jonghwan Kim, Vishwanath R. Iyer, Hong Qiao
Software Mentions: 4
Published: over 9 years ago

10.1371/journal.pbio.3000153

Time-dependent Pax3-mediated chromatin remodeling and cooperation with Six4 and Tead2 specify the skeletal myogenic lineage in developing mesoderm
Cited by: 17
Author(s): Alessandro Magli, June Baik, Lauren J. Mills, Il-Youp Kwak, Bridget S. Dillon, Ricardo Mondragón-González, David Stafford, Scott Swanson, Ron Stewart, James A. Thomson, Daniel J. Garry, Brian David Dynlacht, Rita C.R. Perlingeiro
Software Mentions: 4
Published: over 7 years ago

10.1186/s40168-017-0340-0

Feed in summer, rest in winter: microbial carbon utilization in forest topsoil
Cited by: 104
Author(s): Lucia Žifčáková, Tomáš Větrovský, Vincent Lombard, Bernard Henrissat, Adina Howe, Petr Baldrián
Software Mentions: 4
Published: about 9 years ago

10.1534/g3.114.013508

De Novo Assembly and Annotation of the Transcriptome of the Agricultural Weed Ipomoea purpurea Uncovers Gene Expression Changes Associated with Herbicide Resistance
Cited by: 41
Author(s): Trent A Leslie, Regina S. Baucom
Software Mentions: 4
Published: about 12 years ago

10.1534/g3.118.200789

Dynamic Interactions Between the Genome and an Endogenous Retrovirus: Tirant in Drosophila simulans Wild-Type Strains
Cited by: 4
Author(s): Marie Fablet, Angelo Jacquet, Rita Rebollo, Annabelle Haudry, Colette Rey, Judit Salces-Ortiz, Prajakta Bajad, Nelly Burlet, Michael F. Jantsch, Maria Pilar García Guerreiro, Cristina Vieira
Software Mentions: 4
Published: over 7 years ago

10.3390/genes8020068

Differential Binding of Three Major Human ADAR Isoforms to Coding and Long Non-Coding Transcripts
Cited by: 34
Author(s): Josephine Galipon, Rintaro Ishii, Yutaka Suzuki, Masaru Tomita, Kumiko Ui-Tei
Software Mentions: 4
Published: over 9 years ago

10.1016/j.mex.2019.01.009

RppH can faithfully replace TAP to allow cloning of 5′-triphosphate carrying small RNAs
Cited by: 18
Author(s): Miguel Vasconcelos Almeida, António Miguel de Jesus Domingues, Hanna Lukas, María Méndez-Lago, René F. Ketting
Software Mentions: 4
Published: almost 8 years ago

10.3389/fpls.2012.00202

A High-Throughput Method for Illumina RNA-Seq Library Preparation
Cited by: 134
Author(s): Ravi Kumar, Yasunori Ichihashi, Seisuke Kimura, Daniel H. Chitwood, Lauren R. Headland, Jie Peng, Julin N. Maloof, Neelima Sinha
Software Mentions: 4
Published: almost 15 years ago

10.1186/s12864-015-1660-8

Sex and parasites: genomic and transcriptomic analysis of Microbotryum lychnidis-dioicae, the biotrophic and plant-castrating anther smut fungus
Cited by: 59
Author(s): Michael H. Perlin, Joëlle Amselem, Eric Fontanillas, Su San Toh, Zehua Chen, Jonathan M. Goldberg, Sébastien Duplessis, Bernard Henrissat, Sarah Young, Qiandong Zeng, Gabriela Aguileta, Elsa Petit, Hélène Badouin, Jared Andrews, Dominique Razeeq, Toni Gabaldón, Hadi Quesneville, Tatiana Giraud, Michael E. Hood, David J. Schultz, Christina A. Cuomo
Software Mentions: 4
Published: over 11 years ago

10.3389/fpls.2021.727302

Identification of Genes and MicroRNAs Affecting Pre-harvest Sprouting in Rice (Oryza sativa L.) by Transcriptome and Small RNAome Analyses
Cited by: 4
Author(s): Minsu Park, Wookap Choi, Sang Yoon Shin, Hongman Moon, Dowhan Lee, Yun Shil Gho, Ki Hong Jung, Jong Seong Jeon, Chanseok Shin
Software Mentions: 4
Published: about 5 years ago

10.3389/fpls.2020.01003

The MADS-Box Gene MdDAM1 Controls Growth Cessation and Bud Dormancy in Apple
Cited by: 33
Author(s): Mirko Moser, Elisa Asquini, Giulia Valentina Miolli, Kathleen Weigl, Magda‐Viola Hanke, Henryk Flachowsky, Azeddine Si‐Ammour
Software Mentions: 4
Published: over 6 years ago

10.3389/fnmol.2017.00091

Identification of the Spinal Expression Profile of Non-coding RNAs Involved in Neuropathic Pain Following Spared Nerve Injury by Sequence Analysis
Cited by: 114
Author(s): Jun Zhou, Qingming Xiong, Hongtao Chen, Cheng-xiang Yang, Yu Fan
Software Mentions: 4
Published: over 9 years ago

10.3389/fmicb.2021.668644

Ecological Divergence Within the Enterobacterial Genus Sodalis: From Insect Symbionts to Inhabitants of Decomposing Deadwood
Cited by: 9
Author(s): Vojtěch Tláskal, Victor Satler Pylro, Lucia Žifčáková, Petr Baldrián
Software Mentions: 4
Published: over 5 years ago

10.3389/fmicb.2018.00593

Genome Sequence, Assembly and Characterization of Two Metschnikowia fructicola Strains Used as Biocontrol Agents of Postharvest Diseases
Cited by: 51
Author(s): Edoardo Piombo, Noa Sela, Michael Wisniewski, Maria Hoffmann, M. L. Gullino, Marc W. Allard, E.J. Levin, D. Spadaro, Samir Droby
Software Mentions: 4
Published: over 8 years ago

10.1186/s12862-016-0700-6

Surprisingly rich repertoire of Wnt genes in the demosponge Halisarca dujardini
Cited by: 40
Author(s): Ilya Borisenko, Marcin Adamski, Alexander Ereskovsky, Maja Adamska
Software Mentions: 4
Published: over 10 years ago

10.1371/journal.pone.0187542

Effects of glucose availability in Lactobacillus sakei; metabolic change and regulation of the proteome and transcriptome
Cited by: 10
Author(s): Anette McLeod, Ellen Færgestad Mosleth, Ida Rud, Filipe Branco dos Santos, Lars-Gustav Snipen, Kristian Hovde Liland, Lars Axelsson
Software Mentions: 4
Published: almost 9 years ago

10.1093/bib/bbv019

Optimization of miRNA-seq data preprocessing
Cited by: 100
Author(s): Susan H. Tam, Ming‐Sound Tsao, John Douglas Mcpherson
Software Mentions: 4
Published: over 11 years ago

10.1093/bib/bbz155

Current challenges and best-practice protocols for microbiome analysis
Cited by: 219
Author(s): Richa Bharti, Dominik G. Grimm
Software Mentions: 4
Published: almost 7 years ago

10.1186/s12864-019-5775-1

Translation of upstream open reading frames in a model of neuronal differentiation
Cited by: 25
Author(s): Caitlin M. Rodriguez, Sang-Young Chun, Ryan E. Mills, Peter K. Todd
Software Mentions: 4
Published: over 7 years ago

10.3389/fphar.2021.673831

MMP24 Contributes to Neuropathic Pain in an FTO-Dependent Manner in the Spinal Cord Neurons
Cited by: 6
Author(s): Longfei Ma, Yangyuxin Huang, Fengjiang Zhang, Dave Schwinn Gao, Na Sun, Jinxuan Ren, Suyun Xia, Jia Li, Xiujuan Peng, Yu Lu, Bao‐Chun Jiang, Min Yan
Software Mentions: 4
Published: over 5 years ago

10.1371/journal.ppat.1008984

Characterising the epidemic spread of influenza A/H3N2 within a city through phylogenetics
Cited by: 13
Author(s): Nicola F. Müller, Daniel Wüthrich, Nina Goldman, Nadine Sailer, Claudia Saalfrank, Myrta Brunner, Noémi Augustin, Helena M. B. Seth-Smith, Yvonne Hollenstein, Mohammedyaseen Syedbasha, Daniela Lang, Richard A. Neher, Olivier Dubuis, Michael Naegele, Andreas Buser, Christian H. Nickel, Nicole Ritz, Andreas Zeller, Brian M. Lang, James Hadfield, Trevor Bedford, Manuel Battegay, Rita Schneider-Sliwa, Adrian Egli, Tanja Stadler
Software Mentions: 4
Published: almost 6 years ago

10.1186/s12864-018-4660-7

Analysis of human ES cell differentiation establishes that the dominant isoforms of the lncRNAs RMST and FIRRE are circular
Cited by: 41
Author(s): Osagie Izuogu, Abd A. Alhasan, Carla Mellough, Joseph Collin, Richard Gallon, Jonathon Hyslop, Francesco K. Mastrorosa, Ingrid Ehrmann, Majlinda Lako, David Elliott, Mauro Santibanez‐Koref, Michael S. Jackson
Software Mentions: 4
Published: over 8 years ago

10.1186/s12859-017-1772-z

Evaluation of high-throughput isomiR identification tools: illuminating the early isomiRome of Tribolium castaneum
Cited by: 13
Author(s): Daniel Amsel, Andreas Vilcinskas, André Billion
Software Mentions: 4
Published: about 9 years ago

Projects: pypi: bowtie

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Papers Mentioning bowtie 1,566