pypi: bowtie | Projects | Ecosyste.ms: Papers

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 6 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 11 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: over 7 years ago

10.1186/s12859-019-3180-z

DEEPSEN: a convolutional neural network based method for super-enhancer prediction
Cited by: 13
Author(s): Hongda Bu, Jiaqi Hao, Yanglan Gan, Shuigeng Zhou, Jihong Guan
Software Mentions: 4
Published: almost 5 years ago

10.1186/s12864-015-1491-7

Leaps and lulls in the developmental transcriptome of Dictyostelium discoideum
Cited by: 53
Author(s): Rafael D. Rosengarten, Balaji Santhanam, Danny Fuller, Mariko Katoh-Kurasawa, William F. Loomis, Blaž Zupan, Gad Shaulsky
Software Mentions: 4
Published: over 9 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: almost 8 years ago

10.1186/s12862-020-01739-9

Genomic variation in the American pika: signatures of geographic isolation and implications for conservation
Cited by: 4
Author(s): Kelly B. Klingler, Joshua P. Jahner, Thomas L. Parchman, Chris Ray, Mary M. Peacock
Software Mentions: 4
Published: almost 4 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: about 4 years ago

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: almost 7 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: about 5 years ago

10.1371/journal.pone.0238546

MITF and TFEB cross-regulation in melanoma cells
Cited by: 12
Author(s): Josué Ballesteros‐Álvarez, Ramile Dilshat, Valerie Fock, Katrín Möller, Ludwig Karl, Lionel Larue, Margrét H. Ögmundsdóttir, Eirı́kur Steingrı́msson
Software Mentions: 4
Published: about 4 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 7 years ago

10.1371/journal.pone.0140077

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

10.1186/s12885-017-3711-9

Integrative microRNA and mRNA deep-sequencing expression profiling in endemic Burkitt lymphoma
Cited by: 22
Author(s): Cliff I. Oduor, Yasin Kaymaz, Kiprotich Chelimo, Juliana A. Otieno, John Michael Ong’echa, Ann M. Moormann, Jeffrey A. Bailey
Software Mentions: 3
Published: about 7 years ago

10.1038/srep09100

Genomic analysis of LPS-stimulated myeloid cells identifies a common pro-inflammatory response but divergent IL-10 anti-inflammatory responses
Cited by: 41
Author(s): Andrew Paul Hutchins, Yoshiko Takahashi, Diego Miranda‐Saavedra
Software Mentions: 3
Published: over 9 years ago

10.1186/s12864-018-4856-x

Genome-wide expression profiling of leaves and roots of watermelon in response to low nitrogen
Cited by: 25
Author(s): Muhammad Azher Nawaz, Chen Chen, Fareeha Shireen, Zhuhua Zheng, Hamza Sohail, Muhammad Afzal, Muhammad Amjad Ali, Zhilong Bie, Yuan Huang
Software Mentions: 3
Published: over 6 years ago

10.1186/s13062-017-0195-0

ASXL gain-of-function truncation mutants: defective and dysregulated forms of a natural ribosomal frameshifting product?
Cited by: 12
Author(s): Adam M. Dinan, John F. Atkins, Andrew E. Firth
Software Mentions: 3
Published: about 7 years ago

10.1038/srep16324

Revisiting the reference genomes of human pathogenic Cryptosporidium species: reannotation of C. parvum Iowa and a new C. hominis reference
Cited by: 42
Author(s): Juan Pablo Isaza, Ana Luz Galván, Víctor Polanco, Bernice Huang, Andrey V. Matveyev, Myrna G. Serrano, Patrício Manque, Gregory A. Buck, Juan F. Alzate
Software Mentions: 3
Published: about 9 years ago

10.1038/sdata.2017.161

Nasopharyngeal metagenomic deep sequencing data, Lancaster, UK, 2014–2015
Cited by: 2
Author(s): Kate V. Atkinson, L.A. Bishop, Glenn Rhodes, Nicolas Salez, Neil McEwan, Matthew J. Hegarty, Julie Robey, Nicola Harding, Simon Wetherell, Robert M. Lauder, Roger W. Pickup, Mark Wilkinson, Derek Gatherer
Software Mentions: 3
Published: about 7 years ago

10.1038/s41597-020-0480-0

An improved high-quality genome assembly and annotation of Tibetan hulless barley
Cited by: 23
Author(s): Xingquan Zeng, Tong Xu, Zhihao Ling, Yulin Wang, Xiangfeng Li, Shuqing Xu, Qijun Xu, Zha Sang, Wangmu Qimei, Yuzhen Basang, Jiabu Dunzhu, Mingzhai Yu, Hongjun Yuan, Nyima Tashi
Software Mentions: 3
Published: over 4 years ago

10.1093/bioinformatics/btt650

MEDIPS: genome-wide differential coverage analysis of sequencing data derived from DNA enrichment experiments
Cited by: 246
Author(s): Matthias Lienhard, Christina Grimm, Markus Morkel, Ralf Herwig, Lukas Chávez
Software Mentions: 3
Published: about 11 years ago

10.1371/journal.pgen.1005166

Systematic Profiling of Poly(A)+ Transcripts Modulated by Core 3’ End Processing and Splicing Factors Reveals Regulatory Rules of Alternative Cleavage and Polyadenylation
Cited by: 207
Author(s): Wencheng Li, Bo You, Mainul Hoque, Dinghai Zheng, Wenting Luo, Zhe Ji, Ji Yeon Park, Samuel Gunderson, Auinash Kalsotra, James L. Manley, Bin Tian
Software Mentions: 3
Published: over 9 years ago

10.1371/journal.pone.0016344

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

10.1126/sciadv.aau8317

The gut microbiome from patients with schizophrenia modulates the glutamate-glutamine-GABA cycle and schizophrenia-relevant behaviors in mice
Cited by: 387
Author(s): Peng Zheng, Benhua Zeng, Meiling Liu, Jianjun Chen, Junxi Pan, Han Yu, Yiyun Liu, Ke Cheng, Chanjuan Zhou, Haiyang Wang, Xinyu Zhou, Siwen Gui, Seth W. Perry, Ma‐Li Wong, Júlio Licinio, Hong Wei, Peng Xie
Software Mentions: 3
Published: almost 6 years ago

10.1038/srep12524

Transcriptional profiling of macrophages derived from monocytes and iPS cells identifies a conserved response to LPS and novel alternative transcription
Cited by: 79
Author(s): Kaur Alasoo, Fernando O. Martínez, Christine Hale, Siamon Gordon, Fiona Powrie, Gordon Dougan, Subhankar Mukhopadhyay, Daniel J. Gaffney
Software Mentions: 3
Published: over 9 years ago

10.1098/rspb.2020.3169

Conservation and turnover of miRNAs and their highly complementary targets in early branching animals
Cited by: 5
Author(s): Daniela Praher, Bob Zimmermann, Rohit Dnyansagar, David J. Miller, Aurélie Moya, Vengamanaidu Modepalli, Arie Fridrich, Daniel Sher, Lene Friis-Møller, Per Sundberg, Sylvain Forêt, Regan Ashby, Yehu Moran, Ulrich Technau
Software Mentions: 3
Published: over 3 years ago

10.1186/s12864-015-1983-5

Identification of the meiotic toolkit in diatoms and exploration of meiosis-specific SPO11 and RAD51 homologs in the sexual species Pseudo-nitzschia multistriata and Seminavis robusta
Cited by: 49
Author(s): Shrikant Patil, Sara Moeys, Peter von Dassow, Marie J. J. Huysman, Daniel Mapleson, Lieven De Veylder, Remo Sanges, Wim Vyverman, Marina Montresor, Maria Immacolata Ferrante
Software Mentions: 3
Published: about 9 years ago

10.1371/journal.pone.0143811

The Clinical Significance and Molecular Features of the Spatial Tumor Shapes in Breast Cancers
Cited by: 14
Author(s): Hyeong‐Gon Moon, Namshin Kim, Seongmun Jeong, Min-Ju Lee, Hyunhye Moon, Jong-Jin Kim, Tae-Kyung Yoo, Han‐Byoel Lee, Ji Sun Kim, Dong‐Young Noh, Wonshik Han
Software Mentions: 3
Published: almost 9 years ago

10.1371/journal.pgen.1009650

DAF-18/PTEN inhibits germline zygotic gene activation during primordial germ cell quiescence
Cited by: 7
Author(s): Amanda L. Fry, Amy K. Webster, Julia Burnett, Rojin Chitrakar, L. Ryan Baugh, E. Jane Albert Hubbard
Software Mentions: 3
Published: over 3 years ago

10.1371/journal.pone.0193527

Circulating miRNAs, isomiRs and small RNA clusters in human plasma and breast milk
Cited by: 48
Author(s): Mercedes Rubio, Mariona Bustamante, Carles Hernandez‐Ferrer, Dietmar Fernández‐Orth, Lorena Pantano, Yaris Sarria, Maria Riera Piqué-Borràs, Kilian Vellvé, Sílvia Agramunt, Ramón Carreras, Xavier Estivill, Juan R. González, Alfredo Mayor
Software Mentions: 3
Published: over 6 years ago

10.1186/s12977-017-0378-x

Modulation of the functional association between the HIV-1 intasome and the nucleosome by histone amino-terminal tails
Cited by: 14
Author(s): Mohamed Salah Benleulmi, Julien Matysiak, Xavier Robert, Csaba Miskey, Eric Mauro, Delphine Lapaillerie, Paul Lesbats, Stéphane Chaignepain, Daniel R. Henríquez, Christina Calmels, Oyindamola Oladosu, Eloïse Thierry, Óscar León, Marc Lavigne, Marie‐Line Andréola, Olivier Delelis, Zoltán Ivics, Marc Ruff, Patrice Gouet, Vincent Parissi
Software Mentions: 3
Published: almost 7 years ago

10.1371/journal.ppat.1008660

Identification of oncolytic vaccinia restriction factors in canine high-grade mammary tumor cells using single-cell transcriptomics
Cited by: 3
Author(s): Béatrice Cambien, Kévin Lebrigand, Alberto Baeri, Nicolas Nottet, Catherine Compin, Audrey Lamit, Olivier Ferraris, Christophe N. Peyrefitte, Virginie Magnone, Jérôme Henriques, Laure‐Emmanuelle Zaragosi, Sophie Giorgetti‐Peraldi, Fréd́eric Bost, Marine Gautier-Isola, Roger Rezzonico, Pascal Barbry, Robert Barthel, Bernard Mari, Georges Vassaux
Software Mentions: 3
Published: about 4 years ago

10.1371/journal.pgen.1006179

Recombination Rate Heterogeneity within Arabidopsis Disease Resistance Genes
Cited by: 83
Author(s): Kyuha Choi, Carsten Reinhard, Heïdi Serra, Piotr A Ziolkowski, Charles J Underwood, Xiaohui Zhao, Thomas J. Hardcastle, Nataliya E. Yelina, Catherine Griffin, Matthew A. Jackson, Christine Mézard, Gil McVean, Gregory P. Copenhaver, Ian Henderson
Software Mentions: 3
Published: over 8 years ago

10.1186/1471-2407-14-880

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

10.1371/journal.pone.0100864

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

10.1093/aobpla/plab048

Analyses of open-access multi-omics data sets reveal genetic and expression characteristics of maize ZmCCT family genes
Cited by: 1
Author(s): Ming-You Dong, Lei Ling, Xian‐Wei Fan, Youzhi Li
Software Mentions: 3
Published: over 3 years ago

10.1186/s12870-019-2121-3

Twelve complete chloroplast genomes of wild peanuts: great genetic resources and a better understanding of Arachis phylogeny
Cited by: 14
Author(s): Juan Wang, Yuan Li, Chunjuan Li, Yan Cheng, Xiaobo Zhao, Cuiling Yuan, Quanxi Sun, Chengren Shi, Shiguang Shan
Software Mentions: 3
Published: about 5 years ago

10.1371/journal.pone.0089755

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

10.1371/journal.pgen.1009438

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

10.1242/jcs.252767

N1-acetylspermidine is a determinant of hair follicle stem cell fate
Cited by: 11
Author(s): Kira Allmeroth, Christine S. Kim, Andrea Annibal, Andromachi Pouikli, Janis Koester, Maxime Derisbourg, Carlos Andrés Chacón‐Martínez, Christian Latza, Adam Antebi, Peter Tessarz, Sara A. Wickström, Martin S. Denzel
Software Mentions: 3
Published: over 3 years ago

10.1371/journal.pgen.1002742

Genome-Wide Analysis of GLD-1–Mediated mRNA Regulation Suggests a Role in mRNA Storage
Cited by: 43
Author(s): Claudia Scheckel, Dimos Gaidatzis, Jane E. Wright, Rafal Ciosk
Software Mentions: 3
Published: over 12 years ago

10.1371/journal.pone.0195003

Improved methods of DNA extraction from human spermatozoa that mitigate experimentally-induced oxidative DNA damage
Cited by: 5
Author(s): Miguel J Xavier, Brett Nixon, Shaun D. Roman, R. John Aitken
Software Mentions: 3
Published: over 6 years ago

10.1093/gigascience/giy074

Long-read sequencing and de novo genome assembly of Ammopiptanthus nanus, a desert shrub
Cited by: 18
Author(s): Fei Gao, Xue Wang, Xuming Li, Mingyue Xu, Huayun Li, Merhaba Abla, Han Sun, Shanjun Wei, Jinchao Feng, Yijun Zhou
Software Mentions: 3
Published: over 6 years ago

10.1371/journal.pone.0113800

ViVar: A Comprehensive Platform for the Analysis and Visualization of Structural Genomic Variation
Cited by: 44
Author(s): Tom Sante, Sarah Vergult, Pieter-Jan Volders, Wigard P. Kloosterman, Geert Trooskens, Katleen De Preter, Annelies Dheedene, Franki Speleman, Tim De Meyer, Björn Menten
Software Mentions: 3
Published: almost 10 years ago

10.1186/s13073-015-0168-9

Widespread intron retention diversifies most cancer transcriptomes
Cited by: 254
Author(s): Heidi Dvinge, Robert K. Bradley
Software Mentions: 3
Published: over 9 years ago

10.1186/s13073-015-0180-0

The oxidative demethylase ALKBH3 marks hyperactive gene promoters in human cancer cells
Cited by: 14
Author(s): Robert Liefke, Indra M. Windhof-Jaidhauser, Jochen Gaedcke, Gabriela Salinas-Riester, Feizhen Wu, Michael Ghadimi, Sebastian Dango
Software Mentions: 3
Published: over 9 years ago

10.1093/gigascience/giy095

Draft genome assembly of the invasive cane toad, Rhinella marina
Cited by: 56
Author(s): Richard J. Edwards, Daniel Enosi Tuipulotu, Timothy G. Amos, Denis O’Meally, Mark F. Richardson, Tonia Russell, Marcelo Vallinoto, Miguel Carneiro, Nuno Ferrand, Marc R. Wilkins, Fernando Sequeira, Lee A. Rollins, Edward C. Holmes, Richard Shine
Software Mentions: 3
Published: over 6 years ago

10.1186/1471-2229-14-141

Dehydration stress memory genes of Zea mays; comparison with Arabidopsis thaliana
Cited by: 86
Author(s): Yong Ding, Laëtitia Virlouvet, Ning Liu, Jean-Jack M. Riethoven, Michael Fromm, Zoya Avramova
Software Mentions: 3
Published: over 10 years ago

10.1371/journal.pone.0094646

Post-Translational Decrease in Respiratory Chain Proteins in the Polg Mutator Mouse Brain
Cited by: 12
Author(s): David N. Hauser, Allissa Dillman, Jinhui Ding, Li Yan, Mark Cookson
Software Mentions: 3
Published: over 10 years ago

10.1371/journal.pgen.1005395

Genome-Wide Reprogramming of Transcript Architecture by Temperature Specifies the Developmental States of the Human Pathogen Histoplasma
Cited by: 35
Author(s): Sarah A. Gilmore, Mark Voorhies, Dana Gebhart, Anita Sil
Software Mentions: 3
Published: over 9 years ago

10.1186/s12864-021-08010-5

Metagenomic investigation of potential abortigenic pathogens in foetal tissues from Australian horses
Cited by: 5
Author(s): Rumana Akter, Charles El-Hage, Fiona M. Sansom, Joan Carrick, Joanne M. Devlin, Alistair R. Legione
Software Mentions: 3
Published: about 3 years ago

10.1371/journal.pgen.1006988

Genome-wide chromatin mapping with size resolution reveals a dynamic sub-nucleosomal landscape in Arabidopsis
Cited by: 28
Author(s): Daniel Antony Pass, Emily Sornay, Angela Marchbank, Margaret Crawford, Konrad Paszkiewicz, Nicholas A. Kent, James A. H. Murray
Software Mentions: 3
Published: about 7 years ago

10.1371/journal.pone.0211430

Role of CsrA in stress responses and metabolism important for Salmonella virulence revealed by integrated transcriptomics
Cited by: 36
Author(s): Anastasia H. Potts, Yinping Guo, Brian M. M. Ahmer, Tony Romeo
Software Mentions: 3
Published: almost 6 years ago

10.1186/s13059-021-02465-1

NucHMM: a method for quantitative modeling of nucleosome organization identifying functional nucleosome states distinctly associated with splicing potentiality
Cited by: 5
Author(s): Kun Fang, Tianbao Li, Yufei Huang, Victor X. Jin
Software Mentions: 3
Published: about 3 years ago

10.1186/s12870-017-1187-z

De novo transcriptome assembly from flower buds of dioecious, gynomonoecious and chemically masculinized female Coccinia grandis reveals genes associated with sex expression and modification
Cited by: 16
Author(s): Ravi Suresh Devani, Sangram Sinha, Jayeeta Banerjee, Rabindra Kumar Sinha, Abdelhafid Bendahmane, Anjan K. Banerjee
Software Mentions: 3
Published: almost 7 years ago

10.1371/currents.md.d0c203c018bc024f2f4c9791ecb05f88

Exploratory Profiling of Urine MicroRNAs in the dy2J/dy2J Mouse Model of LAMA2-CMD: Relation to Disease Progression
Cited by: 5
Author(s): Bernardo Moreira Soares Oliveira, Kinga I. Gawlik, Madeleine Durbeej, Johan Holmberg
Software Mentions: 3
Published: almost 7 years ago

10.1371/journal.pone.0062547

p63 Attenuates Epithelial to Mesenchymal Potential in an Experimental Prostate Cell Model
Cited by: 29
Author(s): Jan Roger Olsen, Anne Margrete Øyan, Kari Rostad, Margrete R. Hellem, Jie Liu, Lisha Li, David Micklem, Hallvard Haugen, James B. Lorens, Varda Rotter, Xisong Ke, Biaoyang Lin, Karl‐Henning Kalland
Software Mentions: 3
Published: over 11 years ago

10.1186/s13073-015-0167-x

JAFFA: High sensitivity transcriptome-focused fusion gene detection
Cited by: 130
Author(s): N. Davidson, Ian J. Majewski, Alicia Oshlack
Software Mentions: 3
Published: over 9 years ago

10.1371/journal.ppat.1008402

Human cytomegalovirus IE2 drives transcription initiation from a select subset of late infection viral promoters by host RNA polymerase II
Cited by: 30
Author(s): Ming Li, Christopher B. Ball, Geoffrey S Collins, Qiaolin Hu, Donal S. Luse, David H. Price, Jeffery L. Meier
Software Mentions: 3
Published: over 4 years ago

10.1186/s12870-020-02528-8

Identification of tRFs and phasiRNAs in tomato (Solanum lycopersicum) and their responses to exogenous abscisic acid
Cited by: 7
Author(s): Weiling Luan, Yan Dai, Xinyu Li, Yan Wang, Tao Xiang, Caixia Li, Ping Mao, Xinrong Ma
Software Mentions: 3
Published: over 4 years ago

10.1186/s13059-020-02256-0

Disome-seq reveals widespread ribosome collisions that promote cotranslational protein folding
Cited by: 55
Author(s): Taolan Zhao, Yanming Chen, Yü Liu, Jia Wang, Siyu Chen, Ning Gao, Wenfeng Qian
Software Mentions: 3
Published: almost 4 years ago

10.1371/journal.pcbi.1002714

Confidence-based Somatic Mutation Evaluation and Prioritization
Cited by: 30
Author(s): Martin Löwer, Bernhard Y. Renard, Jos de Graaf, Meike Wagner, Claudia Paret, Kneip Christoph, Özlem Türeci, Mustafa Diken, Cedrik M. Britten, Sebastian Kreiter, Michael Koslowski, John C. Castle, Uğur Şahin
Software Mentions: 3
Published: about 12 years ago

10.1186/s13059-020-02142-9

RNA G-quadruplex structures exist and function in vivo in plants
Cited by: 63
Author(s): Xiaofei Yang, Jitender Cheema, Yueying Zhang, Huiyong Deng, Susan Duncan, Mubarak Ishaq Umar, Jieyu Zhao, Qi Liu, Xiaofeng Cao, Chun Kit Kwok, Yiliang Ding
Software Mentions: 3
Published: about 4 years ago

10.1186/s12870-019-2166-3

Transcriptomic and proteomic analysis reveals mechanisms of low pollen-pistil compatibility during water lily cross breeding
Cited by: 10
Author(s): Caixia Sun, Fadi Chen, Nianjun Teng, Yue-Mei Yao, Xi Shan, Zhigang Dai
Software Mentions: 3
Published: almost 5 years ago

10.1371/journal.pone.0077490

Transcriptional Reprogramming of CD11b+Esamhi Dendritic Cell Identity and Function by Loss of Runx3
Cited by: 29
Author(s): Joseph Dicken, Alexander Mildner, Dena Leshkowitz, Ivo P. Touw, Shay Hantisteanu, Steffen Jung, Yoram Groner
Software Mentions: 3
Published: about 11 years ago

10.1186/s13059-020-02036-w

Protection from DNA re-methylation by transcription factors in primordial germ cells and pre-implantation embryos can explain trans-generational epigenetic inheritance
Cited by: 38
Author(s): Isaac Kremsky, Victor G. Corcés
Software Mentions: 3
Published: over 4 years ago

10.1186/s12870-016-0932-z

Characterization of the cytokinin-responsive transcriptome in rice
Cited by: 34
Author(s): Tracy Raines, Ivory C. Blakley, Yu‐Chang Tsai, Jennifer M. Worthen, José Manuel Franco-Zorrilla, Roberto Solano, G. Schäller, Ann E. Loraine, Joseph J. Kieber
Software Mentions: 3
Published: almost 8 years ago

10.1371/journal.pcbi.1007309

miRWoods: Enhanced precursor detection and stacked random forests for the sensitive detection of microRNAs
Cited by: 8
Author(s): Jimmy D. Bell, Maureen K. Larson, Michelle Anne Kutzler, Massimo Bionaz, Christiane V. Löhr, David A. Hendrix
Software Mentions: 3
Published: about 5 years ago

10.1186/s13059-019-1726-z

Codon usage optimization in pluripotent embryonic stem cells
Cited by: 37
Author(s): Susanne Bornelöv, Tommaso Selmi, Sophia Flad, Sabine Dietmann, Michaela Frye
Software Mentions: 3
Published: over 5 years ago

10.1371/journal.pone.0083723

Function of GATA Factors in the Adult Mouse Liver
Cited by: 39
Author(s): Rena Zheng, Boris Rebolledo‐Jaramillo, Yiwei Zong, Liqing Wang, Pierre Russo, Wayne W. Hancock, Ben Z. Stanger, Ross C. Hardison, Gerd A. Blobel
Software Mentions: 3
Published: almost 11 years ago

10.1371/journal.pcbi.1007543

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

10.1186/s13059-018-1464-7

DNMT3A and TET1 cooperate to regulate promoter epigenetic landscapes in mouse embryonic stem cells
Cited by: 109
Author(s): Tianpeng Gu, Xueqiu Lin, Shay Cullen, Min Luo, Mira Jeong, Marcos R.H. Estécio, Jianjun Shen, Swanand Hardikar, Deqiang Sun, Jianzhong Su, Danielle Rux, Anna Guzman, Minjung Lee, Lei Qi, Jiajia Chen, Michael Kyba, Yun Huang, Taiping Chen, Wei Li, Margaret A. Goodell
Software Mentions: 3
Published: over 6 years ago

10.1186/s12860-020-00251-8

Identification of universal and cell-type specific p53 DNA binding
Cited by: 14
Author(s): Antonina Hafner, Lyubov Kublo, Michael Tsabar, Galit Lahav, Jacob Stewart-Ornstein
Software Mentions: 3
Published: almost 5 years ago

10.1186/s13059-017-1186-2

Epigenetic aging signatures in mice livers are slowed by dwarfism, calorie restriction and rapamycin treatment
Cited by: 232
Author(s): Tina Wang, Brian Tsui, Jason F. Kreisberg, Neil Robertson, Andrew M. Gross, Michael Yu, Hannah Carter, Holly M. Brown–Borg, Peter D. Adams, Trey Ideker
Software Mentions: 3
Published: over 7 years ago

10.1186/s13059-017-1173-7

Functional variation in allelic methylomes underscores a strong genetic contribution and reveals novel epigenetic alterations in the human epigenome
Cited by: 70
Author(s): Warren A. Cheung, Xiaojian Shao, Andréanne Morin, Valérie Siroux, Tony Kwan, Bing Ge, Dylan Aïssi, Lu Chen, Louella Vasquez, Fiona Allum, Frédéric Guénard, Emmanuelle Bouzigon, Simon Maguire, Elodie Boulier, Adriana Redensek, Stephen Watt, Avik Datta, Laura Clarke, Paul Flicek, Daniel Mead, Dirk S. Paul, Stephan Beck, Guillaume Bourque, Mark Lathrop, André Tchernof, Marie‐Claude Vohl, Florence Demenais, Isabelle Pin, Kate Downes, Hendrick G. Stunnenberg, Nicole Soranzo, Tomi Pastinen, Elin Grundberg
Software Mentions: 3
Published: over 7 years ago

10.1186/s13059-018-1553-7

Holo-Seq: single-cell sequencing of holo-transcriptome
Cited by: 26
Author(s): Zhengyun Xiao, Cheng Guo, Jiao Yang, Ci Pan, Ran Li, Danmei Jia, Jing Zhu, Chao Wu, Min Zheng, Junling Jia
Software Mentions: 3
Published: about 6 years ago

10.1371/journal.pone.0142262

High-Throughput Profiling of Caenorhabditis elegans Starvation-Responsive microRNAs
Cited by: 16
Author(s): Laura García-Segura, Cei Abreu‐Goodger, Armando Hernández-Mendoza, Tzvetanka D. Dinkova, Luis Padilla-Noriega, Martha Elva Pérez-Andrade, Juan Miranda-Ríos
Software Mentions: 3
Published: about 9 years ago

10.1186/1471-2164-15-406

Differential gene expression between functionally specialized polyps of the colonial hydrozoan Hydractinia symbiolongicarpus (Phylum Cnidaria)
Cited by: 43
Author(s): Steven M. Sanders, Mariya Shcheglovitova, Paulyn Cartwright
Software Mentions: 3
Published: almost 11 years ago

10.1371/journal.pbio.2002039

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

10.1371/journal.pone.0150591

Analysis of the Phialocephala subalpina Transcriptome during Colonization of Its Host Plant Picea abies
Cited by: 11
Author(s): Vanessa Reininger, Markus Schlegel
Software Mentions: 3
Published: over 8 years ago

10.1186/s12866-015-0370-3

New insights into the fungal community from the raw genomic sequence data of fig wasp Ceratosolen solmsi
Cited by: 5
Author(s): Lihua Niu, Xiufeng Song, Shunmin He, Peng Zhang, Ningxin Wang, Yi Li, Dawei Huang
Software Mentions: 3
Published: almost 10 years ago

10.1371/journal.pbio.3000689

Telomeric TART elements target the piRNA machinery in Drosophila
Cited by: 7
Author(s): Chris Ellison, Meenakshi S. Kagda, Weihuan Cao
Software Mentions: 3
Published: almost 4 years ago

10.1186/s12915-020-00897-y

Long-term experimental evolution reveals purifying selection on piRNA-mediated control of transposable element expression
Cited by: 7
Author(s): Ulfar Bergthorsson, Caroline J. Sheeba, Anke Konrad, Tony Bélicard, Toni Beltran, Vaishali Katju, Peter Sarkies
Software Mentions: 3
Published: about 4 years ago

10.1186/s13059-016-1059-0

Widespread natural variation of DNA methylation within angiosperms
Cited by: 398
Author(s): Chad E. Niederhuth, Adam J. Bewick, Lexiang Ji, Magdy S. Alabady, Kyung Do Kim, Qing Li, Nicholas A. Rohr, Aditi Rambani, John M. Burke, Joshua A. Udall, Chiedozie Egesi, Jeremy Schmutz, Jane Grimwood, Scott A. Jackson, Nathan M. Springer, Robert J. Schmitz
Software Mentions: 3
Published: about 8 years ago

10.1186/s13059-018-1598-7

Analysis of 3D genomic interactions identifies candidate host genes that transposable elements potentially regulate
Cited by: 38
Author(s): Ramya Raviram, Pedro P. Rocha, Vincent Luo, Emily Swanzey, Emily R. Miraldi, Edward B. Chuong, Cédric Feschotte, Richard Bonneau, Jane A. Skok
Software Mentions: 3
Published: almost 6 years ago

10.1186/s13059-021-02409-9

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

10.3390/plants9091080

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

10.1186/1755-8794-4-19

Integrative analysis of next generation sequencing for small non-coding RNAs and transcriptional regulation in Myelodysplastic Syndromes
Cited by: 40
Author(s): Dominik Beck, Steve Ayers, Jianguo Wen, Miriam Brandl, Tuan D. Pham, Paul Webb, Chung Che Chang, Xiaobo Zhou
Software Mentions: 3
Published: over 13 years ago

10.1371/journal.pcbi.1005706

Multidomain analyses of a longitudinal human microbiome intestinal cleanout perturbation experiment
Cited by: 62
Author(s): Julia Fukuyama, Laurie Rumker, Kris Sankaran, P. Jeganathan, Les Dethlefsen, David A. Relman, Susan Holmes
Software Mentions: 3
Published: over 7 years ago

10.1186/s12915-014-0079-z

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

10.3389/fmicb.2018.01739

The Culture Environment Influences Both Gene Regulation and Phenotypic Heterogeneity in Escherichia coli
Cited by: 37
Author(s): Ashley Smith, Agnieszka Kaczmar, Rosemary A. Bamford, Christopher Smith, Simona Frustaci, Andrea Kovacs-Simon, Paul O’Neill, Karen Moore, Konrad Paszkiewicz, Richard W. Titball, Stefano Pagliara
Software Mentions: 3
Published: over 6 years ago

10.1371/journal.pcbi.1001138

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

10.3389/fmicb.2020.02069

Transcriptomic Analysis and Functional Characterization Reveal the Duck Interferon Regulatory Factor 1 as an Important Restriction Factor in the Replication of Tembusu Virus
Cited by: 8
Author(s): Chengwei Xiang, Mei Huang, Tingting Xiong, Rong Fang, Linyu Li, Ding Xiang Liu, Rui Ai Chen
Software Mentions: 3
Published: about 4 years ago

10.1186/1746-4811-8-12

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

10.1186/1471-2350-15-43

Identification of transcription factors and single nucleotide polymorphisms of Lrh1 and its homologous genes in Lrh1-knockout pancreas of mice
Cited by: 1
Author(s): Maochun Tang, Li Cheng, Rongrong Jia, Lei Qiu, Hua Liu, Zhou Shu, Xiaolong Ma, Guoyong Hu, Xingpeng Wang, Yan Zhao
Software Mentions: 3
Published: over 10 years ago

10.3389/fmicb.2020.00163

Synthesis, Regulation and Degradation of Carotenoids Under Low Level UV-B Radiation in the Filamentous Cyanobacterium Chlorogloeopsis fritschii PCC 6912
Cited by: 26
Author(s): Carole A. Llewellyn, Ruth L. Airs, Garry Farnham, Carolyn Greig
Software Mentions: 3
Published: almost 5 years ago

10.1111/tpj.14632

Translational regulation contributes to the elevated CO 2 response in two Solanum species
Cited by: 12
Author(s): Sharon B. Gray, Joel Rodríguez-Medina, Samuel Rusoff, Ted Toal, Kaisa Kajala, Daniel E. Runcie, Siobhán M. Brady
Software Mentions: 3
Published: almost 5 years ago

10.1186/s12864-015-2214-9

Analysis of nucleosome positioning landscapes enables gene discovery in the human malaria parasite Plasmodium falciparum
Cited by: 5
Author(s): Xueqing Maggie Lu, Evelien M. Bunnik, Neeti Pokhriyal, Sara Nasseri, Stefano Lonardi, Karine G. Le Roch
Software Mentions: 3
Published: almost 9 years ago

10.3389/fgene.2020.00133

Comparison of Adult Testis and Ovary MicroRNA Expression Profiles in Reeves’ Pond Turtles (Mauremys reevesii) With Temperature-Dependent Sex Determination
Cited by: 6
Author(s): Lei Xiong, Mengli Yang, Kai Zheng, Ziming Wang, Shengli Gu, Jiucui Tong, Jianjun Li, Nadar Ali Shah, Liuwang Nie
Software Mentions: 3
Published: over 4 years ago

10.1111/pbi.12742

Assembly and comparison of two closely related Brassica napus genomes
Cited by: 129
Author(s): Philipp E. Bayer, Bhavna Hurgobin, Agnieszka A. Golicz, Chon‐Kit Kenneth Chan, Yuxuan Yuan, HueyTyng Lee, Michael Renton, Jianghong Meng, Ruiyuan Li, Yan Long, Jun Zou, Ian Bancroft, Boulos Chalhoub, Graham J. King, Jacqueline Batley, David Edwards
Software Mentions: 3
Published: over 7 years ago

Projects: pypi: bowtie

Papers Mentioning bowtie 1,566