pypi: bowtie | Projects | Ecosyste.ms: Papers

10.1038/s41389-020-0205-4

Post-transcriptional regulation of BRG1 by FIRΔexon2 in gastric cancer
Cited by: 9
Author(s): Guzhanuer Ailiken, Kazuo Kïtamura, Tyuji Hoshino, Mamoru Satoh, Nobuko Tanaka, Toshinari Minamoto, Bahityar Rahmutulla, Sohei Kobayashi, Masayuki Kano, Tomoaki Tanaka, Atsushi Kaneda, Fumio Nomura, Hisahiro Matsubara, Hiroshi Matsushita
Software Mentions: 2
Published: over 6 years ago

10.3892/or.2019.7300

In�vivo effects of mutant RHOA on tumor formation in an orthotopic inoculation model
Cited by: 2
Author(s): Takashi Nishizawa, Kiyotaka Nakano, Etsuko Fujii, Daisuke Komura, Yoshie Kuroiwa, Chisako Ishimaru, Makoto Monnai, Hiroyuki Aburatani, Shumpei Ishikawa, Masami Suzuki
Software Mentions: 2
Published: about 7 years ago

10.7554/eLife.48725

Tyr1 phosphorylation promotes phosphorylation of Ser2 on the C-terminal domain of eukaryotic RNA polymerase II by P-TEFb
Cited by: 21
Author(s): Joshua E. Mayfield, Seema Irani, Edwin E. Escobar, Zhao Zhang, Nathaniel T. Burkholder, Michelle Robinson, M. Rachel Mehaffey, Sarah N. Sipe, Weiwei Yang, Nicholas Adrian Prescott, Karan R. Kathuria, Zhijie Liu, Jennifer S. Brodbelt, Yan Zhang
Software Mentions: 2
Published: over 7 years ago

10.7554/eLife.06205

In vivo targeting of de novo DNA methylation by histone modifications in yeast and mouse
Cited by: 142
Author(s): Marco Morselli, William A. Pastor, Barbara Montanini, Kevin Nee, Roberto Ferrari, Kai Fu, Giancarlo Bonora, Liudmilla Rubbi, Amander T. Clark, Simone Ottonello, Steven E. Jacobsen, Matteo Pellegrini
Software Mentions: 2
Published: over 11 years ago

10.7554/eLife.29938

Msn2/4 regulate expression of glycolytic enzymes and control transition from quiescence to growth
Cited by: 47
Author(s): Zheng Kuang, Sudarshan Pinglay, Hongkai Ji, Jef D. Boeke
Software Mentions: 2
Published: about 9 years ago

10.7554/eLife.06722

Quality control of transcription start site selection by nonsense-mediated-mRNA decay
Cited by: 105
Author(s): Christophe Malabat, Frank Feuerbach, Laurence Ma, Cosmin Saveanu, Alain Jacquier
Software Mentions: 2
Published: over 11 years ago

10.7554/eLife.09003

A gene-expression screen identifies a non-toxic sumoylation inhibitor that mimics SUMO-less human LRH-1 in liver
Cited by: 32
Author(s): Miyuki Suzawa, Diego A. Miranda, Karmela A Ramos, Kenny K-H Ang, Emily J. Faivre, Christopher G. Wilson, Laura Caboni, Michelle R. Arkin, Yeong-Sang Kim, Robert J. Fletterick, Aaron A. Diaz, John S. Schneekloth, Holly A. Ingraham
Software Mentions: 2
Published: almost 11 years ago

10.7554/eLife.52212

MS-275, a class 1 histone deacetylase inhibitor augments glucagon-like peptide-1 receptor agonism to improve glycemic control and reduce obesity in diet-induced obese mice
Cited by: 9
Author(s): Shilpak Dilip Bele, Shravan Babu Girada, Arnab Ray, Abhishek Gupta, Srinivas Oruganti, Phanithi Prakash Babu, Rahul Sr Rayalla, Shashi Vardhan Kalivendi, Ahamed Ibrahim, Vishwajeet Puri, Venkateswar Adalla, Madhumohan R. Katika, Richard D. DiMarchi, Prasenjit Mitra
Software Mentions: 2
Published: almost 6 years ago

10.7554/eLife.21615

TGF-β reduces DNA ds-break repair mechanisms to heighten genetic diversity and adaptability of CD44+/CD24− cancer cells
Cited by: 33
Author(s): Debjani Pal, Anja Pertot, Nitin H. Shirole, Zhan Yao, Naishitha Anaparthy, Tyler Garvin, Hilary Cox, Kenneth Chang, Fred Rollins, Jude Kendall, Leyla Edwards, Vijay A Singh, Gary C. Stone, Michael C. Schatz, James Hicks, Gregory J. Hannon, Raffaella Sordella
Software Mentions: 2
Published: almost 10 years ago

10.7554/eLife.18270

MYC activation and BCL2L11 silencing by a tumour virus through the large-scale reconfiguration of enhancer-promoter hubs
Cited by: 74
Author(s): C. David Wood, Hildegonda Veenstra, Sarika Khasnis, Andrea Gunnell, Helen Webb, Claire Shannon-Lowe, Simon Andrews, Cameron S. Osborne, Michelle J. West
Software Mentions: 2
Published: over 10 years ago

10.7554/eLife.67236

High-resolution, genome-wide mapping of positive supercoiling in chromosomes
Cited by: 27
Author(s): Monica S. Guo, Ryo Kawamura, Megan L Littlehale, John F. Marko, Michael T. Laub
Software Mentions: 2
Published: over 5 years ago

10.7554/eLife.06068

Release of human cytomegalovirus from latency by a KAP1/TRIM28 phosphorylation switch
Cited by: 85
Author(s): Benjamin Rauwel, Suk Min Jang, Marco Cassano, Adamandia Kapopoulou, Isabelle Barde, Didier Trono
Software Mentions: 2
Published: over 11 years ago

10.7554/eLife.57858

Functional interrogation of HOXA9 regulome in MLLr leukemia via reporter-based CRISPR/Cas9 screen
Cited by: 21
Author(s): Hao Zhang, Yang Zhang, Xinyue Zhou, Shaela Wright, Judith Hyle, Lianzhong Zhao, Jie An, Xujie Zhao, Ying Shao, Beisi Xu, Hyeong-Min Lee, Taosheng Chen, Yang Zhou, Xiang Chen, Rui Lu, Chunliang Li
Software Mentions: 2
Published: about 6 years ago

10.7554/eLife.62994

The Arabidopsis active demethylase ROS1 cis-regulates defence genes by erasing DNA methylation at promoter-regulatory regions
Cited by: 54
Author(s): Thierry Halter, Jingyu Wang, Delase Amesefe, Emmanuelle Lastrucci, Magali Charvin, Meenu Singla Rastogi, Lionel Navarro
Software Mentions: 2
Published: almost 6 years ago

10.7554/eLife.33361

G9a regulates temporal preimplantation developmental program and lineage segregation in blastocyst
Cited by: 27
Author(s): J. Ż̷ylicz, Maud Borensztein, Frederick C K Wong, Yun Huang, Caroline Lee, Sabine Dietmann, M. Azim Surani
Software Mentions: 2
Published: over 8 years ago

10.7554/eLife.11275

Comparative analysis of viral RNA signatures on different RIG-I-like receptors
Cited by: 79
Author(s): Raul Y. Sanchez David, Chantal Combredet, Odile Sismeiro, Marie‐Agnès Dillies, Bernd Jagla, Jean‐Yves Coppée, Marie Mura, Mathilde Guerbois Galla, Philippe Desprès, Frédéric Tangy, Anastassia V. Komarova
Software Mentions: 2
Published: over 10 years ago

10.7554/eLife.17548

Co-transcriptional R-loops are the main cause of estrogen-induced DNA damage
Cited by: 208
Author(s): Caroline Townsend Stork, M Bocek, Madzia P Crossley, Julie Sollier, Lionel A. Sanz, Frédéric Chédin, Tomek Swigut, Karlene A. Cimprich
Software Mentions: 2
Published: about 10 years ago

10.7554/eLife.09571

Chromatin dynamics and the role of G9a in gene regulation and enhancer silencing during early mouse development
Cited by: 95
Author(s): J. Ż̷ylicz, Sabine Dietmann, Ufuk Günesdogan, Jim Hackett, Delphine Cougot, Caroline Lee, M. Azim Surani
Software Mentions: 2
Published: about 11 years ago

10.7554/eLife.01257

Distinct stages of the translation elongation cycle revealed by sequencing ribosome-protected mRNA fragments
Cited by: 262
Author(s): Liana F. Lareau, Dustin H Hite, Gregory J. Hogan, Patrick O. Brown
Software Mentions: 2
Published: over 12 years ago

10.7554/eLife.68285

A modified fluctuation assay reveals a natural mutator phenotype that drives mutation spectrum variation within Saccharomyces cerevisiae
Cited by: 21
Author(s): Pengyao Jiang, Anja R Ollodart, Vidha Sudhesh, Alan J. Herr, Maitreya J. Dunham, Kelley Harris
Software Mentions: 2
Published: about 5 years ago

10.3390/ijms151018819

Metaphylogenomic and Potential Functionality of the Limpet Patella pellucida’s Gastrointestinal Tract Microbiome
Cited by: 14
Author(s): Magda Dudek, Jessica Adams, Martin Swain, Matthew J. Hegarty, Sharon Huws, Joe Gallagher
Software Mentions: 2
Published: about 12 years ago

10.3390/ijms18071475

Transcriptome Differences in Porcine Alveolar Macrophages from Tongcheng and Large White Pigs in Response to Highly Pathogenic Porcine Reproductive and Respiratory Syndrome Virus (PRRSV) Infection
Cited by: 29
Author(s): Wan Liang, Likai Ji, Yu Zhang, Yueran Zhen, Qingde Zhang, Xuewen Xu, Bang Liu
Software Mentions: 2
Published: over 9 years ago

10.3390/ijms18081634

Transcriptome Analysis Reveals Increases in Visceral Lipogenesis and Storage and Activation of the Antigen Processing and Presentation Pathway during the Mouth-Opening Stage in Zebrafish Larvae
Cited by: 16
Author(s): Hao Xu, Enxiu Liu, Yun Li, Xiaojie Li, Chenyu Ding
Software Mentions: 2
Published: over 9 years ago

10.3390/ijms19051481

Exploration of ABA Responsive miRNAs Reveals a New Hormone Signaling Crosstalk Pathway Regulating Root Growth of Populus euphratica
Cited by: 20
Author(s): Conglong Lian, Kun Yao, Hui Duan, Qing Li, Chao Liu, Weilun Yin, Xinli Xia
Software Mentions: 2
Published: over 8 years ago

10.3390/ijms20020369

Comprehensive Analysis of Differentially Expressed Unigenes under NaCl Stress in Flax (Linum usitatissimum L.) Using RNA-Seq
Cited by: 24
Author(s): Jianzhong Wu, Qian Zhao, Guangwen Wu, Hongmei Yuan, Yan Ma, Hong Lin, Liyan Pan, Suiyan Li, Dequan Sun
Software Mentions: 2
Published: almost 8 years ago

10.3390/ijms20051106

Transcriptome and Proteome-Based Network Analysis Reveals a Model of Gene Activation in Wheat Resistance to Stripe Rust
Cited by: 21
Author(s): Hong Zhang, Ying Fu, Huan Guo, Lu Zhang, Changyou Wang, Weining Song, Zhaogui Yan, Yajuan Wang, Wanquan Ji
Software Mentions: 2
Published: over 7 years ago

10.3390/ijms20122912

Cell-Free, Embryo-Specific sncRNA as a Molecular Biological Bridge between Patient Fertility and IVF Efficiency
Cited by: 17
Author(s): Timofeeva A.V. Timofeeva, Vitaliy Chagovets, Yulia S. Drapkina, Н. П. Макарова, Kalinina E.A. Kalinina, Г. Т. Сухих
Software Mentions: 2
Published: over 7 years ago

10.3390/ijms20215357

Genome-Wide Analysis of Cotton miRNAs During Whitefly Infestation Offers New Insights into Plant-Herbivore Interaction
Cited by: 9
Author(s): Jianying Li, J. Joe Hull, Shi-Dong Liang, Qiongqiong Wang, Chen Luo, Qinghua Zhang, Maojun Wang, Shahid Mansoor, Xianlong Zhang, Shuangxia Jin
Software Mentions: 2
Published: about 7 years ago

10.3390/ijms21083029

Elimination of Viroids from Tobacco Pollen Involves a Decrease in Propagation Rate and an Increase of the Degradation Processes
Cited by: 13
Author(s): Jaroslav Matoušek, Lenka Steinbachová, Lenka Záveská Drábková, Tomáš Kocábek, David Potěšil, Ajay Kumar Mishra, David Honys, Gerhard Steger
Software Mentions: 2
Published: over 6 years ago

10.3390/ijms21103513

Small RNA Sequencing Analysis of miRNA Expression Reveals Novel Insihts into Root Formation under Root Restriction Cultivation in Grapevine (Vitis vinifera L.)
Cited by: 6
Author(s): Hui Li, Zhen Gao, Muhammad Zahid, Dongmei Li, Hafiz Umer Javed, Lei Wang, Shiren Song, Liping Zhao, Wenping Xu, Caixi Zhang, Chao Ma, Shiping Wang
Software Mentions: 2
Published: over 6 years ago

10.3390/ijms21113846

MiRNAs Expression Profiling of Bovine (Bos taurus) Testes and Effect of bta-miR-146b on Proliferation and Apoptosis in Bovine Male Germline Stem Cells
Cited by: 21
Author(s): Yuan Gao, Fei Wu, Yaxuan Ren, Ziqing Zhou, Ningbo Chen, Yongzhen Huang, Chuzhao Lei, Hong Chen, Ruihua Dang
Software Mentions: 2
Published: over 6 years ago

10.3390/ijms21165914

Comparative Transcriptomic Analysis of the Development of Sepal Morphology in Tomato (Solanum Lycopersicum L.)
Cited by: 9
Author(s): Jingyi Liu, Meijing Shi, Jing Wang, Bo Zhang, Yushun Li, Jin Wang, Ahmed H. El-Sappah, Yan Liang
Software Mentions: 2
Published: about 6 years ago

10.3390/ijms22041563

Plasma miR-9-3p and miR-136-3p as Potential Novel Diagnostic Biomarkers for Experimental and Human Mild Traumatic Brain Injury
Cited by: 19
Author(s): Shalini Gupta, Robert Ciszek, Mette Heiskanen, Niina Lapinlampi, Janne Kukkonen, Ville Leinonen, Noora Puhakka, Asla Pitkänen
Software Mentions: 2
Published: almost 6 years ago

10.3390/ijms22073568

A Tale of Two Transcriptomic Responses in Agricultural Pests via Host Defenses and Viral Replication
Cited by: 5
Author(s): Pramod Pantha, Chalivendra C. Subbaiah, Dong Ha Oh, Bret D. Elderd, Maheshi Dassanayake
Software Mentions: 2
Published: over 5 years ago

10.1523/JNEUROSCI.2673-17.2018

Loss of eIF4E Phosphorylation Engenders Depression-like Behaviors via Selective mRNA Translation
Cited by: 52
Author(s): Inês S. Amorim, Sonal Kedia, Stella Kouloulia, Konstanze Simbriger, Ilse Gantois, Seyed Mehdi Jafarnejad, Yupeng Li, Agniete Kampaite, Tine Pooters, Nicola Romanò, Christos G. Gkogkas
Software Mentions: 2
Published: almost 9 years ago

10.1016/j.isci.2021.102790

ZBTB32 performs crosstalk with the glucocorticoid receptor and is crucial in glucocorticoid responses to starvation
Cited by: 1
Author(s): Lise Van Wyngene, Tineke Vanderhaeghen, Ιωάννα Πέττα, Steven Timmermans, Katrien Corbeels, Bart Van der Schueren, Jolien Vandewalle, Kelly Van Looveren, Charlotte Wallaeys, Melanie Eggermont, Sylviane Dewaele, Leen Catrysse, Geert Loo, Rudi Beyaert, Pieter Gillard, Toshinori Nakayama, Jan Tavernier, Karolien De Bosscher, Claude Libert
Software Mentions: 2
Published: over 5 years ago

10.1016/j.isci.2021.103093

Ezh2 harnesses the intranuclear actin cytoskeleton to remodel chromatin in differentiating Th cells
Cited by: 5
Author(s): Moran Titelbaum, Boris Brant, Daniel Baumel, Alina Burstein-Willensky, Shira Perez, Yiftah Barsheshet, Orly Avni
Software Mentions: 2
Published: about 5 years ago

10.1186/s13048-020-00709-5

Identification of circular RNAs in the ovarian follicles of Meishan and Duroc sows during the follicular phase
Cited by: 2
Author(s): Shuai Xie, Mengxun Li, Yansen Chen, Yi Liu, Ligeng Ma, Xiaomei Sun, Yishan Sun, Ruonan Gao, Tao Huang
Software Mentions: 2
Published: about 6 years ago

10.18632/oncotarget.8124

Non-invasive prostate cancer detection by measuring miRNA variants (isomiRs) in urine extracellular vesicles
Cited by: 108
Author(s): Danijela Koppers-Lalić, Michael Hackenberg, Renée X. de Menezes, Branislav Mišovic, Magda Wąchalska, Albert A. Geldof, Nicoletta Zini, Theo de Reijke, Thomas Würdinger, Andrè N. Vis, Jeroen van Moorselaar, D. Michiel Pegtel, Irene V. Bijnsdorp
Software Mentions: 2
Published: over 10 years ago

10.18632/oncotarget.14788

Acquired resistance to LY2874455 in <i>FGFR2</i>-amplified gastric cancer through an emergence of novel <i>FGFR2-ACSL5</i> fusion
Cited by: 40
Author(s): Sun Young Kim, Tae-Jin Ahn, Heejin Bang, Jun Soo Ham, Jusun Kim, Seung Tae Kim, Jiryeon Jang, Moonhee Shim, So Young Kang, Se Hoon Park, Byung Hoon Min, Hyuk Lee, Won Ki Kang, Woong-Yang Park
Software Mentions: 2
Published: almost 10 years ago

10.18632/oncotarget.24973

Comprehensive genomic transcriptomic tumor-normal gene panel analysis for enhanced precision in patients with lung cancer
Cited by: 9
Author(s): Shahrooz Rabizadeh, Chad Garner, J. Zachary Sanborn, Stephen C. Benz, Sandeep K. Reddy, Patrick Soon‐Shiong
Software Mentions: 2
Published: over 8 years ago

10.4172/2157-7633.S10-009

Transcriptional Regulation of Human NANOG by Alternate Promoters in Embryonic Stem Cells
Cited by: 5
Author(s): Satyabrata Das, Snehalata Jena, Eun‐Mi Kim, Nicholas Zavazava, Dana N. Levasseur
Software Mentions: 2
Published: almost 15 years ago

10.1128/JVI.01515-20

Identification of a Functional Small Noncoding RNA of African Swine Fever Virus
Cited by: 8
Author(s): Laura Dunn, Alasdair Ivens, Christopher L. Netherton, Dave Chapman, Philippa M. Beard
Software Mentions: 2
Published: about 6 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 8 years ago

10.1186/s13059-015-0606-4

A haplotype map of allohexaploid wheat reveals distinct patterns of selection on homoeologous genomes
Cited by: 196
Author(s): Katherine Jordan, Shichen Wang, Yanni Lun, Laura‐Jayne Gardiner, Ron MacLachlan, P. Hucl, Krysta Wiebe, Debbie Wong, Kerrie Forrest, Andrew Sharpe, Christine Sidebottom, Neil Hall, Christopher Toomajian, Timothy J. Close, Jorge Dubcovsky, Alina Akhunova, L. E. Talbert, Urmil Bansal, Harbans Bariana, Matthew Hayden, Curtis Pozniak, Jeffrey A. Jeddeloh, Anthony Hall, Eduard Akhunov
Software Mentions: 1
Published: over 11 years ago

10.1186/s13059-015-0651-z

Oxygen and glucose deprivation induces widespread alterations in mRNA translation within 20 minutes
Cited by: 105
Author(s): Dmitry E. Andreev, Patrick B F O‘Connor, Alexander V. Zhdanov, Ruslan I. Dmitriev, Ivan N. Shatsky, Dmitri B. Papkovsky, Pavel V. Baranov
Software Mentions: 1
Published: over 11 years ago

10.1371/journal.pone.0141915

Transcriptomic Analysis of Myocardial Ischemia Using the Blood of Rat
Cited by: 2
Author(s): Jincai Hou, Jianhua Fu, Dan Li, Xiao Han, Lei Li, Wenjing Song, Mingjiang Yao, Jianxun Liu
Software Mentions: 1
Published: about 11 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 9 years ago

10.1371/journal.pone.0012984

Weakly Positioned Nucleosomes Enhance the Transcriptional Competency of Chromatin
Cited by: 8
Author(s): Yaakov Belch, Jingyi Yang, Yang Liu, Sridhar A. Malkaram, Rong Liu, Jean-Jack M. Riethoven, István Ladunga
Software Mentions: 1
Published: about 16 years ago

10.1371/journal.pone.0122170

De Novo Characterization of Fall Dormant and Nondormant Alfalfa (Medicago sativa L.) Leaf Transcriptome and Identification of Candidate Genes Related to Fall Dormancy
Cited by: 34
Author(s): Senhao Zhang, Shi Ya, Ningning Cheng, Hao Du, Wenna Fan, Chengzhang Wang
Software Mentions: 1
Published: over 11 years ago

10.1371/journal.pone.0151826

A Bayesian Assignment Method for Ambiguous Bisulfite Short Reads
Cited by: 1
Author(s): Hong T. Tran, Xiaowei Wu, Saima Sultana Tithi, Miao‐Kun Sun, Hehuang Xie, Liqing Zhang
Software Mentions: 1
Published: over 10 years ago

10.1371/journal.pone.0024883

A Comprehensive Expression Profile of MicroRNAs in Porcine Pituitary
Cited by: 22
Author(s): Hongyi Li, Qianyun Xi, Yuanyan Xiong, Xiao Cheng, Qien Qi, Lin Yang, Gang Shu, Lina Wang, Ping Gao, Xiaotong Zhu, Qingyan Jiang, Yongliang Zhang, Yuan Li
Software Mentions: 1
Published: about 15 years ago

10.1371/journal.pone.0173238

RNA-Seq analysis of salinity stress–responsive transcriptome in the liver of spotted sea bass (Lateolabrax maculatus)
Cited by: 56
Author(s): Xiaoyan Zhang, Haishen Wen, Hailiang Wang, Yuanyuan Ren, Ji Zhao, Yun Li
Software Mentions: 1
Published: over 9 years ago

10.1186/s12864-018-4431-5

High-sensitivity HLA typing by Saturated Tiling Capture Sequencing (STC-Seq)
Cited by: 8
Author(s): Jiao Yang, Ran Li, Chao Wu, Yibin Ding, Yanning Liu, Danmei Jia, Lifeng Wang, Xiang Xu, Jing Zhu, Min Zheng, Junling Jia
Software Mentions: 1
Published: almost 9 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 9 years ago

10.1371/journal.pone.0166770

Intraluminal Flagellin Differentially Contributes to Gut Dysbiosis and Systemic Inflammation following Burn Injury
Cited by: 16
Author(s): Logan Grimes, Allie Doyle, Aaron L. Miller, Richard B. Pyles, Gábor Oláh, Csaba Szabó, Sarah Hoskins, Tonyia Eaves-Pyles
Software Mentions: 1
Published: almost 10 years ago

10.1371/journal.pone.0072781

Genome-Wide SNP and STR Discovery in the Japanese Crested Ibis and Genetic Diversity among Founders of the Japanese Population
Cited by: 7
Author(s): Yoshinori Taniguchi, Hideaki Matsuda, Takahisa Yamada, Toshie Sugiyama, Kosuke Homma, Yoshinori Kaneko, Satoshi Yamagishi, Hiroaki Iwaisaki
Software Mentions: 1
Published: about 13 years ago

10.1371/journal.pone.0184917

Comparative analysis of miRNAs of two rapeseed genotypes in response to acetohydroxyacid synthase-inhibiting herbicides by high-throughput sequencing
Cited by: 2
Author(s): Meijiao Hu, Pu Huang, Jianqin Gao, Wei Long, Feng Chen, Wei Zhang, Xiaoyin Zhou, Qi Peng, Song Chen, Jiefu Zhang
Software Mentions: 1
Published: about 9 years ago

10.1371/journal.pone.0028318

Comparative Analysis of Human Protein-Coding and Noncoding RNAs between Brain and 10 Mixed Cell Lines by RNA-Seq
Cited by: 27
Author(s): Geng Chen, Kangping Yin, Leming Shi, Yunzhang Fang, Ya Qi, Peng Li, Jian Luo, Bing He, Mingyao Liu, Tieliu Shi
Software Mentions: 1
Published: almost 15 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 9 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 9 years ago

10.1186/s12864-018-5400-8

A dynamic degradome landscape on miRNAs and their predicted targets in sugarcane caused by Sporisorium scitamineum stress
Cited by: 12
Author(s): Yachun Su, Xinhuan Xiao, Hui Ling, Ning Huang, Feng Liu, Weihua Su, Yuye Zhang, Liping Xu, Khushi Muhammad, Youxiong Que
Software Mentions: 1
Published: almost 8 years ago

10.1371/journal.pone.0171566

Comparison of whole genome amplification techniques for human single cell exome sequencing
Cited by: 59
Author(s): Erik Borgström, Marta Paterlini, Jeff E. Mold, Jonas Frisén, Joakim Lundeberg
Software Mentions: 1
Published: over 9 years ago

10.1371/journal.pone.0255914

Nested PCR followed by NGS: Validation and application for HPV genotyping of Tunisian cervical samples
Cited by: 6
Author(s): M. Ardhaoui, Emna Ennaifer, Anna Christina de Matos Salim, Flávio Marcom Gomez, T. Laasili, Mohamed Samir Boubaker, Ikram Guizani
Software Mentions: 1
Published: over 5 years ago

10.1371/journal.pone.0129190

p53 Represses the Oncogenic Sno-MiR-28 Derived from a SnoRNA
Cited by: 52
Author(s): Yu Feng, Cameron P. Bracken, Katherine A. Pillman, David Lawrence, Gregory J. Goodall, David F. Callen, Paul M. Neilsen
Software Mentions: 1
Published: over 11 years ago

10.1155/2021/8845520

Changes in the Small RNA Expression in Endothelial Cells in Response to Inflammatory Stimulation
Cited by: 1
Author(s): Peixi Liu, Lingli Hu, Yuan Shi, Yingjun Liu, Guangrong Yu, Yingjie Zhou, Qingzhu An, Wei Zhu
Software Mentions: 1
Published: over 5 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 8 years ago

10.1371/journal.pone.0054950

Human Trace Amine-Associated Receptor TAAR5 Can Be Activated by Trimethylamine
Cited by: 93
Author(s): Ivonne Wallrabenstein, Jonas Kuklan, Lea Weber, Sandra Zborala, Markus Werner, Janine Altmüller, Christian Becker, Anna Schmidt, Hanns Hatt, Thomas Hummel, Günter Gisselmann
Software Mentions: 1
Published: almost 14 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: about 8 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: about 8 years ago

10.1186/1471-2164-14-2

Saturated linkage map construction in Rubus idaeus using genotyping by sequencing and genome-independent imputation
Cited by: 144
Author(s): J. A. Ward, J. S. Bhangoo, Felicidad Fernández-Fernández, Patrick P. Moore, Jd. Swanson, Roberto Viola, Riccardo Velasco, Nahla V. Bassil, Courtney Weber, Daniel J. Sargent
Software Mentions: 1
Published: almost 14 years ago

10.1371/journal.pone.0206110

Genomic heterogeneity differentiates clinical and environmental subgroups of Legionella pneumophila sequence type 1
Cited by: 8
Author(s): Jeffrey W. Mercante, Jason Caravas, Maliha K. Ishaq, Natalia A. Kozak-Muiznieks, Brian Raphael, Jonas M. Winchell
Software Mentions: 1
Published: about 8 years ago

10.1371/journal.pntd.0007480

Field diagnosis and genotyping of chikungunya virus using a dried reverse transcription loop-mediated isothermal amplification (LAMP) assay and MinION sequencing
Cited by: 17
Author(s): Kyoko Hayashida, Yasuko Orba, Patrícia Carvalho de Sequeira, Chihiro Sugimoto, William W. Hall, Yuki Eshita, Yutaka Suzuki, Lucky Ronald Runtuwene, Patrícia Brasil, Guilherme Amaral Calvet, Cíntia D. S. Rodrigues, Carolina Cardoso dos Santos, Maria Angélica Monteiro de Mello Mares-Guia, Junya Yamagishi, Ana María Bispo de Filippis, Hirofumi Sawa
Software Mentions: 1
Published: over 7 years ago

10.1186/s13059-018-1619-6

Systematic evaluation of C. elegans lincRNAs with CRISPR knockout mutants
Cited by: 24
Author(s): Wei Shuai, He Chen, Emmanuel Enoch Dzakah, Bin Yu, Xiaolin Wang, Tao Fu, Jingxin Li, Lei Liu, Shu-Cheng Fang, Weihong Liu, Shengfang Ge
Software Mentions: 1
Published: almost 8 years ago

10.1186/1471-2164-12-158

Composite transcriptome assembly of RNA-seq data in a sheep model for delayed bone healing
Cited by: 64
Author(s): Marten Jäger, Claus‐Eric Ott, Johannes Grünhagen, Jochen Hecht, Hanna Schell, Stefan Mundlos, Georg N. Duda, Peter N. Robinson, Jasmin Lienau
Software Mentions: 1
Published: over 15 years ago

10.1186/1471-2164-15-743

The I2 resistance gene homologues in Solanum have complex evolutionary patterns and are targeted by miRNAs
Cited by: 20
Author(s): Chunhua Wei, Hanhui Kuang, Li Feng, Jiongjiong Chen
Software Mentions: 1
Published: about 12 years ago

10.1371/journal.pntd.0002489

Whole Genome Sequencing of Field Isolates Reveals a Common Duplication of the Duffy Binding Protein Gene in Malagasy Plasmodium vivax Strains
Cited by: 103
Author(s): Didier Ménard, E. Ricky Chan, Christophe Benedet, Arsène Ratsimbasoa, Saorin Kim, Pheaktra Chim, Catherine Do, Benoît Witkowski, Rémy Durand, Marc Thellier, Carlo Severini, Eric Legrand, Lise Musset, Bakri Y. M. Nour, Odile Mercereau–Puijalon, David Serre, Peter A. Zimmerman
Software Mentions: 1
Published: almost 13 years ago

10.1371/journal.pgen.1003697

Masculinization of Gene Expression Is Associated with Exaggeration of Male Sexual Dimorphism
Cited by: 106
Author(s): Marie A. Pointer, Peter W. Harrison, Alison E. Wright, Judith E. Mank
Software Mentions: 1
Published: about 13 years ago

10.1186/s12864-017-3869-1

Profiling of drought-responsive microRNA and mRNA in tomato using high-throughput sequencing
Cited by: 89
Author(s): Minmin Liu, Huiyang Yu, Gangjun Zhao, Qiufeng Huang, Yongen Lu, Bo Ouyang
Software Mentions: 1
Published: over 9 years ago

10.1371/journal.pgen.1004515

A System for Genome-Wide Histone Variant Dynamics In ES Cells Reveals Dynamic MacroH2A2 Replacement at Promoters
Cited by: 26
Author(s): Özlem Yıldırım, Jui-Hung Hung, Ryan J. Cedeno, Zhiping Weng, Christopher J. Lengner, Oliver J. Rando
Software Mentions: 1
Published: over 12 years ago

10.1371/journal.pgen.1005443

Functional Activation of the Flagellar Type III Secretion Export Apparatus
Cited by: 14
Author(s): Andrew Phillips, Rebecca A. Calvo, Daniel B. Kearns
Software Mentions: 1
Published: over 11 years ago

10.1371/journal.pgen.1003512

Drosophila Functional Elements Are Embedded in Structurally Constrained Sequences
Cited by: 11
Author(s): Ephraim Kenigsberg, Amos Tanay
Software Mentions: 1
Published: over 13 years ago

10.7554/eLife.33684

Gene network analysis identifies a central post-transcriptional regulator of cellular stress survival
Cited by: 16
Author(s): Matthew Tien, Aretha Fiebig, Sean Crosson
Software Mentions: 1
Published: over 8 years ago

10.1371/journal.pgen.1004831

The Global Regulatory Architecture of Transcription during the Caulobacter Cell Cycle
Cited by: 108
Author(s): Bo Zhou, Jared M. Schrader, Virginia S. Kalogeraki, Eduardo Abeliuk, Cong B. Dinh, James Q. Pham, Zhongying Z. Cui, David L. Dill, Harley H. McAdams, Lucy Shapiro
Software Mentions: 1
Published: almost 12 years ago

10.1371/journal.pgen.1004355

A Lack of Parasitic Reduction in the Obligate Parasitic Green Alga Helicosporidium
Cited by: 49
Author(s): Jean‐François Pombert, Nicolas A. Blouin, Christopher E. Lane, Drion G. Boucias, Patrick J. Keeling
Software Mentions: 1
Published: over 12 years ago

10.1371/journal.pgen.1005064

Bacterial Infection Drives the Expression Dynamics of microRNAs and Their isomiRs
Cited by: 57
Author(s): Katherine J. Siddle, Ludovic Tailleux, Matthieu Deschamps, Yong-Hwee Eddie Loh, Cécile Deluen, Brigitte Gicquel, Christophe Antoniewski, Luis B. Barreiro, Laurent Farinelli, Lluı́s Quintana-Murci
Software Mentions: 1
Published: over 11 years ago

10.1371/journal.pgen.1004204

RBPJ, the Major Transcriptional Effector of Notch Signaling, Remains Associated with Chromatin throughout Mitosis, Suggesting a Role in Mitotic Bookmarking
Cited by: 70
Author(s): Robert J. Lake, Pei-Fang Tsai, In-Chan Choi, Kyoung Jae Won, Hua-Ying Fan
Software Mentions: 1
Published: over 12 years ago

10.1186/s12864-021-07481-w

Pi-starvation induced transcriptional changes in barley revealed by a comprehensive RNA-Seq and degradome analyses
Cited by: 10
Author(s): Paweł Sega, Katarzyna Kruszka, Dawid Bielewicz, Wojciech M. Karłowski, Przemysław Nuc, Zofia Szweykowska-Kulińska, Andrzej Pacak
Software Mentions: 1
Published: over 5 years ago

10.1371/journal.pgen.1007170

Cdc73 suppresses genome instability by mediating telomere homeostasis
Cited by: 14
Author(s): Rahul V. Nene, Christopher D. Putnam, Bin-Zhong Li, Katarina G. Nguyen, Anjana Srivatsan, Christopher S. Campbell, Arshad Desai, Richard D. Kolodner
Software Mentions: 1
Published: almost 9 years ago

10.1371/journal.pgen.1004096

New MicroRNAs in Drosophila—Birth, Death and Cycles of Adaptive Evolution
Cited by: 52
Author(s): Yang Lyu, Yang Shen, Heng Li, Yuxin Chen, Li Guo, Yixin Zhao, Eric Hungate, Suhua Shi, Chung‐I Wu, Tian Tang
Software Mentions: 1
Published: almost 13 years ago

10.1186/1471-2164-15-271

SFGD: a comprehensive platform for mining functional information from soybean transcriptome data and its use in identifying acyl-lipid metabolism pathways
Cited by: 36
Author(s): Juan Yu, Zhenhai Zhang, Jiangang Wei, Yi Ling, Wenying Xu, Zhen Su
Software Mentions: 1
Published: over 12 years ago

10.1371/journal.pgen.1002331

Genetic Rearrangements Can Modify Chromatin Features at Epialleles
Cited by: 21
Author(s): Andrea M. Foerster, Huy Q. Dinh, Laura Sedman, Bonnie Wohlrab, Ortrun Mittelsten Scheid
Software Mentions: 1
Published: about 15 years ago

10.1186/s12864-019-6433-3

A crustacean annotated transcriptome (CAT) database
Cited by: 12
Author(s): Wenyan Nong, Zacary Y. H. Chai, Xiaoying Jiang, Jing Qin, Ka Yan, King Ming Chan, Ting Fung Chan, Billy K. C. Chow, Hoi Shan Kwan, Chris K C Wong, Jian‐Wen Qiu, Jerome H.L. Hui, Ka Hou Chu
Software Mentions: 1
Published: almost 7 years ago

10.1371/journal.pgen.1006227

A Conserved Nuclear Cyclophilin Is Required for Both RNA Polymerase II Elongation and Co-transcriptional Splicing in Caenorhabditis elegans
Cited by: 7
Author(s): Jeong Hyun Ahn, Andreas Rechsteiner, Susan Strome, William G. Kelly
Software Mentions: 1
Published: about 10 years ago

10.1371/journal.pgen.1005079

Escape from X Inactivation Varies in Mouse Tissues
Cited by: 211
Author(s): Joel B. Berletch, Wenxiu Ma, Fan Yang, Jay Shendure, William Stafford Noble, Christine M. Distèche, Xinxian Deng
Software Mentions: 1
Published: over 11 years ago

10.1186/s13059-021-02454-4

Integrative approach identifies SLC6A20 and CXCR6 as putative causal genes for the COVID-19 GWAS signal in the 3p21.31 locus
Cited by: 35
Author(s): Silva Kasela, Zharko Daniloski, Sailalitha Bollepalli, Tristan X. Jordan, Benjamin R. tenOever, Neville E. Sanjana, Tuuli Lappalainen
Software Mentions: 1
Published: about 5 years ago

10.1371/journal.pgen.1007781

RNase H1 directs origin-specific initiation of DNA replication in human mitochondria
Cited by: 55
Author(s): Viktor Posse, Ali Al-Behadili, Jay P. Uhler, Anders R. Clausen, Aurelio Reyes, Massimo Zeviani, Maria Falkenberg, Claes M. Gustafsson
Software Mentions: 1
Published: almost 8 years ago

10.1371/journal.pgen.1004518

Requirements for Pseudomonas aeruginosa Acute Burn and Chronic Surgical Wound Infection
Cited by: 255
Author(s): Keith H. Turner, Jake Everett, Urvish Trivedi, Kendra P. Rumbaugh, Marvin Whiteley
Software Mentions: 1
Published: over 12 years ago

10.1371/journal.pgen.1002329

Transcriptome-Wide Binding Sites for Components of the Saccharomyces cerevisiae Non-Poly(A) Termination Pathway: Nrd1, Nab3, and Sen1
Cited by: 137
Author(s): Tyler J. Creamer, Miranda M. Darby, Nuttara Jamonnak, Paul Schaughency, Haiping Hao, Sarah J. Wheelan, Jeffry L. Corden
Software Mentions: 1
Published: about 15 years ago

10.1371/journal.pgen.1004773

Functional Diversity of Carbohydrate-Active Enzymes Enabling a Bacterium to Ferment Plant Biomass
Cited by: 79
Author(s): Magali Boutard, Tristan Cerisy, Pierre-Yves Nogue, Adriana Alberti, Jean Weissenbach, Marcel Salanoubat, Andrew C. Tolonen
Software Mentions: 1
Published: almost 12 years ago

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Papers Mentioning bowtie 1,566