pypi: bowtie | Projects | Ecosyste.ms: Papers

10.1371/journal.pgen.1006595

Genome-wide exonic small interference RNA-mediated gene silencing regulates sexual reproduction in the homothallic fungus Fusarium graminearum
Cited by: 51
Author(s): Hokyoung Son, Ae Ran Park, Jae Yun Lim, Chanseok Shin, Yin-Won Lee
Software Mentions: 2
Published: almost 8 years ago

10.1371/journal.pgen.1004079

C/EBPα Is Required for Long-Term Self-Renewal and Lineage Priming of Hematopoietic Stem Cells and for the Maintenance of Epigenetic Configurations in Multipotent Progenitors
Cited by: 80
Author(s): Marie Sigurd Hasemann, Felicia Kathrine Bratt Lauridsen, Johannes Waage, Janus Schou Jakobsen, Anne-Katrine Frank, Mikkel Bruhn Schuster, Nicolas Rapin, Frederik Otzen Bagger, Philipp S. Hoppe, Timm Schroeder, Bo T. Porse
Software Mentions: 2
Published: almost 11 years ago

10.1371/journal.pgen.1002558

Genomic Analysis of the Hydrocarbon-Producing, Cellulolytic, Endophytic Fungus Ascocoryne sarcoides
Cited by: 75
Author(s): Tara A. Gianoulis, Michael Griffin, Daniel Spakowicz, Brian F. Dunican, Cambria J. Alpha, Andrea Sboner, A. Michael Sismour, Chinnappa D. Kodira, Michael Egholm, George M. Church, Mark Gerstein, Scott A. Strobel
Software Mentions: 2
Published: over 12 years ago

10.1371/journal.pgen.1009085

DNA supercoiling differences in bacteria result from disparate DNA gyrase activation by polyamines
Cited by: 10
Author(s): Alexandre Duprey, Eduardo A. Groisman
Software Mentions: 2
Published: about 4 years ago

10.1371/journal.pgen.1006783

Global analysis of double-strand break processing reveals in vivo properties of the helicase-nuclease complex AddAB
Cited by: 14
Author(s): Anjana Badrinarayanan, Tung B. K. Le, Jan-Hendrik Spille, Ibrahima Cissé, Michael T. Laub
Software Mentions: 2
Published: over 7 years ago

10.1371/journal.pgen.1003994

Transcription Factor Occupancy Can Mediate Active Turnover of DNA Methylation at Regulatory Regions
Cited by: 201
Author(s): Angelika Feldmann, Robert Ivánek, Rabih Murr, Dimos Gaidatzis, Lukas Burger, Dirk Schübeler
Software Mentions: 2
Published: almost 11 years ago

10.1371/journal.pgen.1006956

Recruitment of Armitage and Yb to a transcript triggers its phased processing into primary piRNAs in Drosophila ovaries
Cited by: 60
Author(s): Radha Raman Pandey, David Homolka, Kuan-Ming Chen, Ravi Sachidanandam, Marie-Odile Fauvarque, Ramesh S. Pillai
Software Mentions: 2
Published: over 7 years ago

10.1371/journal.pgen.1008085

Mitochondrial fusion is required for regulation of mitochondrial DNA replication
Cited by: 99
Author(s): Eduardo Silva Ramos, Elisa Motori, Christian Brüser, Inge Kühl, Assa Yeroslaviz, Benedetta Ruzzenente, Johanna H.K. Kauppila, Jakob D. Busch, Kjell Hultenby, Bianca Habermann, Stefan Jakobs, Nils‐Göran Larsson, Arnaud Mourier
Software Mentions: 2
Published: over 5 years ago

10.1371/journal.pntd.0008669

Molecular action of pyriproxyfen: Role of the Methoprene-tolerant protein in the pyriproxyfen-induced sterilization of adult female mosquitoes
Cited by: 8
Author(s): Tahmina Hossain Ahmed, T. Randolph Saunders, Donald E. Mullins, Mohammad Zillur Rahman, Jinsong Zhu
Software Mentions: 2
Published: about 4 years ago

10.1371/journal.pone.0216267

Identification of flowering-time genes in mast flowering plants using De Novo transcriptomic analysis
Cited by: 4
Author(s): * Samarth, Robyn Lee, Jiancheng Song, Richard C. Macknight, Paula E. Jameson
Software Mentions: 2
Published: over 5 years ago

10.1371/journal.pone.0191570

Target discovery screens using pooled shRNA libraries and next-generation sequencing: A model workflow and analytical algorithm
Cited by: 10
Author(s): Christiane Schaefer, Nikhil Mallela, Jochen Seggewiß, Birgit Lechtape, Heymut Omran, Uta Dirksen, Eberhard Korsching, Jenny Potratz
Software Mentions: 2
Published: almost 7 years ago

10.1371/journal.pone.0242171

Age-associated changes in the transcriptomes of non-cultured adipose-derived stem cells from young and old mice assessed via single-cell transcriptome analysis
Cited by: 4
Author(s): Yuta Doshida, Haruka Sano, Sadahiro Iwabuchi, Toshiro Aigaki, Masayuki Yoshida, Shinichi Hashimoto, Akihito Ishigami
Software Mentions: 2
Published: almost 4 years ago

10.1371/journal.pone.0074183

High-Throughput RNA Sequencing of Pseudomonas-Infected Arabidopsis Reveals Hidden Transcriptome Complexity and Novel Splice Variants
Cited by: 75
Author(s): Brian E. Howard, Qiwen Hu, Ahmet Can Babaoglu, Manan Chandra, Monica Borghi, Xiaoping Tan, Ling He, Heike Sederoff, Walter Gassmann, Paola Veronese, Steffen Heber
Software Mentions: 2
Published: about 11 years ago

10.1371/journal.pone.0064643

Transcriptomic Analysis of Cadmium Stress Response in the Heavy Metal Hyperaccumulator Sedum alfredii Hance
Cited by: 86
Author(s): Jun Gao, Ling Sun, Xiaoe Yang, Jian‐Xiang Liu
Software Mentions: 2
Published: over 11 years ago

10.1371/journal.pone.0023409

Systematic Clustering of Transcription Start Site Landscapes
Cited by: 58
Author(s): Xiaobei Zhao, Eivind Valen, Brian J. Parker, Albin Sandelin
Software Mentions: 2
Published: over 13 years ago

10.1371/journal.pone.0157290

Phosphoproteome and Transcriptome of RA-Responsive and RA-Resistant Breast Cancer Cell Lines
Cited by: 24
Author(s): Marilyn Carrier, Mathilde Joint, Régis Lutzing, Adeline Page, Cécile Rochette‐Egly
Software Mentions: 2
Published: over 8 years ago

10.1371/journal.pone.0094052

Molecular Evolution of Glycoside Hydrolase Genes in the Western Corn Rootworm (Diabrotica virgifera virgifera)
Cited by: 55
Author(s): Seong‐il Eyun, Haichuan Wang, Yannick Pauchet, Richard H. ffrench-Constant, Andrew K. Benson, Arnubio Valencia-Jiménez, Etsuko N. Moriyama, Blair D. Siegfried
Software Mentions: 2
Published: over 10 years ago

10.1371/journal.pone.0214816

SNP and indel frequencies at transcription start sites and at canonical and alternative translation initiation sites in the human genome
Cited by: 21
Author(s): Kerstin Neininger, Tobias Marschall, Volkhard Helms
Software Mentions: 2
Published: over 5 years ago

10.1371/journal.pone.0135978

Transcriptome Analysis of Liangshan Pig Muscle Development at the Growth Curve Inflection Point and Asymptotic Stages Using Digital Gene Expression Profiling
Cited by: 16
Author(s): Linyuan Shen, Jia Luo, Jing Du, Chendong Liu, Xiaoqian Wu, Qiang Pu, Yuhua Fu, Qianzi Tang, Yuanrui Liu, Qiang Li, Ronghua Yang, Xuewei Li, Guoqing Tang, Yanzhi Jiang, Mingzhou Li, Shunhua Zhang, Li Zhu
Software Mentions: 2
Published: over 9 years ago

10.1371/journal.pone.0105930

Genome-Wide Binding and Transcriptome Analysis of Human Farnesoid X Receptor in Primary Human Hepatocytes
Cited by: 50
Author(s): Lin Zhan, Hui‐Xin Liu, Yaping Fang, Bo Kong, Yuqi He, Xiao Bo Zhong, Jianwen Fang, Yu Wan, Grace L. Guo
Software Mentions: 2
Published: about 10 years ago

10.1371/journal.pone.0145065

One Step Forward, Two Steps Back; Xeno-MicroRNAs Reported in Breast Milk Are Artifacts
Cited by: 26
Author(s): Caner Bağcı, Jens Allmer
Software Mentions: 2
Published: almost 9 years ago

10.1371/journal.pone.0132127

HIV-1 RNAs are Not Part of the Argonaute 2 Associated RNA Interference Pathway in Macrophages
Cited by: 15
Author(s): Valentina Vongrad, Jochen Imig, Pejman Mohammadi, Shivendra Kishore, Łukasz Jaśkiewicz, Jonathan Hall, Huldrych F. Günthard, Niko Beerenwinkel, Karin J. Metzner
Software Mentions: 2
Published: over 9 years ago

10.1371/journal.pone.0132387

MicroRNA Profiling of Neurons Generated Using Induced Pluripotent Stem Cells Derived from Patients with Schizophrenia and Schizoaffective Disorder, and 22q11.2 Del
Cited by: 80
Author(s): Dejian Zhao, Mingyan Lin, Jian Chen, Erika Pedrosa, Anastasia Hrabovsky, H. Matthew Fourcade, Deyou Zheng, Herbert M. Lachman
Software Mentions: 2
Published: over 9 years ago

10.1371/journal.pone.0154129

Comparative Analysis of the miRNome of Bovine Milk Fat, Whey and Cells
Cited by: 67
Author(s): Ran Li, Pier-Luc Dudemaine, Xin Zhao, Chuzhao Lei, Eveline M. Ibeagha‐Awemu
Software Mentions: 2
Published: over 8 years ago

10.1371/journal.pone.0214102

Helicase/SUMO-targeted ubiquitin ligase Uls1 interacts with the Holliday junction resolvase Yen1
Cited by: 6
Author(s): Stefanie Bauer, Chen Jiang, Stefan U. Åström
Software Mentions: 2
Published: over 5 years ago

10.1371/journal.pone.0064546

IMSA: Integrated Metagenomic Sequence Analysis for Identification of Exogenous Reads in a Host Genomic Background
Cited by: 16
Author(s): Michelle Dimon, Henry M. Wood, Pamela Rabbitts, Sarah T. Arron
Software Mentions: 2
Published: over 11 years ago

10.1371/journal.pone.0084160

The Utility of Shallow RNA-Seq for Documenting Differential Gene Expression in Genes with High and Low Levels of Expression
Cited by: 11
Author(s): Joel Atallah, David C. Plachetzki, W. Cameron Jasper, Brian R. Johnson
Software Mentions: 2
Published: almost 11 years ago

10.1371/journal.pone.0214335

Asymmetric birth and death of type I and type II MADS-box gene subfamilies in the rubber tree facilitating laticifer development
Cited by: 4
Author(s): Anuwat Kumpeangkeaw, Tan D, Lili Fu, Bingying Han, Xiaoyan Sun, Xiaowen Hu, Zehong Ding, Jiaming Zhang
Software Mentions: 2
Published: over 5 years ago

10.1371/journal.pone.0084461

Putative Sugar Transporters of the Mustard Leaf Beetle Phaedon cochleariae: Their Phylogeny and Role for Nutrient Supply in Larval Defensive Glands
Cited by: 16
Author(s): Magdalena Stock, René R. Gretscher, Marco Groth, Simone Eiserloh, Wilhelm Boland, Antje Burse
Software Mentions: 2
Published: almost 11 years ago

10.1371/journal.pone.0152147

Odorant Receptors of the New Zealand Endemic Leafroller Moth Species Planotortrix octo and P. excessana
Cited by: 14
Author(s): Bernd Steinwender, Amali H. Thrimawithana, Ross N. Crowhurst, Richard D. Newcomb
Software Mentions: 2
Published: over 8 years ago

10.1371/journal.pone.0130773

Brazilian Anopheles darlingi Root (Diptera: Culicidae) Clusters by Major Biogeographical Region
Cited by: 41
Author(s): Kevin J. Emerson, Jan E. Conn, Eduardo Sterlino Bergo, Melissa A Randel, Maria Anice Mureb Sallum
Software Mentions: 2
Published: over 9 years ago

10.1371/journal.pone.0127214

Differential Nucleosome Occupancies across Oct4-Sox2 Binding Sites in Murine Embryonic Stem Cells
Cited by: 6
Author(s): Amy C. Sebeson, Xi Li, Quanwei Zhang, Audrey M. Sigmund, Ji Ping Wang, Jonathan Widom, Xiaozhong Wang
Software Mentions: 2
Published: over 9 years ago

10.1371/journal.pone.0045486

WaveSeq: A Novel Data-Driven Method of Detecting Histone Modification Enrichments Using Wavelets
Cited by: 10
Author(s): Apratim Mitra, Jiuzhou Song
Software Mentions: 2
Published: about 12 years ago

10.1371/journal.pone.0153881

Identification and Characterization of Two Novel RNA Viruses from Anopheles gambiae Species Complex Mosquitoes
Cited by: 31
Author(s): Guillaume Carissimo, Karin Eiglmeier, Julie Réveillaud, Inge Holm, Mawlouth Diallo, Diawo Diallo, Amélie Vantaux, Saorin Kim, Didier Ménard, Siv Sovannaroth, Eugeni Belda, Emmanuel Bischoff, Christophe Antoniewski, Kenneth D. Vernick
Software Mentions: 2
Published: over 8 years ago

10.1371/journal.pone.0219163

Transcriptional profiling of Salmonella enterica serovar Enteritidis exposed to ethanolic extract of organic cranberry pomace
Cited by: 23
Author(s): Quail Das, Dion Lepp, Yin X, Kelly Ross, Jason McCallum, Keith Warriner, Massimo F. Marcone, Moussa S. Diarra
Software Mentions: 2
Published: over 5 years ago

10.1371/journal.pone.0065433

Analysis and Prediction of Pathways in HeLa Cells by Integrating Biological Levels of Organization with Systems-Biology Approaches
Cited by: 8
Author(s): Juan Carlos Higareda‐Almaraz, Ilse A. Valtierra-Gutiérrez, Magdalena Hernández‐Ortíz, Sandra Contreras, Enrique Martínez Hernández, Sergio Encarnación
Software Mentions: 2
Published: over 11 years ago

10.1371/journal.pone.0101673

Genome-Wide Delineation of Natural Variation for Pod Shatter Resistance in Brassica napus
Cited by: 159
Author(s): Harsh Raman, Rosy Raman, Andrzej Kilian, Frank Detering, Jason Carling, Neil Coombes, Simon Diffey, Gururaj Kadkol, David Edwards, M. E. McCully, Pradeep Ruperao, Isobel A. P. Parkin, Jacqueline Batley, David J. Luckett, Neil Wratten
Software Mentions: 2
Published: over 10 years ago

10.1371/journal.pone.0212053

SLFN11 can sensitize tumor cells towards IFN-γ-mediated T cell killing
Cited by: 31
Author(s): Riccardo Mezzadra, Marjolein de Bruijn, Lucas T. Jae, Raquel Gomez-Eerland, Anja Duursma, Ferenc A. Scheeren, Thijn R. Brummelkamp, Ton N. Schumacher
Software Mentions: 2
Published: almost 6 years ago

10.1371/journal.pone.0074479

Genomewide Variation in an Introgression Line of Rice-Zizania Revealed by Whole-Genome re-Sequencing
Cited by: 13
Author(s): Zhenhui Wang, Di Zhang, Yan Bai, Yunhong Zhang, Ying Liu, Ying Wu, Xiuyun Lin, Jiawei Wen, Chunming Xu, Linfeng Li, Bao Liu
Software Mentions: 2
Published: about 11 years ago

10.1371/journal.pone.0141066

An Orthologous Epigenetic Gene Expression Signature Derived from Differentiating Embryonic Stem Cells Identifies Regulators of Cardiogenesis
Cited by: 5
Author(s): Brian W. Busser, Yongshun Lin, Yanqin Yang, Jun Zhu, Guokai Chen, Alan M. Michelson
Software Mentions: 2
Published: about 9 years ago

10.1371/journal.pone.0181538

Functional differences between PD-1+ and PD-1- CD4+ effector T cells in healthy donors and patients with glioblastoma multiforme
Cited by: 32
Author(s): Brittany A. Goods, Amanda Hernandez, Daniel E. Lowther, Liliana E. Lucca, Benjamin A. Lerner, Murat Günel, Khadir Raddassi, Vlad Coric, David A. Hafler, J. Christopher Love
Software Mentions: 2
Published: about 7 years ago

10.1371/journal.pone.0133491

Identification of MicroRNAs in Meloidogyne incognita Using Deep Sequencing
Cited by: 11
Author(s): Yunsheng Wang, Zhenchuan Mao, Yan Jin, Xinyue Cheng, Feng Liu, Xiangdong Luo, Liangying Dai, Feng Luo, Bingyan Xie
Software Mentions: 2
Published: over 9 years ago

10.1371/journal.pone.0174041

Mechanisms of glycosylase induced genomic instability
Cited by: 7
Author(s): Daniel E. Eyler, Kylie A. Burnham, Thomas E. Wilson, Patrick O’Brien
Software Mentions: 2
Published: over 7 years ago

10.1371/journal.pone.0010563

Deep Sequencing of Human Nuclear and Cytoplasmic Small RNAs Reveals an Unexpectedly Complex Subcellular Distribution of miRNAs and tRNA 3′ Trailers
Cited by: 270
Author(s): Jian-You Liao, Liming Ma, Yanhua Guo, Yuchan Zhang, Hui Zhou, Pengfei Shao, Yue‐Qin Chen, Liang‐Hu Qu
Software Mentions: 2
Published: over 14 years ago

10.1371/journal.pone.0195913

Transcriptome analysis of pecan seeds at different developing stages and identification of key genes involved in lipid metabolism
Cited by: 7
Author(s): Zhongyu Xu, Jun Ni, Faheem Shah, Qiaojian Wang, Lajos Hanzo, Lifang Wu, Songling Fu
Software Mentions: 2
Published: over 6 years ago

10.1371/journal.pone.0031092

The Pseudomonas aeruginosa Transcriptome in Planktonic Cultures and Static Biofilms Using RNA Sequencing
Cited by: 208
Author(s): Andreas Dötsch, Denitsa Eckweiler, Monika Schniederjans, Ariane Zimmermann, Vanessa Jensen, Maren Scharfe, Robert Geffers, Susanne Häußler
Software Mentions: 2
Published: almost 13 years ago

10.1371/journal.pone.0056018

Short-Read Assembly of Full-Length 16S Amplicons Reveals Bacterial Diversity in Subsurface Sediments
Cited by: 115
Author(s): Christopher S. Miller, Kim M. Handley, Kelly Wrighton, Kyle R. Frischkorn, Brian C. Thomas, Jillian F. Banfield
Software Mentions: 2
Published: almost 12 years ago

10.1371/journal.pone.0208602

Transcriptional profiling identifies novel regulators of macrophage polarization
Cited by: 65
Author(s): Kimberline Y. Gerrick, Elias R Gerrick, Anuj Gupta, Sarah J. Wheelan, Srinivasan Yegnasubramanian, Elizabeth M. Jaffee
Software Mentions: 2
Published: almost 6 years ago

10.1371/journal.pone.0057438

Genome Wide Allele Frequency Fingerprints (GWAFFs) of Populations via Genotyping by Sequencing
Cited by: 86
Author(s): Stephen Byrne, Adrian Czaban, Bruno Studer, Frank Panitz, Christian Berthou, Torben Asp
Software Mentions: 2
Published: over 11 years ago

10.1371/journal.pone.0056721

Global and Stage Specific Patterns of Krüppel-Associated-Box Zinc Finger Protein Gene Expression in Murine Early Embryonic Cells
Cited by: 42
Author(s): Andrea Corsinotti, Adamandia Kapopoulou, Carine Gubelmann, Michaël Imbeault, Francesca R. Santoni de Sio, Helen M. Rowe, Yoann Mouscaz, Bart Deplancke, Didier Trono
Software Mentions: 2
Published: almost 12 years ago

10.1371/journal.pone.0091418

Investigation of De Novo Unique Differentially Expressed Genes Related to Evolution in Exercise Response during Domestication in Thoroughbred Race Horses
Cited by: 19
Author(s): Woncheoul Park, Jaemin Kim, Yang Soo Kim, Jae-Young Choi, Jeong-Woong Park, Hyun-Woo Cho, Byeong-Woo Kim, Myung Hum Park, Teak-Soon Shin, Seong-Keun Cho, Jun-Kyu Park, Heebal Kim, Jin-Hee Hwang, Chang Kyu Lee, Hak-Kyo Lee, Seoae Cho, Byung-Wook Cho
Software Mentions: 2
Published: over 10 years ago

10.1371/journal.pone.0192659

KSHV oral shedding and plasma viremia result in significant changes in the extracellular tumorigenic miRNA expression profile in individuals infected with the malaria parasite
Cited by: 9
Author(s): Minako Ikoma, Soren Gantt, Corey Casper, Yuko Ogata, Qing Zhang, Ryan Basom, Michael R. Dyen, Timothy M. Rose, Serge Barcy
Software Mentions: 2
Published: almost 7 years ago

10.1371/journal.pone.0173723

Genome-wide mapping of histone H3K9me2 in acute myeloid leukemia reveals large chromosomal domains associated with massive gene silencing and sites of genome instability
Cited by: 28
Author(s): Anna C. Salzberg, Abigail Harris-Becker, Evgenya Y. Popova, Nikki Keasey, Thomas P. Loughran, David F. Claxton, Sergei A. Grigoryev
Software Mentions: 2
Published: over 7 years ago

10.1371/journal.pone.0133315

Evaluating the Stability of RNA-Seq Transcriptome Profiles and Drug-Induced Immune-Related Expression Changes in Whole Blood
Cited by: 11
Author(s): John F. Bowyer, Karen M. Tranter, Joseph P. Hanig, Nathaniel M. Crabtree, Robert P. Schleimer, Nysia I. George
Software Mentions: 2
Published: over 9 years ago

10.1371/journal.pone.0072699

In-Depth Characterization of microRNA Transcriptome in Melanoma
Cited by: 111
Author(s): James Kozubek, Zhihai Ma, Elizabeth Fleming, Tatiana Duggan, Rong Wu, Dong-Guk Shin, Soheil S. Dadras
Software Mentions: 2
Published: about 11 years ago

10.1371/journal.pone.0154055

Urinary Exosomal microRNA-451-5p Is a Potential Early Biomarker of Diabetic Nephropathy in Rats
Cited by: 71
Author(s): Avvari V. Mohan, Ravi Shankar Singh, Manju Kumari, Devika Garg, Aditya Upadhyay, Carolyn M. Ecelbarger, Sucheta Tripathy, Swasti Tiwari
Software Mentions: 2
Published: over 8 years ago

10.1371/journal.pone.0152893

Remission for Loss of Odontogenic Potential in a New Micromilieu In Vitro
Cited by: 13
Author(s): Yunfei Zheng, Jinglei Cai, Andrew P. Hutchins, Lingfei Jia, Pengfei Liu, Dandan Yang, Shubin Chen, Lihong Ge, Duanqing Pei, Shicheng Wei
Software Mentions: 2
Published: over 8 years ago

10.1371/journal.pone.0170715

Transcriptional regulation of male-sterility in 7B-1 male-sterile tomato mutant
Cited by: 17
Author(s): Vahid Omidvar, Irina Mohorianu, Tamás Dalmay, Yi Zheng, Zhangjun Fei, Anna Pucci, Andrea Mazzucato, Vendula Večeřová, Michaela Sedlářová, Martin Fellner
Software Mentions: 2
Published: almost 8 years ago

10.1371/journal.pone.0129997

zflncRNApedia: A Comprehensive Online Resource for Zebrafish Long Non-Coding RNAs
Cited by: 23
Author(s): Heena Dhiman, Shruti Kapoor, Ambily Sivadas, Sridhar Sivasubbu, Vinod Scaria
Software Mentions: 2
Published: over 9 years ago

10.1371/journal.pone.0161997

Genome-Wide Ultrabithorax Binding Analysis Reveals Highly Targeted Genomic Loci at Developmental Regulators and a Potential Connection to Polycomb-Mediated Regulation
Cited by: 16
Author(s): Daria Shlyueva, Antonio C. A. Meireles-Filho, Michaela Pagani, Alexander Stark
Software Mentions: 2
Published: about 8 years ago

10.1371/journal.pone.0124432

Functional Marker Detection and Analysis on a Comprehensive Transcriptome of Large Yellow Croaker by Next Generation Sequencing
Cited by: 33
Author(s): Shijun Xiao, Zhaofang Han, Panpan Wang, Fang Han, Yang Liu, Jiong-Tang Li, Wenfei Wang
Software Mentions: 2
Published: over 9 years ago

10.1371/journal.pone.0077147

The Fumagillin Gene Cluster, an Example of Hundreds of Genes under veA Control in Aspergillus fumigatus
Cited by: 45
Author(s): Sourabh Dhingra, Abigail Lind, Hsiao‐Ching Lin, Yi Tang, Antonis Rokas, Ana M. Calvo
Software Mentions: 2
Published: about 11 years ago

10.1371/journal.pone.0217978

Social status regulates the hepatic miRNAome in rainbow trout: Implications for posttranscriptional regulation of metabolic pathways
Cited by: 14
Author(s): Daniel J. Kostyniuk, David Zhang, Christopher J. Martyniuk, Kathleen M. Gilmour, Jan A. Mennigen
Software Mentions: 2
Published: over 5 years ago

10.1371/journal.pone.0192439

A tale of two mixotrophic chrysophytes: Insights into the metabolisms of two Ochromonas species (Chrysophyceae) through a comparison of gene expression
Cited by: 39
Author(s): Alle A. Y. Lie, Zhenfeng Liu, Ramón Terrado, Avery O. Tatters, Karla B. Heidelberg, David A. Caron
Software Mentions: 2
Published: almost 7 years ago

10.1371/journal.pone.0126654

A Function for the hnRNP A1/A2 Proteins in Transcription Elongation
Cited by: 33
Author(s): Bruno Lemieux, Marco Blanchette, Anne Monette, Andrew J. Mouland, Raymund J. Wellinger, Benoît Chabot
Software Mentions: 2
Published: over 9 years ago

10.1371/journal.pone.0054174

Identification and Characterization of MicroRNAs in Channel Catfish (Ictalurus punctatus) by Using Solexa Sequencing Technology
Cited by: 61
Author(s): Zhiqiang Xu, Jiaping Chen, Xuguang Li, Jiachun Ge, Jianlin Pan, Xiaofeng Xu
Software Mentions: 2
Published: almost 12 years ago

10.1371/journal.pone.0083784

Low-Bandwidth and Non-Compute Intensive Remote Identification of Microbes from Raw Sequencing Reads
Cited by: 5
Author(s): Laurent Gautier, Ole Lund
Software Mentions: 2
Published: almost 11 years ago

10.1371/journal.pone.0135410

Genome-Wide Profiling of PARP1 Reveals an Interplay with Gene Regulatory Regions and DNA Methylation
Cited by: 50
Author(s): Narasimharao Nalabothula, Taha Al-jumaily, Abdallah M. Eteleeb, Robert M. Flight, Xiaorong Shao, Hunter N. B. Moseley, Eric C. Rouchka, Yvonne Fondufe‐Mittendorf
Software Mentions: 2
Published: over 9 years ago

10.1371/journal.pone.0252674

De novo activated transcription of inserted foreign coding sequences is inheritable in the plant genome
Cited by: 0
Author(s): Takayuki Hata, Naoto Takada, Chihiro Hayakawa, Mei Kazama, Tomohiro Uchikoba, Makoto Tachikawa, Mitsuhiro Matsuo, Shunji Satoh, Junichi Obokata
Software Mentions: 2
Published: over 3 years ago

10.1371/journal.pone.0242276

Molecular consequences of fetal alcohol exposure on amniotic exosomal miRNAs with functional implications for stem cell potency and differentiation
Cited by: 9
Author(s): Honey Tavanasefat, Feng Li, Kikuye Koyano, Bahar Khalilian Gourtani, Vincent Marty, Yatendra Mulpuri, Sung Hee Lee, Kihyuk Shin, David T. Wong, Xinshu Xiao, Igor Spigelman, Yong Kim
Software Mentions: 2
Published: about 4 years ago

10.1371/journal.pone.0180135

Reversible perturbations of gene regulation after genome editing in Drosophila cells
Cited by: 5
Author(s): Stefan Kunzelmann, Klaus Förstemann
Software Mentions: 2
Published: over 7 years ago

10.1371/journal.pone.0125989

Dicer-Dependent Biogenesis of Small RNAs and Evidence for MicroRNA-Like RNAs in the Penicillin Producing Fungus Penicillium chrysogenum
Cited by: 33
Author(s): Tim A. Dahlmann, Ulrich Kück
Software Mentions: 2
Published: over 9 years ago

10.1371/journal.pone.0196518

Differentially expressed microRNAs associated with changes of transcript levels in detoxification pathways and DDT-resistance in the Drosophila melanogaster strain 91-R
Cited by: 15
Author(s): Keon Mook Seong, Brad S. Coates, Do hyup Kim, Allison K. Hansen, Barry R. Pittendrigh
Software Mentions: 2
Published: over 6 years ago

10.1371/journal.pone.0236376

Transfer of endogenous small RNAs between branches of scions and rootstocks in grafted sweet cherry trees
Cited by: 11
Author(s): Dongyan Zhao, Gan-Yuan Zhong, Guo-Qing Song
Software Mentions: 2
Published: over 4 years ago

10.1371/journal.pone.0177733

Transcriptome-microRNA analysis of Sarcoptes scabiei and host immune response
Cited by: 23
Author(s): Ran He, Xiaobin Gu, Weimin Lai, Xuerong Peng, Guangyou Yang
Software Mentions: 2
Published: over 7 years ago

10.3390/cancers13133204

Depletion of DNA Polymerase Theta Inhibits Tumor Growth and Promotes Genome Instability through the cGAS-STING-ISG Pathway in Esophageal Squamous Cell Carcinoma
Cited by: 8
Author(s): Jian Li, Josephine Mun Yee Ko, Wei Dai, V. Y. H. Yu, Hoi Yan Ng, Jean-Sébastien Hoffmann, Maria Li Lung
Software Mentions: 2
Published: over 3 years ago

10.3390/cancers12092545

FANCD2 Confers a Malignant Phenotype in Esophageal Squamous Cell Carcinoma by Regulating Cell Cycle Progression
Cited by: 15
Author(s): Lisa Chan Lei, V. Y. H. Yu, Josephine Mun Yee Ko, Lvwen Ning, Maria Li Lung
Software Mentions: 2
Published: about 4 years ago

10.3390/cancers11121875

Hypoxic Environment and Paired Hierarchical 3D and 2D Models of Pediatric H3.3-Mutated Gliomas Recreate the Patient Tumor Complexity
Cited by: 13
Author(s): Anne-Florence Blandin, Aurélie Durand, Marie Litzler, Aurélien Tripp, Éric Guérin, Elisa Ruhland, Adeline Obrecht, Céline Keime, Quentin Fuchs, Damien Reita, Benoît Lhermitte, Andrés Coca, Chris Jones, Isabelle Lelong Rebel, Pascal Villa, Izzie Jacques Namer, Monique Dontenwill, Dominique Guénot, Natacha Entz‐Werlé
Software Mentions: 2
Published: almost 5 years ago

10.3390/cancers12102980

Distinct Pattern of Endoplasmic Reticulum Protein Processing and Extracellular Matrix Proteins in Functioning and Silent Corticotroph Pituitary Adenomas
Cited by: 8
Author(s): Alexander Kirkeby Eieland, Kjersti Ringvoll Normann, Arvind Y. M. Sundaram, Tuula A. Nyman, Kristin Astrid Berland Øystese, Tove Lekva, Jens Petter Berg, Jens Bollerslev, Nicoleta Cristina Olarescu
Software Mentions: 2
Published: about 4 years ago

10.1016/j.cell.2014.05.004

Variant PRC1 Complex-Dependent H2A Ubiquitylation Drives PRC2 Recruitment and Polycomb Domain Formation
Cited by: 598
Author(s): Neil P. Blackledge, Anca M. Farcas, Takashi Kondo, Hamish W King, Joanna F. McGouran, Lars Hanssen, Shinsuke Ito, Sarah Cooper, K. Kondo, Haruhiko Koseki, Tomoyuki Ishikura, Hannah K. Long, Thomas W. Sheahan, Neil Brockdorff, Benedikt M. Kessler, Robert J. Klose
Software Mentions: 2
Published: over 10 years ago

10.1038/s41419-018-0819-z

Dynamic placement of the linker histone H1 associated with nucleosome arrangement and gene transcription in early Drosophila embryonic development
Cited by: 12
Author(s): Jian Hu, Liang Gu, Youqiong Ye, Min Zheng, Zhu Xu, Jing Lin, Yanhua Du, Ming Tian, Lin Luo, Beibei Wang, Xiaobai Zhang, Zhiping Weng, Cizhong Jiang
Software Mentions: 2
Published: over 6 years ago

10.1038/s41419-021-04108-6

Increased expression of fragmented tRNA promoted neuronal necrosis
Cited by: 6
Author(s): Yanyan Cao, Kai Li, Ying Xiong, Chenglong Zhao, Lei Liu
Software Mentions: 2
Published: about 3 years ago

10.1038/s41419-020-2375-6

A Cdh1–FoxM1–Apc axis controls muscle development and regeneration
Cited by: 14
Author(s): Zhe Chen, Lei Li, Shuangnian Xu, Zhilong Liu, Chengfang Zhou, Zhigang Li, Yuanyuan Liu, Weiru Wu, Yongxiu Huang, Mei Kuang, Shijun Fan, Hui Li, Xi Li, Guanbin Song, Weixin Wu, Jieping Chen, Yu Hou
Software Mentions: 2
Published: over 4 years ago

10.1038/cddis.2015.33

p53 is active in murine stem cells and alters the transcriptome in a manner that is reminiscent of mutant p53
Cited by: 14
Author(s): Hualong Yan, Valeriya Solozobova, Ping Zhang, Olivier Armant, B. Kuehl, Gerald Brenner‐Weiß, Christine Blattner
Software Mentions: 2
Published: over 9 years ago

10.1038/celldisc.2016.37

Canonical Wnt signalling regulates nuclear export of Setdb1 during skeletal muscle terminal differentiation
Cited by: 23
Author(s): Sophie Beyer, Julien Pontis, Elija Schirwis, Valentine Battisti, Anja Rudolf, Fabien Le Grand, Slimane Ait‐Si‐Ali
Software Mentions: 2
Published: about 8 years ago

10.1038/celldisc.2017.43

Transcriptome-wide identification of the RNA-binding landscape of the chromatin-associated protein PARP1 reveals functions in RNA biogenesis
Cited by: 47
Author(s): Manana Melikishvili, Julia H. Chariker, Eric C. Rouchka, Yvonne Fondufe‐Mittendorf
Software Mentions: 2
Published: almost 7 years ago

10.1016/j.celrep.2018.03.056

Transcriptional Dysregulation of MYC Reveals Common Enhancer-Docking Mechanism
Cited by: 134
Author(s): Jurian Schuijers, John C. Manteiga, Abraham S. Weintraub, Daniel S. Day, Alicia V. Zamudio, Denes Hnisz, Tong Ihn Lee, Richard A. Young
Software Mentions: 2
Published: over 6 years ago

10.1016/j.celrep.2014.07.043

Single-Cell, Genome-wide Sequencing Identifies Clonal Somatic Copy-Number Variation in the Human Brain
Cited by: 252
Author(s): Xinjiang Cai, Gilad D. Evrony, Hillel S. Lehmann, Princess C. Elhosary, Bhaven K. Mehta, Annapurna Poduri, Christopher A. Walsh
Software Mentions: 2
Published: about 10 years ago

10.1016/j.celrep.2017.08.026

SMC Progressively Aligns Chromosomal Arms in Caulobacter crescentus but Is Antagonized by Convergent Transcription
Cited by: 112
Author(s): Ngat T. Tran, Michael T. Laub, Tung B. K. Le
Software Mentions: 2
Published: over 7 years ago

10.1016/j.celrep.2020.107980

Molecular Transducers of Human Skeletal Muscle Remodeling under Different Loading States
Cited by: 29
Author(s): Tanner Stokes, James A. Timmons, Hannah Crossland, Thomas R. Tripp, Karen L. Murphy, Chris McGlory, Cameron J. Mitchell, Sara Y. Oikawa, Robert W. Morton, Bethan E. Phillips, Steven K. Baker, Philip J. Atherton, Claes Wahlestedt, Stuart M. Phillips
Software Mentions: 2
Published: over 4 years ago

10.1007/s12192-018-0910-5

Cellular stress responses to chronic heat shock and shell damage in temperate Mya truncata
Cited by: 18
Author(s): Victoria A. Sleight, Lloyd S. Peck, Elisabeth A. Dyrynda, Valerie J. Smith, Melody S. Clark
Software Mentions: 2
Published: over 6 years ago

10.1038/s42003-018-0015-9

A rare missense variant in NR1H4 associates with lower cholesterol levels
Cited by: 6
Author(s): Aimée M. Deaton, Patrick Sulem, Paul Nioi, Stefania Benónísdóttir, Lucas D. Ward, Olafur B. Davidsson, Socheata Lao, Anna Helgadóttir, Fan Fan, Brynjar O. Jensson, Gudmundur L. Norddahl, Áslaug Jónasdóttir, Aðalbjörg Jónasdóttir, Ásgeir Sigurðsson, Ragnar P. Kristjansson, Ásmundur Oddsson, Gudny A. Arnadottir, Hákon Jónsson, Ísleifur Ólafsson, Gudmundur I. Eyjolfsson, Ólöf Sigurðardóttir, Einar Björnsson, Sigurður Ólafsson, Þóra Steingrímsdóttir, Thorunn Rafnar, Guðmundur Þorgeirsson, Gísli Másson, Guðmar Þorleifsson, Daníel F. Guðbjartsson, Hilma Hólm, Unnur Þorsteinsdóttir, Kāri Stefánsson
Software Mentions: 2
Published: almost 7 years ago

10.1038/s42003-021-02516-0

Identification of a transcription factor, PunR, that regulates the purine and purine nucleoside transporter punC in E. coli
Cited by: 11
Author(s): Irina A. Rodionova, Ye Gao, Anand V. Sastry, Ying Hefner, Hyun Gyu Lim, Dmitry A. Rodionov, Milton H. Saier, Jaehyung Kim
Software Mentions: 2
Published: over 3 years ago

10.1093/database/bax074

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

10.1016/j.ydbio.2012.03.024

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

10.1242/dev.136051

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

10.3390/diagnostics10090701

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

10.1038/emboj.2013.177

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

10.15252/embj.201695323

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

10.15252/embj.201592532

Sororin actively maintains sister chromatid cohesion
Cited by: 84
Author(s): René Ladurner, Emanuel Kreidl, Miroslav P Ivanov, Heinz Ekker, Maria Helena Idarraga-Amado, Georg A. Busslinger, Gordana Wutz, David A. Cisneros, Jan‐Michael Peters
Software Mentions: 2
Published: almost 9 years ago

Projects: pypi: bowtie

Papers Mentioning bowtie 1,566