bioconductor: Biostrings | Projects

10.1186/s12864-015-2164-2

The direction of cross affects obesity after puberty in male but not female offspring
Cited by: 5
Author(s): Stefan Kärst, Danny Arends, Sebastian Heise, Jan Trost, Marie–Laure Yaspo, Vyacheslav Amstislavskiy, Thomas S. Risch, Hans Lehrach, Gudrun A. Brockmann
Software Mentions: 4
Published: almost 9 years ago

10.1186/1471-2164-15-37

Comparison of different assembly and annotation tools on analysis of simulated viral metagenomic communities in the gut
Cited by: 74
Author(s): Jorge F. Vázquez-Castellanos, Rodrigo García-López, Vicente Pérez‐Brocal, Miguel Pignatelli, Andrés Moya
Software Mentions: 4
Published: over 10 years ago

10.1186/s12864-020-6662-5

Comprehensive genome-wide identification of angiosperm upstream ORFs with peptide sequences conserved in various taxonomic ranges using a novel pipeline, ESUCA
Cited by: 12
Author(s): Hiro Takahashi, Noriya Hayashi, Yuta Hiragori, Shun Sasaki, Taichiro Motomura, Yoshihisa Yamashita, Shuichi Naito, Atsushi Takahashi, Kazuyuki Fuse, Kenji Satou, Toshinori Endo, Shoko Kojima, Hitoshi Onouchi
Software Mentions: 4
Published: over 4 years ago

10.1186/1471-2164-13-519

Comparison of transcriptome technologies in the pathogenic fungus Aspergillus fumigatus reveals novel insights into the genome and MpkA dependent gene expression
Cited by: 37
Author(s): Sebastian Müller, Clara Baldin, Marco Groth, Reinhard Guthke, Olaf Kniemeyer, Axel A. Brakhage, Vito Valiante
Software Mentions: 4
Published: about 12 years ago

10.1186/s12864-016-2729-8

A systematic, large-scale comparison of transcription factor binding site models
Cited by: 13
Author(s): Daniela Hombach, Jana Marie Schwarz, Peter N. Robinson, Markus Schuelke, Dominik Seelow
Software Mentions: 4
Published: over 8 years ago

10.1186/s12866-019-1500-0

Long-read based de novo assembly of low-complexity metagenome samples results in finished genomes and reveals insights into strain diversity and an active phage system
Cited by: 101
Author(s): Vincent Somerville, Stefanie Lutz, Michael Schmid, Daniel Frei, Aline Moser, Stefan Irmler, Jürg E. Frey, Christian H. Ahrens
Software Mentions: 4
Published: over 5 years ago

10.1155/2014/736798

Computational Evidence of NAGNAG Alternative Splicing in Human Large Intergenic Noncoding RNA
Cited by: 2
Author(s): Xiaoyong Sun, Simon Lin, Xiaoyan Yan
Software Mentions: 4
Published: almost 11 years ago

10.1155/2013/340620

State-of-the-Art Fusion-Finder Algorithms Sensitivity and Specificity
Cited by: 79
Author(s): Matteo Carrara, Marco Beccuti, Fulvio Lazzarato, Federica Cavallo, Francesca Cordero, Susanna Donatelli, Raffaele Calogero
Software Mentions: 4
Published: almost 12 years ago

10.26508/lsa.202000825

The RNA-binding profile of the splicing factor SRSF6 in immortalized human pancreatic β-cells
Cited by: 13
Author(s): Maria Inês Alvelos, Mirko Brüggemann, F. X. Reymond Sutandy, Jonàs Juan-Mateu, Máikel Luís Colli, Anke Busch, Miguel Lopes, Ângela Castela, Annemieke Aartsma‐Rus, Julian König, Kathi Zarnack, Décio L. Eizirik
Software Mentions: 4
Published: almost 4 years ago

10.1007/978-1-4939-9074-0_25

Sharing Programming Resources Between Bio* Projects
Cited by: 4
Author(s): Raoul Jean Pierre Bonnal, Andy Yates, Naohisa Goto, Laurent Gautier, Scooter Willis, Christopher J. Fields, Toshiaki Katayama, Pjotr Prins
Software Mentions: 4
Published: almost 6 years ago

10.3390/plants9111589

Effects of Exogenous Salicylic Acid on Drought Response and Characterization of Dehydrins in Impatiens walleriana
Cited by: 11
Author(s): Dragana D Antonić, Angelina Subotić, Milan Dragićević, Danijel Pantelić, Snežana Milošević, Ana Simonović, Ivana Momčilović
Software Mentions: 4
Published: almost 4 years ago

10.1371/journal.pgen.1002415

A Densely Interconnected Genome-Wide Network of MicroRNAs and Oncogenic Pathways Revealed Using Gene Expression Signatures
Cited by: 30
Author(s): Chia Huey Ooi, Hue Kian Oh, H Wang, Angie Lay Keng Tan, Jeanie Wu, Ming‐Hui Lee, Sun Young Rha, Hyun Cheol Chung, David M. Virshup, Patrick Tan
Software Mentions: 4
Published: almost 13 years ago

10.1371/journal.pone.0250654

Potential G-quadruplexes and i-Motifs in the SARS-CoV-2
Cited by: 25
Author(s): Efres Belmonte-Reche, Israel Serrano‐Chacón, Carlos González, Juan Gallo, Manuel Bañobre‐López
Software Mentions: 4
Published: over 3 years ago

10.1371/journal.pone.0108424

CRISPRseek: A Bioconductor Package to Identify Target-Specific Guide RNAs for CRISPR-Cas9 Genome-Editing Systems
Cited by: 156
Author(s): Lihua Julie Zhu, Benjamin Holmes, Neil Aronin, Michael Brodsky
Software Mentions: 4
Published: about 10 years ago

10.1371/journal.pone.0093975

A Framework Phylogeny of the American Oak Clade Based on Sequenced RAD Data
Cited by: 190
Author(s): Andrew L. Hipp, Deren A. R. Eaton, Jeannine Cavender‐Bares, Elisabeth Fitzek, Rick Nipper, Paul S. Manos
Software Mentions: 4
Published: over 10 years ago

10.1371/journal.pone.0107259

Optimization of Extraction of Circulating RNAs from Plasma – Enabling Small RNA Sequencing
Cited by: 48
Author(s): Melanie Spornraft, Benedikt Kirchner, Bettina Haase, Vladimı́r Beneš, Michael W. Pfaffl, Irmgard Riedmaier
Software Mentions: 4
Published: about 10 years ago

10.1371/journal.pone.0033575

Genetic Dissection of Acute Ethanol Responsive Gene Networks in Prefrontal Cortex: Functional and Mechanistic Implications
Cited by: 78
Author(s): Aaron R. Wolen, Charles Phillips, Michael A. Langston, Alex H. Putman, Paul J. Vorster, Nathan A. Bruce, Timothy P. York, Robert W. Williams, Michael F. Miles
Software Mentions: 4
Published: over 12 years ago

10.1371/journal.pone.0157600

De Novo Assembly of Human Herpes Virus Type 1 (HHV-1) Genome, Mining of Non-Canonical Structures and Detection of Novel Drug-Resistance Mutations Using Short- and Long-Read Next Generation Sequencing Technologies
Cited by: 43
Author(s): Timokratis Karamitros, Ian Harrison, Renata Piorkowska, Aris Katzourakis, Gkikas Magiorkinis, Jean L. Mbisa
Software Mentions: 4
Published: over 8 years ago

10.1093/database/baz053

CropCircDB: a comprehensive circular RNA resource for crops in response to abiotic stress
Cited by: 26
Author(s): Kai Wang, Chong Wang, Baohuan Guo, Kun Song, Chuanhong Shi, Xin Jiang, Keyi Wang, Yacong Tan, Lequn Wang, Lin Wang, Jiangjiao Li, Ying Liu, Yu-Dong Cai, Hongwei Zhao, Xiaoyong Sun
Software Mentions: 4
Published: almost 6 years ago

10.1111/eva.12555

Focusing the diversity ofGardnerella vaginalisthrough the lens of ecotypes
Cited by: 33
Author(s): Omar E. Cornejo, Roxana J. Hickey, Haruo Suzuki, Larry J. Forney
Software Mentions: 4
Published: almost 7 years ago

10.3389/fimmu.2021.705381

Antibody Repertoire Analysis of Tumor-Infiltrating B Cells Reveals Distinct Signatures and Distributions Across Tissues
Cited by: 7
Author(s): Ligal Aizik, Yael Dror, David Taussig, Adi Barzel, Yaron Carmi, Yariv Wine
Software Mentions: 4
Published: about 3 years ago

10.3389/fimmu.2019.01625

Computational Analysis of HLA-presentation of Non-synonymous Recipient Mismatches Indicates Effect on the Risk of Chronic Graft-vs.-Host Disease After Allogeneic HSCT
Cited by: 8
Author(s): Jarmo Ritari, Kati Hyvärinen, Satu Koskela, Riitta Niittyvuopio, Anne Nihtinen, Urpu Salmenniemi, Matti Putkonen, Liisa Volin, Tony Kwan, Tomi Pastinen, Maija Itälä‐Remes, Jukka Partanen
Software Mentions: 4
Published: about 5 years ago

10.1186/s12711-021-00643-0

Genetic variation in recombination rate in the pig
Cited by: 15
Author(s): Martin Johnsson, Andrew Whalen, Roger Ros‐Freixedes, Gregor Gorjanc, Ching-Yi Chen, William Herring, Dirk-Jan de Koning, John M. Hickey
Software Mentions: 4
Published: over 3 years ago

10.1038/srep20064

Digital detection of endonuclease mediated gene disruption in the HIV provirus
Cited by: 21
Author(s): Ruth Hall Sedlak, Shu Liang, Nixon Niyonzima, Harshana S. De Silva Feelixge, Pavitra Roychoudhury, Alexander L. Greninger, Nicholas Weber, Sandrine Boissel, Andrew M. Scharenberg, Anqi Cheng, Amalia Magaret, Roger E. Bumgarner, Daniel Stone, Keith R. Jerome
Software Mentions: 4
Published: over 8 years ago

10.1038/s41598-019-44889-7

Morph-specific protein patterns in the femoral gland secretions of a colour polymorphic lizard
Cited by: 22
Author(s): Marco Mangiacotti, Marco Fumagalli, Maddalena Cagnone, Simona Viglio, Anna Bardoni, Stefano Scali, Roberto Sacchi
Software Mentions: 4
Published: over 5 years ago

10.1038/s41598-020-73307-6

Exhaustive identification of conserved upstream open reading frames with potential translational regulatory functions from animal genomes
Cited by: 6
Author(s): Hiro Takahashi, Shido Miyaki, Hitoshi Onouchi, Taichiro Motomura, Nobuo Idesako, Atsushi Takahashi, Masataka Murase, Shuichi Fukuyoshi, Toshinori Endo, Kenji Satou, Shuichi Naito, Motoyuki Itoh
Software Mentions: 4
Published: about 4 years ago

10.7554/eLife.44279

Plant–necrotroph co-transcriptome networks illuminate a metabolic battlefield
Cited by: 42
Author(s): Wei Zhang, Jason A. Corwin, Daniel Copeland, Julie E. Feusier, Robert Eshbaugh, David E. Cook, Suzi Atwell, Daniel J. Kliebenstein
Software Mentions: 4
Published: over 5 years ago

10.7554/eLife.08932

Codon-level information improves predictions of inter-residue contacts in proteins by correlated mutation analysis
Cited by: 7
Author(s): Etai Jacob, Ron Unger, Amnon Horovitz
Software Mentions: 3
Published: about 9 years ago

10.1371/journal.ppat.1009226

The coronavirus proofreading exoribonuclease mediates extensive viral recombination
Cited by: 173
Author(s): Jennifer Gribble, Laura J. Stevens, Marco Agostini, Jordan Anderson-Daniels, James D. Chappell, Xiaotao Lu, Andrea J. Pruijssers, Andrew Routh, Mark R. Denison
Software Mentions: 3
Published: over 3 years ago

10.1371/journal.pone.0129154

High-Throughput Sequencing and De Novo Assembly of Red and Green Forms of the Perilla frutescens var. crispa Transcriptome
Cited by: 37
Author(s): Atsushi Fukushima, Michimi Nakamura, Hideyuki Suzuki, Kazuki Saito, Mami Yamazaki
Software Mentions: 3
Published: over 9 years ago

10.1093/g3journal/jkaa026

De novo assembly of a chromosome-scale reference genome for the northern flicker Colaptes auratus
Cited by: 3
Author(s): Jack P. Hruska, Joseph D. Manthey
Software Mentions: 3
Published: almost 4 years ago

10.3390/microorganisms9061117

Reassessment of the Columnea latent viroid (CLVd) Taxonomic Classification
Cited by: 1
Author(s): Parichate Tangkanchanapas, Annelies Haegeman, Monica Höfte, Kris De Jonghe
Software Mentions: 3
Published: over 3 years ago

10.3390/v13030437

viromeBrowser: A Shiny App for Browsing Virome Sequencing Analysis Results
Cited by: 1
Author(s): David F. Nieuwenhuijse, Bas B. Oude Munnink, Marion Koopmans
Software Mentions: 3
Published: over 3 years ago

10.1186/s12859-016-0935-7

LowMACA: exploiting protein family analysis for the identification of rare driver mutations in cancer
Cited by: 16
Author(s): Giorgio Melloni, Stefano de Pretis, Laura Riva, Mattia Pelizzola, Arnaud Céol, Jole Costanza, Heiko Müller, Luca Zammataro
Software Mentions: 3
Published: over 8 years ago

10.1371/journal.pgen.1004368

Translational Regulation of Specific mRNAs Controls Feedback Inhibition and Survival during Macrophage Activation
Cited by: 95
Author(s): Johanna Schott, Sonja Reitter, Janine Philipp, Katharina Haneke, Heiner Schäfer, Georg Stoecklin
Software Mentions: 3
Published: over 10 years ago

10.1111/tpj.14546

Characterization of repeat arrays in ultra‐long nanopore reads reveals frequent origin of satellite DNA from retrotransposon‐derived tandem repeats
Cited by: 67
Author(s): Tihana Vondrak, Laura Ávila Robledillo, Petr Novák, Andrea Koblížková, Pavel Neumann, Jiří Macas
Software Mentions: 3
Published: almost 5 years ago

10.1186/1471-2148-12-94

Uninformative polymorphisms bias genome scans for signatures of selection
Cited by: 131
Author(s): Marius Roesti, Walter Salzburger, Daniel Berner
Software Mentions: 3
Published: over 12 years ago

10.3389/fcell.2019.00385

Retinoic Acid Induces Embryonic Stem Cells (ESCs) Transition to 2 Cell-Like State Through a Coordinated Expression of Dux and Duxbl1
Cited by: 23
Author(s): Daniela Tagliaferri, P. Mazzone, Teresa Maria Rosaria Noviello, Martina Addeo, Tiziana Angrisano, Luigi Del Vecchio, Feliciano Visconte, Vitalba Ruggieri, Sabino Russi, Antonella Caivano, Irene Cantone, Mario De Felice, Michele Ceccarelli, Luigi Cerulo, Geppino Falco
Software Mentions: 3
Published: over 4 years ago

10.1128/mBio.02136-21

Protospacer-Adjacent Motif Specificity during Clostridioides difficile Type I-B CRISPR-Cas Interference and Adaptation
Cited by: 3
Author(s): Anna Maikova, Pierre Boudry, Anna Shiriaeva, Aleksandra Vasileva, Anaïs Boutserin, Sofia Medvedeva, Ekaterina Semenova, Konstantin Severinov, Olga Soutourina
Software Mentions: 3
Published: about 3 years ago

10.1371/journal.pone.0176739

Genotypic and phenotypic diversity of Lactobacillus rhamnosus clinical isolates, their comparison with strain GG and their recognition by complement system
Cited by: 21
Author(s): Eija Nissilä, François P. Douillard, Jarmo Ritari, Lars Paulín, Hanna Järvinen, Pia Rasinkangas, Karita Haapasalo, Seppo Meri, Hanna Jarva, Willem M. de Vos
Software Mentions: 3
Published: over 7 years ago

10.1186/s12864-017-4344-8

Bioinformatically predicted deleterious mutations reveal complementation in the interior spruce hybrid complex
Cited by: 15
Author(s): Gina L. Conte, Kathryn A. Hodgins, Sam Yeaman, Jon C. Degner, Sally N. Aitken, Loren H. Rieseberg, Michael C. Whitlock
Software Mentions: 3
Published: almost 7 years ago

10.1186/s12864-016-3440-5

Single genome retrieval of context-dependent variability in mutation rates for human germline
Cited by: 5
Author(s): Aleksandr B. Sahakyan, Shankar Balasubramanian
Software Mentions: 3
Published: over 7 years ago

10.1002/ece3.6855

Genetic drift and bottleneck do not influence diversity in Toll‐like receptor genes at a small spatial scale in a Himalayan passerine
Cited by: 1
Author(s): Mridula Nandakumar, Farah Ishtiaq
Software Mentions: 3
Published: almost 4 years ago

10.1371/journal.pone.0143193

Random Tagging Genotyping by Sequencing (rtGBS), an Unbiased Approach to Locate Restriction Enzyme Sites across the Target Genome
Cited by: 10
Author(s): Elena Hilario, Lorna Barron, Cecilia Deng, Paul M. Datson, Nihal De Silva, Marcus Davy, Roy Storey
Software Mentions: 3
Published: almost 9 years ago

10.1242/dev.116996

Gene activation-associated long noncoding RNAs function in mouse preimplantation development
Cited by: 71
Author(s): Nobuhiko Hamazaki, Masahiro Uesaka, Kinichi Nakashima, Kiyokazu Agata, Takuya Imamura
Software Mentions: 3
Published: almost 10 years ago

10.1038/s41598-021-91208-0

Focused peptide library screening as a route to a superior affinity ligand for antibody purification
Cited by: 3
Author(s): Krištof Bozovičar, Barbara Jenko Bizjan, Anže Meden, Jernej Kovač, Tomaž Bratkovič
Software Mentions: 3
Published: over 3 years ago

10.1186/s12859-017-1653-5

ICoVeR – an interactive visualization tool for verification and refinement of metagenomic bins
Cited by: 20
Author(s): Bertjan Broeksema, Magdalena Całusińska, Fintan McGee, Klaas Winter, Francesco Bongiovanni, Xavier Goux, Paul Wilmes, Philippe Delfosse, Mohammad Ghoniem
Software Mentions: 3
Published: over 7 years ago

10.3389/fimmu.2021.629059

HLA RNA Sequencing With Unique Molecular Identifiers Reveals High Allele-Specific Variability in mRNA Expression
Cited by: 15
Author(s): Tiira Johansson, Dawit A. Yohannes, Satu Koskela, Jukka Partanen, Päivi Saavalainen
Software Mentions: 3
Published: over 3 years ago

10.1186/1471-2164-13-385

Genetic changes during a laboratory adaptive evolution process that allowed fast growth in glucose to an Escherichia coli strain lacking the major glucose transport system
Cited by: 38
Author(s): César Aguilar, Adelfo Escalante, Noemí Flores, R. Anda, Fernando Riveros-Mckay, Guillermo Gosset, Enrique Morett, Francisco Bolívar
Software Mentions: 3
Published: about 12 years ago

10.1186/s12859-020-3493-y

Self-analysis of repeat proteins reveals evolutionarily conserved patterns
Cited by: 4
Author(s): M. Merski, Krzysztof Młynarczyk, Jan Ludwiczak, Jakub Skrzeczkowski, Stanisław Dunin-Horkawicz, Maria W. Górna
Software Mentions: 3
Published: over 4 years ago

10.3389/fmicb.2015.00955

Direct sequencing of human gut virome fractions obtained by flow cytometry
Cited by: 18
Author(s): Mária Džunková, Giuseppe D’Auria, Andrés Moya
Software Mentions: 3
Published: about 9 years ago

10.1186/s12881-015-0236-4

Relationships between putative G-quadruplex-forming sequences, RecQ helicases, and transcription
Cited by: 34
Author(s): John A. Smestad, L. James Maher
Software Mentions: 3
Published: about 9 years ago

10.1186/1471-2180-12-121

Molecular analysis of meso- and thermophilic microbiota associated with anaerobic biowaste degradation
Cited by: 36
Author(s): Jarmo Ritari, Kaisa Koskinen, Jenni Hultman, Jukka Kurola, Maritta Kymäläinen, Martin Romantschuk, Lars Paulín, Petri Auvinen
Software Mentions: 3
Published: almost 13 years ago

10.3389/fmicb.2018.02485

Flexible Symbiotic Associations of Symbiodinium With Five Typical Coral Species in Tropical and Subtropical Reef Regions of the Northern South China Sea
Cited by: 28
Author(s): Sanqiang Gong, Guangjun Chai, Yilin Xiao, Lijia Xu, Kefu Yu, Jinlong Li, Fang Liu, Hao Cheng, Fengli Zhang, Baolin Liao, Zhiyong Li
Software Mentions: 3
Published: almost 6 years ago

10.1371/journal.pone.0089694

PolyaPeak: Detecting Transcription Factor Binding Sites from ChIP-seq Using Peak Shape Information
Cited by: 12
Author(s): Hao Wu, Hongkai Ji
Software Mentions: 3
Published: over 10 years ago

10.1080/22221751.2021.1969868

Host-dependent editing of SARS-CoV-2 in COVID-19 patients
Cited by: 12
Author(s): Josep Gregori, María Francesca Cortese, María Piñana, Carolina Campos, Damir García-Cehic, Cristina Andrés, Josep F. Abril, María Gema Codina, Ariadna Rando, Juliana Esperalba, Elena Sulleiro, Joan Joseph, Narcís Saubi, Sergi Colomer-Castell, Mari Carmen Martin, Carla Castillo, Juan Ignacio Esteban, Tomàs Pumarola, Francisco Rodríguez‐Frías, Andrés Antón, Josep Quer
Software Mentions: 3
Published: almost 4 years ago

10.1155/2021/6667201

Predicting Ovarian/Breast Cancer Pathogenic Risks of Human BRCA1 Gene Variants of Unknown Significance
Cited by: 0
Author(s): Hui-Heng Lin, Hongxing Xu, Hongbo Hu, Zhu Ma, Jie Zhou, Qingyun Liang
Software Mentions: 3
Published: over 3 years ago

10.3390/ijms18071378

Multiple Isoforms of ANRIL in Melanoma Cells: Structural Complexity Suggests Variations in Processing
Cited by: 34
Author(s): Debina Sarkar, Ali Oghabian, Pasani K. Bodiyabadu, Wayne R. Joseph, Euphemia Leung, Graeme J. Finlay, Bruce C. Baguley, Marjan Askarian-Amiri
Software Mentions: 3
Published: over 7 years ago

10.1038/s41598-021-95166-5

Feeding sites promoting wildlife-related tourism might highly expose the endangered Yunnan snub-nosed monkey (Rhinopithecus bieti) to parasite transmission
Cited by: 4
Author(s): Eve Afonso, Rong Fu, Amaël Dupaix, A.-C. Goydadin, ZhongHua Yu, Cécile Callou, Petra Villette, Patrick Giraudoux, Li Li
Software Mentions: 2
Published: about 3 years ago

10.1186/s13072-017-0169-6

A screening system to identify transcription factors that induce binding site-directed DNA demethylation
Cited by: 40
Author(s): Tsuyoshi Suzuki, Shiori Maeda, Erina Furuhata, Yuri Shimizu, Hajime Nishimura, Mami Kishima, Harukazu Suzuki
Software Mentions: 2
Published: almost 7 years ago

10.7554/eLife.59633

Dynamically evolving novel overlapping gene as a factor in the SARS-CoV-2 pandemic
Cited by: 65
Author(s): Chase W. Nelson, Zachary Ardern, Tony L. Goldberg, Chen Meng, Chen-Hao Kuo, Christina Ludwig, Sergios‐Orestis Kolokotronis, Xinzhu Wei
Software Mentions: 2
Published: about 4 years ago

10.3389/fgene.2013.00301

The anti-miR21 antagomir, a therapeutic tool for colorectal cancer, has a potential synergistic effect by perturbing an angiogenesis-associated miR30
Cited by: 26
Author(s): Minsun Song, John J. Rossi
Software Mentions: 2
Published: almost 11 years ago

10.3389/fgene.2021.620253

Capture Sequencing to Explore and Map Rare Casein Variants in Goats
Cited by: 4
Author(s): Siham A. Rahmatalla, Danny Arends, Ammar Said Ahmed, Lubna M. A. Hassan, Stefan Krebs, Monika Reißmann, Gudrun A. Brockmann
Software Mentions: 2
Published: over 3 years ago

10.1371/journal.pgen.1005686

Comparative Genomic Analyses of the Human NPHP1 Locus Reveal Complex Genomic Architecture and Its Regional Evolution in Primates
Cited by: 21
Author(s): Bo Yuan, Pengfei Liu, Aditya Gupta, Christine R. Beck, Anusha Tejomurtula, Ian Campbell, Tomasz Gambin, Alexandra D. Simmons, Marjorie Withers, R. Alan Harris, Jeffrey Rogers, David C. Schwartz, James R. Lupski
Software Mentions: 2
Published: almost 9 years ago

10.3389/fvets.2021.650546

Who Is Dermanyssus gallinae? Genetic Structure of Populations and Critical Synthesis of the Current Knowledge
Cited by: 5
Author(s): Lise Roy, Annunziata Giangaspero, Nathalie Sleeckx, Øivind Øines
Software Mentions: 2
Published: over 3 years ago

10.1371/journal.pgen.1002339

Temporal Coordination of Gene Networks by Zelda in the Early Drosophila Embryo
Cited by: 222
Author(s): Chung Yi Nien, Hsiao Lan Liang, Stephen Butcher, Yujia Sun, Shengbo Fu, Tenzin Gocha, Nikolai Kirov, J. Robert Manak, Christine Rushlow
Software Mentions: 2
Published: almost 13 years ago

10.18632/aging.103203

NAC1 attenuates BCL6 negative autoregulation and functions as a BCL6 coactivator of FOXQ1 transcription in cancer cells
Cited by: 5
Author(s): Min Gao, Alice Laschuk Herlinger, Ren‐Chin Wu, Tian Li Wang, Ie Ming Shih, Beihua Kong, Letícia Batista Azevedo Rangel, Jin Ming Yang
Software Mentions: 2
Published: over 4 years ago

10.7717/peerj.3492

SubVis: an interactive R package for exploring the effects of multiple substitution matrices on pairwise sequence alignment
Cited by: 1
Author(s): Scott Barlowe, H.B. Coan, Robert T. Youker
Software Mentions: 2
Published: over 7 years ago

10.1186/s13073-019-0676-0

Distinct patterns of complex rearrangements and a mutational signature of microhomeology are frequently observed in PLP1 copy number gain structural variants
Cited by: 19
Author(s): Vahid Bahrambeigi, Xiaofei Song, Karen Sperle, Christine R. Beck, Hadia Hijazi, Christopher M. Grochowski, Shen Gu, Pavel Seeman, Karen Woodward, Claudia M.B. Carvalho, Grace M. Hobson, James R. Lupski
Software Mentions: 2
Published: almost 5 years ago

10.1111/jeb.13443

How clonal are clones? A quest for loss of heterozygosity during asexual reproduction in Daphnia magna
Cited by: 13
Author(s): Marinela Dukič, Daniel Berner, Christoph R. Haag, Dieter Ebert
Software Mentions: 2
Published: over 5 years ago

10.1186/1471-2164-14-846

Complex gene expression in the dragline silk producing glands of the Western black widow (Latrodectus hesperus)
Cited by: 27
Author(s): A. Kelly Lane, Cheryl Y. Hayashi, Gregg B. Whitworth, Nadia A. Ayoub
Software Mentions: 2
Published: almost 11 years ago

10.1186/1471-2164-15-750

Characteristics of replication-independent endogenous double-strand breaks in Saccharomyces cerevisiae
Cited by: 8
Author(s): Monnat Pongpanich, Maturada Patchsung, Jirapan Thongsroy, Apiwat Mutirangura
Software Mentions: 2
Published: about 10 years ago

10.1186/1471-2105-14-S11-S2

Fast discovery and visualization of conserved regions in DNA sequences using quasi-alignment
Cited by: 4
Author(s): Anurag Nagar, Michael Hahsler
Software Mentions: 2
Published: about 11 years ago

10.1038/s41598-019-52614-7

Empirical design of a variant quality control pipeline for whole genome sequencing data using replicate discordance
Cited by: 14
Author(s): Robert P. Adelson, Alan E. Renton, Wentian Li, Nir Barzilai, Gil Atzmon, Alison M. Goate, Peter Davies, Yun Freudenberg-Hua
Software Mentions: 2
Published: almost 5 years ago

10.1186/s12864-015-2265-y

Improved taxonomic assignment of human intestinal 16S rRNA sequences by a dedicated reference database
Cited by: 111
Author(s): Jarmo Ritari, Jarkko Salojärvi, Leo Lahti, Willem M. de Vos
Software Mentions: 2
Published: almost 9 years ago

10.18632/oncotarget.7589

hnRNP A1-mediated translational regulation of the G quadruplex-containing RON receptor tyrosine kinase mRNA linked to tumor progression
Cited by: 26
Author(s): Anne Cammas, Magali Lacroix-Triki, Sandra Pierredon, Morgane Le Bras, Jason S. Iacovoni, Marie-Paule Teulade-Fichou, Gilles Favre, Henri Roché, Thomas Filleron, Stefania Millevoi, Stéphan Vagner
Software Mentions: 2
Published: over 8 years ago

10.1038/s41598-020-79268-0

Methyl-CpG-binding protein 2 mediates overlapping mechanisms across brain disorders
Cited by: 9
Author(s): Snow Bach, Niamh Ryan, Paolo Guasoni, Aiden Corvin, Rania A. El-Nemr, Danyal Khan, Albert Sanfeliu, Daniela Tropea
Software Mentions: 2
Published: almost 4 years ago

10.1016/j.jmoldx.2018.07.005

Effects of Collection and Processing Procedures on Plasma Circulating Cell-Free DNA from Cancer Patients
Cited by: 75
Author(s): Bente Risberg, Dana W.Y. Tsui, Heather Biggs, Andrea Ruiz-Valdepenas Martin de Almagro, Sarah-Jane Dawson, Charlotte Hodgkin, Linda Jones, Christine Parkinson, Anna Piskorz, Francesco Marass, Dineika Chandrananda, Elizabeth Moore, James A. Morris, Vincent Plagnol, Nitzan Rosenfeld, Carlos Caldas, James D. Brenton, Davina Gale
Software Mentions: 2
Published: almost 6 years ago

10.1186/s12864-018-4695-9

Genome-wide identification of the auxin response factor gene family in Cicer arietinum
Cited by: 38
Author(s): José V. Die, J. Gil, Teresa Millán
Software Mentions: 2
Published: over 6 years ago

10.1186/s12859-015-0682-1

Odintifier - A computational method for identifying insertions of organellar origin from modern and ancient high-throughput sequencing data based on haplotype phasing
Cited by: 5
Author(s): José Alfredo Samaniego Castruita, Marie Lisandra Zepeda Mendoza, Ross Barnett, Nathan Wales, M. Thomas P. Gilbert
Software Mentions: 2
Published: about 9 years ago

10.1371/journal.pone.0185697

Indigenous species barcode database improves the identification of zooplankton
Cited by: 20
Author(s): Jianghua Yang, Xiaowei Zhang, Wanwan Zhang, Jingying Sun, Yuwei Xie, Yimin Zhang, G.A. Burton, Yu H
Software Mentions: 2
Published: about 7 years ago

10.15252/emmm.201606188

Plasmodium falciparum var genes expressed in children with severe malaria encode <scp>CIDR</scp> α1 domains
Cited by: 74
Author(s): Jakob S. Jespersen, Christian W. Wang, Sixbert I. Mkumbaye, Daniel T. R. Minja, Bent Petersen, Louise Turner, Jens E. V. Petersen, John Lusingu, Thor G. Theander, Thomas Lavstsen
Software Mentions: 2
Published: over 8 years ago

10.1038/srep43395

GS-5734 and its parent nucleoside analog inhibit Filo-, Pneumo-, and Paramyxoviruses
Cited by: 354
Author(s): Michael K. Lo, Robert Jordan, Aaron Arvey, Jawahar Sudhamsu, Punya Shrivastava-Ranjan, Anne L. Hotard, Mike Flint, Laura K. McMullan, Dustin S. Siegel, Michael O. Clarke, Richard L. Mackman, Hon Hui, Michel Perron, Adrian S. Ray, Tomás̆ Cihlář, Stuart T. Nichol, Christina F. Spiropoulou
Software Mentions: 1
Published: over 7 years ago

10.1186/1756-0500-3-337

MethVisual - visualization and exploratory statistical analysis of DNA methylation profiles from bisulfite sequencing
Cited by: 18
Author(s): Arie Zackay, Christine Steinhoff
Software Mentions: 1
Published: almost 14 years ago

10.1038/s41598-017-01808-y

Zooplankton Community Profiling in a Eutrophic Freshwater Ecosystem-Lake Tai Basin by DNA Metabarcoding
Cited by: 47
Author(s): Jianghua Yang, Xiaowei Zhang, Yuwei Xie, Chao Song, Yong Zhang, Yu H, G.A. Burton
Software Mentions: 1
Published: over 7 years ago

10.1371/journal.pone.0227180

Pan-cancer analysis of somatic mutations and epigenetic alterations in insulated neighbourhood boundaries
Cited by: 7
Author(s): Pietro Pinoli, Eirini Stamoulakatou, An-phi Nguyen, María Rodríguez Martínez, Stefano Ceri
Software Mentions: 1
Published: over 4 years ago

10.1186/1755-8794-7-27

Cellular dissection of psoriasis for transcriptome analyses and the post-GWAS era
Cited by: 41
Author(s): William R. Swindell, Philip E. Stuart, Mrinal K. Sarkar, John J. Voorhees, James T. Elder, Andrew Johnston, Jóhann E. Guðjónsson
Software Mentions: 1
Published: over 10 years ago

10.1371/journal.pone.0099808

Expansion of the Preimmune Antibody Repertoire by Junctional Diversity in Bos taurus
Cited by: 28
Author(s): Jenni Liljavirta, Mikael Niku, Tiina Pessa‐Morikawa, Anna Ekman, Antti Iivanainen
Software Mentions: 1
Published: over 10 years ago

10.1186/s12859-017-1627-7

Pan-cancer analysis of systematic batch effects on somatic sequence variations
Cited by: 11
Author(s): Ji-Hye Choi, Su Young Hong, Hyun Goo Woo
Software Mentions: 1
Published: over 7 years ago

10.1371/journal.pone.0023794

Seamless Gene Tagging by Endonuclease-Driven Homologous Recombination
Cited by: 55
Author(s): Anton Khmelinskii, Matthias Meurer, Nurlanbek Duishoev, Nicolas Delhomme, Michael Knop
Software Mentions: 1
Published: about 13 years ago

10.3389/fimmu.2020.579480

Potential CD8+ T Cell Cross-Reactivity Against SARS-CoV-2 Conferred by Other Coronavirus Strains
Cited by: 36
Author(s): Chloe H. Lee, Mariana Pereira Pinho, Paul Buckley, Isaac Woodhouse, Graham S. Ogg, Alison Simmons, Giorgio Napolitani, Hashem Koohy
Software Mentions: 1
Published: almost 4 years ago

10.7554/eLife.37750

Parvovirus minute virus of mice interacts with sites of cellular DNA damage to establish and amplify its lytic infection
Cited by: 30
Author(s): Kinjal Majumder, Juexin Wang, Maria Boftsi, Matthew S. Fuller, Jordan E Rede, Trupti Joshi, David J. Pintel
Software Mentions: 1
Published: about 6 years ago

10.1080/22221751.2020.1806735

Naturally occurring SARS-CoV-2 gene deletions close to the spike S1/S2 cleavage site in the viral quasispecies of COVID19 patients
Cited by: 51
Author(s): Cristina Andrés, Damir García-Cehic, Josep Gregori, María Piñana, Francisco Rodríguez‐Frías, Mercedes Guerrero-Murillo, Juliana Esperalba, Ariadna Rando, Lidia Goterris, María Gema Codina, Susanna Quer, Maria Carmen Martín, Magda Campins, Ricard Ferrer, Benito Almirante, Juan Ignacio Esteban, Tomàs Pumarola, Andrés Antón, Josep Quer
Software Mentions: 1
Published: almost 5 years ago

10.1038/s41423-020-0440-9

Streamlined human antibody generation and optimization by exploiting designed immunoglobulin loci in a B cell line
Cited by: 4
Author(s): Hidetaka Seo, Hitomi Masuda, Kenjiro Asagoshi, Tomoaki Uchiki, Shigehisa Kawata, Goh Sasaki, Takashi Yabuki, Shunsuke Miyai, Naoki Takahashi, Shu-ichi Hashimoto, Atsushi Sawada, Aki Takaiwa, Chika Koyama, Kanako Tamai, Kohei Kurosawa, Ke-Yi Lin, Kunihiro Ohta, Yukoh Nakazaki
Software Mentions: 1
Published: over 4 years ago

10.1371/journal.pone.0121223

Revised Timeline and Distribution of the Earliest Diverged Human Maternal Lineages in Southern Africa
Cited by: 15
Author(s): Eva Chan, Rae-Anne Hardie, Desiree C. Petersen, Karen Beeson, Riana Bornman, Andrew B. Smith, Vanessa M. Hayes
Software Mentions: 1
Published: over 9 years ago

10.1038/s42003-019-0704-z

Placental malaria vaccine candidate antigen VAR2CSA displays atypical domain architecture in some Plasmodium falciparum strains
Cited by: 25
Author(s): Justin Doritchamou, Robert Morrison, Jonathan P. Renn, José M. C. Ribeiro, Junhui Duan, Michal Fried, Patrick E. Duffy
Software Mentions: 1
Published: almost 5 years ago

10.1371/journal.pone.0044878

Computational Prediction of Polycomb-Associated Long Non-Coding RNAs
Cited by: 18
Author(s): Galina Glazko, Boris Zybailov, Igor B. Rogozin
Software Mentions: 1
Published: about 12 years ago

10.1371/journal.pone.0071039

Extinction of Hepatitis C Virus by Ribavirin in Hepatoma Cells Involves Lethal Mutagenesis
Cited by: 60
Author(s): Ana Maria Ortega-Prieto, Julie Sheldon, Ana Grande-Pérez, Héctor Tejero, Josep Gregori, Josep Quer, Juan Ignacio Esteban, Esteban Domingo, Celia Perales
Software Mentions: 1
Published: about 11 years ago

10.1371/journal.pone.0112306

Clinical Application of Estimating Hepatitis B Virus Quasispecies Complexity by Massive Sequencing: Correlation between Natural Evolution and On-Treatment Evolution
Cited by: 26
Author(s): María Homs, Andrea Caballero, Josep Gregori, David Tabernero, Josep Quer, Leonardo Nieto, Rafael Esteban, Marı́a Buti, Francisco Rodríguez‐Frías
Software Mentions: 1
Published: almost 10 years ago

10.1371/journal.pone.0083361

Ultra-Deep Pyrosequencing (UDPS) Data Treatment to Study Amplicon HCV Minor Variants
Cited by: 58
Author(s): Josep Gregori, Juan Ignacio Esteban, Meritxell Cubero, Damir García-Cehic, Celia Perales, Rosario Casillas, Miguel Álvarez-Tejado, Francisco Rodríguez‐Frías, J. Guardia, Esteban Domingo, Josep Quer
Software Mentions: 1
Published: almost 11 years ago

Projects: bioconductor: Biostrings

Papers Mentioning Biostrings 220