Projects: pypi: browser
https://packages.ecosyste.ms/registries/pypi.org/packages/browser
A package to prevent Dependency Confusion attacks against Yandex.
2 versions
Latest release: over 2 years ago
2 dependent packages
Enhanced Analysis
Repository Activity:
Repository Owner:
Francis Tseng (user)
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Science Score: 65/100
Starting Score: 100 points
Penalties:
-
-10
PyPI ecosystem
General-purpose ecosystem -
-15
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No scientific terms found in keywords/classifiers -
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No science terms in description
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Very Likely Science (65)
Papers Mentioning browser 2,125
10.7554/eLife.38340
The origin of the odorant receptor gene family in insectsCited by: 88
Author(s): Philipp Brand, Hugh M. Robertson, Wei Lin, Ratnasri Pothula, William E. Klingeman, Juan Luís Jurat-Fuentes, Brian R. Johnson
Software Mentions: 4
Published: over 7 years ago
10.1186/s13059-015-0671-8
An integrative analysis of post-translational histone modifications in the marine diatom Phaeodactylum tricornutumCited by: 76
Author(s): Alaguraj Veluchamy, Achal Rastogi, Xin Lin, Bérangère Lombard, Omer Murik, Y. Thomas, Florent Dingli, Máximo Rivarola, Sandra Ott, Xinyue Liu, Yan Sun, Pablo D. Rabinowicz, James S. McCarthy, Andrew E. Allen, Damarys Loew, Chris Bowler, Leïla Tirichine
Software Mentions: 4
Published: over 10 years ago
10.1038/s41422-020-0281-1
Refined spatial temporal epigenomic profiling reveals intrinsic connection between PRDM9-mediated H3K4me3 and the fate of double-stranded breaksCited by: 34
Author(s): Yao Chen, Ruitu Lyu, Bowen Rong, Yuxuan Zheng, Zhen Lin, Ruofei Dai, Xi Zhang, Nannan Xie, Siqing Wang, Fuchou Tang, Fei Lan, Ming-Han Tong
Software Mentions: 4
Published: over 5 years ago
10.7554/eLife.29005
Conserved noncoding transcription and core promoter regulatory code in early Drosophila developmentCited by: 10
Author(s): Philippe Batut, T Gingeras
Software Mentions: 4
Published: almost 8 years ago
10.7554/eLife.15614
Hypothalamic transcriptomes of 99 mouse strains reveal trans eQTL hotspots, splicing QTLs and novel non-coding genesCited by: 35
Author(s): Yehudit Hasin-Brumshtein, Khan Ah, Farhad Hormozdiari, Calvin Pan, Brian W. Parks, Vladislav Petyuk, Paul Piehowski, Anneke Brümmer, Matteo Pellegrini, Xinshu Xiao, Eleazar Eskin, Richard Smith, Aldons J. Lusis, Desmond J. Smith
Software Mentions: 4
Published: about 9 years ago
10.1186/s13148-021-01127-0
DNA methylation analysis reveals epimutation hotspots in patients with dilated cardiomyopathy-associated laminopathiesCited by: 7
Author(s): Julien Morival, Halida P. Widyastuti, Christopher Nguyen, Michael V. Zaragoza, Timothy L. Downing
Software Mentions: 4
Published: over 4 years ago
10.7554/eLife.50895
Partial loss of CFIm25 causes learning deficits and aberrant neuronal alternative polyadenylationCited by: 23
Author(s): Callison E Alcott, Hari Krishna Yalamanchili, Ping Ji, Meike E van der Heijden, Alexander B. Saltzman, Nathan D. Elrod, Lin Ai, Mei Leng, Bhoomi Bhatt, Shuang Hao, Qi Wang, Afaf Saliba, Jianrong Tang, Anna Malovannaya, Eric J. Wagner, Zhandong Liu, Huda Y. Zoghbi
Software Mentions: 4
Published: over 5 years ago
10.7554/eLife.04235
Polycomb- and REST-associated histone deacetylases are independent pathways toward a mature neuronal phenotypeCited by: 43
Author(s): James C. McGann, Jon A. Oyer, Saurabh Garg, Huilan Yao, Jun Li, Xin Feng, Lujian Liao, John R. Yates, Gail Mandel
Software Mentions: 4
Published: about 11 years ago
10.1186/gb-2011-12-2-r16
Genomewide characterization of non-polyadenylated RNAsCited by: 358
Author(s): Li Yang, Michael O. Duff, Brenton R. Graveley, Gordon G. Carmichael, Lingling Chen
Software Mentions: 4
Published: almost 15 years ago
10.7554/eLife.47835
Epigenetic silencing of a multifunctional plant stress regulatorCited by: 25
Author(s): Mark Zander, Björn C. Willige, Yiping He, Thu Anh Nguyen, Amber E. Langford, Ramlah Nehring, Elizabeth D. Howell, Robert B. McGrath, Anna Bartlett, Rosa Castanon, Joseph R. Nery, Huaming Chen, Zhuzhu Zhang, Florian Jupe, Anna N. Stepanova, Robert J. Schmitz, Mathew G. Lewsey, Joanne Chory, Joseph R. Ecker
Software Mentions: 4
Published: about 6 years ago
10.1016/j.celrep.2018.07.026
Fine-Tuning Mybl2 Is Required for Proper Mesenchymal-to-Epithelial Transition during Somatic ReprogrammingCited by: 16
Author(s): Carl Ward, Giacomo Volpe, Pierre Cauchy, Anetta Ptasińska, Ruba Almaghrabi, Daniel Blakemore, Monica Nafria, Doris Kestner, Jon Frampton, George J. Murphy, Yosef Buganim, Keisuke Kaji, Paloma García
Software Mentions: 4
Published: over 7 years ago
10.7554/eLife.08904
Complex transcriptional regulation and independent evolution of fungal-like traits in a relative of animalsCited by: 57
Author(s): Alex de Mendoza, Hiroshi Suga, Joan Permanyer, Manuel Irimia, Iñaki Ruiz‐Trillo
Software Mentions: 4
Published: about 10 years ago
10.7554/eLife.43922
Dynamic repression by BCL6 controls the genome-wide liver response to fasting and steatosisCited by: 38
Author(s): Meredith A Sommars, Krithika Ramachandran, Madhavi D. Senagolage, Christopher R. Futtner, Derrik M Germain, Amanda L. Allred, Yasuhiro Omura, Ilya Bederman, Grant D. Barish
Software Mentions: 4
Published: over 6 years ago
10.1186/gb-2014-15-2-r21
Genome-wide analysis links emerin to neuromuscular junction activity in Caenorhabditis elegansCited by: 46
Author(s): Cristina González-Aguilera, Kohta Ikegami, Cristina de la Cruz Ayuso, Alberto de Luis, María Íñiguez, Juan Cabello, Jason D. Lieb, Peter Askjaer
Software Mentions: 4
Published: almost 12 years ago
10.7554/eLife.62438
Regulatory roles of Escherichia coli 5' UTR and ORF-internal RNAs detected by 3' end mappingCited by: 52
Author(s): Philip P. Adams, Gabriele Baniulyte, Caroline Esnault, Kavya Chegireddy, Navjot Singh, Molly Monge, Ryan Dale, Gisela Storz, Joseph T. Wade
Software Mentions: 4
Published: almost 5 years ago
10.1186/s12915-015-0119-3
Distinct genetic architecture underlies the emergence of sleep loss and prey-seeking behavior in the Mexican cavefishCited by: 87
Author(s): Masato Yoshizawa, Beatriz G. Robinson, Erik R. Duboué, Pavel Mašek, James B. Jaggard, Kelly E. O’Quin, Richard Borowsky, William R. Jeffery, Alex C. Keene
Software Mentions: 4
Published: over 10 years ago
10.1186/1471-2164-14-S8-S3
QChIPat: a quantitative method to identify distinct binding patterns for two biological ChIP-seq samples in different experimental conditionsCited by: 28
Author(s): Bin Liu, Jimmy Yi, Aishwarya Sv, Xun Lan, Yiyi Ma, Tim H.M. Huang, Gustavo Leone, Victor X. Jin
Software Mentions: 4
Published: almost 12 years ago
10.1186/s13072-019-0286-5
BRD4 bimodal binding at promoters and drug-induced displacement at Pol II pause sites associates with I-BET sensitivityCited by: 20
Author(s): Pierre Khoueiry, Aoife Ward Gahlawat, Massimo Petretich, Anne-Marie Michon, Daniel F. Simola, Enid Y.N. Lam, Eileen E. M. Furlong, Vladimı́r Beneš, Mark A. Dawson, Rab K. Prinjha, Gerard Drewes, Paola Grandi
Software Mentions: 4
Published: over 6 years ago
10.1186/s12864-015-1374-y
Sequencing, identification and mapping of primed L1 elements (SIMPLE) reveals significant variation in full length L1 elements between individualsCited by: 29
Author(s): Vincent A. Streva, Vallmer E Jordan, Sara B. Linker, Dale J. Hedges, Prescott L. Deininger
Software Mentions: 4
Published: over 10 years ago
10.7717/peerj.2056
SigmoID: a user-friendly tool for improving bacterial genome annotation through analysis of transcription control signalsCited by: 9
Author(s): Yevgeny Nikolaichik, Aliaksandr U. Damienikan
Software Mentions: 4
Published: over 9 years ago
10.1186/1471-2105-12-447
OmniMapFree: A unified tool to visualise and explore sequenced genomesCited by: 12
Author(s): J. F. Antoniw, Andrew M Beacham, Tyler Baldwin, Martin Urban, J. J. Rudd, K. E. Hammond‐Kosack
Software Mentions: 4
Published: almost 14 years ago
10.1002/mgg3.1346
Dysregulated expression of androgen metabolism genes and genetic analysis in hypospadiasCited by: 7
Author(s): Zhongzhong Chen, Xiaoling Lin, Yaping Wang, Hua Xie, Fang Chen
Software Mentions: 4
Published: over 5 years ago
10.1186/1471-2164-15-539
ChIPseek, a web-based analysis tool for ChIP dataCited by: 59
Author(s): Ting-Wen Chen, Hsin Pai Li, Chi-Ching Lee, Ruei Chi Gan, Po-Jung Huang, Timothy Wu, Cheng Yang Lee, Ian Yi‐Feng Chang, Petrus Tang
Software Mentions: 4
Published: over 11 years ago
10.3389/fcell.2018.00020
Improved circRNA Identification by Combining Prediction AlgorithmsCited by: 123
Author(s): Thomas B. Hansen
Software Mentions: 4
Published: over 7 years ago
10.1186/1471-2164-11-50
Integrating multiple genome annotation databases improves the interpretation of microarray gene expression dataCited by: 17
Author(s): Jun Yin, Sarah McLoughlin, Ian B. Jeffery, Antonino Glaviano, Breandán N. Kennedy, Desmond G. Higgins
Software Mentions: 4
Published: almost 16 years ago
10.1186/s12943-019-1115-y
LINC02273 drives breast cancer metastasis by epigenetically increasing AGR2 transcriptionCited by: 118
Author(s): Bingqiu Xiu, Yayun Chi, Lei Liu, Weiru Chi, Qi Zhang, Jiajian Chen, Rong Guo, Jingjing Si, Lun Li, Jian Xue, Zhi‐Ming Shao, Zhao-Hui Wu, Shenglin Huang, Jiong Wu
Software Mentions: 4
Published: almost 6 years ago
10.3389/fendo.2021.679756
Pre-Menopausal Women With Breast Cancers Having High AR/ER Ratios in the Context of Higher Circulating Testosterone Tend to Have Poorer OutcomesCited by: 5
Author(s): Savitha Rajarajan, Aruna Korlimarla, A. Alexander, C E Anupama, Rakesh Ramesh, B S Srinath, T.S. Sridhar, Jyothi S Prabhu
Software Mentions: 4
Published: over 4 years ago
10.1242/dev.175265
A gene expression atlas of embryonic neurogenesis in <i>Drosophila</i> reveals complex spatiotemporal regulation of lncRNAsCited by: 21
Author(s): Alexandra L. McCorkindale, Philipp Wahle, Irwin Jungreis, Peter Menzel, Chinmay Shukla, Rúben Lopes Pereira Abreu, Rafael A. Irizarry, Irmtraud M. Meyer, M Kellis, Robert P. Zinzen
Software Mentions: 4
Published: over 6 years ago
10.1093/database/bax039
GenomeHubs: simple containerized setup of a custom Ensembl database and web server for any speciesCited by: 14
Author(s): Richard Challis, Sujai Kumar, Lewis Stevens, Mark Blaxter
Software Mentions: 4
Published: almost 9 years ago
10.18632/aging.202365
Transcriptomic characterization reveals prognostic molecular signatures of sorafenib resistance in hepatocellular carcinomaCited by: 7
Author(s): Wei Yuan, Ran Tao, Da Huang, Weiming Yan, Shen Gao, Qin Ning
Software Mentions: 4
Published: almost 5 years ago
10.1186/1471-2164-15-631
Analysis of stranded information using an automated procedure for strand specific RNA sequencingCited by: 29
Author(s): Bárður Sigurgeirsson, Olof Emanuelsson, Joakim Lundeberg
Software Mentions: 4
Published: over 11 years ago
10.1186/1471-2164-11-74
Automated design of genomic Southern blot probesCited by: 6
Author(s): Mike D. R. Croning, David Fricker, Noboru H. Komiyama, Seth G. N. Grant
Software Mentions: 4
Published: almost 16 years ago
10.1186/s12859-020-3386-0
GsmPlot: a web server to visualize epigenome data in NCBICited by: 2
Author(s): Jia Li, Yue Yin, Mutian Zhang, Jie Cui, Zhenhai Zhang, Zhiyong Zhang, Deqiang Sun
Software Mentions: 4
Published: over 5 years ago
10.1186/s13100-021-00235-1
Genomic properties of variably methylated retrotransposons in mouseCited by: 13
Author(s): Jessica L. Elmer, Amir D. Hay, Noah J. Kessler, Tessa M. Bertozzi, Eve Ainscough, Anne C. Ferguson-Smith
Software Mentions: 4
Published: over 4 years ago
10.1093/database/bau076
APADB: a database for alternative polyadenylation and microRNA regulation eventsCited by: 88
Author(s): Sören Müller, Lukas Rycak, Fabian Afonso-Grunz, Peter Winter, Adam M. Zawada, Ewa Damrath, Jessica Scheider, Juliane Schmäh, Ina Koch, Günter Kahl, Björn Rotter
Software Mentions: 4
Published: over 11 years ago
10.3389/fgene.2019.00306
Chromatin State-Based Analysis of Epigenetic H3K4me3 Marks of Arabidopsis in Response to Dark StressCited by: 13
Author(s): Hengyu Yan, Yue Liu, Kang Zhang, Jakyoung Song, Wenying Xu, Zhen Su
Software Mentions: 4
Published: over 6 years ago
10.1186/s12859-020-03565-8
ELIXIR-IT HPC@CINECA: high performance computing resources for the bioinformatics communityCited by: 22
Author(s): Tiziana Castrignanò, Silvia Gioiosa, Tiziano Flati, Mirko Cestari, Ernesto Picardi, Matteo Chiara, Maddalena Fratelli, Stefano Amente, Marco Cirilli, M. A. Tangaro, Giovanni Chillemi, Graziano Pesole, Federico Zambelli
Software Mentions: 4
Published: over 5 years ago
10.1371/journal.pone.0098122
A Bayesian Method to Incorporate Hundreds of Functional Characteristics with Association Evidence to Improve Variant PrioritizationCited by: 30
Author(s): Sarah A. Gagliano, Michael R. Barnes, Michael E. Weale, Jo Knight
Software Mentions: 4
Published: over 11 years ago
10.1186/s12864-019-5605-5
Genome-wide association studies targeting the yield of extraembryonic fluid and production traits in Russian White chickensCited by: 20
Author(s): Andrei A. Kudinov, Natalia V. Dementieva, О.В. Митрофанова, Olga I. Stanishevskaya, Е.С. Федорова, Tatiana A. Larkina, Arina I Mishina, Kirill Plemyashov, Darren K. Griffin, Michael N Romanov
Software Mentions: 4
Published: over 6 years ago
10.1186/s13075-015-0677-3
Use of RNA sequencing to evaluate rheumatic disease patientsCited by: 23
Author(s): Ευγενία Γιαννοπούλου, Olivier Elemento, Lionel B. Ivashkiv
Software Mentions: 4
Published: over 10 years ago
10.1371/journal.pone.0021495
MicroRNA Expression Profiling Reveals MiRNA Families Regulating Specific Biological Pathways in Mouse Frontal Cortex and HippocampusCited by: 70
Author(s): Juuso Juhila, Tessa Sipilä, Katherine Icay, Daniel Nicorici, Pekka Ellonen, Aleksi Kallio, Eija Korpelainen, Dario Greco, Iiris Hovatta
Software Mentions: 4
Published: over 14 years ago
10.3389/fgene.2016.00075
Integrated Systems for NGS Data Management and Analysis: Open Issues and Available SolutionsCited by: 35
Author(s): Valerio Bianchi, Arnaud Céol, Alessandro G. E. Ogier, Stefano de Pretis, Eugenia Galeota, Kamal Kishore, Pranami Bora, Ottavio Croci, Stefano Campaner, Bruno Amati, Marco J. Morelli, Mattia Pelizzola
Software Mentions: 4
Published: over 9 years ago
10.1371/journal.pone.0140829
Genomics Virtual Laboratory: A Practical Bioinformatics Workbench for the CloudCited by: 99
Author(s): Enis Afgan, Clare Sloggett, Nuwan Goonasekera, Igor V. Makunin, Derek Benson, Mark L. Crowe, Simon Gladman, Yousef Kowsar, Michael Pheasant, Ron Horst, Andrew Lonie
Software Mentions: 4
Published: about 10 years ago
10.1186/s12864-021-07731-x
Exposure to hypoxia causes stress erythropoiesis and downregulates immune response genes in spleen of miceCited by: 16
Author(s): Haijing Wang, Daoxin Liu, Pengfei Song, Feng Jiang, Xiaowei Chi, Tongzuo Zhang
Software Mentions: 4
Published: over 4 years ago
10.26508/lsa.202000944
In utero exposure to chlordecone affects histone modifications and activates LINE-1 in cord bloodCited by: 6
Author(s): Louis Legoff, Shereen Cynthia D’Cruz, Katia Bouchekhchoukha, Christine Monfort, Christian Jaulin, Luc Multigner, Fátima Smagulova
Software Mentions: 4
Published: over 4 years ago
10.1038/s41598-017-06200-4
Associating transcription factors and conserved RNA structures with gene regulation in the human brainCited by: 12
Author(s): Nikolai Hecker, Stefan E. Seemann, Asli Silahtaroglu, Walter L. Ruzzo, Jan Gorodkin
Software Mentions: 4
Published: over 8 years ago
10.1186/1471-2105-8-456
The Firegoose: two-way integration of diverse data from different bioinformatics web resources with desktop applicationsCited by: 33
Author(s): J. Christopher Bare, Paul Shannon, Amy K. Schmid, Nitin S. Baliga
Software Mentions: 4
Published: almost 18 years ago
10.1186/1471-2164-12-S3-S9
UASIS: Universal Automatic SNP Identification SystemCited by: 5
Author(s): Danny Chiang Choon Poo, Shaojiang Cai, James T. L. Mah
Software Mentions: 4
Published: almost 15 years ago
10.1371/journal.pone.0024542
Comparative Analysis of Serine/Arginine-Rich Proteins across 27 Eukaryotes: Insights into Sub-Family Classification and Extent of Alternative SplicingCited by: 62
Author(s): Dale N. Richardson, Mark F. Rogers, Adam Labadorf, Asa Ben-Hur, Hui Guo, Andrew H. Paterson, Anireddy S. N. Reddy
Software Mentions: 4
Published: about 14 years ago
10.1155/2017/8932583
An Integrative Developmental Genomics and Systems Biology Approach to Identify an In Vivo Sox Trio-Mediated Gene Regulatory Network in Murine EmbryosCited by: 9
Author(s): Wenqing Jean Lee, Satadal Chatterjee, Sook Peng Yap, Siew Lan Lim, Xing Xing, Petra Kraus, Wenjie Sun, Xiaoming Hu, V. Sivakamasundari, Hsiao Yun Chan, Prasanna R. Kolatkar, Shyam Prabhakar, Thomas Lufkin
Software Mentions: 4
Published: almost 9 years ago
10.1186/s12864-020-07100-0
Comparative genomics and community curation further improve gene annotations in the nematode Pristionchus pacificusCited by: 16
Author(s): Marina Athanasouli, Hanh Witte, Christian Weiler, Tobias Loschko, Gabi Eberhardt, Ralf J. Sommer, Christian Rödelsperger
Software Mentions: 4
Published: about 5 years ago
10.18632/oncotarget.9535
Alterations of androgen receptor-regulated enhancer RNAs (eRNAs) contribute to enzalutamide resistance in castration-resistant prostate cancerCited by: 35
Author(s): Jingwen Zhao, Yu Zhao, Liguo Wang, Jun Zhang, Jeffrey Karnes, Manish Kohli, Guixia Wang, Haojie Huang
Software Mentions: 4
Published: over 9 years ago
10.1007/s00401-019-02109-6
Loss of UGP2 in brain leads to a severe epileptic encephalopathy, emphasizing that bi-allelic isoform-specific start-loss mutations of essential genes can cause genetic diseasesCited by: 37
Author(s): Elena Perenthaler, Anita Nikoncuk, Soheil Yousefi, Woutje M. Berdowski, Maysoon Alsagob, Ivan Čapo, Herma C. van der Linde, Paul van den Berg, Edwin H. Jacobs, Darija Putar, Mehrnaz Ghazvini, Eleonora Aronica, Wilfred F. J. van IJcken, Walter G. de Valk, Evita Medici-van den Herik, Marjon van Slegtenhorst, Lauren Brick, Mariya Kozenko, Jennefer N. Kohler, Jonathan A. Bernstein, Kristin G. Monaghan, Amber Begtrup, Rebecca Torene, Amna Al Futaisi, Fathiya Al Murshedi, Renjith Mani, Faisal Al Azri, Erik‐Jan Kamsteeg, Majid Mojarrad, Atieh Eslahi, Zaynab Khazaei, Fateme Massinaei Darmiyan, Mohammad Doosti, Ehsan Ghayoor Karimiani, Jana Vandrovcová, Faisal Zafar, Nuzhat Rana, Krishna Kumar Kandaswamy, Jozef Hertecant, Péter Bauer, Mohammed A. AlMuhaizea, Mustafa A. Salih, Mazhor Aldosary, Rawan Almass, Laila AlQuait, Wafa Qubbaj, Serdar Coşkun, Khaled O. Alahmadi, Muddathir H. Hamad, Salem Alwadaee, Khalid Awartani, Anas Dababo, Futwan Al‐Mohanna, Dilek Çolak, Mohammadreza Dehghani, Mohammad Yahya Vahidi Mehrjardi, Murat Günel, A. Gülhan Ercan-Şençiçek, Gouri Rao Passi, Huma Arshad Cheema, Stéphanie Efthymiou, Henry Houlden, Aida M. Bertoli‐Avella, Alice S. Brooks, Kyle Retterer, Reza Maroofian, Namik Kaya, Tjakko J. van Ham, Tahsin Stefan Barakat
Software Mentions: 4
Published: almost 6 years ago
10.1155/2018/2906292
A Simple Guideline to Assess the Characteristics of RNA-Seq DataCited by: 21
Author(s): Keun Hong Son, Sungryul Yu, Wonseok Shin, Kyudong Han, Keunsoo Kang
Software Mentions: 4
Published: about 7 years ago
10.1186/s12864-020-6687-9
Stable intronic sequence RNAs (sisRNAs) are selected regions in introns with distinct propertiesCited by: 2
Author(s): Jing Jin, Ximiao He, Elena M. Silva
Software Mentions: 4
Published: over 5 years ago
10.1084/jem.20181276
Contrasting requirements during disease evolution identify EZH2 as a therapeutic target in AMLCited by: 78
Author(s): Faisal Basheer, George Giotopoulos, Eshwar Meduri, Haiyang Yun, Milena Mazan, Daniel Sasca, Paolo Gallipoli, Ludovica Marando, Malgorzata Gozdecka, Ryan Asby, Olivia Sheppard, Monika Dudek, Lars Bullinger, Hartmut Döhner, Richard Dillon, Sylvie Freeman, Oliver G. Ottmann, Alan Kenneth Burnett, Nigel H. Russell, Elli Papaemmanuil, Robert Kerrin Hills, Peter J. Campbell, George S. Vassiliou, Brian J. P. Huntly
Software Mentions: 4
Published: over 6 years ago
10.1186/1745-6150-3-24
In silico regulatory analysis for exploring human disease progressionCited by: 8
Author(s): Dustin T. Holloway, Mark A. Kon, Charles DeLisi
Software Mentions: 4
Published: over 17 years ago
10.3390/ijerph17207671
Significant Associations between AXIN1 rs1805105, rs12921862, rs370681 Haplotypes and Variant Genotypes of AXIN2 rs2240308 with Risk of Congenital Heart DefectsCited by: 0
Author(s): George Andrei Crauciuc, Mihaela Iancu, Peter Olah, Florin Tripon, Mădălina Anciuc, Liliana Gozar, Rodica Togănel, Claudia Bănescu
Software Mentions: 4
Published: about 5 years ago
10.1371/journal.pone.0238546
MITF and TFEB cross-regulation in melanoma cellsCited by: 12
Author(s): Josué Ballesteros‐Álvarez, Ramile Dilshat, Valerie Fock, Katrín Möller, Ludwig Karl, Lionel Larue, Margrét H. Ögmundsdóttir, Eirı́kur Steingrı́msson
Software Mentions: 4
Published: about 5 years ago
10.1128/mBio.01650-17
<i>De Novo</i> Assembly and Phasing of Dikaryotic Genomes from Two Isolates of <i>Puccinia coronata</i> f. sp. <i>avenae</i> , the Causal Agent of Oat Crown RustCited by: 45
Author(s): Marisa E. Miller, Ying Zhang, Vahid Omidvar, Jana Sperschneider, Benjamin Schwessinger, Castle Raley, Jonathan M. Palmer, Diana Garnica, Narayana M. Upadhyaya, John P. Rathjen, Jennifer Taylor, Robert Park, Peter N. Dodds, Cory D. Hirsch, Shahryar F. Kianian, Melania Figueroa
Software Mentions: 4
Published: over 7 years ago
10.1038/s41388-019-1005-1
Identifying functions and prognostic biomarkers of network motifs marked by diverse chromatin states in human cell linesCited by: 12
Author(s): Li Wang, Hongying Zhao, Jing Li, Yingqi Xu, Yujia Lan, Wenkang Yin, Xiaoqin Liu, Lei Yu, Shan Lin, Michael Yifei Du, Xia Li, Yun Xiao, Yunpeng Zhang
Software Mentions: 4
Published: about 6 years ago
10.1038/s41598-019-40403-1
A multimodal approach to cardiovascular risk stratification in patients with type 2 diabetes incorporating retinal, genomic and clinical featuresCited by: 19
Author(s): Ahmed E. Fetit, Alex S.F. Doney, Stephen Hogg, Ruixuan Wang, Tom MacGillivray, Joanna M. Wardlaw, Fergus Doubal, Gareth J. McKay, Stephen J. McKenna, Emanuele Trucco
Software Mentions: 4
Published: over 6 years ago
10.1371/journal.pone.0218552
SNP-based mixed model association of growth- and yield-related traits in popcornCited by: 9
Author(s): Gabrielle Sousa Mafra, Antônio Teixeira do Amaral Júnior, Janeo Eustáquio de Almeida Filho, Marcelo Vivas, Pedro Henrique Araújo Diniz Santos, Juliana Saltires Santos, Guilherme Ferreira Pena, Valter Jário de Lima, Samuel Henrique Kamphorst, Fábio Tomaz de Oliveira, Yure Pequeno de Souza, Ismael Albino Schwantes, Talles de Oliveira Santos, Rosimeire Barbosa Bispo, Carlos Maldonado, Freddy Mora
Software Mentions: 4
Published: over 6 years ago
10.1099/acmi.0.000082
Transcriptome analysis of Brucella abortus S19∆per immunized mouse spleen revealed activation of MHC-I and MHC-II pathwaysCited by: 2
Author(s): K. S. Solanki, Ravikumar Gandham, Prasad Thomas, Pallab Chaudhuri
Software Mentions: 4
Published: almost 6 years ago
10.1371/journal.pone.0181902
EINCR1 is an EGF inducible lincRNA overexpressed in lung adenocarcinomasCited by: 4
Author(s): Karol Nowicki-Osuch, Yaoyong Li, Mairi Challinor, Dave T. Gerrard, Neil A. Hanley, Andrew D. Sharrocks
Software Mentions: 4
Published: over 8 years ago
10.1038/s41598-020-79781-2
Novel circRNA discovery in sheep shows evidence of high backsplice junction conservationCited by: 7
Author(s): Endika Varela-Martínez, Giulia I. Corsi, Christian Anthon, Jan Gorodkin, Begoña M. Jugo
Software Mentions: 4
Published: almost 5 years ago
10.3390/s130708060
Context Management Platform for Tourism ApplicationsCited by: 14
Author(s): David Buján, David L. Martin, Ortzi Torices, Diego López-de-Ipiña, Carlos Lamsfus, Joseba Abaitua, Aurkene Alzua-Sorzabal
Software Mentions: 4
Published: over 12 years ago
10.1016/j.jmb.2019.04.043
PhyreRisk: A Dynamic Web Application to Bridge Genomics, Proteomics and 3D Structural Data to Guide Interpretation of Human Genetic VariantsCited by: 19
Author(s): Tochukwu C. Ofoegbu, Alessia David, Lawrence A. Kelley, Stefans Mezulis, Suhail A. Islam, Sophia F. Mersmann, Léonie Strömich, Ilya A. Vakser, Richard S. Houlston, Michael J.E. Sternberg
Software Mentions: 4
Published: over 6 years ago
10.1186/s12859-018-2086-5
An information-theoretic approach to the modeling and analysis of whole-genome bisulfite sequencing dataCited by: 23
Author(s): W. Garrett Jenkinson, Jordi Abante, Andrew P. Feinberg, John Goutsias
Software Mentions: 4
Published: over 7 years ago
10.1038/srep20369
Multidisciplinary investigation links backward-speech trait and working memory through genetic mutationCited by: 5
Author(s): Stefan Prekovic, Dušica Filipović Đurđević, Gábor Csifcsák, Olivera Šveljo, Oliver Stojković, Milica M. Janković, Katarina Koprivšek, Laura Covill, Miloš Lučić, Thomas Van den Broeck, Christine Helsen, Fabiola Ceroni, Frank Claessens, Dianne F. Newbury
Software Mentions: 4
Published: almost 10 years ago
10.1371/journal.pgen.1006964
rahu is a mutant allele of Dnmt3c, encoding a DNA methyltransferase homolog required for meiosis and transposon repression in the mouse male germlineCited by: 56
Author(s): Devanshi Jain, Cem Meydan, Julian Lange, Corentin Claeys Bouuaert, Nathalie Lailler, Christopher E. Mason, Kathryn V. Anderson, Scott Keeney
Software Mentions: 4
Published: about 8 years ago
10.1126/sciadv.abe3516
Genomic profiling of native R loops with a DNA-RNA hybrid recognition sensorCited by: 37
Author(s): Kang Wang, Honghong Wang, Conghui Li, Zhenggang Yin, Ran Xiao, Qiuzi Li, Xiaofang Ying, Wen Wang, Jian Huang, Liang Chen, Pingping Fang, Kaiwei Liang
Software Mentions: 4
Published: over 4 years ago
10.1186/s12920-018-0430-2
CRlncRNA: a manually curated database of cancer-related long non-coding RNAs with experimental proof of functions on clinicopathological and molecular featuresCited by: 20
Author(s): Jun Wang, Xuan Zhang, Wen Chen, Jing Li, Changning Liu
Software Mentions: 4
Published: almost 7 years ago
10.1038/sdata.2014.38
DNA methylation temporal profiling following peripheral versus central nervous system axotomyCited by: 14
Author(s): Ricco Lindner, Radhika Puttagunta, Tuan Nguyen, Simone Di Giovanni
Software Mentions: 4
Published: almost 11 years ago
10.1038/s41598-017-17996-6
Identification of long non-coding RNAs in the immature and mature rat anterior pituitaryCited by: 19
Author(s): Dong-Xu Han, Xiaolong Sun, Yao Fu, Changjiang Wang, Jianbo Li, Hao Jiang, Yan Gao, Chengzhen Chen, Bao Yuan, Jiabao Zhang
Software Mentions: 4
Published: almost 8 years ago
10.1080/15476286.2020.1777768
Targeted RNA sequencing enhances gene expression profiling of ultra-low input samplesCited by: 10
Author(s): Fabiola Curion, Adam E. Handel, Moustafa Attar, Giuseppe Gallone, Rory Bowden, M Z Cader, Michael B. Clark
Software Mentions: 4
Published: over 5 years ago
10.1038/s41438-020-0338-9
Kiwifruit Genome Database (KGD): a comprehensive resource for kiwifruit genomicsCited by: 43
Author(s): Junyang Yue, Jiacheng Liu, Wei Tang, Ya Qing Wu, Xiaofeng Tang, Wei Li, Ying Yang, Lihuan Wang, Shengxiong Huang, Congbing Fang, Kun Zhao, Zhangjun Fei, Yongsheng Liu, Yi Zheng
Software Mentions: 4
Published: over 5 years ago
10.1371/journal.pgen.1007819
The complex architecture and epigenomic impact of plant T-DNA insertionsCited by: 98
Author(s): Florian Jupe, Angeline Rivkin, Todd P. Michael, Mark Zander, S. Timothy Motley, Justin P. Sandoval, R. Keith Slotkin, Huaming Chen, Rosa Castanon, Joseph R. Nery, Joseph R. Ecker
Software Mentions: 4
Published: almost 7 years ago
10.3389/fpls.2016.00889
PlantAPA: A Portal for Visualization and Analysis of Alternative Polyadenylation in PlantsCited by: 19
Author(s): Xiaohui Wu, Yumin Zhang, Qingshun Quinn Li
Software Mentions: 4
Published: over 9 years ago
10.1534/g3.117.039396
Comparative Genomics of the Ectomycorrhizal Sister Species <i>Rhizopogon vinicolor</i> and <i>Rhizopogon vesiculosus</i> (Basidiomycota: Boletales) Reveals a Divergence of the Mating Type <i>B</i> LocusCited by: 16
Author(s): Alija B. Mujic, Alan Kuo, Andrew Tritt, Anna Lipzen, Cindy Chen, Jenifer Johnson, Aarti Sharma, Kerrie Barry, Igor V. Grigoriev, Joseph W. Spatafora
Software Mentions: 4
Published: over 8 years ago
10.1371/journal.pgen.1008273
BCDIN3D regulates tRNAHis 3’ fragment processingCited by: 21
Author(s): Calder Reinsborough, Hélène Ipas, Nathan S. Abell, Ryan M. Nottingham, Jun Yao, Sravan K. Devanathan, Samantha B. Shelton, Alan M. Lambowitz, Blerta Xhemalçe
Software Mentions: 4
Published: over 6 years ago
10.1038/s41598-017-07100-3
Bmal1 regulates inflammatory responses in macrophages by modulating enhancer RNA transcriptionCited by: 59
Author(s): Yumiko Oishi, Shinichiro Hayashi, Takayuki Isagawa, Motohiko Oshima, Atsushi Iwama, Shigeki Shimba, Hitoshi Okamura, Ichiro Manabe
Software Mentions: 4
Published: over 8 years ago
10.1186/1471-2156-13-24
Enhancing the usability and performance of structured association mapping algorithms using automation, parallelization, and visualization in the GenAMap software systemCited by: 4
Author(s): Ross E. Curtis, Anuj Goyal, Eric P. Xing
Software Mentions: 4
Published: over 13 years ago
10.1186/1471-2164-8-265
Inference of transcriptional regulation using gene expression data from the bovine and human genomesCited by: 8
Author(s): Amonida Zadissa, John C. McEwan, Chris M. Brown
Software Mentions: 4
Published: over 18 years ago
10.1186/s12920-015-0139-4
Genome-wide DNA methylome reveals the dysfunction of intronic microRNAs in major psychosisCited by: 27
Author(s): Hongying Zhao, Jiu Hua Xu, Lin Pang, Yunpeng Zhang, Huihui Fan, Ling Liu, Tingting Liu, Fulong Yu, Guanxiong Zhang, Yujia Lan, Jing Bai, Xia Li, Yun Xiao
Software Mentions: 4
Published: about 10 years ago
10.3389/fpls.2018.00005
Abiotic Stresses Modulate Landscape of Poplar Transcriptome via Alternative Splicing, Differential Intron Retention, and Isoform Ratio SwitchingCited by: 84
Author(s): Sergei A. Filichkin, Michael Hamilton, Palitha Dharmawardhana, Sunil Kumar Singh, Christopher Sullivan, Asa Ben‐Hur, Anireddy S. N. Reddy, Pankaj Jaiswal
Software Mentions: 4
Published: over 7 years ago
10.1534/g3.118.200726
Nuclear Transcriptomes of the Seven Neuronal Cell Types That Constitute the<i>Drosophila</i>Mushroom BodiesCited by: 43
Author(s): Min-Yi Shih, Fred P. Davis, Gilbert L. Henry, Josh Dubnau
Software Mentions: 4
Published: almost 7 years ago
10.1186/s12864-015-1954-x
Genome-wide analysis reveals the extent of EAV-HP integration in domestic chickenCited by: 8
Author(s): David Wragg, Andrew S. Mason, Lejun Yu, Richard Kuo, Raman Akinyanju Lawal, Takele Taye Desta, Joram M. Mwacharo, Chang-Yeon Cho, Stephen J. Kemp, David W. Burt, Olivier Hanotte
Software Mentions: 4
Published: about 10 years ago
10.1371/journal.pcbi.1002603
An Integrated Regulatory Network Reveals Pervasive Cross-Regulation among Transcription and Splicing FactorsCited by: 15
Author(s): Idit Kosti, Predrag Radivojac, Yael Mandel-Gutfreund
Software Mentions: 4
Published: over 13 years ago
10.3389/fimmu.2019.01253
Signal Integration of IFN-I and IFN-II With TLR4 Involves Sequential Recruitment of STAT1-Complexes and NFκB to Enhance Pro-inflammatory TranscriptionCited by: 32
Author(s): Anna Piaszyk-Borychowska, Lajos Széles, Attila Csermely, Hsüch‐Ching Chiang, Joanna Wesoły, Chien‐Kuo Lee, László Nagy, Hans A.R. Bluyssen
Software Mentions: 4
Published: over 6 years ago
10.1371/journal.pcbi.1006937
Exon level machine learning analyses elucidate novel candidate miRNA targets in an avian model of fetal alcohol spectrum disorderCited by: 9
Author(s): Abrar E. Al‐Shaer, George R. Flentke, Mark E. Berres, Ana Garic, Susan Smith
Software Mentions: 4
Published: over 6 years ago
10.3389/fimmu.2020.01089
IL-12 Signaling Contributes to the Reprogramming of Neonatal CD8+ T CellsCited by: 4
Author(s): Darely Y. Gutiérrez-Reyna, Alejandra Cedillo-Baños, Linda A Kempis-Calanis, Oscar Ramírez-Pliego, Lisa Bargier, Denis Puthier, José David Abad Flores, Morgane Thomas‐Chollier, Denis Thieffry, Alejandra Medina-Rivera, Salvatore Spicuglia, María Angélica Santana
Software Mentions: 4
Published: over 5 years ago
10.3389/fmicb.2020.586614
Deciphering Microbial Community Dynamics and Biochemical Changes During Nyons Black Olive Natural FermentationsCited by: 18
Author(s): Marine Penland, Stéphanie-Marie Deutsch, Hélène Falentin, Audrey Pawtowski, Elisabeth Poirier, Giorgia Visenti, Christophe Le Meur, Marie-Bernadette Maillard, Anne Thierry, Jérôme Mounier, Monika Coton
Software Mentions: 4
Published: about 5 years ago
10.1371/journal.pbio.2003648
A direct link between MITF, innate immunity, and hair grayingCited by: 37
Author(s): Melissa L. Harris, Temesgen Fufa, Joseph W. Palmer, Sandeep S. Joshi, Denise M. Larson, Arturo Incao, Derek Gildea, Niraj Trivedi, Autumne N Lee, Chi-Ping Day, Helen Michael, Thomas J. Hornyak, Glenn Merlino, Nisc Comparative Sequencing Program, William J. Pavan
Software Mentions: 4
Published: over 7 years ago
10.1186/1471-2164-13-549
Evolutionary force in confamiliar marine vertebrates of different temperature realms: adaptive trends in zoarcid fish transcriptomesCited by: 17
Author(s): Heidrun Sigrid Windisch, Magnus Lucassen, Stephan Frickenhaus
Software Mentions: 4
Published: almost 14 years ago
10.1186/s12864-020-07200-x
iCLIP analysis of RNA substrates of the archaeal exosomeCited by: 2
Author(s): Jochen Bathke, A. Susann Gauernack, Oliver Rupp, Lennart Weber, Christian Preußer, Marcus Lechner, Oliver Roßbach, Alexander Goesmann, Elena Evguenieva‐Hackenberg, Gabriele Klug
Software Mentions: 4
Published: almost 5 years ago
10.1371/journal.pgen.0030087
Whole-Genome Cartography of Estrogen Receptor α Binding SitesCited by: 414
Author(s): Chin-Yo Lin, Vinsensius B. Vega, Jane S. Thomsen, Tao Zhang, Say Li Kong, Ming Xie, King-Wah Chiu, Leonard Lipovich, Daniel H. Barnett, Fabio Stossi, A. Yeo, Joshy George, Vladimir A. Kuznetsov, Yew Kok Lee, Tze Howe Charn, Nallasivam Palanisamy, Lance D. Miller, Edwin Cheung, Benita S. Katzenellenbogen, Yijun Ruan, Guillaume Bourque, Chia Lin Wei, Edison T. Liu
Software Mentions: 4
Published: over 18 years ago
10.1186/s12864-019-6088-0
7C: Computational Chromosome Conformation Capture by Correlation of ChIP-seq at CTCF motifsCited by: 10
Author(s): Jonas Ibn-Salem, Miguel A. Andrade‐Navarro
Software Mentions: 4
Published: about 6 years ago
10.3389/fmicb.2020.01707
Synergic Effects of Temperature and Irradiance on the Physiology of the Marine Synechococcus Strain WH7803Cited by: 16
Author(s): Ulysse Guyet, Ngoc-An Nguyen, Hugo Doré, Julie Haguait, Justine Pittera, Maël Conan, Morgane Ratin, Erwan Corre, Gildas Le Corguillé, Loraine Brillet-Guéguen, Mark Hoebeke, Christophe Six, Claudia Steglich, Anne Siegel, Damien Eveillard, Frédéric Partensky, Laurence Garczarek
Software Mentions: 4
Published: over 5 years ago
10.3389/fgene.2015.00331
Mapping Mammalian Cell-type-specific Transcriptional Regulatory Networks Using KD-CAGE and ChIP-seq Data in the TC-YIK Cell LineCited by: 12
Author(s): Marina Lizio, Yuri Ishizu, Masayoshi Itoh, Timo Lassmann, Akira Hasegawa, Atsutaka Kubosaki, Jessica Severin, Hideya Kawaji, Yukio Nakamura, Harukazu Suzuki, Yoshihide Hayashizaki, Piero Carninci, Alistair R.R. Forrest
Software Mentions: 4
Published: almost 10 years ago