Ecosyste.ms: Papers

An open API service providing mapping between scientific papers and software projects that are mentioned in them.
All mentions data is based on the CZI Software Mentions dataset.

Projects: pypi: bowtie

https://packages.ecosyste.ms/registries/pypi.org/packages/bowtie

Interactive Dashboard Toolkit.
43 versions
Latest release: about 6 years ago
1 dependent package
221 downloads last month

Papers Mentioning bowtie 1,566

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 5 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 5 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 9 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 7 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 9 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 9 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 4 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 8 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 8 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 3 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 9 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 4 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 4 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 6 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 8 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 8 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 9 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 10 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 3 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 10 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 7 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 7 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 6 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 6 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 5 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 5 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 5 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 4 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 4 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 4 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: over 4 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 4 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 3 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 7 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 3 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 3 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 4 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 8 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 8 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 6 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 13 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 4 years ago
10.3390/nu13020614
Acute Effects of Cheddar Cheese Consumption on Circulating Amino Acids and Human Skeletal Muscle
Cited by: 8
Author(s): Naomi M.M.P. de Hart, Ziad Mahmassani, Paul T. Reidy, Joshua Kelley, Alison McKenzie, Jonathan J Petrocelli, M.J. Bridge, Lisa Baird, Eric D. Bastian, Loren S. Ward, Michael Howard, Micah J. Drummond
Software Mentions: 2
Published: almost 4 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 3 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 10 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 9 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 10 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 7 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 6 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 11 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 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 10 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: over 8 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 5 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 9 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 6 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 3 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 10 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 13 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: about 10 years ago
10.1371/journal.pgen.1004138
Euchromatic Transposon Insertions Trigger Production of Novel Pi- and Endo-siRNAs at the Target Sites in the Drosophila Germline
Cited by: 122
Author(s): Sergey Shpiz, Sergei Ryazansky, Ivan Olovnikov, Yuri Abramov, Alla Kalmykova
Software Mentions: 1
Published: almost 11 years ago
10.1186/s12864-020-6580-6
Biased visibility in Hi-C datasets marks dynamically regulated condensed and decondensed chromatin states genome-wide
Cited by: 8
Author(s): Keerthivasan Raanin Chandradoss, Prashanth Kumar Guthikonda, Srinivas Kethavath, Monika Dass, Harpreet Singh, Rakhee Nayak, Sreenivasulu Kurukuti, Kuljeet Singh Sandhu
Software Mentions: 1
Published: over 4 years ago
10.1093/aobpla/ply077
Association analysis uncovers the genetic basis of general combining ability of 11 yield-related traits in parents of hybrid rice
Cited by: 4
Author(s): Imdad Ullah Zaid, Weijie Tang, Jianbo He, Sana Ullah Khan, Delin Hong
Software Mentions: 1
Published: almost 6 years ago
10.1371/journal.pgen.1004476
Apomictic and Sexual Germline Development Differ with Respect to Cell Cycle, Transcriptional, Hormonal and Epigenetic Regulation
Cited by: 63
Author(s): Anja Schmidt, Marc W. Schmid, Ulrich C. Klostermeier, Weihong Qi, Daniela Guthörl, Christian Sailer, Manuel Waller, Philip Rosenstiel, Ueli Grossniklaus
Software Mentions: 1
Published: over 10 years ago
10.1371/journal.pgen.1004463
The Coding and Noncoding Architecture of the Caulobacter crescentus Genome
Cited by: 131
Author(s): Jared M. Schrader, Bo Zhou, Gene-Wei Li, Keren Lasker, W. Seth Childers, Brandon Williams, Tao Long, Sean Crosson, Harley H. McAdams, Jonathan S. Weissman, Lucy Shapiro
Software Mentions: 1
Published: over 10 years ago
10.1371/journal.pgen.1007250
SUMO E3 ligase Mms21 prevents spontaneous DNA damage induced genome rearrangements
Cited by: 16
Author(s): Jason Liang, Bin-Zhong Li, Alexander P. Tan, Richard D. Kolodner, Christopher D. Putnam, Huilin Zhou
Software Mentions: 1
Published: over 6 years ago
10.1186/gm403
HLA typing from RNA-Seq sequence reads
Cited by: 193
Author(s): Sebastian Boegel, Martin Löwer, Michael K. E. Schäfer, Thomas Bukur, Jos de Graaf, Valesca Boisguérin, Özlem Türeci, Mustafa Diken, John C. Castle, Uğur Şahin
Software Mentions: 1
Published: almost 13 years ago
10.1371/journal.pgen.1006731
Natural variation of piRNA expression affects immunity to transposable elements
Cited by: 22
Author(s): Sergei Ryazansky, Elizaveta Radion, Anastasia Mironova, Natalia Akulenko, Yuri Abramov, Valeriya Morgunova, M. Yu. Kordyukova, Ivan Olovnikov, Alla Kalmykova
Software Mentions: 1
Published: over 7 years ago
10.1371/journal.pgen.1006551
An Arabidopsis Natural Epiallele Maintained by a Feed-Forward Silencing Loop between Histone and DNA
Cited by: 26
Author(s): Astrid Agorio, Simon Durand, Elisa Fiume, Cécile Brousse, Isabelle Gy, Matthieu Simon, Sarit Anava, Oded Rechavi, Olivier Loudet, Christine Camilleri, Nicolas Bouché
Software Mentions: 1
Published: almost 8 years ago
10.1371/journal.pgen.1006437
Phosphorylation of CBP20 Links MicroRNA to Root Growth in the Ethylene Response
Cited by: 28
Author(s): Fan Zhang, Likai Wang, Jae Yun Lim, Tae-Wook Kim, Youngjae Pyo, Sibum Sung, Chanseok Shin, Hong Qiao
Software Mentions: 1
Published: about 8 years ago
10.1371/journal.pgen.1002576
Polycomb-Like 3 Promotes Polycomb Repressive Complex 2 Binding to CpG Islands and Embryonic Stem Cell Self-Renewal
Cited by: 90
Author(s): Julie Hunkapiller, Yin Shen, Aaron A. Diaz, Gerard Cagney, David McCleary, Miguel Ramalho-Santos, Nevan J. Krogan, Bing Ren, Jun S. Song, Jeremy F. Reiter
Software Mentions: 1
Published: over 12 years ago
10.1186/s13073-021-00932-9
Genome-wide sequencing as a first-tier screening test for short tandem repeat expansions
Cited by: 23
Author(s): Indhu‐Shree Rajan‐Babu, Junran J. Peng, Readman Chiu, Patricia Birch, Madeline Couse, Colleen Guimond, Anna Lehman, Jill Mwenifumbo, Clara van Karnebeek, Jan M. Friedman, Shelin Adam, Christèle du Souich, Alison M Elliott, Anna Lehman, Jill Mwenifumbo, Tanya N. Nelson, Clara van Karnebeek, Jan M. Friedman, Chenkai Li, Arezoo Mohajeri, Egor Dolzhenko, Michael A. Eberle, İnanç Birol, Jan M. Friedman
Software Mentions: 1
Published: over 3 years ago
10.1186/s12864-016-2822-z
Network-based bioinformatics analysis of spatio-temporal RNA-Seq data reveals transcriptional programs underpinning normal and aberrant retinal development
Cited by: 6
Author(s): Devi Krishna Priya Karunakaran, Sahar Al Seesi, Abdul Rouf Banday, Marybeth Baumgartner, Anouk M. Olthof, Christopher Lemoine, Ion Măndoiu, Rahul N. Kanadia
Software Mentions: 1
Published: over 8 years ago
10.1371/journal.pgen.1006466
The Transcription Factor Nfatc2 Regulates β-Cell Proliferation and Genes Associated with Type 2 Diabetes in Mouse and Human Islets
Cited by: 39
Author(s): Mark P. Keller, Pradyut K. Paul, Mary E. Rabaglia, Donnie S. Stapleton, Kathryn L. Schueler, Aimee Teo Broman, Shuyun Isabella Ye, Ning Leng, Christopher Brandon, Elias Chaibub Neto, Christopher L. Plaisier, Shane P. Simonett, Melkam A. Kebede, Gloria Sheynkman, Milton M. Klein, Nitin S. Baliga, Lloyd M. Smith, Karl W. Broman, Brian S. Yandell, Christina Kendziorski, Alan D. Attie
Software Mentions: 1
Published: almost 8 years ago
10.1186/s13742-015-0068-3
Comparison of variations detection between whole-genome amplification methods used in single-cell resequencing
Cited by: 129
Author(s): Yong Hou, Kui Wu, Shi Xiao-li, Fuqiang Li, Liying Song, Huawei Wu, Michael Dean, Guibo Li, Shirley Tsang, Runze Jiang, Xiaolong Zhang, Bo Li, Geng Li, Niharika Bedekar, Na Lü, Guoyun Xie, Han Liang, Liao Chang, Ting Wang, Jianghao Chen, Yingrui Li, Xiuqing Zhang, Huanming Yang, Xun Xu, Ling Wang, Jun Wang
Software Mentions: 1
Published: over 9 years ago
10.1186/s12864-015-1835-3
MicroRNAs in the oriental fruit fly, Bactrocera dorsalis: extending Drosophilid miRNA conservation to the Tephritidae
Cited by: 11
Author(s): Bernarda Calla, Scott M. Geib
Software Mentions: 1
Published: about 9 years ago
10.1093/gigascience/giy053
Independent assessment and improvement of wheat genome sequence assemblies using Fosill jumping libraries
Cited by: 12
Author(s): Fu-Hao Lu, Neil McKenzie, George Kettleborough, Darren Heavens, Matt Clark, Michael W. Bevan
Software Mentions: 1
Published: over 6 years ago
10.1371/journal.pgen.1004277
DNA Repair Pathway Selection Caused by Defects in TEL1, SAE2, and De Novo Telomere Addition Generates Specific Chromosomal Rearrangement Signatures
Cited by: 19
Author(s): Christopher D. Putnam, Katielee Pallis, Tikvah K. Hayes, Richard D. Kolodner
Software Mentions: 1
Published: over 10 years ago
10.1371/journal.pcbi.1000598
An Abundance of Ubiquitously Expressed Genes Revealed by Tissue Transcriptome Sequence Data
Cited by: 773
Author(s): Daniel Ramsköld, Eric T. Wang, Christopher B. Burge, Rickard Sandberg
Software Mentions: 1
Published: almost 15 years ago
10.1371/journal.pcbi.1003030
Distinct Types of Disorder in the Human Proteome: Functional Implications for Alternative Splicing
Cited by: 61
Author(s): Recep Çolak, TaeHyung Kim, Magali Michaut, Mark Sun, Manuel Irimia, Jeremy Bellay, Chad L. Myers, Benjamin J. Blencowe, Philip M. Kim
Software Mentions: 1
Published: over 11 years ago
10.7554/eLife.13065
Spatial organization shapes the turnover of a bacterial transcriptome
Cited by: 132
Author(s): Jeffrey R. Moffitt, Shristi Pandey, Alistair N. Boettiger, Siyuan Wang, Xiaowei Zhuang
Software Mentions: 1
Published: over 8 years ago
10.1523/JNEUROSCI.1821-20.2020
<i>Tet1</i>Isoforms Differentially Regulate Gene Expression, Synaptic Transmission, and Memory in the Mammalian Brain
Cited by: 19
Author(s): Celeste B. Greer, Jeffrey G. Wright, Joscha Weiss, Roman M. Lazarenko, Sean P. Moran, Junqin Zhu, Keagan S. Chronister, Aiwu Jin, Andrew Kennedy, J. David Sweatt, Garrett A. Kaas
Software Mentions: 1
Published: almost 4 years ago
10.7554/eLife.10557
Discovery and validation of sub-threshold genome-wide association study loci using epigenomic signatures
Cited by: 97
Author(s): Xinchen Wang, Nathan R. Tucker, Gizem Rizki, Robert W. Mills, Peter H.L. Krijger, Elzo de Wit, Vidya Subramanian, Eric Bartell, Xinh Xinh Nguyen, Jiangchuan Ye, Jordan Leyton‐Mange, Elena Dolmatova, Pim van der Harst, Wouter de Laat, Patrick T. Ellinor, Christopher Newton‐Cheh, David J. Milan, M Kellis, Laurie A. Boyer
Software Mentions: 1
Published: over 8 years ago
10.1186/1471-2164-14-168
De-novo assembly and characterization of the transcriptome of Metschnikowia fructicola reveals differences in gene expression following interaction with Penicillium digitatumand grapefruit peel
Cited by: 66
Author(s): Vera Hershkovitz, Noa Sela, Leena Taha-Salaime, Jia Liu, G. Rafael, Clarita Kessler, Radi Aly, Maggie Levy, Michael Wisniewski, Samir Droby
Software Mentions: 1
Published: over 11 years ago
10.1186/s43008-019-0002-x
A multigene phylogeny toward a new phylogenetic classification of Leotiomycetes
Cited by: 118
Author(s): Peter R. Johnston, Luis Quijada, Chris Smith, Hans-Otto Baral, Tsuyoshi Hosoya, Christiane Baschien, Kadri Pärtel, Wen-Ying Zhuang, Danny Haelewaters, Park DuckChul, Steffen Carl, Francesc López-Giráldez, Zheng Wang, Jeffrey P. Townsend
Software Mentions: 1
Published: over 5 years ago
10.3390/insects11030161
First Report of Aleurocanthus spiniferus on Ailanthus altissima: Profiling of the Insect Microbiome and MicroRNAs
Cited by: 10
Author(s): Giovanni Bubici, Maria Isabella Prigigallo, Francesca Garganese, Francesco Nugnes, M. G. M. Jansen, Francesco Porcelli
Software Mentions: 1
Published: over 4 years ago
10.3390/insects12060533
Male-Biased microRNA Discovery in the Pea Aphid
Cited by: 3
Author(s): Xiaomi Liu, Erica L. Culbert, Jennifer A. Brisson
Software Mentions: 1
Published: over 3 years ago
10.1186/1471-2164-15-942
Characterizing the developmental transcriptome of the oriental fruit fly, Bactrocera dorsalis (Diptera: Tephritidae) through comparative genomic analysis with Drosophila melanogaster utilizing modENCODE datasets
Cited by: 36
Author(s): Scott M. Geib, Bernarda Calla, Brian E. Hall, Shaobin Hou, Nicholas C. Manoukis
Software Mentions: 1
Published: almost 11 years ago
10.1371/journal.pcbi.1002779
Bioinformatics for the Human Microbiome Project
Cited by: 74
Author(s): Dirk Gevers, Mihai Pop, Patrick D. Schloss, Curtis Huttenhower
Software Mentions: 1
Published: almost 12 years ago
10.1371/journal.pcbi.1006472
Ten quick tips for sharing open genomic data
Cited by: 8
Author(s): Anne V. Brown, Jacqueline Campbell, Teshale Assefa, David Grant, Rex T. Nelson, Nathan T. Weeks, Steven B. Cannon
Software Mentions: 1
Published: almost 6 years ago
10.1016/j.jbc.2021.100566
Nutrient availability regulates proline/alanine transporters in Trypanosoma brucei
Cited by: 5
Author(s): Alexander C. Haindrich, Viona Ernst, Arunasalam Naguleswaran, Quentin-Florian Oliveres, Isabel Roditi, Doris Rentsch
Software Mentions: 1
Published: almost 4 years ago
10.1111/jcmm.14252
5‐Hydroxymethylcytosine profiling from genomic and cell‐free DNA for colorectal cancers patients
Cited by: 17
Author(s): Ping Gao, Shengli Lin, Ming‐Yan Cai, Yan Zhu, Yanqun Song, Yi Sui, Jing Lin, Jiaxiuyu Liu, Xingyu Lu, Yun‐Shi Zhong, Yuehong Cui, Ping‐Hong Zhou
Software Mentions: 1
Published: over 5 years ago
10.1111/jcmm.15828
Decreased long non‐coding RNA lincFOXF1 indicates poor progression and promotes cell migration and metastasis in osteosarcoma
Cited by: 4
Author(s): Shu-Li Yang, Jian Chen, Bin Lv, Jun Zhang, Deli Li, Meng‐Yuan Huang, Yuan Li, Guoyong Yin
Software Mentions: 1
Published: about 4 years ago
10.1242/jcs.208066
Phosphorylation of the RNA binding protein Zfs1 modulates sexual differentiation in fission yeast
Cited by: 9
Author(s): Francisco J. Navarro, Probir Chakravarty, Paul Nurse
Software Mentions: 1
Published: almost 8 years ago
10.1371/journal.pcbi.1005480
MAGERI: Computational pipeline for molecular-barcoded targeted resequencing
Cited by: 35
Author(s): Mikhail Shugay, Andrew R. Zaretsky, Dmitry A. Shagin, Irina A. Shagina, Ivan A. Volchenkov, Andrey Shelenkov, Mikhail Lebedin, Dmitriy V. Bagaev, Sergey Lukyanov, Dmitriy M. Chudakov
Software Mentions: 1
Published: over 7 years ago
10.1186/2043-9113-2-21
Genome-wide Profiling of RNA splicing in prostate tumor from RNA-seq data using virtual microarrays
Cited by: 2
Author(s): Subhashini Srinivasan, Arun H. Patil, Mohit Verma, Jonathan Bingham, Srivatsan Raghunathan
Software Mentions: 1
Published: almost 13 years ago
10.3390/jcm4091798
Bioinformatic Interrogation of 5p-arm and 3p-arm Specific miRNA Expression Using TCGA Datasets
Cited by: 18
Author(s): Wei‐Ting Kuo, Ming-Wei Su, Yungling Leo Lee, Chien-Hsiun Chen, Chew-Wun Wu, Wen‐Liang Fang, Kai Huang, Wen-Chiao Lin
Software Mentions: 1
Published: about 9 years ago
10.1128/JCM.00104-18
Control of Artifactual Variation in Reported Intersample Relatedness during Clinical Use of a Mycobacterium tuberculosis Sequencing Pipeline
Cited by: 11
Author(s): David Wyllie, Nicholas D. Sanderson, Richard Myers, Tim Peto, Esther Robinson, Derrick W. Crook, E. Grace Smith, A Sarah Walker
Software Mentions: 1
Published: over 6 years ago
10.1128/JCM.00683-19
Whole-Genome Sequencing Reveals a Prolonged and Persistent Intrahospital Transmission of Corynebacterium striatum, an Emerging Multidrug-Resistant Pathogen
Cited by: 21
Author(s): Xuebing Wang, Haijian Zhou, Dongke Chen, Pengcheng Du, Ruiting Lan, Xiaotong Qiu, Xuexin Hou, Zhiguo Liu, Lina Sun, Shuai Xu, Xingzhao Ji, Heqiao Li, Dan Li, Jingshan Zhang, Hui Zeng, Zhenjun Li
Software Mentions: 1
Published: about 5 years ago
10.1093/jxb/eru193
Was low CO2 a driving force of C4 evolution: Arabidopsis responses to long-term low CO2 stress
Cited by: 51
Author(s): Yuanyuan Li, Jiajia Xu, Noor ul Haq, Hui Zhang, Xin‐Guang Zhu
Software Mentions: 1
Published: over 10 years ago