Works by Bush, Stephen J

Results: 46

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

Maximum lifespan and brain size in mammals are associated with gene family size expansion related to immune system functions.

Published in:

Scientific Reports, 2025, v. 15, n. 1, p. 1, doi. 10.1038/s41598-025-98786-3

By:

Kilili, Huseyin;
Padilla-Morales, Benjamin;
Castillo-Morales, Atahualpa;
Monzón-Sandoval, Jimena;
Díaz-Barba, Karina;
Cornejo-Paramo, Paola;
Vincze, Orsolya;
Giraudeau, Mathieu;
Bush, Stephen J.;
Li, Zhidan;
Chen, Lu;
Mourkas, Evangelos;
Ancona, Sergio;
Gonzalez-Voyer, Alejandro;
Cortez, Diego;
Gutierrez, Humberto;
Székely, Tamás;
Acuña-Alonzo, Alín P.;
Urrutia, Araxi O.

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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