cran: ggseqlogo | Projects | Ecosyste.ms: Papers

10.7554/eLife.43966

Unified single-cell analysis of testis gene regulation and pathology in five mouse strains
Cited by: 91
Author(s): Min Jung, Daniel Wells, Jannette Rusch, Suhaira Ahmad, Jonathan Marchini, Simon Myers, Donald F. Conrad
Software Mentions: 22
Published: over 5 years ago

10.3390/genes12030413

Spt4 Promotes Pol I Processivity and Transcription Elongation
Cited by: 5
Author(s): Abigail K. Huffines, Yvonne J. K. Edwards, David A. Schneider
Software Mentions: 18
Published: over 3 years ago

10.3389/fimmu.2020.00082

Fc Receptor-Like 6 (FCRL6) Discloses Progenitor B Cell Heterogeneity That Correlates With Pre-BCR Dependent and Independent Pathways of Natural Antibody Selection
Cited by: 7
Author(s): Kazuhito Honjo, Woong-Jai Won, R. Glenn King, Lara Ianov, David K. Crossman, Juliet Easlick, Mikhail A. Shakhmatov, Mohamed Khass, André M. Vale, Robert P. Stephan, Ran Li, Randall S. Davis
Software Mentions: 15
Published: almost 5 years ago

10.1016/j.celrep.2020.107885

CD4+ T Cells Recognize Conserved Influenza A Epitopes through Shared Patterns of V-Gene Usage and Complementary Biochemical Features
Cited by: 9
Author(s): Alexander Greenshields‐Watson, Meriem Attaf, Bruce J. MacLachlan, Thomas Whalley, Cristina Rius, Aaron Wall, Alun G. Lloyd, Hywel Hughes, Kathryn E. Strange, Georgina H Mason, Andrea J. A. Schauenburg, Sarah Hulin-Curtis, James Geary, Yuan Chen, Sarah N. Lauder, Kathryn Smart, Dhanasekaran Vijaykrishna, Miguel L. Grau, Mikhail Shugay, Robert Andrews, Garry Dolton, P.J. Rizkallah, Awen Gallimore, Andrew K. Sewell, Andrew Godkin, David K. Cole
Software Mentions: 10
Published: over 4 years ago

10.7554/eLife.50004

Casposase structure and the mechanistic link between DNA transposition and spacer acquisition by CRISPR-Cas
Cited by: 15
Author(s): A.B. Hickman, Shweta Kailasan, Pavol Genzor, Astrid D. Haase, Fred Dyda
Software Mentions: 9
Published: almost 5 years ago

10.3389/fcell.2021.643603

Developmental Accumulation of Gene Body and Transposon Non-CpG Methylation in the Zebrafish Brain
Cited by: 8
Author(s): Samuel E. Ross, Daniel Hesselson, Ozren Bogdanović
Software Mentions: 9
Published: over 3 years ago

10.1186/s13059-021-02309-y

Deep sequencing of pre-translational mRNPs reveals hidden flux through evolutionarily conserved alternative splicing nonsense-mediated decay pathways
Cited by: 11
Author(s): Carrie Kovalak, Scott Donovan, Alicia A. Bicknell, Mihir Metkar, Melissa J. Moore
Software Mentions: 7
Published: over 3 years ago

10.1172/jci.insight.138066

Effector Vγ9Vδ2 T cell response to congenital Toxoplasma gondii infection
Cited by: 3
Author(s): Lifang Ma, Maria V. Papadopoulou, Martin Taton, Francesca Genco, Arnaud Marchant, Valeria Meroni, David Vermijlen
Software Mentions: 7
Published: about 3 years ago

10.1186/s13073-019-0695-x

FIREVAT: finding reliable variants without artifacts in human cancer samples using etiologically relevant mutational signatures
Cited by: 7
Author(s): Hyunbin Kim, Andy Jinseok Lee, Jongkeun Lee, Hyonho Chun, Young Seok Ju, Dong Ho Hong
Software Mentions: 7
Published: almost 5 years ago

10.1186/s13059-021-02437-5

SCAPTURE: a deep learning-embedded pipeline that captures polyadenylation information from 3′ tag-based RNA-seq of single cells
Cited by: 11
Author(s): Guo-Wei Li, Nan Fang, Guo-Hua Yuan, Chu-Xiao Liu, Xindong Liu, Lingling Chen, Bin Tian, Li Yang
Software Mentions: 7
Published: over 3 years ago

10.7554/eLife.42499

A combination of transcription factors mediates inducible interchromosomal contacts
Cited by: 15
Author(s): Seungsoo Kim, Maitreya J. Dunham, Jay Shendure
Software Mentions: 5
Published: over 5 years ago

10.1186/s12915-020-00769-5

Multiple links between 5-methylcytosine content of mRNA and translation
Cited by: 71
Author(s): Ulrike Schümann, He-Na Zhang, Tennille Sibbritt, Anyu Pan, Attila Horváth, Simon Gross, Susan J. Clark, Li Yang, Thomas Preiß
Software Mentions: 5
Published: over 4 years ago

10.1038/s41598-018-38458-7

High-throughput, Efficient, and Unbiased Capture of Small RNAs from Low-input Samples for Sequencing
Cited by: 15
Author(s): Cassandra D. Belair, Hu Tao, Brandon Chu, Jacob W. Freimer, Matthew R. Cooperberg, Robert Blelloch
Software Mentions: 5
Published: almost 6 years ago

10.1186/s12859-018-2489-3

A new sequence logo plot to highlight enrichment and depletion
Cited by: 43
Author(s): Kushal Kumar Dey, Dongyue Xie, Matthew Stephens
Software Mentions: 4
Published: almost 6 years ago

10.1093/molbev/msaa324

Repeated Evolution of Inactive Pseudonucleases in a Fungal Branch of the Dis3/RNase II Family of Nucleases
Cited by: 8
Author(s): Elizabeth R. Ballou, Atlanta G. Cook, Eric Wallace
Software Mentions: 4
Published: almost 4 years ago

10.1093/ve/vey033

Modeling site-specific amino-acid preferences deepens phylogenetic estimates of viral sequence divergence
Cited by: 11
Author(s): Sarah K Hilton, Jesse D. Bloom
Software Mentions: 4
Published: over 6 years ago

10.1371/journal.pbio.3000382

LATS1/2 suppress NFκB and aberrant EMT initiation to permit pancreatic progenitor differentiation
Cited by: 19
Author(s): Caitlin M. Braitsch, D. Berfin Azizoglu, Yadanar Htike, Haley R. Barlow, Ulrike Schnell, Christopher Chaney, Thomas J. Carroll, Ben Z. Stanger, Ondine Cleaver
Software Mentions: 4
Published: over 5 years ago

10.1371/journal.pcbi.1007496

Recurrent somatic mutations reveal new insights into consequences of mutagenic processes in cancer
Cited by: 15
Author(s): Miranda D. Stobbe, Gian Andri Thun, Andrea Diéguez-Docampo, Meritxell Oliva, Justin P. Whalley, Emanuele Raineri, Marta Gut
Software Mentions: 4
Published: almost 5 years ago

10.1016/j.csbj.2020.07.010

MU-PseUDeep: A deep learning method for prediction of pseudouridine sites
Cited by: 8
Author(s): Saad Khan, Fei He, Duolin Wang, Yongbing Chen, Dong Xu
Software Mentions: 4
Published: almost 5 years ago

10.1002/ece3.7037

FastD: Fast detection of insecticide target‐site mutations and overexpressed detoxification genes in insect populations from RNA‐Seq data
Cited by: 1
Author(s): Longfei Chen, Kun Lang, Mei Yang, Zhanghong Shi, Kang He, Fei Li, Huamei Xiao, Gōngyín Yè, Zhaojun Han
Software Mentions: 4
Published: about 4 years ago

10.3390/ijms21239331

Genomic and Transcriptomic Survey Provides New Insight into the Organization and Transposition Activity of Highly Expressed LTR Retrotransposons of Sunflower (Helianthus annuus L.)
Cited by: 13
Author(s): Ilya Kirov, Murad Omarov, Pavel Merkulov, Maxim Dudnikov, Sofya Gvaramiya, Elizaveta Kolganova, Р. А. Комахин, Г. И. Карлов, A. A. Soloviev
Software Mentions: 4
Published: almost 4 years ago

10.3389/fmicb.2019.01603

Next Generation DNA-Seq and Differential RNA-Seq Allow Re-annotation of the Pyrococcus furiosus DSM 3638 Genome and Provide Insights Into Archaeal Antisense Transcription
Cited by: 14
Author(s): Felix Grünberger, Robert Reichelt, Boyke Bunk, Cathrin Spröer, Jörg Overmann, Reinhard Rachel, Dina Grohmann, Winfried Hausner
Software Mentions: 3
Published: over 5 years ago

10.1371/journal.ppat.1007159

Complete functional mapping of infection- and vaccine-elicited antibodies against the fusion peptide of HIV
Cited by: 42
Author(s): Adam S. Dingens, Priyamvada Acharya, Hugh K. Haddox, Reda Rawi, Kai Xu, Gwo-Yu Chuang, Hui Wei, Baoshan Zhang, John R. Mascola, Bridget Carragher, Clinton S. Potter, Julie Overbaugh, Peter D. Kwong, Jesse D Bloom
Software Mentions: 3
Published: over 6 years ago

10.7554/eLife.34420

Mapping mutational effects along the evolutionary landscape of HIV envelope
Cited by: 87
Author(s): Hugh K. Haddox, Adam S. Dingens, Sarah K Hilton, Julie Overbaugh, Jesse D. Bloom
Software Mentions: 3
Published: over 6 years ago

10.1093/bioinformatics/btz921

Logomaker: beautiful sequence logos in Python
Cited by: 218
Author(s): Ammar Tareen, Justin B. Kinney
Software Mentions: 3
Published: almost 5 years ago

10.3389/fmolb.2021.670940

Profiling Thermus thermophilus Argonaute Guide DNA Sequence Preferences by Functional Screening
Cited by: 6
Author(s): Eric A. Hunt, Esta Tamanaha, Kevin Bonanno, Eric J. Cantor, Nathan A. Tanner
Software Mentions: 3
Published: over 3 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

10.1099/jgv.0.001491

Predicting the recombination potential of severe acute respiratory syndrome coronavirus 2 and Middle East respiratory syndrome coronavirus
Cited by: 12
Author(s): Arinjay Banerjee, Andrew C. Doxey, Benjamin Tremblay, Michael J. Mansfield, Sonu Subudhi, Jeremy A. Hirota, Matthew S. Miller, Andrew G. McArthur, Samira Mubareka, Karen Mossman
Software Mentions: 3
Published: almost 4 years ago

10.1186/s13059-019-1873-2

The majority of A-to-I RNA editing is not required for mammalian homeostasis
Cited by: 55
Author(s): Alistair M. Chalk, Scott Taylor, Jacki Heraud-Farlow, Carl R. Walkley
Software Mentions: 3
Published: almost 5 years ago

10.3390/v11030264

The Transcriptional Landscape of Marek’s Disease Virus in Primary Chicken B Cells Reveals Novel Splice Variants and Genes
Cited by: 29
Author(s): Luca D. Bertzbach, Florian Pfaff, Viktoria Isabella Pauker, Ahmed Kheimar, Dirk W. Höper, Sonja Härtle, Axel Karger, Benedikt B. Kaufer
Software Mentions: 3
Published: over 5 years ago

10.15252/embj.2018100847

Strong anion exchange‐mediated phosphoproteomics reveals extensive human non‐canonical phosphorylation
Cited by: 115
Author(s): Gemma Hardman, Simon Perkins, Philip Brownridge, Christopher J. Clarke, Dominic P. Byrne, Amy E. Campbell, Anton Kalyuzhnyy, Ashleigh C Myall, Patrick A. Eyers, Andrew R. Jones
Software Mentions: 3
Published: over 5 years ago

10.15252/msb.20209866

TATA and paused promoters active in differentiated tissues have distinct expression characteristics
Cited by: 12
Author(s): Vivekanandan Ramalingam, Malini Natarajan, Jeff Johnston, Julia Zeitlinger
Software Mentions: 3
Published: almost 4 years ago

10.1038/s42003-021-02588-y

Burkholderia PglL enzymes are Serine preferring oligosaccharyltransferases which target conserved proteins across the Burkholderia genus
Cited by: 3
Author(s): Andrew Hayes, Jessica M Lewis, Mark R. Davies, Nichollas E. Scott
Software Mentions: 3
Published: about 3 years ago

10.3390/ijms22031461

ESR1 ChIP-Seq Identifies Distinct Ligand-Free ESR1 Genomic Binding Sites in Human Hepatocytes and Liver Tissue
Cited by: 7
Author(s): Joseph M. Collins, Zhiguang Huo, Daqing Wang
Software Mentions: 2
Published: almost 4 years ago

10.1038/s42003-021-02486-3

Expression of a human cDNA in moss results in spliced mRNAs and fragmentary protein isoforms
Cited by: 8
Author(s): Oguz Top, Stella W. L. Milferstaedt, Nico van Gessel, Sebastian N. W. Hoernstein, Buğra Özdemir, Eva L. Decker, Ralf Reski
Software Mentions: 2
Published: over 3 years ago

10.1007/s00018-019-03150-0

The PCNA interaction motifs revisited: thinking outside the PIP-box
Cited by: 69
Author(s): Andreas Prestel, Nanna Wichmann, João M. Martins, Riccardo Marabini, Noah Kassem, Sebastian S. Broendum, Marit Otterlei, Olaf Nielsen, Martin Willemoës, Michael Ploug, Wouter Boomsma
Software Mentions: 2
Published: over 5 years ago

10.15252/msb.202010025

CIGAR‐seq, a CRISPR/Cas‐based method for unbiased screening of novel mRNA modification regulators
Cited by: 15
Author(s): Liang Fang, Wen Wang, Guipeng Li, Li Zhang, Jun Li, Diwen Gan, Yang Jiao, Yisen Tang, Zewen Ding, Min Zhang, Wenhao Zhang, Daqi Deng, Zhenlong Song, Qionghua Zhu, Huanhuan Cui, Yuhui Hu, Wei Chen
Software Mentions: 2
Published: about 4 years ago

10.1074/jbc.RA120.015053

Development of a novel mammalian display system for selection of antibodies against membrane proteins
Cited by: 12
Author(s): NJ Robertson, Nancy López-Antón, Shalom A. Gurjar, Hena Khalique, Zainab A. Khalaf, Siobhan Clerkin, Vaughan R. Leydon, Richard P. Parker-Manuel, Alexander Raeside, Tom Payne, Timothy D. Jones, Len Seymour, Ryan Cawood
Software Mentions: 2
Published: almost 4 years ago

10.1038/s41598-021-86217-y

Protein cleavage influences surface protein presentation in Mycoplasma pneumoniae
Cited by: 4
Author(s): Iain J. Berry, Michael Widjaja, Veronica M. Jarocki, Joel R. Steele, Matthew P. Padula, Steven P. Djordjevic
Software Mentions: 2
Published: over 3 years ago

10.1128/mBio.02119-17

The Ancient Link between G-Protein-Coupled Receptors and C-Terminal Phospholipid Kinase Domains
Cited by: 13
Author(s): Johan van den Hoogen, H.J.G. Meijer, Michael Seidl, F. Govers
Software Mentions: 2
Published: over 6 years ago

10.1186/s12864-021-07850-5

Genome-wide analysis of MYB transcription factors of Vaccinium corymbosum and their positive responses to drought stress
Cited by: 10
Author(s): Aibin Wang, Kehao Liang, Shiwen Yang, Yibo Cao, Lei Wang, Ming Zhang, Jing Zhou, Lingyun Zhang
Software Mentions: 2
Published: over 3 years ago

10.1128/mBio.00788-21

Identification of a High-Frequency Intrahost SARS-CoV-2 Spike Variant with Enhanced Cytopathic and Fusogenic Effects
Cited by: 18
Author(s): Lynda Rocheleau, Geneviève Laroche, Kathy Fu, Corina M Stewart, Abdulhamid O Mohamud, Marceline Côté, Patrick M. Giguère, Marc‐André Langlois, Martin Pelchat
Software Mentions: 1
Published: over 3 years ago

10.1038/s41598-019-40950-7

Regulation of folate and methionine metabolism by multisite phosphorylation of human methylenetetrahydrofolate reductase
Cited by: 18
Author(s): Yuxiang Zheng, Shivan Ramsamooj, Qian Li, Jared L. Johnson, Tomer M. Yaron, Klaus Sharra, Lewis C. Cantley
Software Mentions: 1
Published: over 5 years ago

10.7554/eLife.31662

Functional role of the type 1 pilus rod structure in mediating host-pathogen interactions
Cited by: 63
Author(s): Caitlin N. Spaulding, Henry L. Schreiber, Weili Zheng, Karen W. Dodson, Jennie E Hazen, Matt S. Conover, Fengbin Wang, Pontus Svenmarker, Areli Luna-Rico, Olivera Francetić, Magnus Andersson, Scott J. Hultgren, Edward H. Egelman
Software Mentions: 1
Published: almost 7 years ago

10.1038/s12276-021-00658-z

Mutational spectrum of SARS-CoV-2 during the global pandemic
Cited by: 26
Author(s): Kijong Yi, Su Yeon Kim, Thomas Bleazard, Taewoo Kim, Jeonghwan Youk, Young Seok Ju
Software Mentions: 1
Published: over 3 years ago

10.3390/molecules25153465

Custom G4 Microarrays Reveal Selective G-Quadruplex Recognition of Small Molecule BMVC: A Large-Scale Assessment of Ligand Binding Selectivity
Cited by: 15
Author(s): Guanhui Wu, Desiree Tillo, Sreejana Ray, Ta‐Chau Chang, John S. Schneekloth, Charles Vinson, Danzhou Yang
Software Mentions: 1
Published: over 4 years ago

10.1186/s12896-019-0504-z

Ex vivo evolution of human antibodies by CRISPR-X: from a naive B cell repertoire to affinity matured antibodies
Cited by: 14
Author(s): Marie‐Claire Devilder, Mélinda Moyon, Laetitia Gautreau‐Rolland, Benjamin Navet, Jeanne Perroteau, Florent Delbos, Marie-Claude Gesnel, Richard Breathnach, Xavier Saulquin
Software Mentions: 1
Published: almost 6 years ago

10.3390/vaccines8040568

Progress in L2-Based Prophylactic Vaccine Development for Protection against Diverse Human Papillomavirus Genotypes and Associated Diseases
Cited by: 18
Author(s): Pola Olczak, Richard B.S. Roden
Software Mentions: 1
Published: about 4 years ago

10.1128/mSystems.00039-20

Abundant and Diverse RNA Viruses in Insects Revealed by RNA-Seq Analysis: Ecological and Evolutionary Implications
Cited by: 57
Author(s): Haoming Wu, Rui Pang, Tong Cheng, Xue Li, Haiyan Zeng, Ling Tao, Moutong Chen, Shi Wu, Yu Ding, Jumei Zhang, Mǎng Shī, Qingping Wu
Software Mentions: 1
Published: about 4 years ago

Projects: cran: ggseqlogo

Papers Mentioning ggseqlogo 49