Works by Bush, Stephen J

Results: 45

Editorial: Emerging talents in human and medical genomics.
Published in:
Frontiers in Genetics, 2024, p. 1, doi. 10.3389/fgene.2024.1497486
By:
- Meyer, Vanessa;
- Bush, Stephen J.;
- Botes, Angela;
- Kaur, Mandeep
Publication type:
Article
Editorial: Emerging talents in human and medical genomics.
Published in:
Frontiers in Genetics, 2024, p. 1, doi. 10.3389/fgene.2024.1497486
By:
- Meyer, Vanessa;
- Bush, Stephen J.;
- Botes, Angela;
- Kaur, Mandeep
Publication type:
Article
Genetic and genomic analyses underpin the feasibility of concomitant genetic improvement of milk yield and mastitis resistance in dairy sheep.
Published in:
PLoS ONE, 2019, v. 14, n. 11, p. 1, doi. 10.1371/journal.pone.0214346
By:
- Banos, Georgios;
- Clark, Emily L.;
- Bush, Stephen J.;
- Dutta, Prasun;
- Bramis, Georgios;
- Arsenos, Georgios;
- Hume, David A.;
- Psifidi, Androniki
Publication type:
Article
Combination of novel and public RNA-seq datasets to generate an mRNA expression atlas for the domestic chicken.
Published in:
BMC Genomics, 2018, v. 19, n. 1, p. 1, doi. 10.1186/s12864-018-4972-7
By:
- Bush, Stephen J.;
- Freem, Lucy;
- MacCallum, Amanda J.;
- O'Dell, Jenny;
- Wu, Chunlei;
- Afrasiabi, Cyrus;
- Psifidi, Androniki;
- Stevens, Mark P.;
- Smith, Jacqueline;
- Summers, Kim M.;
- Hume, David A.
Publication type:
Article
Cross-species inference of long non-coding RNAs greatly expands the ruminant transcriptome.
Published in:
Genetics Selection Evolution, 2018, v. 50, n. 1, p. N.PAG, doi. 10.1186/s12711-018-0391-0
By:
- Bush, Stephen J.;
- Muriuki, Charity;
- McCulloch, Mary E. B.;
- Farquhar, Iseabail L.;
- Clark, Emily L.;
- Hume, David A.
Publication type:
Article
ADGRE1 (EMR1, F4/80) Is a Rapidly-Evolving Gene Expressed in Mammalian Monocyte-Macrophages.
Published in:
Frontiers in Immunology, 2018, p. N.PAG, doi. 10.3389/fimmu.2018.02246
By:
- Waddell, Lindsey A.;
- Lefevre, Lucas;
- Bush, Stephen J.;
- Raper, Anna;
- Young, Rachel;
- Lisowski, Zofia M.;
- McCulloch, Mary E. B.;
- Muriuki, Charity;
- Sauter, Kristin A.;
- Clark, Emily L.;
- Irvine, Katharine M.;
- Pridans, Clare;
- Hope, Jayne C.;
- Hume, David A.
Publication type:
Article
Arginine to Glutamine Variant in Olfactomedin Like 3 (OLFML3) Is a Candidate for Severe Goniodysgenesis and Glaucoma in the Border Collie Dog Breed.
Published in:
G3: Genes | Genomes | Genetics, 2019, v. 9, n. 3, p. 943, doi. 10.1534/g3.118.200944
By:
- Pugh, Carys A.;
- Farrell, Lindsay L.;
- Carlisle, Ailsa J.;
- Bush, Stephen J.;
- Ewing, Adam;
- Trejo-Reveles, Violeta;
- Matika, Oswald;
- de Kloet, Arne;
- Walsh, Caitlin;
- Bishop, Stephen C.;
- Prendergast, James G. D.;
- Rainger, Joe;
- Schoenebeck, Jeffrey J.;
- Summers, Kim M.
Publication type:
Article
Comprehensive Transcriptional Profiling of the Gastrointestinal Tract of Ruminants from Birth to Adulthood Reveals Strong Developmental Stage Specific Gene Expression.
Published in:
G3: Genes | Genomes | Genetics, 2019, v. 9, n. 2, p. 359, doi. 10.1534/g3.118.200810
By:
- Bush, Stephen J.;
- McCulloch, Mary E. B.;
- Muriuki, Charity;
- Salavati, Mazdak;
- Davis, Gemma M.;
- Farquhar, Iseabail L.;
- Lisowski, Zofia M.;
- Archibald, Alan L.;
- Hume, David A.;
- Clark, Emily L.
Publication type:
Article
Centromere Landscapes Resolved from Hundreds of Human Genomes.
Published in:
Genomics, Proteomics & Bioinformatics, 2024, v. 22, n. 5, p. 1, doi. 10.1093/gpbjnl/qzae071
By:
- Gao, Shenghan;
- Zhang, Yimeng;
- Bush, Stephen J;
- Wang, Bo;
- Yang, Xiaofei;
- Ye, Kai
Publication type:
Article
Wild-type bone marrow cells repopulate tissue resident macrophages and reverse the impacts of homozygous CSF1R mutation.
Published in:
PLoS Genetics, 2025, v. 21, n. 1, p. 1, doi. 10.1371/journal.pgen.1011525
By:
- Carter-Cusack, Dylan;
- Huang, Stephen;
- Keshvari, Sahar;
- Patkar, Omkar;
- Sehgal, Anuj;
- Allavena, Rachel;
- Byrne, Robert A. J.;
- Morgan, B. Paul;
- Bush, Stephen J.;
- Summers, Kim M.;
- Irvine, Katharine M.;
- Hume, David A.
Publication type:
Article
Modern Solutions for Ancient Pathogens: Direct Pathogen Sequencing for Diagnosis of Lepromatous Leprosy and Cerebral Coenurosis.
Published in:
Open Forum Infectious Diseases, 2022, v. 9, n. 9, p. 1, doi. 10.1093/ofid/ofac428
By:
- Young, Bernadette C;
- Bush, Stephen J;
- Lipworth, Sam;
- George, Sophie;
- Dingle, Kate E;
- Sanderson, Nick;
- Brankin, Alice;
- Walker, Timothy;
- Sharma, Srilakshmi;
- Leong, James;
- Plaha, Puneet;
- Hofer, Monika;
- Chiodini, Peter;
- Gottstein, B;
- Furrer, Lavinia;
- Crook, Derrick;
- Brent, Andrew
Publication type:
Article
Adult Human, but Not Rodent, Spermatogonial Stem Cells Retain States with a Foetal-like Signature.
Published in:
Cells (2073-4409), 2024, v. 13, n. 9, p. 742, doi. 10.3390/cells13090742
By:
- Bush, Stephen J.;
- Nikola, Rafail;
- Han, Seungmin;
- Suzuki, Shinnosuke;
- Yoshida, Shosei;
- Simons, Benjamin D.;
- Goriely, Anne
Publication type:
Article
Evolutionary analysis of conserved non‐coding elements subsequent to whole‐genome duplication in opium poppy.
Published in:
Plant Journal, 2023, v. 116, n. 6, p. 1804, doi. 10.1111/tpj.16466
By:
- Xu, Yu;
- Bush, Stephen J.;
- Yang, Xinyi;
- Xu, Linfeng;
- Wang, Bo;
- Ye, Kai
Publication type:
Article
CSF1R-dependent macrophages control postnatal somatic growth and organ maturation.
Published in:
PLoS Genetics, 2021, v. 17, n. 6, p. 1, doi. 10.1371/journal.pgen.1009605
By:
- Keshvari, Sahar;
- Caruso, Melanie;
- Teakle, Ngari;
- Batoon, Lena;
- Sehgal, Anuj;
- Patkar, Omkar L.;
- Ferrari-Cestari, Michelle;
- Snell, Cameron E.;
- Chen, Chen;
- Stevenson, Alex;
- Davis, Felicity M.;
- Bush, Stephen J.;
- Pridans, Clare;
- Summers, Kim M.;
- Pettit, Allison R.;
- Irvine, Katharine M.;
- Hume, David A.
Publication type:
Article
Characterisation of the British honey bee metagenome.
Published in:
Nature Communications, 2018, v. 9, n. 1, p. 1, doi. 10.1038/s41467-018-07426-0
By:
- Regan, Tim;
- Barnett, Mark W.;
- Laetsch, Dominik R.;
- Bush, Stephen J.;
- Wragg, David;
- Budge, Giles E.;
- Highet, Fiona;
- Dainat, Benjamin;
- de Miranda, Joachim R.;
- Watson, Mick;
- Blaxter, Mark;
- Freeman, Tom C.
Publication type:
Article
Rats exhibit age-related mosaic loss of chromosome Y.
Published in:
Communications Biology, 2021, v. 4, n. 1, p. 1, doi. 10.1038/s42003-021-02936-y
By:
- Orta, Alberto H.;
- Bush, Stephen J.;
- Gutiérrez-Mariscal, Mariana;
- Castro-Obregón, Susana;
- Jaimes-Hoy, Lorraine;
- Grande, Ricardo;
- Vázquez, Gloria;
- Gorostieta-Salas, Elisa;
- Martínez-Pacheco, Mónica;
- Díaz-Barba, Karina;
- Cornejo-Páramo, Paola;
- Sanchez-Flores, Alejandro;
- Székely, Tamas;
- Urrutia, Araxi O.;
- Cortez, Diego
Publication type:
Article
Personalized recurrence risk assessment following the birth of a child with a pathogenic de novo mutation.
Published in:
Nature Communications, 2023, v. 14, n. 1, p. 1, doi. 10.1038/s41467-023-36606-w
By:
- Bernkopf, Marie;
- Abdullah, Ummi B.;
- Bush, Stephen J.;
- Wood, Katherine A.;
- Ghaffari, Sahar;
- Giannoulatou, Eleni;
- Koelling, Nils;
- Maher, Geoffrey J.;
- Thibaut, Loïc M.;
- Williams, Jonathan;
- Blair, Edward M.;
- Kelly, Fiona Blanco;
- Bloss, Angela;
- Burkitt-Wright, Emma;
- Canham, Natalie;
- Deng, Alexander T.;
- Dixit, Abhijit;
- Eason, Jacqueline;
- Elmslie, Frances;
- Gardham, Alice
Publication type:
Article
A Note on the UK Local BMD: A Full Name Onomastic Resource.
Published in:
Names: A Journal of Onomastics, 2024, v. 72, n. 2, p. 61, doi. 10.5195/names.2024.2543
By:
- Bush, Stephen J.
Publication type:
Article
Name Transmission Relationships in England (1838-2014).
Published in:
Names: A Journal of Onomastics, 2023, v. 71, n. 3, p. 20, doi. 10.5195/names.2023.2500
By:
- Bush, Stephen J.
Publication type:
Article
Ambivalence, Avoidance, and Appeal: Alliterative Aspects of Anglo Anthroponyms.
Published in:
Names: A Journal of Onomastics, 2020, v. 68, n. 3, p. 141, doi. 10.1080/00277738.2020.1775471
By:
- Bush, Stephen J.
Publication type:
Article
Re-using the names of newborns: symbolic reincarnation in an age of infant mortality.
Published in:
Names: A Journal of Onomastics, 2019, v. 67, n. 2, p. 100, doi. 10.1080/00277738.2018.1536186
By:
- Bush, Stephen J.
Publication type:
Article
A high resolution atlas of gene expression in the domestic sheep (Ovis aries).
Published in:
PLoS Genetics, 2017, v. 13, n. 9, p. 1, doi. 10.1371/journal.pgen.1006997
By:
- Clark, Emily L.;
- Bush, Stephen J.;
- McCulloch, Mary E. B.;
- Farquhar, Iseabail L.;
- Young, Rachel;
- Lefevre, Lucas;
- Pridans, Clare;
- Tsang, Hiu;
- Wu, Chunlei;
- Afrasiabi, Cyrus;
- Watson, Mick;
- Whitelaw, C. Bruce;
- Freeman, Tom C.;
- Summers, Kim M.;
- Archibald, Alan L.;
- Hume, David A.
Publication type:
Article
Network analysis of transcriptomic diversity amongst resident tissue macrophages and dendritic cells in the mouse mononuclear phagocyte system.
Published in:
PLoS Biology, 2020, v. 18, n. 10, p. 1, doi. 10.1371/journal.pbio.3000859
By:
- Summers, Kim M.;
- Bush, Stephen J.;
- Hume, David A.
Publication type:
Article
Generation and network analysis of an RNA-seq transcriptional atlas for the rat.
Published in:
NAR Genomics & Bioinformatics, 2022, v. 4, n. 1, p. 1, doi. 10.1093/nargab/lqac017
By:
- Summers, Kim M;
- Bush, Stephen J;
- Wu, Chunlei;
- Hume, David A
Publication type:
Article
Optimization of next-generation sequencing transcriptome annotation for species lacking sequenced genomes.
Published in:
Molecular Ecology Resources, 2016, v. 16, n. 2, p. 446, doi. 10.1111/1755-0998.12465
By:
- Ockendon, Nina F.;
- O'Connell, Lauren A.;
- Bush, Stephen J.;
- Monzón‐Sandoval, Jimena;
- Barnes, Holly;
- Székely, Tamás;
- Hofmann, Hans A.;
- Dorus, Steve;
- Urrutia, Araxi O.
Publication type:
Article
Correcting for Differential Transcript Coverage Reveals a Strong Relationship between Alternative Splicing and Organism Complexity.
Published in:
Molecular Biology & Evolution, 2014, v. 31, n. 6, p. 1402, doi. 10.1093/molbev/msu083
By:
- Chen, Lu;
- Bush, Stephen J.;
- Tovar-Corona, Jaime M.;
- Castillo-Morales, Atahualpa;
- Urrutia, Araxi O.
Publication type:
Article
Presence–Absence Variation in A. thaliana Is Primarily Associated with Genomic Signatures Consistent with Relaxed Selective Constraints.
Published in:
Molecular Biology & Evolution, 2014, v. 31, n. 1, p. 59, doi. 10.1093/molbev/mst166
By:
- Bush, Stephen J.;
- Castillo-Morales, Atahualpa;
- Tovar-Corona, Jaime M.;
- Chen, Lu;
- Kover, Paula X.;
- Urrutia, Araxi O.
Publication type:
Article
Haplotype-resolved assemblies and variant benchmark of a Chinese Quartet.
Published in:
Genome Biology, 2023, v. 24, n. 1, p. 1, doi. 10.1186/s13059-023-03116-3
By:
- Jia, Peng;
- Dong, Lianhua;
- Yang, Xiaofei;
- Wang, Bo;
- Bush, Stephen J.;
- Wang, Tingjie;
- Lin, Jiadong;
- Wang, Songbo;
- Zhao, Xixi;
- Xu, Tun;
- Che, Yizhuo;
- Dang, Ningxin;
- Ren, Luyao;
- Zhang, Yujing;
- Wang, Xia;
- Liang, Fan;
- Wang, Yang;
- Ruan, Jue;
- Xia, Han;
- Zheng, Yuanting
Publication type:
Article
Quantitative trait loci and transcriptome signatures associated with avian heritable resistance to Campylobacter.
Published in:
Scientific Reports, 2021, v. 11, n. 1, p. 1, doi. 10.1038/s41598-020-79005-7
By:
- Psifidi, Androniki;
- Kranis, Andreas;
- Rothwell, Lisa M.;
- Bremner, Abi;
- Russell, Kay;
- Robledo, Diego;
- Bush, Stephen J.;
- Fife, Mark;
- Hocking, Paul M.;
- Banos, Georgios;
- Hume, David A.;
- Kaufman, Jim;
- Bailey, Richard A.;
- Avendano, Santiago;
- Watson, Kellie A.;
- Kaiser, Pete;
- Stevens, Mark. P.
Publication type:
Article
Expression of Calcification and Extracellular Matrix Genes in the Cardiovascular System of the Healthy Domestic Sheep (Ovis aries).
Published in:
Frontiers in Genetics, 2020, v. 11, p. N.PAG, doi. 10.3389/fgene.2020.00919
By:
- Tsang, Hiu-Gwen;
- Clark, Emily L.;
- Markby, Greg R.;
- Bush, Stephen J.;
- Hume, David A.;
- Corcoran, Brendan M.;
- MacRae, Vicky E.;
- Summers, Kim M.
Publication type:
Article
Functional Annotation of the Transcriptome of the Pig, Sus scrofa , Based Upon Network Analysis of an RNAseq Transcriptional Atlas.
Published in:
Frontiers in Genetics, 2020, v. 10, p. 1, doi. 10.3389/fgene.2019.01355
By:
- Summers, Kim M.;
- Bush, Stephen J.;
- Wu, Chunlei;
- Su, Andrew I.;
- Muriuki, Charity;
- Clark, Emily L.;
- Finlayson, Heather A.;
- Eory, Lel;
- Waddell, Lindsey A.;
- Talbot, Richard;
- Archibald, Alan L.;
- Hume, David A.
Publication type:
Article
Analysis of the Progeny of Sibling Matings Reveals Regulatory Variation Impacting the Transcriptome of Immune Cells in Commercial Chickens.
Published in:
Frontiers in Genetics, 2019, v. 10, p. 1, doi. 10.3389/fgene.2019.01032
By:
- Freem, Lucy;
- Summers, Kim M.;
- Gheyas, Almas A.;
- Psifidi, Androniki;
- Boulton, Kay;
- MacCallum, Amanda;
- Harne, Rakhi;
- O'Dell, Jenny;
- Bush, Stephen J.;
- Hume, David A.
Publication type:
Article
A Mini-Atlas of Gene Expression for the Domestic Goat (Capra hircus).
Published in:
Frontiers in Genetics, 2019, v. 10, p. 1, doi. 10.3389/fgene.2019.01080
By:
- Muriuki, Charity;
- Bush, Stephen J.;
- Salavati, Mazdak;
- McCulloch, Mary E.B.;
- Lisowski, Zofia M.;
- Agaba, Morris;
- Djikeng, Appolinaire;
- Hume, David A.;
- Clark, Emily L.
Publication type:
Article
Elimination of Reference Mapping Bias Reveals Robust Immune Related Allele-Specific Expression in Crossbred Sheep.
Published in:
Frontiers in Genetics, 2019, p. 1, doi. 10.3389/fgene.2019.00863
By:
- Salavati, Mazdak;
- Bush, Stephen J.;
- Palma-Vera, Sergio;
- McCulloch, Mary E. B.;
- Hume, David A.;
- Clark, Emily L.
Publication type:
Article
A Gene Expression Atlas of the Domestic Water Buffalo (Bubalus bubalis).
Published in:
Frontiers in Genetics, 2019, p. 1, doi. 10.3389/fgene.2019.00668
By:
- Young, Rachel;
- Lefevre, Lucas;
- Bush, Stephen J.;
- Joshi, Akshay;
- Singh, Salam Herojeet;
- Jadhav, Santosh Kumar;
- Dhanikachalam, Velu;
- Lisowski, Zofia M.;
- Iamartino, Daniela;
- Summers, Kim M.;
- Williams, John L.;
- Archibald, Alan L.;
- Gokhale, Suresh;
- Kumar, Satish;
- Hume, David A.
Publication type:
Article
MeDAS: a Metazoan Developmental Alternative Splicing database.
Published in:
Nucleic Acids Research, 2021, v. 49, n. D1, p. D144, doi. 10.1093/nar/gkaa886
By:
- Li, Zhidan;
- Zhang, Yiming;
- Bush, Stephen J;
- Tang, Chao;
- Chen, Li;
- Zhang, Dan;
- Urrutia, Araxi O;
- Lin, Jing-wen;
- Chen, Lu
Publication type:
Article
Network analysis of the social and demographic influences on name choice within the UK (1838-2016).
Published in:
PLoS ONE, 2018, v. 13, n. 10, p. 1, doi. 10.1371/journal.pone.0205759
By:
- Bush, Stephen J.;
- Powell-Smith, Anna;
- Freeman, Tom C.
Publication type:
Article
Linezolid for Infants and Toddlers With Disseminated Tuberculosis: First Steps.
Published in:
Clinical Infectious Diseases, 2016, v. 63, p. S80, doi. 10.1093/cid/ciw482
By:
- Deshpande, Devyani;
- Srivastava, Shashikant;
- Pasipanodya, Jotam G.;
- Bush, Stephen J.;
- Nuermberger, Eric;
- Swaminathan, Soumya;
- Gumbo, Tawanda
Publication type:
Article
Near telomere-to-telomere genome assemblies of two Chlorella species unveil the composition and evolution of centromeres in green algae.
Published in:
BMC Genomics, 2024, v. 25, n. 1, p. 1, doi. 10.1186/s12864-024-10280-8
By:
- Wang, Bo;
- Jia, Yanyan;
- Dang, Ningxin;
- Yu, Jie;
- Bush, Stephen J.;
- Gao, Shenghan;
- He, Wenxi;
- Wang, Sirui;
- Guo, Hongtao;
- Yang, Xiaofei;
- Ma, Weimin;
- Ye, Kai
Publication type:
Article
Transcriptomic Analysis of Rat Macrophages.
Published in:
Frontiers in Immunology, 2021, v. 11, p. N.PAG, doi. 10.3389/fimmu.2020.594594
By:
- Pridans, Clare;
- Irvine, Katharine M.;
- Davis, Gemma M.;
- Lefevre, Lucas;
- Bush, Stephen J.;
- Hume, David A.
Publication type:
Article
Contrasting gene‐level signatures of selection with reproductive fitness.
Published in:
Molecular Ecology, 2022, v. 31, n. 5, p. 1515, doi. 10.1111/mec.16329
By:
- Bush, Stephen J.;
- Murren, Courtney J.;
- Urrutia, Araxi O.;
- Kover, Paula X.
Publication type:
Article
Lineage-specific sequence evolution and exon edge conservation partially explain the relationship between evolutionary rate and expression level in A. thaliana.
Published in:
Molecular Ecology, 2015, v. 24, n. 12, p. 3093, doi. 10.1111/mec.13221
By:
- Bush, Stephen J.;
- Kover, Paula X.;
- Urrutia, Araxi O.
Publication type:
Article
De novo and somatic structural variant discovery with SVision-pro.
Published in:
Nature Biotechnology, 2025, v. 43, n. 2, p. 181, doi. 10.1038/s41587-024-02190-7
By:
- Wang, Songbo;
- Lin, Jiadong;
- Jia, Peng;
- Xu, Tun;
- Li, Xiujuan;
- Liu, Yuezhuangnan;
- Xu, Dan;
- Bush, Stephen J.;
- Meng, Deyu;
- Ye, Kai
Publication type:
Article
Spatial Network Mapping of Pulmonary Multidrug-Resistant Tuberculosis Cavities Using RNA Sequencing.
Published in:
2019
By:
- Dheda, Keertan;
- Lenders, Laura;
- Srivastava, Shashikant;
- Magombedze, Gesham;
- Wainwright, Helen;
- Raj, Prithvi;
- Bush, Stephen J.;
- Pollara, Gabriele;
- Steyn, Rachelle;
- Davids, Malika;
- Pooran, Anil;
- Pennel, Timothy;
- Linegar, Anthony;
- McNerney, Ruth;
- Moodley, Loven;
- Pasipanodya, Jotam G.;
- Turner, Carolin T.;
- Noursadeghi, Mahdad;
- Warren, Robin M.;
- Wakeland, Edward
Publication type:
journal article
Integration of quantitated expression estimates from polyA-selected and rRNAdepleted RNA-seq libraries.
Published in:
BMC Bioinformatics, 2017, v. 18, p. 1, doi. 10.1186/s12859-017-1714-9
By:
- Bush, Stephen J.;
- McCulloch, Mary E. B.;
- Summers, Kim M.;
- Hume, David A.;
- Clark, Emily L.
Publication type:
Article