pypi: bowtie | Projects | Ecosyste.ms: Papers

10.1038/s41598-019-49886-4

The Human Papillomavirus (HPV) E1 protein regulates the expression of cellular genes involved in immune response
Cited by: 23
Author(s): Leonardo Josué Castro-Muñoz, Joaquín Manzo-Merino, J. Omar Muñoz-Bello, Leslie Olmedo-Nieva, Alberto Cedro‐Tanda, Luis Alfaro-Ruiz, Alfredo Hidalgo-Miranda, Vicente Madrid‐Marina, Marcela Lizano
Software Mentions: 2
Published: about 7 years ago

10.1038/s41598-019-51470-9

Transcriptome profiling of mouse samples using nanopore sequencing of cDNA and RNA molecules
Cited by: 77
Author(s): Camille Sessegolo, Corinne Cruaud, Corinne Da Silva, Audric Cologne, Marion Dubarry, Thomas Derrien, Vincent Lacroix, Jean‐Marc Aury
Software Mentions: 2
Published: about 7 years ago

10.1038/s41598-019-51984-2

Effects of codon optimization on coagulation factor IX translation and structure: Implications for protein and gene therapies
Cited by: 35
Author(s): Aikaterini Alexaki, Gaya Hettiarachchi, John C. Athey, Upendra Katneni, Vijaya L. Simhadri, Nobuko Hamasaki-Katagiri, Puja Nanavaty, Brian C. Lin, Kazuyo Takeda, Darón I. Freedberg, Dougald M. Monroe, Joseph R. McGill, Robert Peters, Jacob Kames, David D. Holcomb, Ryan Hunt, Zuben E. Sauna, Amy D. Gelinas, Nebojša Janjić, Michael DiCuccio, Haim Bar, Anton A. Komar, Chava Kimchi-Sarfaty
Software Mentions: 2
Published: about 7 years ago

10.1038/s41598-019-56030-9

Transcriptome analysis-identified long noncoding RNA CRNDE in maintaining endothelial cell proliferation, migration, and tube formation
Cited by: 6
Author(s): Matthew Moran, Xiangdong Cheng, Mohamed Sham Shihabudeen Haider Ali, Nishikant Wase, Nghi M. Nguyen, Wenchao Yang, Chi Zhang, Concetta C. DiRusso, Xinghui Sun
Software Mentions: 2
Published: almost 7 years ago

10.1038/s41598-020-59678-w

PDCD4 controls the G1/S-phase transition in a telomerase-immortalized epithelial cell line and affects the expression level and translation of multiple mRNAs
Cited by: 7
Author(s): Astrid Haas, Benedikt S. Nilges, Sebastian A. Leidel, Karl‐Heinz Klempnauer
Software Mentions: 2
Published: over 6 years ago

10.1038/s41598-020-73549-4

Assembly of the durian chloroplast genome using long PacBio reads
Cited by: 10
Author(s): Jeremy R. Shearman, Chutima Sonthirod, Chaiwat Naktang, Duangjai Sangsrakru, Thippawan Yoocha, Ratchanee Chatbanyong, Siriporn Vorakuldumrongchai, O. Chusri, Sithichoke Tangphatsornruang, Wirulda Pootakham
Software Mentions: 2
Published: about 6 years ago

10.1038/s41598-021-81637-2

Evaluation on reprogramed biological processes in transgenic maize varieties using transcriptomics and metabolomics
Cited by: 4
Author(s): Wei Fu, Pengyu Zhu, Mingnan Qu, Zhi Wang, Yongjiang Zhang, Feiwu Li, Shuifang Zhu
Software Mentions: 2
Published: almost 6 years ago

10.1038/s41598-021-89672-9

Osteocytes as main responders to low-intensity pulsed ultrasound treatment during fracture healing
Cited by: 18
Author(s): Tatsuya Shimizu, Naomasa Fujita, Kiyomi Tsuji‐Tamura, Yoshimasa Kitagawa, Toshiaki Fujisawa, Masato Tamura, Mari Sato
Software Mentions: 2
Published: over 5 years ago

10.1038/s41598-021-90270-y

Integrated RNA and miRNA sequencing analysis reveals a complex regulatory network of Magnolia sieboldii seed germination
Cited by: 4
Author(s): Mei Mei, Jun S. Wei, Wanfeng Ai, Lijie Zhang, Xiujun Lu
Software Mentions: 2
Published: over 5 years ago

10.1038/s41598-021-92832-6

Transcriptome analysis insight into ethylene metabolism and pectinase activity of apricot (Prunus armeniaca L.) development and ripening
Cited by: 1
Author(s): Min Xu, Weiquan Zhou, Geng WenJuan, Shirong Zhao, Yan Pan, Guoquan Fan, Shikui Zhang, Yatong Wang
Software Mentions: 2
Published: over 5 years ago

10.1038/s41598-021-95779-w

Comparison of gene expression in the red imported fire ant (Solenopsis invicta) under different temperature conditions
Cited by: 5
Author(s): Mohammad Vatanparast, Robert T. Puckett, Deuk‐Soo Choi, Youngjin Park
Software Mentions: 2
Published: about 5 years ago

10.1186/s40064-016-2902-1

Comparative profiling of differentially expressed microRNAs between the follicular and luteal phases ovaries of goats
Cited by: 10
Author(s): Long Zhu, Tao Chen, Menghua Sui, Chunyang Han, Fugui Fang, Yuehui Ma, Mingxing Chu, Xiaorong Zhang, Cuiyan Liu, Yinghui Ling
Software Mentions: 2
Published: over 10 years ago

10.1016/j.stemcr.2016.11.014

Cytosine-5 RNA Methylation Regulates Neural Stem Cell Differentiation and Motility
Cited by: 118
Author(s): Joana V. Flores, Lucía Cordero-Espinoza, Feride Oeztuerk-Winder, Amanda Andersson-Rolf, Tommaso Selmi, Sandra Blanco, Jignesh Tailor, Sabine Dietmann, Michaela Frye
Software Mentions: 2
Published: almost 10 years ago

10.1186/s13287-015-0116-z

Human bone marrow- and adipose-mesenchymal stem cells secrete exosomes enriched in distinctive miRNA and tRNA species
Cited by: 559
Author(s): S. Rubina Baglio, Koos Rooijers, Danijela Koppers-Lalić, Frederik J. Verweij, M Pérez Lanzón, Nicoletta Zini, B.A. Naaijkens, Francesca Perut, Hans W.M. Niessen, Nicola Baldini, D. Michiel Pegtel
Software Mentions: 2
Published: over 11 years ago

10.7150/thno.43577

Exercise protects proliferative muscle satellite cells against exhaustion via the Igfbp7-Akt-mTOR axis
Cited by: 24
Author(s): Zhe Chen, Lei Li, Weiru Wu, Zhilong Liu, Yongxiu Huang, Li Yang, Qing Luo, Jieping Chen, Yu Hou, Guanbin Song
Software Mentions: 2
Published: almost 7 years ago

10.3390/toxins12010041

Aberrant Expressional Profiling of Known MicroRNAs in the Liver of Silver Carp (Hypophthalmichthys molitrix) Following Microcystin-LR Exposure Based on samllRNA Sequencing
Cited by: 6
Author(s): Yiyi Feng, Xi Chen, Jing Ma, Bangjun Zhang, Xiaoyü Li
Software Mentions: 2
Published: almost 7 years ago

10.1101/2020.11.16.385278

High resolution profiling of pathways of escape for SARS-CoV-2 spike-binding antibodies
Cited by: 8
Author(s): Meghan Garrett, Jared Galloway, Helen Y. Chu, Hannah L. Itell, Caitlin I. Stoddard, Caitlin R Wolf, Jennifer K. Logue, Dylan McDonald, F. A. Matsen, Julie Overbaugh
Software Mentions: 2
Published: almost 6 years ago

10.1128/mBio.02027-20

Survey of Early-Diverging Lineages of Fungi Reveals Abundant and Diverse Mycoviruses
Cited by: 32
Author(s): Jillian M. Myers, Anne E. Bonds, Rebecca A. Clemons, Natasha Thapa, D. Rabern Simmons, Derreck Carter-House, Jericho Ortañez, P. Liu, Alejandro Miralles-Durán, Alessandro Desirò, Joyce E. Longcore, Gregory Bonito, Jason E. Stajich, J. W. Spatafora, Ying Chang, Luis M. Corrochano, Andrii P. Gryganskyi, Igor V. Grigoriev, Timothy Y. James
Software Mentions: 2
Published: about 6 years ago

10.1128/mBio.03649-20

Whole-Genome Transformation Promotes tRNA Anticodon Suppressor Mutations under Stress
Cited by: 2
Author(s): Quinten Deparis, Jorge Duitama, María R. Foulquié-Moreno, Johan M. Thevelein
Software Mentions: 2
Published: over 5 years ago

10.1128/mSphere.00855-20

Structured RNA Contaminants in Bacterial Ribo-Seq
Cited by: 15
Author(s): Brayon J. Fremin, Ami S. Bhatt
Software Mentions: 2
Published: about 6 years ago

10.1128/mSystems.00673-19

Selection Is a Significant Driver of Gene Gain and Loss in the Pangenome of the Bacterial Genus <i>Sulfurovum</i> in Geographically Distinct Deep-Sea Hydrothermal Vents
Cited by: 33
Author(s): Alief Moulana, R. Anderson, Caroline S. Fortunato, Julie A. Huber
Software Mentions: 2
Published: over 6 years ago

10.1128/mSystems.01078-20

Complementary Roles of Wood-Inhabiting Fungi and Bacteria Facilitate Deadwood Decomposition
Cited by: 61
Author(s): Vojtěch Tláskal, Vendula Brabcová, Tomáš Větrovský, Mayuko Jomura, Rubén López-Mondéjar, Lummy Maria Oliveira Monteiro, J. Saraiva, Zander Rainier Human, Tomáš Cajthaml, Ulisses Nunes da Rocha, Petr Baldrián
Software Mentions: 2
Published: over 5 years ago

10.1128/mSystems.00704-21

Identification and Differentiation of Pseudomonas Species in Field Samples Using an <i>rpoD</i> Amplicon Sequencing Methodology
Cited by: 9
Author(s): Jonas Greve Lauritsen, Morten Lindqvist Hansen, Pernille Kjersgaard Bech, Lars Jelsbak, Lone Gram, Mikael Lenz Strube
Software Mentions: 2
Published: about 5 years ago

10.1093/hmg/ddy405

Dynamic transcriptomic analysis reveals suppression of PGC1α/ERRα drives perturbed myogenesis in facioscapulohumeral muscular dystrophy
Cited by: 46
Author(s): Christopher R. S. Banerji, Maryna Panamarova, Johanna Prüller, Nicolas Figeac, Husam Hebaishi, Efthymios Fidanis, Alka Saxena, Julian Contet, Sabrina Sacconi, Simone Severini, Peter S. Zammit
Software Mentions: 2
Published: almost 8 years ago

10.1155/2015/527054

Genome-Wide Identification of Genes Probably Relevant to the Uniqueness of Tea Plant (Camellia sinensis) and Its Cultivars
Cited by: 2
Author(s): Yan Wei, Jing Wang, Youxiang Zhou, Mingming Zhao, Yan Gong, Hua Ding, Lijun Peng, HU Ding-jin
Software Mentions: 2
Published: almost 12 years ago

10.1038/s41388-018-0530-7

Acetylation of AGO2 promotes cancer progression by increasing oncogenic miR-19b biogenesis
Cited by: 50
Author(s): Hailong Zhang, Yanli Wang, Jinzhuo Dou, Yanmin Guo, Jianfeng He, Lian Li, Xiaojia Liu, Ran Chen, Rong Deng, Jian Huang, Ruiyu Xie, Xian Zhao, Jianxiu Yu
Software Mentions: 2
Published: about 8 years ago

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

10.1371/journal.pone.0073455

Detection of Bacillus anthracis DNA in Complex Soil and Air Samples Using Next-Generation Sequencing
Cited by: 25
Author(s): Nicholas A. Be, James B. Thissen, Shea N. Gardner, Kevin McLoughlin, Viacheslav Y. Fofanov, Heather Koshinsky, Sally R. Ellingson, Thomas Brettin, Paul J. Jackson, Crystal Jaing
Software Mentions: 1
Published: about 13 years ago

10.1093/humrep/dew056

Depolarization of sperm membrane potential is a common feature of men with subfertility and is associated with low fertilization rate at IVF
Cited by: 46
Author(s): Sean G. Brown, Stephen J. Publicover, Steven A. Mansell, Polina V. Lishko, Hannah Williams, Mythili Ramalingam, Stuart M. Wilson, Christopher L.R. Barratt, Keith A. Sutton, Sarah Martins da Silva
Software Mentions: 1
Published: over 10 years ago

10.1371/journal.pone.0008632

Gene Expression Profiles Deciphering Rice Phenotypic Variation between Nipponbare (Japonica) and 93-11 (Indica) during Oxidative Stress
Cited by: 52
Author(s): Fengxia Liu, Wenying Xu, Qiang Wang, Zhenghai Zhang, Zhuo Xing, Lubin Tan, Chao Di, Dongxia Yao, Chunchao Wang, Yuanjun Tan, Yanbin Hong, Yi Ling, Chuanqing Sun, Yongbiao Xue, Zhen Su
Software Mentions: 1
Published: almost 17 years ago

10.1371/journal.pone.0042030

A Transgenic Transcription Factor (TaDREB3) in Barley Affects the Expression of MicroRNAs and Other Small Non-Coding RNAs
Cited by: 35
Author(s): Michael Hackenberg, Bu‐Jun Shi, Perry Gustafson, Peter Langridge
Software Mentions: 1
Published: over 14 years ago

10.1186/s12870-019-2056-8

Overexpression of rice jacalin-related mannose-binding lectin (OsJAC1) enhances resistance to ionizing radiation in Arabidopsis
Cited by: 12
Author(s): In‐Ha Jung, Joon-Woo Ahn, Sera Jung, Jin-Woo Hwang, Min Jeong Hong, Hong‐Il Choi, Jin-Baek Kim
Software Mentions: 1
Published: almost 7 years ago

10.1371/journal.pone.0199866

Genetics instability of wtAAV2 genome and AAV promoter activities in the Baculovirus/Sf9 cells system
Cited by: 5
Author(s): Adrien Savy, Minna U. Kaikkonen, Adrien Léger, Yohann Dickx, Lionel Galibert, Otto‐Wilhelm Merten
Software Mentions: 1
Published: over 8 years ago

10.1186/s12860-021-00381-7

An alternative D. melanogaster 7SK snRNP
Cited by: 1
Author(s): Duy Nguyen, Nicolas Buisine, Olivier Fayol, Annemieke A. Michels, Olivier Bensaude, David H. Price, Patricia Uguen
Software Mentions: 1
Published: about 5 years ago

10.1371/journal.pone.0108411

Next-Generation Sequencing Analysis of MiRNA Expression in Control and FSHD Myogenesis
Cited by: 17
Author(s): Veronica Colangelo, Stéphanie François, Giulia Soldà, Raffaella Picco, Francesca Roma, Enrico Ginelli, Raffaella Meneveri
Software Mentions: 1
Published: about 12 years ago

10.1371/journal.pone.0110163

Integrated microRNA and mRNA Transcriptome Sequencing Reveals the Potential Roles of miRNAs in Stage I Endometrioid Endometrial Carcinoma
Cited by: 35
Author(s): Hanzhen Xiong, Qiulian Li, Shaoyan Liu, Fang Wang, Zhongtang Xiong, Juan Chen, Hui Chen, Yuexin Yang, Xuexian Tan, Qiaojie Luo, Juan Peng, Guohong Xiao, Qingping Jiang
Software Mentions: 1
Published: about 12 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.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

10.1371/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

10.1186/s12866-020-02061-6

Host cell response and distinct gene expression profiles at different stages of Chlamydia trachomatis infection reveals stage-specific biomarkers of infection
Cited by: 10
Author(s): Emmanuel Enoch Dzakah, Liping Huang, Yaohua Xue, Wei Shuai, Xiaolin Wang, Hongliang Chen, Jingwei Shui, Foster Kyei, Farooq Rashid, Heping Zheng, Bing Yang, Shixing Tang
Software Mentions: 1
Published: almost 6 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.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

10.1371/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

10.1186/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 15 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

10.1371/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

10.1186/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 5 years ago

10.7150/ijms.50248

MicroRNA expression profile of Lacrimal Glands in rabbit autoimmune dacryoadenitis model
Cited by: 2
Author(s): Bo Liu, Lu Zhao, Yankai Wei, Sisi Chen, Lingzhai Bian, Di Guo, Min Gao, Hong Nian
Software Mentions: 1
Published: almost 7 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

10.1186/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 11 years ago

10.3892/ijmm.2014.1973

Profiling of alternative polyadenylation sites in luminal B breast cancer using the SAPAS method
Cited by: 6
Author(s): Xinmei Wang, Mingyue Li, Yingchun Yin, Liang Li, Youshan Tao, Dengguo Chen, Jianzhao Li, Hongmei Han, Zhenbo Hou, Baohua Zhang, Yu Ding, Haiyan Cui, Hengming Zhang
Software Mentions: 1
Published: about 12 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 8 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

10.1371/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

10.1371/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

10.1186/1755-8794-8-S2-S14

PDEGEM: Modeling non-uniform read distribution in RNA-Seq data
Cited by: 1
Author(s): Yuchao Xia, Fugui Wang, Minping Qian, Zhaohui Qin, Minghua Deng
Software Mentions: 1
Published: over 11 years ago

10.1186/s12864-015-2025-z

Combined ultra-low input mRNA and whole-genome sequencing of human embryonic stem cells
Cited by: 4
Author(s): Florián Mertes, Björn Lichtner, Heiner Kuhl, Mirjam Blattner, Jörg Otte, Wasco Wruck, Bernd Timmermann, Hans Lehrach, James Adjaye
Software Mentions: 1
Published: almost 11 years ago

10.1186/1471-2164-14-S1-S2

A computational approach for identifying microRNA-target interactions using high-throughput CLIP and PAR-CLIP sequencing
Cited by: 46
Author(s): Chih Hung Chou, Feng Lin, Min Te Chou, Sheng Da Hsu, Tzu Hao Chang, Shun Long Weng, Sirjana Shrestha, Chiung Chih Hsiao, Jui Hung Hung, Hsien Da Huang
Software Mentions: 1
Published: almost 14 years ago

10.1186/s12859-017-1801-y

Identification of genome-wide non-canonical spliced regions and analysis of biological functions for spliced sequences using Read-Split-Fly
Cited by: 5
Author(s): Yongsheng Bai, Jeff Kinne, Lizhong Ding, Ethan Rath, Aaron R. Cox, Siva Dharman Naidu
Software Mentions: 1
Published: about 9 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 7 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 6 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 5 years ago

10.1186/1471-2105-14-31

Estimation of data-specific constitutive exons with RNA-Seq data
Cited by: 6
Author(s): Ellis Patrick, Michael Buckley, Jean Yee Hwa Yang
Software Mentions: 1
Published: almost 14 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

10.1371/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

10.1016/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 6 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 7 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 6 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 10 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

10.1186/2043-9113-2-21

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 15 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 11 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 8 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 7 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 12 years ago

10.1093/jxb/erx117

Enhancing faba bean (Vicia faba L.) genome resources
Cited by: 33
Author(s): James W. Cooper, Michael Wilson, Martijn F.L. Derks, Sandra Smit, K. Kunert, Christopher A. Cullis, Christine H. Foyer
Software Mentions: 1
Published: over 9 years ago

10.1186/1471-2105-13-S6-S4

Biases in read coverage demonstrated by interlaboratory and interplatform comparison of 117 mRNA and genome sequencing experiments
Cited by: 7
Author(s): Ekaterina E. Khrameeva, Mikhail S. Gelfand
Software Mentions: 1
Published: over 14 years ago

10.1371/journal.ppat.1004130

Cathepsin-L Can Resist Lysis by Human Serum in Trypanosoma brucei brucei
Cited by: 31
Author(s): Sam Alsford, Rachel B. Currier, José Afonso Guerra-Assunção, Taane G. Clark, David Horn
Software Mentions: 1
Published: over 12 years ago

10.1371/journal.ppat.1004230

A Virulent Strain of Deformed Wing Virus (DWV) of Honeybees (Apis mellifera) Prevails after Varroa destructor-Mediated, or In Vitro, Transmission
Cited by: 276
Author(s): Eugene V. Ryabov, Graham R. Wood, Jessica Fannon, Jonathan D. Moore, James C. Bull, Dave Chandler, Andrew Mead, Nigel John Burroughs, David J. Evans
Software Mentions: 1
Published: over 12 years ago

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