Europe PMC requires Javascript to function effectively.

Either your web browser doesn't support Javascript or it is currently turned off. In the latter case, please turn on Javascript support in your web browser and reload this page.

Search life-sciences literature (45,104,145 articles, preprints and more)

Search results

1-25 of 285 results

Sort by:

Relevance ^{Relevance: This is determined based on a ranking of criteria including term frequency, rarity of term, recency of article, whether there is a Title or Author field match, etc.}

Times cited

Date

1 2 3 Next ...

Peripheral immune cell abundance differences link blood mitochondrial DNA copy number and Parkinson's disease.
Wang L, Han J, Fearnley LG, Milton M, Rafehi H, Reid J, Gerring ZF, Masaldan S, Lang T, Speed TP, Bahlo M
NPJ Parkinsons Dis, 10(1):219, 14 Nov 2024
Cited by: 0 articles | PMID: 39543161 | PMCID: PMC11564539
Add to export list
This article is in the Europe PMC Open access subset. Refer to the copyright information in the article for licensing details.
Free full text in Europe PMC
Venetoclax Dose Escalation Rapidly Activates a BAFF/BCL-2 Survival Axis in Chronic Lymphocytic Leukemia.
Luo MX, Tan T, Trussart M, Poch A, Nguyen MT, Speed TP, Hicks DG, Bandala-Sanchez E, Peng H, Chappaz S, Slade C, Utzschneider DT, Koldej RM, Ritchie D, Strasser A, Thijssen R, Ritchie ME, Tam CSL, Lindeman GJ, [...] Gray DHD
Blood, blood.2024024341, 29 Oct 2024
Cited by: 0 articles | PMID: 39471335
Add to export list
Retinoic acid and TGF-β orchestrate organ-specific programs of tissue residency.
Obers A, Poch T, Rodrigues G, Christo SN, Gandolfo LC, Fonseca R, Zaid A, Kuai JEY, Lai H, Zareie P, Yakou MH, Dryburgh L, Burn TN, Dosser J, Buquicchio FA, Lareau CA, Walsh C, Judd L, Theodorou MR, [...] Mackay LK
Immunity, 57(11):2615-2633.e10, 14 Oct 2024
Cited by: 0 articles | PMID: 39406245
Add to export list
Myeloid-instructed CD14⁺CD4⁺T cells within the tumor microenvironment are associated with TNF⍺ signaling and prolonged survival in non-small cell lung cancer
Marceaux C, Yokote K, Gayevskiy V, Batey D, Tarasova I, Choux L, Riley L, Ribera NT, Hywood J, Christie M, Antippa P, Speed TP, Rogers KL, Phipson B, Asselin-Labat M
bioRxiv, 06 Aug 2024
Cited by: 0 articles | PPR: PPR891192
Add to export list Preprint
Unveiling Peripheral Immune Dysfunction in Parkinson’s Disease through Analysis of Blood-based Mitochondrial DNA Copy Number
Wang L, Han J, Fearnley LG, Milton M, Rafehi H, Reid J, Gerring Z, Masaldan S, Lang T, Speed TP, Bahlo M
medRxiv, 30 Apr 2024
Cited by: 0 articles | PPR: PPR845855
Add to export list Preprint
GLMsim: a GLM-based single cell RNA-seq simulator incorporating batch and biological effects
Wang J, Chen L, Thijssen R, Phipson B, Speed TP
bioRxiv, 23 Mar 2024
Cited by: 0 articles | PPR: PPR826548
Add to export list Preprint
MAssively-Parallel Flow cytometry Xplorer (MAPFX): A Toolbox for Analysing Data from the Massively-Parallel Cytometry Experiments
Liao H, Speed TP, McCarthy DJ, Salim A
bioRxiv, 03 Mar 2024
Cited by: 0 articles | PPR: PPR813666
Add to export list Preprint
Early cytokine-driven adaptation of survival pathways in lymphoid cells during targeted therapies
Luo M, Tan T, Trussart M, Poch A, Nguyen TMH, Speed TP, Hicks DG, Bandala-Sanchez E, Peng H, Chappaz S, Slade C, Utzschneider DT, Strasser A, Thijssen R, Ritchie ME, Tam CS, Lindeman G, Huang DC, Lew TE, [...] Gray DH
bioRxiv, 06 Mar 2024
Cited by: 0 articles | PPR: PPR817220
Add to export list Preprint
This article is in the Europe PMC Open access subset. Refer to the copyright information in the article for licensing details.
Free full text in Europe PMC
The current landscape and emerging challenges of benchmarking single-cell methods
Cao Y, Yu L, Torkel M, Kim S, Lin Y, Yang P, Speed TP, Ghazanfar S, Yang JYH
bioRxiv, 19 Dec 2023
Cited by: 0 articles | PPR: PPR775883
Add to export list Preprint
Full 16S and 23S rRNA gene-based,strain-level resolution of the microbiota of a mock bacterial microbiome using ONT nanopore sequencing
Woodruff CJ, Zhang Z, Speed TP
bioRxiv, 09 Feb 2024
Cited by: 0 articles | PPR: PPR803549
Add to export list Preprint
Divergent molecular networks program functionally distinct CD8⁺ skin-resident memory T cells.
Park SL, Christo SN, Wells AC, Gandolfo LC, Zaid A, Alexandre YO, Burn TN, Schröder J, Collins N, Han SJ, Guillaume SM, Evrard M, Castellucci C, Davies B, Osman M, Obers A, McDonald KM, Wang H, Mueller SN, [...] Mackay LK
Science, 382(6674):1073-1079, 30 Nov 2023
Cited by: 10 articles | PMID: 38033053
Add to export list
Establishing the Link between X-Chromosome Aberrations and TP53 Status, with Breast Cancer Patient Outcomes.
Caramia F, Speed TP, Shen H, Haupt Y, Haupt S
Cells, 12(18):2245, 11 Sep 2023
Cited by: 2 articles | PMID: 37759468 | PMCID: PMC10526523
Add to export list
This article is in the Europe PMC Open access subset. Refer to the copyright information in the article for licensing details.
Free full text in Europe PMC
sccomp: Robust differential composition and variability analysis for single-cell data.
Mangiola S, Roth-Schulze AJ, Trussart M, Zozaya-Valdés E, Ma M, Gao Z, Rubin AF, Speed TP, Shim H, Papenfuss AT
Proc Natl Acad Sci U S A, 120(33):e2203828120, 07 Aug 2023
Cited by: 4 articles | PMID: 37549298 | PMCID: PMC10438834
Add to export list
This article is in the Europe PMC Open access subset. Refer to the copyright information in the article for licensing details.
Free full text in Europe PMC
An open protocol for modeling T Cell Clonotype repertoires using TCRβ CDR3 sequences.
Gurun B, Horton W, Murugan D, Zhu B, Leyshock P, Kumar S, Byrne KT, Vonderheide RH, Margolin AA, Mori M, Spellman PT, Coussens LM, Speed TP
BMC Genomics, 24(1):349, 26 Jun 2023
Cited by: 0 articles | PMID: 37365517 | PMCID: PMC10291816
Add to export list
This article is in the Europe PMC Open access subset. Refer to the copyright information in the article for licensing details.
Free full text in Europe PMC
Spatial analysis with SPIAT and spaSim to characterize and simulate tissue microenvironments.
Feng Y, Yang T, Zhu J, Li M, Doyle M, Ozcoban V, Bass GT, Pizzolla A, Cain L, Weng S, Pasam A, Kocovski N, Huang YK, Keam SP, Speed TP, Neeson PJ, Pearson RB, Sandhu S, Goode DL, Trigos AS
Nat Commun, 14(1):2697, 15 May 2023
Cited by: 19 articles | PMID: 37188662 | PMCID: PMC10185501
Add to export list
This article is in the Europe PMC Open access subset. Refer to the copyright information in the article for licensing details.
Free full text in Europe PMC
Early immune pressure initiated by tissue-resident memory T cells sculpts tumor evolution in non-small cell lung cancer.
Weeden CE, Gayevskiy V, Marceaux C, Batey D, Tan T, Yokote K, Ribera NT, Clatch A, Christo S, Teh CE, Mitchell AJ, Trussart M, Rankin L, Obers A, McDonald JA, Sutherland KD, Sharma VJ, Starkey G, D'Costa R, [...] Asselin-Labat ML
Cancer Cell, 41(5):837-852.e6, 21 Apr 2023
Cited by: 10 articles | PMID: 37086716
Add to export list
Intratumoral CD8⁺ T cells with a tissue-resident memory phenotype mediate local immunity and immune checkpoint responses in breast cancer.
Virassamy B, Caramia F, Savas P, Sant S, Wang J, Christo SN, Byrne A, Clarke K, Brown E, Teo ZL, von Scheidt B, Freestone D, Gandolfo LC, Weber K, Teply-Szymanski J, Li R, Luen SJ, Denkert C, Loibl S, [...] Loi S
Cancer Cell, 41(3):585-601.e8, 23 Feb 2023
Cited by: 40 articles | PMID: 36827978
Add to export list
An open protocol for modeling T Cell Clonotype repertoires using TCRβ CDR3 sequences
Gurun B, Horton W, Murugan D, Zhu B, Leyshock P, Kumar S, Byrne KT, Vonderheide RH, Margolin AA, Mori M, Spellman PT, Coussens LM, Speed TP
Research Square, 16 Feb 2023
Cited by: 0 articles | PPR: PPR617744
Add to export list Preprint v1
Stem cell plasticity, acetylation of H3K14, and de novo gene activation rely on KAT7.
Kueh AJ, Bergamasco MI, Quaglieri A, Phipson B, Li-Wai-Suen CSN, Lönnstedt IM, Hu Y, Feng ZP, Woodruff C, May RE, Wilcox S, Garnham AL, Snyder MP, Smyth GK, Speed TP, Thomas T, Voss AK
Cell Rep, 42(1):111980, 14 Jan 2023
Cited by: 5 articles | PMID: 36641753
Add to export list
Genomic characterisation of hormone receptor-positive breast cancer arising in very young women.
Luen SJ, Viale G, Nik-Zainal S, Savas P, Kammler R, Dell'Orto P, Biasi O, Degasperi A, Brown LC, Láng I, MacGrogan G, Tondini C, Bellet M, Villa F, Bernardo A, Ciruelos E, Karlsson P, Neven P, Climent M, [...] Loi S
Ann Oncol, 34(4):397-409, 25 Jan 2023
Cited by: 11 articles | PMID: 36709040 | PMCID: PMC10619213
Add to export list Free full text in Europe PMC
Removing unwanted variation from large-scale RNA sequencing data with PRPS.
Molania R, Foroutan M, Gagnon-Bartsch JA, Gandolfo LC, Jain A, Sinha A, Olshansky G, Dobrovic A, Papenfuss AT, Speed TP
Nat Biotechnol, 41(1):82-95, 15 Sep 2022
Cited by: 19 articles | PMID: 36109686 | PMCID: PMC9849124
Add to export list
This article is in the Europe PMC Open access subset. Refer to the copyright information in the article for licensing details.
Free full text in Europe PMC
RUV-III-NB: normalization of single cell RNA-seq data.
Salim A, Molania R, Wang J, De Livera A, Thijssen R, Speed TP
Nucleic Acids Res, 50(16):e96, 01 Sep 2022
Cited by: 4 articles | PMID: 35758618 | PMCID: PMC9458465
Add to export list
This article is in the Europe PMC Open access subset. Refer to the copyright information in the article for licensing details.
Free full text in Europe PMC
Runx3 drives a CD8⁺ T cell tissue residency program that is absent in CD4⁺ T cells.
Fonseca R, Burn TN, Gandolfo LC, Devi S, Park SL, Obers A, Evrard M, Christo SN, Buquicchio FA, Lareau CA, McDonald KM, Sandford SK, Zamudio NM, Zanluqui NG, Zaid A, Speed TP, Satpathy AT, Mueller SN, Carbone FR, Mackay LK
Nat Immunol, 23(8):1236-1245, 26 Jul 2022
Cited by: 41 articles | PMID: 35882933
Add to export list
Estimation of tumor cell total mRNA expression in 15 cancer types predicts disease progression.
Cao S, Wang JR, Ji S, Yang P, Dai Y, Guo S, Montierth MD, Shen JP, Zhao X, Chen J, Lee JJ, Guerrero PA, Spetsieris N, Engedal N, Taavitsainen S, Yu K, Livingstone J, Bhandari V, Hubert SM, [...] Wang W
Nat Biotechnol, 40(11):1624-1633, 13 Jun 2022
Cited by: 28 articles | PMID: 35697807 | PMCID: PMC9646498
Add to export list
This article is in the Europe PMC Open access subset. Refer to the copyright information in the article for licensing details.
Free full text in Europe PMC
An open protocol for modeling T Cell Clonotype repertoires using TCRβ CDR3 sequences
Gurun B, Horton W, Murugan D, Zhu B, Leyshock P, Kumar S, Byrne KT, Vonderheide RH, Margolin AA, Mori M, Spellman PT, Coussens LM, Speed TP
bioRxiv, 01 Apr 2022
Cited by: 0 articles | PPR: PPR476147
Add to export list Preprint

1-25 of 285 results

1 2 3 Next ...

Search life-sciences literature (45,104,145 articles, preprints and more)

Search results

Peripheral immune cell abundance differences link blood mitochondrial DNA copy number and Parkinson's disease.

Venetoclax Dose Escalation Rapidly Activates a BAFF/BCL-2 Survival Axis in Chronic Lymphocytic Leukemia.

Retinoic acid and TGF-β orchestrate organ-specific programs of tissue residency.

Myeloid-instructed CD14⁺CD4⁺T cells within the tumor microenvironment are associated with TNF⍺ signaling and prolonged survival in non-small cell lung cancer

Unveiling Peripheral Immune Dysfunction in Parkinson’s Disease through Analysis of Blood-based Mitochondrial DNA Copy Number

GLMsim: a GLM-based single cell RNA-seq simulator incorporating batch and biological effects

MAssively-Parallel Flow cytometry Xplorer (MAPFX): A Toolbox for Analysing Data from the Massively-Parallel Cytometry Experiments

Early cytokine-driven adaptation of survival pathways in lymphoid cells during targeted therapies

The current landscape and emerging challenges of benchmarking single-cell methods

Full 16S and 23S rRNA gene-based,strain-level resolution of the microbiota of a mock bacterial microbiome using ONT nanopore sequencing

Divergent molecular networks program functionally distinct CD8⁺ skin-resident memory T cells.

Establishing the Link between X-Chromosome Aberrations and TP53 Status, with Breast Cancer Patient Outcomes.

sccomp: Robust differential composition and variability analysis for single-cell data.

An open protocol for modeling T Cell Clonotype repertoires using TCRβ CDR3 sequences.

Spatial analysis with SPIAT and spaSim to characterize and simulate tissue microenvironments.

Early immune pressure initiated by tissue-resident memory T cells sculpts tumor evolution in non-small cell lung cancer.

Intratumoral CD8⁺ T cells with a tissue-resident memory phenotype mediate local immunity and immune checkpoint responses in breast cancer.

An open protocol for modeling T Cell Clonotype repertoires using TCRβ CDR3 sequences

Stem cell plasticity, acetylation of H3K14, and de novo gene activation rely on KAT7.

Genomic characterisation of hormone receptor-positive breast cancer arising in very young women.

Removing unwanted variation from large-scale RNA sequencing data with PRPS.

RUV-III-NB: normalization of single cell RNA-seq data.

Runx3 drives a CD8⁺ T cell tissue residency program that is absent in CD4⁺ T cells.

Estimation of tumor cell total mRNA expression in 15 cancer types predicts disease progression.

An open protocol for modeling T Cell Clonotype repertoires using TCRβ CDR3 sequences

Partnerships & funding