Virag Sharma

发表

A pilot study of bacterial genes with disrupted ORFs reveals a surprising profusion of protein sequence recoding mediated by ribosomal frameshifting and transcriptional realignment.

M. Borodovsky, J. F. Atkins, P. Baranov, 2011, Molecular biology and evolution.

A genomics approach reveals insights into the importance of gene losses for mammalian adaptations

Bjoern E. Langer, M. Hiller, Virag Sharma, 2018, Nature Communications.

Coding exon-structure aware realigner (CESAR) utilizes genome alignments for accurate comparative gene annotation

Anas Elghafari, M. Hiller, Virag Sharma, 2016, Nucleic acids research.

Convergent gene losses illuminate metabolic and physiological changes in herbivores and carnivores

M. Hiller, Virag Sharma, Nikolai Hecker, 2019, Proceedings of the National Academy of Sciences.

Convergent losses of TLR5 suggest altered extracellular flagellin detection in four mammalian lineages

M. Hiller, Virag Sharma, Nikolai Hecker, 2020, bioRxiv.

Convergent losses of TLR5 suggest altered extracellular flagellin detection in four mammalian lineages.

M. Hiller, Virag Sharma, Nikolai Hecker, 2020, Molecular biology and evolution.

Insights into Sex Chromosome Evolution and Aging from the Genome of a Short-Lived Fish

D. Chalopin, J. Volff, M. Schartl, 2015, Cell.

Retapamulin-Assisted Rib osome Profiling Reveals the Alternative Bacterial Proteome Graphical

D. Klepacki, P. Baranov, A. Mankin, 2019 .

Gene Expression-Based Identification of Antigen-Responsive CD8+ T Cells on a Single-Cell Level

E. Bonifacio, Virag Sharma, A. Dahl, 2019, Front. Immunol..

Losses of human disease-associated genes in placental mammals

M. Hiller, Virag Sharma, 2019, NAR genomics and bioinformatics.

Transition to an Aquatic Habitat Permitted the Repeated Loss of the Pleiotropic KLK8 Gene in Mammals

M. Hiller, Virag Sharma, Nikolai Hecker, 2017, Genome biology and evolution.

LeishBase: Leishmania major structural database.

Virag Sharma, S. Kaur, N. Roy, 2009 .

Retapamulin-assisted ribosome profiling reveals the alternative bacterial proteome

D. Klepacki, P. Baranov, A. Mankin, 2019, bioRxiv.

Integrating gene annotation with orthology inference at scale

K. Lindblad-Toh, M. Hiller, E. Karlsson, 2023, bioRxiv.

Functional and metabolic fitness of human CD4+ T lymphocytes during metabolic stress

E. Bonifacio, A. Ziegler, Virag Sharma, 2021, Life Science Alliance.

Maximum depth sequencing reveals an ON/OFF replication slippage switch and apparent in vivo selection for bifidobacterial pilus expression

J. F. Atkins, Virag Sharma, G. Loughran, 2022, Scientific Reports.

Loss of Enzymes in the Bile Acid Synthesis Pathway Explains Differences in Bile Composition among Mammals

M. Hiller, Virag Sharma, 2018, Genome biology and evolution.

Genes lost during the transition from land to water in cetaceans highlight genomic changes associated with aquatic adaptations

M. Hiller, M. Springer, Virag Sharma, 2019, Science Advances.

Productive mRNA stem loop-mediated transcriptional slippage: Crucial features in common with intrinsic terminators

J. F. Atkins, P. Baranov, Virag Sharma, 2015, Proceedings of the National Academy of Sciences.

Loss of RXFP2 and INSL3 genes in Afrotheria shows that testicular descent is the ancestral condition in placental mammals

M. Hiller, Virag Sharma, T. Lehmann, 2018, PLoS biology.

Resource Insights into Sex Chromosome Evolution and Aging from the Genome of a Short-Lived Fish Graphical

D. Chalopin, J. Volff, M. Schartl, 2015 .

CodonLogo: a sequence logo-based viewer for codon patterns

Gregory M. Provan, David P. Murphy, Virag Sharma, 2012, Bioinform..

Distinguishing activated T regulatory cell and T conventional cells by single‐cell technologies

E. Bonifacio, Virag Sharma, A. Eugster, 2022, Immunology.

Interspecies transcriptomics identify genes that underlie disproportionate foot growth in jerboas

M. Hiller, T. Capellini, A. Birmingham, 2021, Current Biology.

Interspecies transcriptome analyses identify genes that control the development and evolution of limb skeletal proportion

M. Hiller, A. Birmingham, Virag Sharma, 2019, bioRxiv.

Analysis of tetra- and hepta-nucleotides motifs promoting -1 ribosomal frameshifting in Escherichia coli

J. F. Atkins, P. Baranov, A. Firth, 2014, Nucleic acids research.

Increased alignment sensitivity improves the usage of genome alignments for comparative gene annotation

Michael Hiller, Virag Sharma, M. Hiller, 2017, Nucleic acids research.

CESAR 2.0 substantially improves speed and accuracy of comparative gene annotation

Michael Hiller, Virag Sharma, Peter Schwede, 2017, Bioinform..

Benchmarking solutions to the T-cell receptor epitope prediction problem: IMMREP22 workshop report

T. Mora, A. Walczak, M. Nielsen, 2022, bioRxiv.

Gene Expression-Based Identification of Antigen-Responsive CD8+ T Cells on a Single-Cell Level

E. Bonifacio, Virag Sharma, A. Dahl, 2019, bioRxiv.

Comparative de novo assembly and annotation of mantle tissue transcriptomes from the Mytilus edulis species complex (M. edulis, M. galloprovincialis, M. trossulus)

M. Hiller, Virag Sharma, C. Breusing, 2020 .

Genes lost during the transition from land to water in cetaceans highlight genomic changes involved in aquatic adaptations

M. Hiller, M. Springer, Virag Sharma, 2019, bioRxiv.

SubCellProt: Predicting Protein Subcellular Localization Using Machine Learning Approaches

Nilanjan Roy, Prabha Garg, Virag Sharma, 2009, Silico Biol..

A genomics approach reveals insights into the importance of gene losses for mammalian adaptations

Bjoern E. Langer, M. Hiller, Virag Sharma, 2018, Nature Communications.

Increased alignment sensitivity improves the usage of genome alignments for comparative gene annotation

M. Hiller, Virag Sharma, 2017, Nucleic acids research.

Coding Exon-Structure Aware Realigner (CESAR): Utilizing Genome Alignments for Comparative Gene Annotation.

Michael Hiller, Virag Sharma, M. Hiller, 2019, Methods in molecular biology.

Integrating gene annotation with orthology inference at scale

K. Lindblad-Toh, M. Hiller, E. Karlsson, 2023, bioRxiv.