pypi: bowtie | Projects | Ecosyste.ms: Papers

10.1101/mcs.a002444

Resistance-promoting effects of ependymoma treatment revealed through genomic analysis of multiple recurrences in a single patient
Cited by: 15
Author(s): Christopher A. Miller, Sonika Dahiya, Tiandao Li, Robert S. Fulton, Matthew D. Smyth, Gavin P. Dunn, Joshua B. Rubin, Elaine R. Mardis
Software Mentions: 4
Published: over 8 years ago

10.7554/eLife.36828

Hypoxia-inducible factor cell non-autonomously regulates C. elegans stress responses and behavior via a nuclear receptor
Cited by: 12
Author(s): Corinne L Pender, H. Robert Horvitz
Software Mentions: 4
Published: over 8 years ago

10.7554/eLife.59111

Bisulfite treatment and single-molecule real-time sequencing reveal D-loop length, position, and distribution
Cited by: 5
Author(s): Shanaya Shital Shah, Stella R. Hartono, Frédéric Chédin, Wolf Dietrich Heyer
Software Mentions: 4
Published: almost 6 years ago

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

10.1038/s42003-021-02112-2

Deep ocean metagenomes provide insight into the metabolic architecture of bathypelagic microbial communities
Cited by: 82
Author(s): Silvia G. Acinas, Pablo Sánchez, Guillem Salazar, Francisco M. Cornejo‐Castillo, Marta Sebastián, Ramiro Logares, Marta Royo-Llonch, Lucas Paoli, Shinichi Sunagawa, Pascal Hingamp, Hiroyuki Ogata, Gipsi Lima‐Mendez, Simon Roux, José M. González, Jesús M. Arrieta, Intikhab Álam, Allan Kamau, Chris Bowler, Jeroen Raes, Stéphane Pesant, Peer Bork, Susana Agustı́, Takashi Gojobori, Dolors Vaqué, Matthew B. Sullivan, Carlos Pedrós‐Alió, Ramón Massana, Carlos M. Duarte, Josep M. Gasol
Software Mentions: 4
Published: over 5 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

10.7554/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 <i>Zymomonas mobilis</i> : 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

10.1038/s41598-021-88709-3

Regulatory role of non-coding RNA in ginseng rusty root symptom tissue
Cited by: 5
Author(s): Xingbo Bian, Pengcheng Yu, Ling Dong, Yan Zhao, Yang He, Yongzhong Han, Lianxue Zhang
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

10.1080/15384101.2016.1261765

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

10.1038/s41598-021-92932-3

Dietary phosphorus and calcium in feed affects miRNA profiles and their mRNA targets in jejunum of two strains of laying hens
Cited by: 6
Author(s): Muhammad Arsalan Iqbal, Asghar Ali, Frieder Hadlich, Michael Oster, Henry Reyer, Nares Trakooljul, Vera Sommerfeld, M. Rodehutscord, Klaus Wimmers, Siriluck Ponsuksili
Software Mentions: 4
Published: over 5 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

10.1038/s41598-020-79436-2

Transcriptomic analysis of early stages of intestinal regeneration in Holothuria glaberrima
Cited by: 12
Author(s): David J. Quispe-Parra, Joshua G. Medina-Feliciano, Sebastián Cruz-González, Humberto Ortíz-Zuazaga, José E. García‐Arrarás
Software Mentions: 4
Published: almost 6 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

10.7554/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

10.1038/s41598-019-40127-2

Unravelling paralogous gene expression dynamics during three-spined stickleback embryogenesis
Cited by: 7
Author(s): Elisavet Kaitetzidou, Ioanna Katsiadaki, Jacques Lagnel, Efthimia Antonopoulou, Elena Sarropoulou
Software Mentions: 4
Published: over 7 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

10.1038/s41598-019-48979-4

Comparative analysis demonstrates cell type-specific conservation of SOX9 targets between mouse and chicken
Cited by: 22
Author(s): Satoshi Yamashita, Kensuke Kataoka, Hiroto Yamamoto, Tomoko Kato, Satoshi Hara, Katsushi Yamaguchi, Claire Renard-Guillet, Yuki Katou, Katsuhiko Shirahige, Haruki Ochi, Hitoshi Ogino, Tatsuo Uchida, Masafumi Inui, Shuji Takada, Shuji Shigenobu, Hiroshi Asahara
Software Mentions: 4
Published: about 7 years ago

10.1038/s41598-019-39395-9

Extensive epigenomic integration of the glucocorticoid response in primary human monocytes and in vitro derived macrophages
Cited by: 24
Author(s): Cheng Wang, Luca Nanni, Boris Novakovic, Wout Megchelenbrink, Т. Н. Кузнецова, Hendrik G. Stunnenberg, Stefano Ceri, Colin Logie
Software Mentions: 4
Published: over 7 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

10.1038/s41598-019-48283-1

De novo transcriptome assembly for four species of crustose coralline algae and analysis of unique orthologous genes
Cited by: 9
Author(s): Tessa M. Page, Carmel McDougall, Guillermo Díaz-Pulido
Software Mentions: 4
Published: about 7 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

10.1371/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

10.1007/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

10.1038/s41598-017-02110-7

Revealing genome-scale transcriptional regulatory landscape of OmpR highlights its expanded regulatory roles under osmotic stress in Escherichia coli K-12 MG1655
Cited by: 31
Author(s): Sang Woo Seo, Ye Gao, Donghyuk Kim, Richard Szubin, Joseph Yang, Byung-Kwan Cho, Bernhard Ø. Palsson
Software Mentions: 4
Published: over 9 years ago

10.1038/s41598-017-07100-3

Bmal1 regulates inflammatory responses in macrophages by modulating enhancer RNA transcription
Cited by: 59
Author(s): Yumiko Oishi, Shinichiro Hayashi, Takayuki Isagawa, Motohiko Oshima, Atsushi Iwama, Shigeki Shimba, Hitoshi Okamura, Ichiro Manabe
Software Mentions: 4
Published: about 9 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

10.1038/srep42110

Blubber transcriptome response to acute stress axis activation involves transient changes in adipogenesis and lipolysis in a fasting-adapted marine mammal
Cited by: 37
Author(s): Jane Khudyakov, Cory D. Champagne, Lorenzo Meneghetti, Daniel E. Crocker
Software Mentions: 4
Published: over 9 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

10.1007/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

10.1186/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

10.1038/srep17901

Identification of Genes Associated with Smad3-dependent Renal Injury by RNA-seq-based Transcriptome Analysis
Cited by: 19
Author(s): Qin Zhou, Yuanyan Xiong, Xiao Ru Huang, Patrick Ming‐Kuen Tang, Xueqing Yu, Hui‐Yao Lan
Software Mentions: 4
Published: almost 11 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

10.1371/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

10.1371/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

10.1371/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

10.1038/srep25866

Hot spots of DNA double-strand breaks in human rDNA units are produced in vivo
Cited by: 16
Author(s): Nickolai A. Tchurikov, Dmitry V. Yudkin, М. А. Горбачева, Anastasia I. Kulemzina, I. V. Grischenko, Д. М. Федосеева, D. V. Sosin, Yuri V. Kravatsky, О. В. Кретова
Software Mentions: 4
Published: over 10 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

10.1074/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

10.1186/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

10.1371/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

10.1093/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

10.1186/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

10.1371/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

10.1038/srep38439

RNA sequencing of chorionic villi from recurrent pregnancy loss patients reveals impaired function of basic nuclear and cellular machinery
Cited by: 40
Author(s): Siim Sõber, Kristiina Rull, Mario Reiman, Piret Ilisson, Pirkko Mattila, Maris Laan
Software Mentions: 4
Published: almost 10 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

10.1186/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

10.1186/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/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/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/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

10.1186/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

10.1186/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

10.3389/fimmu.2021.663736

MicroRNA Expression Differences in Blood-Derived CD19+ B Cells of Methotrexate Treated Rheumatoid Arthritis Patients
Cited by: 8
Author(s): Fatima Heinicke, Xiao Zhong, Siri Tennebø Flåm, Johannes Breidenbach, Magnus Leithaug, Marthe Thoresen Mæhlen, Siri Lillegraven, Anna‐Birgitte Aga, Ellen Sauar Norli, Maria D Mjaavatten, Espen A. Haavardsholm, Manuela Zucknick, Simon Rayner, Benedicte A. Lie
Software Mentions: 4
Published: over 5 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

10.1038/s41598-018-36912-0

DNA damage and transcriptional regulation in iPSC-derived neurons from Ataxia Telangiectasia patients
Cited by: 10
Author(s): Alessandro Corti, Raina Sota, Matteo Dugo, Raffaele Calogero, Benedetta Terragni, Massimo Mantegazza, Silvana Franceschetti, Michela Restelli, Patrizia Gasparini, Daniele Lecis, Krystyna Chrzanowska, Domenico Delia
Software Mentions: 4
Published: over 7 years ago

Projects: pypi: bowtie

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Papers Mentioning bowtie 1,566