pypi: weblogo | Projects | Ecosyste.ms: Papers

10.1099/mgen.0.000492

Quantitative analysis of the splice variants expressed by the major hepatitis B virus genotypes
Cited by: 13
Author(s): Chun Shen Lim, Vitina Sozzi, Margaret Littlejohn, Lilly Yuen, Nadia Warner, Brigid Betz‐Stablein, Fabio Luciani, Peter Revill, Chris M. Brown
Software Mentions: 13
Published: almost 4 years ago

10.3390/v13040553

Profile of Small RNAs, vDNA Forms and Viral Integrations in Late Chikungunya Virus Infection of Aedes albopictus Mosquitoes
Cited by: 11
Author(s): Michele Marconcini, Elisa Pischedda, Vincent Houé, Umberto Palatini, Nabor Lozada-Chávez, Davide Sogliani, Anna‐Bella Failloux, Mariangela Bonizzoni
Software Mentions: 5
Published: over 3 years ago

10.1186/s12859-015-0590-4

Software for the analysis and visualization of deep mutational scanning data
Cited by: 101
Author(s): Jesse D. Bloom
Software Mentions: 5
Published: over 9 years ago

10.1002/2211-5463.12521

In silico identification and biochemical characterization of the human dicarboxylate clamp TPR protein interaction network
Cited by: 4
Author(s): Alexandra Bernadotte, Rajnish Kumar, Bengt Winblad, Pavel F. Pavlov
Software Mentions: 4
Published: about 6 years ago

10.3389/fgene.2020.566320

Transcriptomic and Epigenomic Dynamics of Honey Bees in Response to Lethal Viral Infection
Cited by: 11
Author(s): Hongmei Li-Byarlay, Humberto Boncristiani, Gary W. Howell, Jacob Herman, Lindsay V. Clark, Micheline K. Strand, David R. Tarpy, Olav Rueppell
Software Mentions: 4
Published: about 4 years ago

10.1371/journal.pgen.1002984

The Paramecium Germline Genome Provides a Niche for Intragenic Parasitic DNA: Evolutionary Dynamics of Internal Eliminated Sequences
Cited by: 142
Author(s): Olivier Arnaiz, Nathalie Mathy, Céline Baudry, Sophie Malinsky, Jean‐Marc Aury, Cyril Denby Wilkes, Olivier Garnier, Karine Labadie, Benjamin E. Lauderdale, Anne Le Mouël, Antoine Marmignon, Mariusz Nowacki, Julie Poulain, M Prajer, Patrick Wincker, Éric Meyer, Sandra Duharcourt, Laurent Duret, Mireille Bétermier, Linda Sperling
Software Mentions: 4
Published: about 12 years ago

10.1186/1471-2105-13-317

A Monte Carlo-based framework enhances the discovery and interpretation of regulatory sequence motifs
Cited by: 18
Author(s): Phillip Seitzer, Elizabeth G. Wilbanks, David Larsen, Marc T. Facciotti
Software Mentions: 4
Published: almost 12 years ago

10.1016/j.jmb.2018.06.007

The FapF Amyloid Secretion Transporter Possesses an Atypical Asymmetric Coiled Coil
Cited by: 10
Author(s): Sarah L. Rouse, Fisentzos Stylianou, Howie Wu, Jamie-Lee Berry, Lee Sewell, Rhodri M. L. Morgan, Andrea C. Sauerwein, Steve Matthews
Software Mentions: 4
Published: about 6 years ago

10.7554/eLife.37927

Six domesticated PiggyBac transposases together carry out programmed DNA elimination in Paramecium
Cited by: 36
Author(s): Julien Bischerour, Simran Bhullar, Cyril Denby Wilkes, Vinciane Régnier, Nathalie Mathy, Emeline Dubois, Aditi Singh, Estienne C. Swart, Olivier Arnaiz, Linda Sperling, Mariusz Nowacki, Mireille Bétermier
Software Mentions: 4
Published: about 6 years ago

10.1186/s12864-017-4393-z

Exploring the relationship between intron retention and chromatin accessibility in plants
Cited by: 41
Author(s): Fahad Ullah, Michael Hamilton, Anireddy S. N. Reddy, Asa Ben-Hur
Software Mentions: 3
Published: almost 7 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

10.1128/mBio.02047-18

Nucleotide Resolution Comparison of Transcription of Human Cytomegalovirus and Host Genomes Reveals Universal Use of RNA Polymerase II Elongation Control Driven by Dissimilar Core Promoter Elements
Cited by: 25
Author(s): Mrutyunjaya Parida, Kyle A. Nilson, Ming Li, Christopher B. Ball, Harrison A. Fuchs, Christine Lawson, Donal S. Luse, Jeffery L. Meier, David H. Price
Software Mentions: 3
Published: over 5 years ago

10.1002/2211-5463.12690

Comparative analysis of <scp>CDR</scp>3 regions in paired human αβ <scp>CD</scp>8 T cells
Cited by: 6
Author(s): Kun Yu, Jingwei Shi, Dan Lü, Qiong Yang
Software Mentions: 3
Published: over 5 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

10.3389/fnagi.2020.603793

Sporadic Parkinson’s Disease Potential Risk Loci Identified in Han Ancestry of Chinese Mainland
Cited by: 2
Author(s): Bo Wang, Xin Liu, Shengyuan Xu, Zheng Liu, Yong Zhu, Xiong Zhang, Renshi Xu
Software Mentions: 3
Published: almost 4 years ago

10.3390/pathogens10020242

An Integrated Sequencing Approach for Updating the Pseudorabies Virus Transcriptome
Cited by: 8
Author(s): Gábor Torma, Dóra Tombácz, Zsolt Csabai, Dániel Göbhardter, Zoltán Deim, M Snyder, Zsolt Boldogkői
Software Mentions: 3
Published: over 3 years ago

10.1371/journal.pone.0022046

Spliceosomal Intron Insertions in Genome Compacted Ray-Finned Fishes as Evident from Phylogeny of MC Receptors, Also Supported by a Few Other GPCRs
Cited by: 18
Author(s): Abhishek Kumar, Anita Bhandari, Rahul Sinha, Pankaj Goyal, Alessandro Grapputo
Software Mentions: 3
Published: over 13 years ago

10.3389/fnmol.2018.00113

The LILI Motif of M3-S2 Linkers Is a Component of the NMDA Receptor Channel Gate
Cited by: 24
Author(s): Marek Ladislav, Jiří Černý, Jan Krůšek, Martin Hořák, Aleš Balík, Ladislav Vyklicky
Software Mentions: 2
Published: over 6 years ago

10.1371/journal.pone.0073227

Functional Characterization of the Human Mariner Transposon Hsmar2
Cited by: 2
Author(s): Estel Gil-Guiñón, Assumpció Bosch, David J. Lampe, José M. Lizcano, José C. Perales, Olivier Danos, Miguel Chillón
Software Mentions: 2
Published: about 11 years ago

10.1371/journal.pcbi.1005600

Rosetta:MSF: a modular framework for multi-state computational protein design
Cited by: 38
Author(s): Patrick Löffler, Samuel Schmitz, Enrico Hupfeld, Reinhard Sterner, Rainer Merkl
Software Mentions: 2
Published: over 7 years ago

10.1534/g3.112.002881

Genomes of <i>Ashbya</i> Fungi Isolated from Insects Reveal Four Mating-Type Loci, Numerous Translocations, Lack of Transposons, and Distinct Gene Duplications
Cited by: 31
Author(s): Fred S. Dietrich, Sylvia Voegeli, Sidney Kuo, Peter Philippsen
Software Mentions: 2
Published: over 11 years ago

10.1186/s12915-017-0416-0

Ribosome signatures aid bacterial translation initiation site identification
Cited by: 22
Author(s): Adam Giess, Veronique Jonckheere, Elvis Ndah, Katarzyna Chyżyńska, Petra Van Damme, Eivind Valen
Software Mentions: 2
Published: about 7 years ago

10.1371/journal.pgen.1002390

Identification of Evolutionarily Conserved Exons as Regulated Targets for the Splicing Activator Tra2β in Development
Cited by: 61
Author(s): Sushma Nagaraja Grellscheid, Caroline Dalgliesh, Markus Storbeck, Andrew Best, Yilei Liu, Miriam Jakubik, Ylva Mende, Ingrid Ehrmann, Tomaž Curk, Kristina Roßbach, Cyril F. Bourgeois, James Stévenin, David Grellscheid, Michael S. Jackson, Brunhilde Wirth, David J. Elliott
Software Mentions: 2
Published: almost 13 years ago

10.3390/ijms21144831

Characterizing the Fused TvG6PD::6PGL Protein from the Protozoan Trichomonas vaginalis, and Effects of the NADP+ Molecule on Enzyme Stability
Cited by: 5
Author(s): Laura Morales-Luna, Beatriz Hernández-Ochoa, Edson Jiovany Ramírez-Nava, Víctor Martínez‐Rosas, Paulina Ortiz-Ramírez, Fabiola Fernández-Rosario, Abigail González‐Valdez, Noemí Cárdenas-Rodríguez, Hugo Serrano‐Posada, Sara Centeno-Leija, Roberto Arreguín-Espinosa, Miguel Cuevas-Cruz, Daniel Ortega-Cuéllar, Verónica Pérez de la Cruz, Luz María Rocha-Ramírez, Edgar Sierra-Palacios, Rosa Angélica Castillo-Rodríguez, Vanesa Vega-García, Yadira Rufino-González, Jaime Marcial-Quino, Saúl Gómez-Manzo
Software Mentions: 1
Published: over 4 years ago

10.1074/mcp.M117.067355

Phosphoproteomic Analysis Reveals the Importance of Kinase Regulation During Orbivirus Infection
Cited by: 12
Author(s): Bjorn-Patrick Mohl, Edward Emmott, Polly Roy
Software Mentions: 1
Published: about 7 years ago

10.3390/ph3103324

Allosteric Modulation of G Protein Coupled Receptors by Cytoplasmic, Transmembrane and Extracellular Ligands
Cited by: 15
Author(s): Naveena Yanamala, Judith Klein‐Seetharaman
Software Mentions: 1
Published: about 14 years ago

10.1016/j.plasmid.2007.12.001

PepA and ArgR do not regulate Cre recombination at the bacteriophage P1 loxP site
Cited by: 3
Author(s): Alasdair A. MacDonald, Yangjie Lü, Elizabeth Kilbride, Aram Akopian, Sean D. Colloms
Software Mentions: 1
Published: over 16 years ago

10.1371/journal.pone.0096931

Directed Evolution of Improved Zinc Finger Methyltransferases
Cited by: 27
Author(s): Brian Chaikind, Marc Ostermeier
Software Mentions: 1
Published: over 10 years ago

10.1371/journal.pone.0161913

A Computational Model for Predicting RNase H Domain of Retrovirus
Cited by: 4
Author(s): Sijia Wu, Xinman Zhang, Jiuqiang Han
Software Mentions: 1
Published: about 8 years ago

10.1371/journal.pone.0126248

Characterization of Mutants of Human Small Heat Shock Protein HspB1 Carrying Replacements in the N-Terminal Domain and Associated with Hereditary Motor Neuron Diseases
Cited by: 40
Author(s): Lydia K. Muranova, S.D. Weeks, S.V. Strelkov, Nikolai B. Gusev
Software Mentions: 1
Published: over 9 years ago

10.1371/journal.pone.0007627

Proteomic and Phospho-Proteomic Profile of Human Platelets in Basal, Resting State: Insights into Integrin Signaling
Cited by: 126
Author(s): Amir Qureshi, Vineet Chaoji, Dony Maiguel, Mohd Hafeez Faridi, Constantinos J. Barth, Saeed Salem, Mudita Singhal, Darren Stoub, Bryan Krastins, Mitsunori Ogihara, Mohammed J. Zaki, Vineet Gupta
Software Mentions: 1
Published: about 15 years ago

10.1371/journal.pone.0061850

A Global Transcriptional Switch between the Attack and Growth Forms of Bdellovibrio bacteriovorus
Cited by: 77
Author(s): Iris Karunker, Or Rotem, Mally Dori-Bachash, Édouard Jurkevitch, Rotem Sorek
Software Mentions: 1
Published: over 11 years ago

10.1371/journal.pone.0229812

The PP2A/4/6 subfamily of phosphoprotein phosphatases regulates DAF-16 and confers resistance to environmental stress in postreproductive adult C. elegans
Cited by: 1
Author(s): Rebecca S. Rivard, Julia Morris, Matthew J. Youngman
Software Mentions: 1
Published: almost 4 years ago

10.1186/2045-9769-3-2

Characterization of a novel cell penetrating peptide derived from human Oct4
Cited by: 23
Author(s): Eva Harreither, Hanna Rydberg, Helene L. Åmand, Vaibhav Jadhav, Lukas Fliedl, Christina Benda, Miguel A. Esteban, Duanqing Pei, Nicole Borth, Regina Grillari‐Voglauer, Oliver Hommerding, Frank Edenhofer, Bengt Nordén, Johannes Grillari
Software Mentions: 1
Published: almost 11 years ago

10.3389/fpls.2016.00868

Misannotation Awareness: A Tale of Two Gene-Groups
Cited by: 24
Author(s): Tânia Nobre, Maria Doroteia Campos, Eva Lucic-Mercy, Birgit Arnholdt‐Schmitt
Software Mentions: 1
Published: over 8 years ago

10.1534/g3.115.026849

Genome-Wide Analysis of Transposon and Retroviral Insertions Reveals Preferential Integrations in Regions of DNA Flexibility
Cited by: 17
Author(s): Pavle Vrljicak, Shijie Tao, Gaurav K. Varshney, Helen Ngoc Bao Quach, Adita Joshi, Shawn M. Burgess, Karuna Sampath
Software Mentions: 1
Published: over 8 years ago

10.1534/g3.118.200347

An Anopheles stephensi Promoter-Trap: Augmenting Genome Annotation and Functional Genomics
Cited by: 6
Author(s): William Reid, Kristina L. Pilitt, Robert T. Alford, Adriana Cervantes-Medina, Huilin Yu, Channa Aluvihare, Robert A. Harrell, David A. O’Brochta
Software Mentions: 1
Published: about 6 years ago

10.1371/journal.ppat.1006461

The Staphylococcus aureus superantigen SElX is a bifunctional toxin that inhibits neutrophil function
Cited by: 36
Author(s): Stephen W. Tuffs, David B. A. James, Jovanka Bestebroer, Amy C. Richards, Mariya I. Goncheva, Marie A. O’Shea, Bryan A. Wee, Keun Seok Seo, Patrick M. Schlievert, Andreas Lengeling, Jos A. van Strijp, Victor J. Torres, J. Ross Fitzgerald
Software Mentions: 1
Published: about 7 years ago

10.1371/journal.ppat.1006792

Effect of analytical treatment interruption and reinitiation of antiretroviral therapy on HIV reservoirs and immunologic parameters in infected individuals
Cited by: 70
Author(s): Katherine E. Clarridge, Jana Blažková, Kevin Einkauf, Mary E. Petrone, Eric W. Refsland, J. Shawn Justement, Victoria Shi, Erin Huiting, Catherine Seamon, Guinevere Q. Lee, Xu G. Yu, Susan Moir, Michael C. Sneller, Mathias Lichterfeld, Tae‐Wook Chun
Software Mentions: 1
Published: almost 7 years ago

10.1038/s41598-017-02052-0

A genome scan for milk production traits in dairy goats reveals two new mutations in Dgat1 reducing milk fat content
Cited by: 48
Author(s): Pauline Martin, Isabelle Palhière, Cyrielle Maroteau, Philippe Bardou, Kamila Canale-Tabet, Julien Sarry, Florent Woloszyn, Justine Bertrand‐Michel, Ines Racke, Hüseyin Besir, Rachel Rupp, Gwenola Tosser‐Klopp
Software Mentions: 1
Published: over 7 years ago

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