pypi: bowtie | Projects | Ecosyste.ms: Papers

10.1038/s42003-020-01125-7

Improving the diversity of captured full-length isoforms using a normalized single-molecule RNA-sequencing method
Cited by: 8
Author(s): Yueming Hu, Xing-sheng Shu, Jiaxian Yu, Ming-an Sun, Zewei Chen, Xianming Liu, Qiongfang Fang, Wei Zhang, Xinjie Hui, Ying Ying, Li Fu, Desheng Lu, Rakesh Kumar, Yejun Wang
Software Mentions: 1
Published: over 4 years ago

10.1186/s13287-021-02452-0

LINGO-1 regulates Wnt5a signaling during neural stem and progenitor cell differentiation by modulating miR-15b-3p levels
Cited by: 4
Author(s): Chenguang Zhao, Jie Qin, Jia Li, Shan Jiang, Fengkui Ju, Wei Sun, Zhen Ren, Yibing Ji, Rui Wang, Xiaolong Sun, Xiang Mou, Hua Yuan
Software Mentions: 1
Published: over 3 years ago

10.1002/2211-5463.13139

CRISPR‐based knock‐in mutagenesis of the pioneer transcription factor FOXA1: optimization of strategies for multi‐allelic proteins in cancer cells
Cited by: 4
Author(s): Li Shen, Joseph P. Garay, Colby A. Tubbs, Hector L. Franco
Software Mentions: 1
Published: over 3 years ago

10.1155/2014/948408

Exploring the miRNA-mRNA Regulatory Network in Clear Cell Renal Cell Carcinomas by Next-Generation Sequencing Expression Profiles
Cited by: 36
Author(s): Sören Müller, Katharina Nowak
Software Mentions: 1
Published: almost 11 years ago

10.1038/s42003-019-0500-9

Genome assembly of Nannochloropsis oceanica provides evidence of host nucleus overthrow by the symbiont nucleus during speciation
Cited by: 26
Author(s): Li Guo, Sijie Liang, Zhongyi Zhang, Huan Liu, Songwen Wang, Kehou Pan, Jian Xu, Xue Ren, Surui Pei, Guanpin Yang
Software Mentions: 1
Published: over 5 years ago

10.7150/thno.36639

Glyoxalase 1 Prevents Chronic Hyperglycemia Induced Heart-Explant Derived Cell Dysfunction
Cited by: 10
Author(s): Melanie Villanueva, Connor Michie, Sandrine Parent, Georges N. Kanaan, Ghazaleh Rafatian, Pushpinder Kanda, Bin Ye, Wenbin Liang, Mary‐Ellen Harper, Darryl R. Davis
Software Mentions: 1
Published: almost 6 years ago

10.3389/fbioe.2015.00007

Computational Prediction of miRNA Genes from Small RNA Sequencing Data
Cited by: 33
Author(s): Wenjing Kang, Marc R. Friedländer
Software Mentions: 1
Published: almost 10 years ago

10.1038/s42003-020-01525-9

Natural epialleles of Arabidopsis SUPERMAN display superwoman phenotypes
Cited by: 9
Author(s): Ramesh Bondada, Saravanakumar Somasundaram, Mohan Premanand Marimuthu, Mohammed Afsal Badarudeen, Vaishak Kanjirakol Puthiyaveedu, Maruthachalam Ravi
Software Mentions: 1
Published: almost 4 years ago

10.1186/s13148-021-01134-1

Genome wide DNA methylation analysis of alveolar capillary dysplasia lung tissue reveals aberrant methylation of genes involved in development including the FOXF1 locus
Cited by: 5
Author(s): E Slot, Ruben Boers, Joachim Boers, Wilfred F. J. van IJcken, Dick Tibboel, Joost Gribnau, Robbert J. Rottier, Annelies de Klein
Software Mentions: 1
Published: over 3 years ago

10.3389/fcell.2021.670435

PERK Signaling Controls Myoblast Differentiation by Regulating MicroRNA Networks
Cited by: 9
Author(s): Ying Tan, Yin Zhang, Bin Li, Yangwen Ou, Shu‐Juan Xie, Peipei Chen, Shi-Qiang Mei, Qiao-Juan Huang, Ling‐Ling Zheng, Liang‐Hu Qu
Software Mentions: 1
Published: over 3 years ago

10.1039/d0sc03509b

Single-nucleotide resolution of N6-adenine methylation sites in DNA and RNA by nitrite sequencing
Cited by: 21
Author(s): Yasaman Mahdavi‐Amiri, Kimberley Chung, Ryan Hili
Software Mentions: 1
Published: almost 4 years ago

10.3389/fcell.2021.679325

Meis2 Is Required for Inner Ear Formation and Proper Morphogenesis of the Cochlea
Cited by: 6
Author(s): María Beatriz Durán Alonso, Victor Vendrell, Iris López‐Hernández, Donna M. Martin, Fernando Giráldez, Laura Carramolino, Giovanna Giovinazzo, Enrique Vázquez, Miguel Torres, Thomas Schimmang
Software Mentions: 1
Published: over 3 years ago

10.7554/eLife.54761

Global phenotypic profiling identifies a conserved actinobacterial cofactor for a bifunctional PBP-type cell wall synthase
Cited by: 8
Author(s): Joel W Sher, Hoong Chuin Lim, Thomas G. Bernhardt
Software Mentions: 1
Published: over 4 years ago

10.3390/cells10071757

FOS Rescues Neuronal Differentiation of Sox2-Deleted Neural Stem Cells by Genome-Wide Regulation of Common SOX2 and AP1(FOS-JUN) Target Genes
Cited by: 7
Author(s): Miriam Pagin, Mattias Pernebrink, Mattia Pitasi, Federica Malighetti, Chew-Yee Ngan, Sergio Ottolenghi, Giulio Pavesi, Claudio Cantù, Silvia K. Nicolis
Software Mentions: 1
Published: over 3 years ago

10.7150/thno.47845

Elevated IgE promotes cardiac fibrosis by suppressing miR-486a-5p
Cited by: 12
Author(s): Hongmei Zhao, Hongqin Yang, Chi Geng, Yang Chen, Yaqin Tang, Zhiwei Li, Junling Pang, Ting Shu, Yu Nie, Yongshuo Liu, Jia Ke, Jing Wang
Software Mentions: 1
Published: almost 4 years ago

10.3390/toxins10030096

True Lies: Using Proteomics to Assess the Accuracy of Transcriptome-Based Venomics in Centipedes Uncovers False Positives and Reveals Startling Intraspecific Variation in Scolopendra subspinipes
Cited by: 39
Author(s): Jennifer J. Smith, Eivind A. B. Undheim
Software Mentions: 1
Published: over 6 years ago

10.7554/eLife.24869

Contact-dependent killing by Caulobacter crescentus via cell surface-associated, glycine zipper proteins
Cited by: 61
Author(s): Leonor García-Bayona, Monica S. Guo, Michael T. Laub
Software Mentions: 1
Published: over 7 years ago

10.1155/2013/270805

A Guide RNA Sequence Design Platform for the CRISPR/Cas9 System for Model Organism Genomes
Cited by: 57
Author(s): Ming Ma, Adam Yongxin Ye, Weiguo Zheng, Lei Kong
Software Mentions: 1
Published: almost 12 years ago

10.1007/s11248-020-00196-w

CRISPR/Cas9-mediated targeted mutagenesis of TAS4 and MYBA7 loci in grapevine rootstock 101-14
Cited by: 29
Author(s): Sukumaran Sunitha, Christopher D. Rock
Software Mentions: 1
Published: over 4 years ago

10.3390/biology10090896

Bioinformatics and Machine Learning Approaches to Understand the Regulation of Mobile Genetic Elements
Cited by: 2
Author(s): Ilektra-Chara Giassa, Panagiotis Alexiou
Software Mentions: 1
Published: about 3 years ago

10.3390/biology9110358

Cloning of Thalassiosira pseudonana’s Mitochondrial Genome in Saccharomyces cerevisiae and Escherichia coli
Cited by: 3
Author(s): Ryan R. Cochrane, Stephanie L. Brumwell, Arina Shrestha, Daniel J. Giguere, Samir Hamadache, Gregory B. Gloor, David R. Edgell, Bogumil J. Karas
Software Mentions: 1
Published: about 4 years ago

10.3389/fendo.2019.00485

Growth Hormone Promotes in vitro Maturation of Human Oocytes
Cited by: 29
Author(s): Yue Li, Hui Liu, Qingqing Yu, Hongbin Liu, Tao Huang, Shigang Zhao, Jinlong Ma, Han Zhao
Software Mentions: 1
Published: over 5 years ago

10.3906/biy-2103-3

Transcriptome profiling of Stevia rebaudiana MS007 revealed genes involved in flower development
Cited by: 2
Author(s): Nurul Hidayah Samsulrizal, Khairul Shahyidi Khadzran, Tamil Chelvan Meenakshi Sundram, Zarina Zainuddin, Siti Hajar Nor Shaarani, Nur Sabrina Ahmad Azmi, Sarahani Harun
Software Mentions: 1
Published: over 3 years ago

10.1016/j.stem.2017.09.004

Distinct Cell-Cycle Control in Two Different States of Mouse Pluripotency
Cited by: 61
Author(s): Menno ter Huurne, James Chappell, Stephen Dalton, Hendrik G. Stunnenberg
Software Mentions: 1
Published: about 7 years ago

10.1016/j.celrep.2014.11.033

Rfx6 Maintains the Functional Identity of Adult Pancreatic β Cells
Cited by: 106
Author(s): Julie Piccand, Perrine Strasser, David J. Hodson, A. Meunier, Tao Ye, Céline Keime, Marie‐Christine Birling, Guy A. Rutter, Gérard Gradwohl
Software Mentions: 1
Published: almost 10 years ago

10.1186/s12864-018-4838-z

Genome sequencing analysis of Streptomyces coelicolor mutants that overcome the phosphate-depending vancomycin lethal effect
Cited by: 20
Author(s): Fernando Santos-Beneit
Software Mentions: 1
Published: over 6 years ago

10.1128/mBio.00897-17

On the Origin of Reverse Transcriptase-Using CRISPR-Cas Systems and Their Hyperdiverse, Enigmatic Spacer Repertoires
Cited by: 47
Author(s): Sukrit Silas, Kira S. Makarova, Sergey Shmakov, David Páez-Espino, Georg Mohr, Yi Liu, Michelle Davison, Simon Roux, Siddharth R. Krishnamurthy, Becky Xu Hua Fu, Larry G. Hansen, David Wang, Matthew B. Sullivan, Andrew Millard, Martha R. J. Clokie, Devaki Bhaya, Alan M. Lambowitz, Nikos C. Kyrpides, Eugene V. Koonin, Andrew Fire
Software Mentions: 1
Published: about 7 years ago

10.3389/fgene.2020.00947

MicroRNA Expression Profiling of Bone Marrow–Derived Proangiogenic Cells (PACs) in a Mouse Model of Hindlimb Ischemia: Modulation by Classical Cardiovascular Risk Factors
Cited by: 3
Author(s): Michel Desjarlais, Sylvie Dussault, José Carlos Rivera, Sylvain Chemtob, Alain Rivard
Software Mentions: 1
Published: over 4 years ago

10.1038/s41419-021-03636-5

A family harboring an MLKL loss of function variant implicates impaired necroptosis in diabetes
Cited by: 21
Author(s): Joanne M Hildebrand, Bernice Lo, Sara Tomei, Valentina Di Mattei, Samuel N. Young, Cheree Fitzgibbon, James M. Murphy, Abeer A. Fadda
Software Mentions: 1
Published: over 3 years ago

10.1093/bioinformatics/bts452

SpliceSeq: a resource for analysis and visualization of RNA-Seq data on alternative splicing and its functional impacts
Cited by: 172
Author(s): Michaël Ryan, James Cleland, RyangGuk Kim, Wing Chung Wong, John N. Weinstein
Software Mentions: 1
Published: over 12 years ago

10.1038/s41419-019-1964-8

Stromal cells downregulate miR-23a-5p to activate protective autophagy in acute myeloid leukemia
Cited by: 28
Author(s): Saravanan Ganesan, Hamenth Kumar Palani, Vairavan Lakshmanan, Nithya Balasundaram, Ansu Abu Alex, Sachin David, Arvind Venkatraman, Anu Korula, Biju George, Poonkuzhali Balasubramanian, Dasaradhi Palakodeti, Neha Vyas, Vikram Mathews
Software Mentions: 1
Published: about 5 years ago

10.1093/bioinformatics/btv199

Cellular phenotype database: a repository for systems microscopy data
Cited by: 10
Author(s): Catherine Kirsanova, Alvis Brāzma, Gabriella Rustici, Ugis Sarkans
Software Mentions: 1
Published: over 9 years ago

10.1016/j.cell.2012.06.018

piRNAs Can Trigger a Multigenerational Epigenetic Memory in the Germline of C. elegans
Cited by: 663
Author(s): Alyson Ashe, Alexandra Sapetschnig, Eva-Maria Weick, Jacinth Mitchell, Marloes P. Bagijn, Amy Cording, Anna-Lisa Doebley, Leonard D. Goldstein, Nicolas J Lehrbach, Jérémie Le Pen, Greta Pintacuda, Aisa Sakaguchi, Peter Sarkies, Shawn Ahmed, Eric A. Miska
Software Mentions: 1
Published: over 12 years ago

10.3389/fgene.2013.00150

The detection of microRNA associated with Alzheimer's disease in biological fluids using next-generation sequencing technologies
Cited by: 104
Author(s): Lesley Cheng, Camelia Quek, Xin Sun, Shayne A. Bellingham, Andrew F. Hill
Software Mentions: 1
Published: almost 12 years ago

10.3390/cancers11020209

Metformin Treatment Suppresses Melanoma Cell Growth and Motility Through Modulation of microRNA Expression
Cited by: 49
Author(s): Hui‐Wen Tseng, Sung‐Chou Li, Kuo‐Wang Tsai
Software Mentions: 1
Published: almost 6 years ago

10.1371/journal.pone.0172721

Identification of the ER-resident E3 ubiquitin ligase RNF145 as a novel LXR-regulated gene
Cited by: 20
Author(s): Emma C. L. Cook, Jessica K. Nelson, Vincenzo Sorrentino, Duco S. Koenis, Martina Moeton, Saskia Scheij, Roelof Ottenhoff, Boris Bleijlevens, Anke Loregger, Noam Zelcer
Software Mentions: 1
Published: over 7 years ago

10.1186/1752-0509-6-S2-S14

MicroRNA 3' end nucleotide modification patterns and arm selection preference in liver tissues
Cited by: 35
Author(s): Sung‐Chou Li, Kuo‐Wang Tsai, Hung‐Wei Pan, Yung‐Ming Jeng, Meng‐Ru Ho, Wen-Hsiung Li
Software Mentions: 1
Published: almost 13 years ago

10.1371/journal.pone.0088462

De Novo Assembly and Transcriptome Analysis of Contrasting Sugarcane Varieties
Cited by: 108
Author(s): Cláudio Benício Cardoso-Silva, Everardo Andrade da Costa, Melina Cristina Mancini, Thiago Willian Almeida Balsalobre, Lucas Eduardo Costa Canesin, Luciana Rossini Pinto, Monalisa Sampaio Carneiro, Antônio Augusto Franco Garcia, Anete Pereira de Souza, Renato Vicentini
Software Mentions: 1
Published: almost 11 years ago

10.1371/journal.pone.0169242

Generation of a Stable Transgenic Swine Model Expressing a Porcine Histone 2B-eGFP Fusion Protein for Cell Tracking and Chromosome Dynamics Studies
Cited by: 12
Author(s): Renan Sper, Sehwon Koh, Xia Zhang, Sean Simpson, Bruce Collins, Jeff Sommer, Robert M. Petters, Ignacio Caballero, Jeffrey L. Platt, Jorge A. Piedrahita
Software Mentions: 1
Published: almost 8 years ago

10.3389/fgene.2012.00226

Lack of miRNA Misregulation at Early Pathological Stages in Drosophila Neurodegenerative Disease Models
Cited by: 20
Author(s): Anita Reinhardt, Sébastien Feuillette, Marlène Cassar, Céline Callens, Hélène Thomassin, Serge Birman, Magalie Lecourtois, Christophe Antoniewski, Hervé Tricoire
Software Mentions: 1
Published: almost 13 years ago

10.1371/journal.pone.0107365

Vernalization Mediated Changes in the Lolium perenne Transcriptome
Cited by: 17
Author(s): Cristiana Paina, Stephen Byrne, C. Domnisoru, Torben Asp
Software Mentions: 1
Published: about 10 years ago

10.3389/fgene.2021.675027

Rapid Evolution of Autosomal Binding Sites of the Dosage Compensation Complex in Drosophila melanogaster and Its Association With Transcription Divergence
Cited by: 1
Author(s): Aimei Dai, Yushuai Wang, Anthony J. Greenberg, Zhongqi Liufu, Tian Tang
Software Mentions: 1
Published: over 3 years ago

10.1128/mBio.00201-20

Virulence as a Side Effect of Interspecies Interaction in Vibrio Coral Pathogens
Cited by: 18
Author(s): Esther Rubio-Portillo, Ana Belén Martín‐Cuadrado, Andrés Mauricio Caraballo‐Rodríguez, Forest Rohwer, Pieter C. Dorrestein, Josefa Antón
Software Mentions: 1
Published: about 4 years ago

10.1186/1756-0500-2-257

Impact of genome assembly status on ChIP-Seq and ChIP-PET data mapping
Cited by: 5
Author(s): Nicolas Buisine, Laurent M. Sachs
Software Mentions: 1
Published: almost 16 years ago

10.1371/journal.pone.0158846

Analysis of Genetic Variation across the Encapsidated Genome of Microplitis demolitor Bracovirus in Parasitoid Wasps
Cited by: 3
Author(s): Gaelen R. Burke
Software Mentions: 1
Published: over 8 years ago

10.3389/fgene.2019.00222

Novel and Conserved miRNAs Among Brazilian Pine and Other Gymnosperms
Cited by: 13
Author(s): José Henrique Galdino, María Eguiluz, Frank Guzmán, Rogério Margis
Software Mentions: 1
Published: over 5 years ago

10.7554/eLife.27590

A novel role for Ets4 in axis specification and cell migration in the spider Parasteatoda tepidariorum
Cited by: 25
Author(s): Matthias Pechmann, Matthew A. Benton, Nathan J. Kenny, Nico Posnien, Siegfried Roth
Software Mentions: 1
Published: about 7 years ago

10.1186/s12864-018-4600-6

RNA-Seq analysis validates the use of culture-derived Trypanosoma brucei and provides new markers for mammalian and insect life-cycle stages
Cited by: 57
Author(s): Arunasalam Naguleswaran, Nicholas Doiron, Isabel Roditi
Software Mentions: 1
Published: over 6 years ago

10.1371/journal.pone.0040366

Prevalence and Clinical Features of Hearing Loss Patients with CDH23 Mutations: A Large Cohort Study
Cited by: 55
Author(s): Maiko Miyagawa, Shin‐ya Nishio, Shin‐ichi Usami
Software Mentions: 1
Published: over 12 years ago

10.1371/journal.pone.0167088

Determination of a Screening Metric for High Diversity DNA Libraries
Cited by: 0
Author(s): Nicholas Guido, Steven Handerson, Elaine M. Joseph, Devin Leake, Li Kung
Software Mentions: 1
Published: almost 8 years ago

10.1371/journal.pone.0090859

Circular RNA Is Expressed across the Eukaryotic Tree of Life
Cited by: 533
Author(s): Peter L. Wang, Yun Bao, Muh-Ching Yee, Steven P. Barrett, Gregory J. Hogan, Mari Olsen, José R. Dinneny, Patrick O. Brown, Julia Salzman
Software Mentions: 1
Published: over 10 years ago

10.7554/eLife.55002

Translational initiation in E. coli occurs at the correct sites genome-wide in the absence of mRNA-rRNA base-pairing
Cited by: 61
Author(s): Kazuki Saito, Rachel Green, Allen R. Buskirk
Software Mentions: 1
Published: almost 5 years ago

10.1371/journal.pone.0158142

Mining and Analysis of SNP in Response to Salinity Stress in Upland Cotton (Gossypium hirsutum L.)
Cited by: 10
Author(s): Xiaoge Wang, Xuke Lu, Junjuan Wang, Delong Wang, Zujun Yin, Weili Fan, Shuai Wang, Wuwei Ye
Software Mentions: 1
Published: over 8 years ago

10.1371/journal.pone.0136383

MicroRNA-Sequence Profiling Reveals Novel Osmoregulatory MicroRNA Expression Patterns in Catadromous Eel Anguilla marmorata
Cited by: 10
Author(s): Xiaolu Wang, Danqing Yin, Peng Li, Shaowu Yin, Li Wang, Yong Jia, Xinhua Shu
Software Mentions: 1
Published: over 9 years ago

10.1371/journal.pone.0227749

Molecular and biological analysis revealed genetic diversity and high virulence strain of Toxoplasma gondii in Japan
Cited by: 6
Author(s): Junpei Fukumoto, Akinori Yamano, Motomichi Matsuzaki, Hisako Kyan, Tsutomu Matsui, Tomohide Matsuo, Toshihiro Matsui, Mami Murakami, Yasuhiro Takashima, Ryuma Matsubara, Michiru Tahara, Takaya Sakura, Fumihiko Takeuchi, Kisaburo Nagamune
Software Mentions: 1
Published: almost 5 years ago

10.1371/journal.pone.0022544

Integrated Expression Profiling and Genome-Wide Analysis of ChREBP Targets Reveals the Dual Role for ChREBP in Glucose-Regulated Gene Expression
Cited by: 123
Author(s): Yun Seung Jeong, Deokhoon Kim, Yong Seok Lee, Ha Jung Kim, Jung Youn Han, Seung Soon Im, Hansook Kim Chong, Je Keun Kwon, Yun Ho Cho, Woo Kyung Kim, Timothy F. Osborne, Jay D. Horton, Hee-Sook Jun, Yeon Soon Ahn, Sung Min Ahn, Jung Han Young
Software Mentions: 1
Published: over 13 years ago

10.1371/journal.pone.0116528

Development of Genetic Markers in Eucalyptus Species by Target Enrichment and Exome Sequencing
Cited by: 28
Author(s): Modhumita Ghosh Dasgupta, Veeramuthu Dharanishanthi, Ishangi Agarwal, Konstantin V. Krutovsky
Software Mentions: 1
Published: almost 10 years ago

10.3389/fimmu.2017.02010

Benzyl-2-Acetamido-2-Deoxy-α-d-Galactopyranoside Increases Human Immunodeficiency Virus Replication and Viral Outgrowth Efficacy In Vitro
Cited by: 5
Author(s): Àlex Olvera, Javier P Martínez, María Casadellà, Anuska Llano, Míriam Rosás, Beatriz Mothe, Marta Ruiz-Riol, Gemma Arsequell, Gregorio Valencia, Marc Noguera‐Julian, Roger Paredes, Andreas Meyerhans, Christian Berthou
Software Mentions: 1
Published: almost 7 years ago

10.1371/journal.pone.0114612

Genome-Wide Identification of Different Dormant Medicago sativa L. MicroRNAs in Response to Fall Dormancy
Cited by: 18
Author(s): Wenna Fan, Senhao Zhang, Hao Du, Xuejun Sun, Shi Ya, Chengzhang Wang
Software Mentions: 1
Published: almost 10 years ago

10.1371/journal.pone.0050013

Function Annotation of Hepatic Retinoid x Receptor α Based on Genome-Wide DNA Binding and Transcriptome Profiling
Cited by: 10
Author(s): Qimin Zhan, Yaping Fang, Yuqi He, Hui‐Xin Liu, Jianwen Fang, Yu‐Jui Yvonne Wan
Software Mentions: 1
Published: about 12 years ago

10.1186/1756-0500-5-275

BowStrap v1.0: Assigning statistical significance to expressed genes using short-read transcriptome data
Cited by: 6
Author(s): Peter E. Larsen, F. Collart
Software Mentions: 1
Published: over 12 years ago

10.1371/journal.pone.0238753

PFRED: A computational platform for siRNA and antisense oligonucleotides design
Cited by: 18
Author(s): Simone Sciabola, Hualin Simon Xi, Dario A. Cruz, Qing Cao, Christine Lawrence, Tianhong Zhang, Sergio H. Rotstein, Jason D. Hughes, Daniel R. Caffrey, Robert V. Stanton
Software Mentions: 1
Published: almost 4 years ago

10.1371/journal.pone.0017570

Sequencing Illustrates the Transcriptional Response of Legionella pneumophila during Infection and Identifies Seventy Novel Small Non-Coding RNAs
Cited by: 81
Author(s): Barbara Weissenmayer, James Prendergast, Amanda J. Lohan, Brendan J. Loftus
Software Mentions: 1
Published: over 13 years ago

10.1371/journal.pone.0227592

A genome-wide enrichment screen identifies NUMA1-loss as a resistance mechanism against mitotic cell-death induced by BMI1 inhibition
Cited by: 3
Author(s): Santiago Gisler, Alexandra S. Maia, G. Chandrasekaran, Jawahar Kopparam, Maarten van Lohuizen
Software Mentions: 1
Published: over 4 years ago

10.1371/journal.pone.0149146

Bcl6 Is Required for Somatic Hypermutation and Gene Conversion in Chicken DT40 Cells
Cited by: 8
Author(s): Alan M Williams, Yaakov Maman, Jukka Alinikula, David G. Schatz
Software Mentions: 1
Published: almost 9 years ago

10.3389/fmicb.2017.00501

Human and Epstein-Barr Virus miRNA Profiling as Predictive Biomarkers for Endemic Burkitt Lymphoma
Cited by: 16
Author(s): Cliff I. Oduor, Mercedeh Movassagh, Yasin Kaymaz, Kiprotich Chelimo, Juliana A. Otieno, John Michael Ong’echa, Ann M. Moormann, Jeffrey A. Bailey
Software Mentions: 1
Published: over 7 years ago

10.1186/1753-6561-8-S4-P96

Advancing palm genomics by developing a high-density battery of molecular markers for Elaeis oleifera for future downstream applications
Cited by: 0
Author(s): Alexandre Alonso Alves, Valquíria Martins Pereira, André Pereira Leão, Eduardo Fernandes Formigheri, Guy de Capdeville, Manoel Teixeira Souza Júnior
Software Mentions: 1
Published: about 10 years ago

10.3389/fmicb.2016.01873

The Use of Transposon Insertion Sequencing to Interrogate the Core Functional Genome of the Legume Symbiont Rhizobium leguminosarum
Cited by: 28
Author(s): Benjamin J. Perry, Mir S. Akter, Christopher K. Yost
Software Mentions: 1
Published: about 8 years ago

10.3389/fmicb.2020.01739

Genomic Characteristics and Potential Metabolic Adaptations of Hadal Trench Roseobacter and Alteromonas Bacteria Based on Single-Cell Genomics Analyses
Cited by: 6
Author(s): Mingming Chen, Yu Song, Xiaoyuan Feng, Kai Tang, Nianzhi Jiao, Jie Tian, Yao Zhang
Software Mentions: 1
Published: over 4 years ago

10.3389/fmicb.2016.01905

RNAseq Analysis of Endornavirus-Infected vs. Endornavirus-Free Common Bean (Phaseolus vulgaris) Cultivar Black Turtle Soup
Cited by: 11
Author(s): Surasak Khankhum, Noa Sela, Juan M. Osorno, R. A. Valverde
Software Mentions: 1
Published: almost 8 years ago

10.1186/s12870-021-03136-w

Integrated ionomic and transcriptomic dissection reveals the core transporter genes responsive to varying cadmium abundances in allotetraploid rapeseed
Cited by: 3
Author(s): Ting Zhou, Caipeng Yue, Tianyu Zhang, Ying Liu, Jinyong Huang, Yingpeng Hua
Software Mentions: 1
Published: over 3 years ago

10.1371/journal.pone.0192730

Transcriptome analysis in different developmental stages of Batocera horsfieldi (Coleoptera: Cerambycidae) and comparison of candidate olfactory genes
Cited by: 23
Author(s): Hua Yang, Yan Cai, Zhihang Zhuo, Wei Yang, Chunping Yang, Zhangdong Jin, Yang Yang, Baoxin Wang, Fengrong Guan
Software Mentions: 1
Published: over 6 years ago

10.3389/fmicb.2014.00108

The microbial nitrogen cycling potential is impacted by polyaromatic hydrocarbon pollution of marine sediments
Cited by: 63
Author(s): Nicole M. Scott, Matthias Hess, N. Bouskill, Olivia U. Mason, Janet Jansson, Jack A. Gilbert
Software Mentions: 1
Published: over 10 years ago

10.1371/journal.pone.0007767

BFAST: An Alignment Tool for Large Scale Genome Resequencing
Cited by: 489
Author(s): Nils Homer, Barry Merriman, Stanley F. Nelson
Software Mentions: 1
Published: about 15 years ago

10.1371/journal.pone.0205570

De novo genome and transcriptome analyses provide insights into the biology of the trematode human parasite Fasciolopsis buski
Cited by: 3
Author(s): Devendra Kumar Biswal, Tanmoy Roychowdhury, Priyatama Pandey, Veena Tandon
Software Mentions: 1
Published: about 6 years ago

10.1371/journal.pone.0187157

Overlapping RdDM and non-RdDM mechanisms work together to maintain somatic repression of a paramutagenic epiallele of maize pericarp color1
Cited by: 6
Author(s): Po Hao Wang, Kameron T Wittmeyer, Tzuu fen Lee, Blake C. Meyers, Surinder Chopra
Software Mentions: 1
Published: about 7 years ago

10.1371/journal.pone.0104580

Plant Virology and Next Generation Sequencing: Experiences with a Potyvirus
Cited by: 71
Author(s): Monica A. Kehoe, B. A. Coutts, Bevan Buirchell, R. A. C. Jones
Software Mentions: 1
Published: over 10 years ago

10.1371/journal.pone.0230537

Sergentomyia schwetzi: Salivary gland transcriptome, proteome and enzymatic activities in two lineages adapted to different blood sources
Cited by: 6
Author(s): Nikola Polanská, Aygul Ishemgulova, Věra Volfová, Pavel Flegontov, Jan Votýpka, Vyacheslav Yurchenko, Petr Volf
Software Mentions: 1
Published: over 4 years ago

10.1371/journal.pone.0158151

Puffy Skin Disease Is an Emerging Transmissible Condition in Rainbow Trout Oncorhynchus mykiss Walbaum
Cited by: 8
Author(s): Irene Cano, David W. Verner–Jeffreys, Ronny van Aerle, Richard Paley, E. J. Peeler, Matthew Green, Georgina S. E. Rimmer, Jacqueline Savage, C. Joiner, Amanda Bayley, J Mewett, J Hulland, Stephen W. Feist
Software Mentions: 1
Published: over 8 years ago

10.1371/journal.pone.0147007

Intrinsic Viral Factors Are the Dominant Determinants of the Hepatitis C Virus Response to Interferon Alpha Treatment in Chimeric Mice
Cited by: 1
Author(s): Ran Chen, Michelle Kobewka, William R. Addison, Gerald LaChance, D. Lorne Tyrrell
Software Mentions: 1
Published: almost 9 years ago

10.1128/mSystems.00459-19

Global Screening of Genomic and Transcriptomic Factors Associated with Phenotype Differences between Multidrug-Resistant and -Susceptible Candida haemulonii Strains
Cited by: 8
Author(s): Hao Zhang, Y. Niu, Jingwen Tan, Weixia Liu, Miao‐Kun Sun, Ence Yang, Qian Wang, Ruoyu Li, Yejun Wang, Wei Liu
Software Mentions: 1
Published: almost 5 years ago

10.1186/s12863-016-0364-7

Combined small RNA and degradome sequencing to identify miRNAs and their targets in response to drought in foxtail millet
Cited by: 53
Author(s): Yongqiang Wang, Li Lin, Sha Tang, Jianguang Liu, Hanshuang Zhang, Hui Zhi, Guanqing Jia, Xianmin Diao
Software Mentions: 1
Published: over 8 years ago

10.1371/journal.pone.0139850

Synergistic Gene Expression Signature Observed in TK6 Cells upon Co-Exposure to UVC-Irradiation and Protein Kinase C-Activating Tumor Promoters
Cited by: 9
Author(s): Kyle P. Glover, Zhongqiang Chen, Lauren K. Markell, Xing Han
Software Mentions: 1
Published: about 9 years ago

10.1371/journal.pone.0139771

Identification of Novel and Conserved microRNAs in Homalodisca vitripennis, the Glassy-Winged Sharpshooter by Expression Profiling
Cited by: 4
Author(s): Raja Sekhar Nandety, Almas Sharif, Shizuo G. Kamita, R. Asokan, Bryce W. Falk
Software Mentions: 1
Published: about 9 years ago

10.1371/journal.pone.0055214

On Measuring miRNAs after Transient Transfection of Mimics or Antisense Inhibitors
Cited by: 101
Author(s): Daniel Thomson, Cameron P. Bracken, Jan M. Szubert, Gregory J. Goodall
Software Mentions: 1
Published: almost 12 years ago

10.1371/journal.pone.0139044

Metagenomic Human Repiratory Air in a Hospital Environment
Cited by: 6
Author(s): Yi Yu Lai, Yanming Liu, Jidong Lang, Xunliang Tong, Lína Zhang, Jau–Shiung Fang, Jingli Xing, Meng Cai, Huji Xu, Yuxin Deng, Fei Xiao, Geng Tian
Software Mentions: 1
Published: about 9 years ago

10.1186/s13059-017-1243-x

MicroRNAs control mRNA fate by compartmentalization based on 3′ UTR length in male germ cells
Cited by: 38
Author(s): Ying Zhang, Chong Tang, Tian Yu, Ruirui Zhang, Huili Zheng, Wei Yan
Software Mentions: 1
Published: over 7 years ago

10.1186/s13059-017-1278-z

Large scale genomic reorganization of topological domains at the HoxD locus
Cited by: 29
Author(s): Pierre J. Fabre, Marion Leleu, Benjamin Mormann, Lucille Lopez-Delisle, Daan Noordermeer, Léonardo Beccari, Denis Duboule
Software Mentions: 1
Published: over 7 years ago

10.1186/s12870-015-0553-y

Developmental profiling of gene expression in soybean trifoliate leaves and cotyledons
Cited by: 27
Author(s): Anne V. Brown, Karen A. Hudson
Software Mentions: 1
Published: over 9 years ago

10.1371/journal.pone.0066389

Validation of Reference Genes for Expression Studies during Craniofacial Development in Arctic Charr
Cited by: 36
Author(s): Ehsan Pashay Ahi, Jóhannes Guðbrandsson, Kalina H. Kapralova, Sigríður Rut Franzdóttir, Sigurður S. Snorrason, Valerie H. Maier, Zophonı́as O. Jónsson
Software Mentions: 1
Published: over 11 years ago

10.1371/journal.pone.0146064

Epigenetic Segregation of Microbial Genomes from Complex Samples Using Restriction Endonucleases HpaII and McrB
Cited by: 8
Author(s): Guohong Liu, Christopher Q. Weston, Long Pham, Shannon Waltz, Helen Barnes, Paula King, Dan Sphar, R. T. Yamamoto, R. Allyn Forsyth
Software Mentions: 1
Published: almost 9 years ago

10.1371/journal.pone.0201417

Quillworts from the Amazon: A multidisciplinary populational study on Isoetes serracarajensis and Isoetes cangae
Cited by: 17
Author(s): Gisele Nunes, Renato R. M. Oliveira, José Tasso Felix Guimarães, Ana María Giulietti, Cecílio Fróis Caldeira, Santelmo Vasconcelos, Eder S. Pires, Mariana Costa Dias, Maurício Takashi Coutinho Watanabe, José A. Pereira, Rodolfo Jaffé, Cinthia Helena M. M. Bandeira, Nelson Carvalho-Filho, Edilson Freitas da Silva, Tarcísio Magevski Rodrigues, Fernando Marino Gomes dos Santos, Taís Nogueira Fernandes, Alexandre Castilho, Pedro Walfir M. Souza‐Filho, Vera Lúcia Imperatriz-Fonseca, José Oswaldo Siqueira, Ronnie Alves, Guilherme Oliveira
Software Mentions: 1
Published: over 6 years ago

10.1186/s12876-020-01460-3

Effects of proton pump inhibitor use on the esophageal microbial community
Cited by: 8
Author(s): Sadia Tasnim, Aaron L. Miller, Daniel C. Jupiter, Catherine Hamilton, Gabriel Reep, Timothy Krill, Richard B. Pyles, Ikenna Okereke
Software Mentions: 1
Published: about 4 years ago

10.1186/s13059-018-1402-8

Developmental transcriptomics of the brittle star Amphiura filiformis reveals gene regulatory network rewiring in echinoderm larval skeleton evolution
Cited by: 28
Author(s): David Dylus, Anna Czarkwiani, Liisa M. Blowes, Maurice R. Elphick, Paola Oliveri
Software Mentions: 1
Published: over 6 years ago

10.1371/journal.pone.0087744

The Atlantic Bonito (Sarda sarda, Bloch 1793) Transcriptome and Detection of Differential Expression during Larvae Development
Cited by: 14
Author(s): Elena Sarropoulou, Hooman K. Moghadam, Nikos Papandroulakis, Fernando de la Gándara, Aurelio Ortega García, Pavlos Makridis
Software Mentions: 1
Published: almost 11 years ago

10.1186/s13059-018-1495-0

QsRNA-seq: a method for high-throughput profiling and quantifying small RNAs
Cited by: 17
Author(s): Ayelet Fishman, Dean Light, Ayelet T. Lamm
Software Mentions: 1
Published: over 6 years ago

10.1186/s13059-018-1494-1

Functional CRISPR screen identifies AP1-associated enhancer regulating FOXF1 to modulate oncogene-induced senescence
Cited by: 34
Author(s): Ruiqi Han, Li Li, Alejandro P. Ugalde, A. Tal, Zohar Manber, Eric Pintó Barberà, Veronica Della Chiara, Ran Elkon, Reuven Agami
Software Mentions: 1
Published: over 6 years ago

10.1186/s12862-018-1274-2

Diverse RNA interference strategies in early-branching metazoans
Cited by: 20
Author(s): Andrew Calcino, Selene L. Fernández-Valverde, Ryan J. Taft, Bernard M. Degnan
Software Mentions: 1
Published: about 6 years ago

10.1371/journal.pone.0136798

Allele-Selective Transcriptome Recruitment to Polysomes Primed for Translation: Protein-Coding and Noncoding RNAs, and RNA Isoforms
Cited by: 13
Author(s): Roshan Mascarenhas, Maciej Pietrzak, Ryan M. Smith, Amy Webb, Daqing Wang, Audrey C. Papp, Julia K. Pinsonneault, Michał Seweryn, Grzegorz A. Rempała, Wolfgang Sadée
Software Mentions: 1
Published: about 9 years ago

10.1371/journal.pone.0044017

Allele-Biased Expression in Differentiating Human Neurons: Implications for Neuropsychiatric Disorders
Cited by: 64
Author(s): Mingyan Lin, Anastasia Hrabovsky, Erika Pedrosa, Tao Wang, Deyou Zheng, Herbert M. Lachman
Software Mentions: 1
Published: about 12 years ago

Projects: pypi: bowtie

Papers Mentioning bowtie 1,566