By Dr David Humphreys

Journal articles

Zhuang X; Wang Q; Joost S; Ferrena A; Humphreys DT; Li Z; Blum M; Bastl K; Ding S; Landais Y; Zhan Y; Zhao Y; Chaligne R; Lee J-H; Carrasco SE; Bhanot UK; Koche RP; Bott MJ; Katajisto P; Soto-Feliciano YM; Pisanic T; Thomas T; Zheng D; Wong ES; Tammela T, 2024, 'Aging limits stemness and tumorigenesis in the lung by reprogramming iron homeostasis.', bioRxiv, http://dx.doi.org/10.1101/2024.06.23.600305

Patrick R; Janbandhu V; Tallapragada V; Tan SSM; McKinna EE; Contreras O; Ghazanfar S; Humphreys DT; Murray NJ; Tran YTH; Hume RD; Chong JJH; Harvey RP, 2024, 'Integration mapping of cardiac fibroblast single-cell transcriptomes elucidates cellular principles of fibrosis in diverse pathologies', Science Advances, 10, http://dx.doi.org/10.1126/sciadv.adk8501

Lewis A; Humphreys DT; Pan-Castillo B; Berti G; Felice C; Gordon H; Gadhok R; Nijhuis A; Mehta S S; Eleid L; Iqbal S; Armuzzi A; Minicozzi A; Giannoulatou E; Chinaleong J; Feakins R; Sagi-Kiss V; Barisic D; Koufaki MI; Bundy JG; Lindsay JO; Silver A, 2024, 'Epigenetic and Metabolic Reprogramming of Fibroblasts in Crohn's Disease Strictures Reveals Histone Deacetylases as Therapeutic Targets', Journal of Crohn's and Colitis, 18, pp. 895 - 907, http://dx.doi.org/10.1093/ecco-jcc/jjad209

Humphreys DT; Lewis A; Pan-Castillo B; Berti G; Mein C; Wozniak E; Gordon H; Gadhok R; Minicozzi A; ChinAleong J; Feakins R; Giannoulatou E; James LK; Stagg AJ; Lindsay JO; Silver A, 2024, 'Single cell sequencing data identify distinct B cell and fibroblast populations in stricturing Crohn's disease', Journal of Cellular and Molecular Medicine, 28, http://dx.doi.org/10.1111/jcmm.18344

Zhuang X; Wang Q; Joost S; Ferrena A; Humphreys DT; Li Z; Blum M; Krause K; Ding S; Landais Y; Zhan Y; Zhao Y; Chaligne R; Lee JH; Carrasco SE; Bhanot UK; Koche RP; Bott MJ; Katajisto P; Soto-Feliciano YM; Pisanic T; Thomas T; Zheng D; Wong ES; Tammela T, 2024, 'Ageing limits stemness and tumorigenesis by reprogramming iron homeostasis', Nature, http://dx.doi.org/10.1038/s41586-024-08285-0

Mullari M; Fossat N; Skotte NH; Asenjo-Martinez A; Humphreys DT; Bukh J; Kirkeby A; Scheel TKH; Nielsen ML, 2023, 'Characterising the RNA-binding protein atlas of the mammalian brain uncovers RBM5 misregulation in mouse models of Huntington’s disease', Nature Communications, 14, http://dx.doi.org/10.1038/s41467-023-39936-x

Murtha LA; Hardy SA; Mabotuwana NS; Bigland MJ; Bailey T; Raguram K; Liu S; Ngo DT; Sverdlov AL; Tomin T; Birner-Gruenberger R; Hume RD; Iismaa SE; Humphreys DT; Patrick R; Chong JJH; Lee RJ; Harvey RP; Graham RM; Rainer PP; Boyle AJ, 2023, 'Fibulin-3 is necessary to prevent cardiac rupture following myocardial infarction', Scientific Reports, 13, http://dx.doi.org/10.1038/s41598-023-41894-9

Chiang IKN; Humphrey D; Mills RJ; Kaltzis P; Pachauri S; Graus M; Saha D; Wu Z; Young P; Sim CB; Davidson T; Hernandez-Garcia A; Shaw CA; Renwick A; Scott DA; Porrello ER; Wong ES; Hudson JE; Red-Horse K; del Monte-Nieto G; Francois M, 2023, 'Sox7-positive endothelial progenitors establish coronary arteries and govern ventricular compaction', EMBO Reports, 24, http://dx.doi.org/10.15252/embr.202255043

Moradi Marjaneh M; Kirk EP; Patrick R; Alankarage D; Humphreys DT; Del Monte-Nieto G; Cornejo-Paramo P; Janbandhu V; Doan TB; Dunwoodie SL; Wong ES; Moran C; Martin ICA; Thomson PC; Harvey RP, 2023, 'Quantitative trait and transcriptome analysis of genetic complexity underpinning cardiac interatrial septation in mice using an advanced intercross line', eLife, 12, http://dx.doi.org/10.7554/eLife.83606

Ridone P; Ishida T; Lin A; Humphreys DT; Giannoulatou E; Sowa Y; Baker MAB, 2022, 'The rapid evolution of flagellar ion selectivity in experimental populations of E. coli', Science Advances, 8, http://dx.doi.org/10.1126/sciadv.abq2492

Alankarage D; Enriquez A; Steiner RD; Raggio C; Higgins M; Milnes D; Humphreys DT; Duncan EL; Sparrow DB; Giampietro PF; Chapman G; Dunwoodie SL, 2022, 'Myhre syndrome is caused by dominant-negative dysregulation of SMAD4 and other co-factors', Differentiation, 128, pp. 1 - 12, http://dx.doi.org/10.1016/j.diff.2022.09.002

Nicks AM; Holman SR; Chan AY; Tsang M; Young PE; Humphreys DT; Naqvi N; Husain A; Li M; Smith NJ; Iismaa SE; Graham RM, 2022, 'Standardised method for cardiomyocyte isolation and purification from individual murine neonatal, infant, and adult hearts', Journal of Molecular and Cellular Cardiology, 170, pp. 47 - 59, http://dx.doi.org/10.1016/j.yjmcc.2022.05.012

Tarr I; Hesselson S; Iismaa SE; Rath E; Monger S; Troup M; Mishra K; Wong CMY; Hsu PC; Junday K; Humphreys DT; Adlam D; Webb TR; Baranowska-Clarke AA; Hamby SE; Carss KJ; Samani NJ; Bax M; McGrath-Cadell L; Kovacic JC; Dunwoodie SL; Fatkin D; Muller DWM; Graham RM; Giannoulatou E, 2022, 'Exploring the Genetic Architecture of Spontaneous Coronary Artery Dissection Using Whole-Genome Sequencing', Circulation: Genomic and Precision Medicine, 15, pp. 267 - 277, http://dx.doi.org/10.1161/CIRCGEN.121.003527

Yang A; Alankarage D; Cuny H; Ip EKK; Almog M; Lu J; Das D; Enriquez A; Szot JO; Humphreys DT; Blue GM; Ho JWK; Winlaw DS; Dunwoodie SL; Giannoulatou E, 2022, 'CHDgene: A Curated Database for Congenital Heart Disease Genes', Circulation: Genomic and Precision Medicine, 15, pp. E003539 - E003539, http://dx.doi.org/10.1161/CIRCGEN.121.003539

Janbandhu V; Tallapragada V; Patrick R; Li Y; Abeygunawardena D; Humphreys DT; Martin EMMA; Ward AO; Contreras O; Farbehi N; Yao E; Du J; Dunwoodie SL; Bursac N; Harvey RP, 2022, 'Hif-1a suppresses ROS-induced proliferation of cardiac fibroblasts following myocardial infarction', Cell Stem Cell, 29, pp. 281 - 297.e12, http://dx.doi.org/10.1016/j.stem.2021.10.009

Nicks AM; Holman SR; Chan AY; Pang C-HJ; Tsang M; Naqvi N; Husain A; Li M; Humphreys DT; Smith NJ; Iismaa SE; Graham RM, 2021, 'Abstract 11948: A Standardized Method to Isolate and Purify Cardiomyocytes from Individual Mouse Hearts Irrespective of Postnatal Age', Circulation, 144, http://dx.doi.org/10.1161/circ.144.suppl_1.11948

Ogawa M; Geng FS; Humphreys DT; Kristianto E; Sheng DZ; Hui SP; Zhang Y; Sugimoto K; Nakayama M; Zheng D; Hesselson D; Hodson MP; Bogdanovic O; Kikuchi K, 2021, 'Krüppel-like factor 1 is a core cardiomyogenic trigger in zebrafish', Science, 372, http://dx.doi.org/10.1126/science.abe2762

Ridone P; Ishida T; Lin A; Humphreys D; Giannoulatou E; Sowa Y; Baker M, 2021, 'The rapid evolution of flagellar ion-selectivity in experimental populations ofE. coli', , http://dx.doi.org/10.1101/2021.01.26.427765

Santiago C; Huttner I; Chand R; Humphreys D; Young P; Ward A; Fatkin D, 2021, 'TTNtv Carriers do not Have Increased Susceptibility to Chemotherapy-Induced Cardiomyopathy', Heart, Lung and Circulation, 30, pp. S97 - S97, http://dx.doi.org/10.1016/j.hlc.2021.06.018

Martin EMMA; Enriquez A; Sparrow DB; Humphreys DT; McInerney-Leo AM; Leo PJ; Duncan EL; Iyer KR; Greasby JA; Ip E; Giannoulatou E; Sheng D; Wohler E; Dimartino C; Amiel J; Capri Y; Lehalle D; Mory A; Wilnai Y; Lebenthal Y; Gharavi AG; Krzemień GG; Miklaszewska M; Steiner RD; Raggio C; Blank R; Baris Feldman H; Milo Rasouly H; Sobreira NLM; Jobling R; Gordon CT; Giampietro PF; Dunwoodie SL; Chapman G, 2020, 'Heterozygous loss of WBP11 function causes multiple congenital defects in humans and mice', Human Molecular Genetics, 29, pp. 3662 - 3678, http://dx.doi.org/10.1093/hmg/ddaa258

Patrick R; Humphreys DT; Janbandhu V; Oshlack A; Ho JWK; Harvey RP; Lo KK, 2020, 'Sierra: Discovery of differential transcript usage from polyA-captured single-cell RNA-seq data', Genome Biology, 21, http://dx.doi.org/10.1186/s13059-020-02071-7

Santiago C; Chand R; Humphreys D; Young P; Ward A; Huttner I; Fatkin D, 2020, '002 Titin Truncation Provides a Sensitised Template for Cardio-Depressant Effects of Alcohol', Heart, Lung and Circulation, 29, pp. S37 - S38, http://dx.doi.org/10.1016/j.hlc.2020.09.009

Humphreys DT; Fossat N; Demuth M; Tam PPL; Ho JWK, 2019, 'Ularcirc: Visualization and enhanced analysis of circular RNAs via back and canonical forward splicing', Nucleic Acids Research, 47, http://dx.doi.org/10.1093/nar/gkz718

Alankarage D; Ip E; Szot JO; Munro J; Blue GM; Harrison K; Cuny H; Enriquez A; Troup M; Humphreys DT; Wilson M; Harvey RP; Sholler GF; Graham RM; Ho JWK; Kirk EP; Pachter N; Chapman G; Winlaw DS; Giannoulatou E; Dunwoodie SL, 2019, 'Identification of clinically actionable variants from genome sequencing of families with congenital heart disease', Genetics in Medicine, 21, pp. 1111 - 1120, http://dx.doi.org/10.1038/s41436-018-0296-x

Coleman JLJ; Mouat MA; Wu J; Jancovski N; Bassi JK; Chan AY; Humphreys DT; Mrad N; Yu ZY; Ngo T; Iismaa S; Dos Remedios CG; Feneley MP; Allen AM; Graham RM; Smith NJ, 2018, 'Orphan receptor GPR37L1 contributes to the sexual dimorphism of central cardiovascular control', Biology of Sex Differences, 9, pp. 14, http://dx.doi.org/10.1186/s13293-018-0173-y

Szot JO; Cuny H; Blue GM; Humphreys DT; Ip E; Harrison K; Sholler GF; Giannoulatou E; Leo P; Duncan EL; Sparrow DB; Ho JWK; Graham RM; Pachter N; Chapman G; Winlaw DS; Dunwoodie SL, 2018, 'A Screening Approach to Identify Clinically Actionable Variants Causing Congenital Heart Disease in Exome Data', Circulation. Genomic and precision medicine, 11, pp. e001978, http://dx.doi.org/10.1161/CIRCGEN.117.001978

Humphreys D; Fossat N; Tam P; Ho J, 2018, 'Ularcirc: Visualisation and enhanced analysis of circular RNAs via back and canonical forward splicing', , http://dx.doi.org/10.1101/318436

Shi H; Enriquez A; Rapadas M; Martin EMMA; Wang R; Moreau J; Lim CK; Szot JO; Ip E; Hughes JN; Sugimoto K; Humphreys DT; McInerney-Leo AM; Leo PJ; Maghzal GJ; Halliday J; Smith J; Colley A; Mark PR; Collins F; Sillence DO; Winlaw DS; Ho JWK; Guillemin GJ; Brown MA; Kikuchi K; Thomas PQ; Stocker R; Giannoulatou E; Chapman G; Duncan EL; Sparrow DB; Dunwoodie SL, 2017, 'NAD deficiency, congenital malformations, and niacin supplementation', New England Journal of Medicine, 377, pp. 544 - 552, http://dx.doi.org/10.1056/NEJMoa1616361

Muthiah K; Humphreys DT; Robson D; Dhital K; Spratt P; Jansz P; Macdonald PS; Hayward CS, 2017, 'Longitudinal structural, functional, and cellular myocardial alterations with chronic centrifugal continuous-flow left ventricular assist device support', Journal of Heart and Lung Transplantation, 36, pp. 722 - 731, http://dx.doi.org/10.1016/j.healun.2016.05.017

Blue GM; Humphreys D; Szot J; Major J; Chapman G; Bosman A; Kirk EP; Sholler GF; Harvey RP; Dunwoodie SL; Winlaw DS, 2017, 'The promises and challenges of exome sequencing in familial, non-syndromic congenital heart disease', International Journal of Cardiology, 230, pp. 155 - 163, http://dx.doi.org/10.1016/j.ijcard.2016.12.024

Cropley JE; Eaton SA; Aiken A; Young PE; Giannoulatou E; Ho JWK; Buckland ME; Keam SP; Hutvagner G; Humphreys DT; Langley KG; Henstridge DC; Martin DIK; Febbraio MA; Suter CM, 2016, 'Male-lineage transmission of an acquired metabolic phenotype induced by grand-paternal obesity', Molecular Metabolism, 5, pp. 699 - 708, http://dx.doi.org/10.1016/j.molmet.2016.06.008

Soetanto R; Hynes CJ; Patel HR; Humphreys DT; Evers M; Duan G; Parker BJ; Archer SK; Clancy JL; Graham RM; Beilharz TH; Smith NJ; Preiss T, 2016, 'Role of miRNAs and alternative mRNA 3'-end cleavage and polyadenylation of their mRNA targets in cardiomyocyte hypertrophy', Biochimica et Biophysica Acta - Gene Regulatory Mechanisms, 1859, pp. 744 - 756, http://dx.doi.org/10.1016/j.bbagrm.2016.03.010

Lie S; Morrison JL; Williams-Wyss O; Suter CM; Humphreys DT; Ozanne SE; Zhang S; Maclaughlin SM; Kleemann DO; Walker SK; Roberts CT; McMillen IC, 2016, 'Impact of maternal undernutrition around the time of conception on factors regulating hepatic lipid metabolism and microRNAs in singleton and twin fetuses', American Journal of Physiology - Endocrinology and Metabolism, 310, pp. E148 - E159, http://dx.doi.org/10.1152/ajpendo.00600.2014

Cropley J; Eaton S; Aiken A; Young P; Giannoulatou E; Ho JWK; Buckland M; Keam S; Hutvagner G; Humphreys D; Langley K; Henstridge D; Martin D; Febbraio M; Suter C, 2016, 'Grand paternal inheritance of an acquired metabolic trait induced by ancestral obesity is associated with sperm RNA', , http://dx.doi.org/10.1101/042101

Lie S; Morrison JL; Williams-Wyss O; Suter CM; Humphreys DT; Ozanne SE; Zhang S; MacLaughlin SM; Kleemann DO; Walker SK; Roberts CT; McMillen IC, 2015, 'Impact of periconceptional and preimplantation undernutrition on factors regulating myogenesis and protein synthesis in muscle of singleton and twin fetal sheep', Physiological Reports, 3, http://dx.doi.org/10.14814/phy2.12495

Djordjevic D; Deshpande V; Szczesnik T; Yang A; Humphreys DT; Giannoulatou E; Ho JWK, 2015, 'Decoding the complex genetic causes of heart diseases using systems biology', Biophysical Reviews, 7, pp. 141 - 159

Deakin CT; Deakin JJ; Ginn SL; Young P; Humphreys D; Suter CM; Alexander IE; Hallwirth CV, 2014, 'Impact of next-generation sequencing error on analysis of barcoded plasmid libraries of known complexity and sequence', NUCLEIC ACIDS RESEARCH, 42, http://dx.doi.org/10.1093/nar/gku607

Keam SP; Young PE; McCorkindale AL; Dang THY; Clancy JL; Humphreys DT; Preiss T; Hutvagner G; Martin DIK; Cropley JE; Suter CM, 2014, 'The human Piwi protein Hiwi2 associates with tRNA-derived piRNAs in somatic cells', Nucleic Acids Research, 42, pp. 8984 - 8995, http://dx.doi.org/10.1093/nar/gku620

Lie S; Morrison JL; Williams-Wyss O; Zhang S; MacLaughlin SM; McMillen IC; Suter CM; Humphreys DT; Ozanne SE; Kleemann DO; Walker SK; Roberts CT, 2014, 'Impact of embryo number and maternal undernutrition around the time of conception on insulin signaling and gluconeogenic factors and microRNAs in the liver of fetal sheep', American Journal of Physiology - Endocrinology and Metabolism, 306, http://dx.doi.org/10.1152/ajpendo.00456.2013

Lie S; Morrison JL; Williams-Wyss O; Suter CM; Humphreys DT; Ozanne SE; Zhang S; MacLaughlin SM; Kleemann DO; Walker SK; Roberts CT; McMillen IC, 2014, 'Impact of embryo number and maternal undernutrition around the time of conception on insulin signaling and gluconeogenic factors and microRNAs in the liver of fetal sheep', American Journal of Physiology - Endocrinology and Metabolism, 306, http://dx.doi.org/10.1152/ajpendo.00553.2013

Lie S; Morrison JL; Williams-Wyss O; Suter CM; Humphreys DT; Ozanne SE; Zhang S; MacLaughlin SM; Kleemann DO; Walker SK; Roberts CT; Caroline McMillen I, 2014, 'Periconceptional undernutrition programs changes in insulin-signaling molecules and micrornas in skeletal muscle in singleton and twin fetal sheep', Biology of Reproduction, 90, http://dx.doi.org/10.1095/biolreprod.113.109751

Muthiah K; Humphreys D; Robson D; Macdonald P; Dhital K; Jansz P; Hayward CS, 2014, 'Regression of Cellular Hypertrophy Leads to Functional Recovery Following Implantation with Centrifugal Continuous Flow Left Ventricular Assist Devices', The Journal of Heart and Lung Transplantation, 33, pp. S236 - S236, http://dx.doi.org/10.1016/j.healun.2014.01.614

Giannoulatou E; Park S-H; Humphreys DT; Ho JWK, 2014, 'Verification and validation of bioinformatics software without a gold standard: a case study of BWA and Bowtie', BMC bioinformatics, 15, pp. S15 - S15

Liang B; Soka M; Christensen AH; Olesen MS; Larsen AP; Knop FK; Wang F; Nielsen JB; Andersen MN; Humphreys D; Mann SA; Huttner IG; Vandenberg JI; Svendsen JH; Haunsø S; Preiss T; Seebohm G; Olesen SP; Schmitt N; Fatkin D, 2013, 'Genetic variation in the two-pore domain potassium channel, TASK-1, may contribute to an atrial substrate for arrhythmogenesis.', J Mol Cell Cardiol, http://dx.doi.org/10.1016/j.yjmcc.2013.12.014

Olesen M; Liang B; Soka M; Larsen AP; Knop FK; Wang F; Nielsen JB; Andersen MN; Humphreys D; Mann SA; Vandenberg JI; Svendsen JH; Haunso S; Preiss T; Seebohm G; Olesen S-P; Schmitt N; Fatkin D, 2013, 'TASK-1 potassium channel mutations in atrial fibrillation', European Heart Journal, 34, pp. 3411 - 3411, http://dx.doi.org/10.1093/eurheartj/eht309.3411

Humphreys DT; Suter CM, 2013, 'MiRspring: A compact standalone research tool for analyzing miRNA-seq data', Nucleic Acids Research, 41, http://dx.doi.org/10.1093/nar/gkt485

Ohanian M; Humphreys DT; Anderson E; Preiss T; Fatkin D, 2013, 'A heterozygous variant in the human cardiac miR-133 gene, MIR133A2, alters miRNA duplex processing and strand abundance.', BMC genetics, 14, http://dx.doi.org/10.1186/1471-2156-14-18

Li CCY; Eaton SA; Young PE; Lee M; Shuttleworth R; Humphreys DT; Grau GE; Combes V; Bebawy M; Gong J; Brammah S; Buckland ME; Suter CM, 2013, 'Glioma microvesicles carry selectively packaged coding and noncoding RNAs which alter gene expression in recipient cells', RNA Biology, 10, pp. 1333 - 1344, http://dx.doi.org/10.4161/rna.25281

Samaraweera SE; O'Keefe LV; Van Eyk CL; Lawlor KT; Humphreys DT; Suter CM; Richards RI, 2013, 'Modeling and analysis of repeat RNA toxicity in drosophila', Methods in Molecular Biology, 1017, pp. 173 - 192, http://dx.doi.org/10.1007/978-1-62703-438-8_13

Humphreys DT; Hynes CJ; Patel HR; Wei G; Cannon LE; Fatkin D; Suter CM; Clancy JL; Preiss T, 2012, 'Complexity of murine cardiomyocyte miRNA biogenesis, sequence variant expression and function', PLoS One, 7, pp. e30933, http://dx.doi.org/10.1371/journal.pone.0030933

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