Malene Lindholm

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About me

I am a translational scientist with a PhD in medical science working at the intersection of cardiometabolic disease, bioinformatics and molecular biology, currently serving as junior faculty and Director of the Human Molecular Moonshot at Stanford University.

Articles

Journal article: BMC BIOLOGY. 2024;22(1):147

DNA methylation of exercise-responsive genes differs between trained and untrained men.

Geiger C; Needhamsen M; Emanuelsson EB; Norrbom J; Steindorf K; Sundberg CJ; Reitzner SM; Lindholm ME
Journal article: CELL GENOMICS. 2024;4(6):100421

Molecular adaptations in response to exercise training are associated with tissue-specific transcriptomic and epigenomic signatures.

Nair VD; Pincas H; Smith GR; Zaslavsky E; Ge Y; Amper MAS; Vasoya M; Chikina M; Sun Y; Raja AN; Mao W; Gay NR; Esser KA; Smith KS; Zhao B; Wiel L; Singh A; Lindholm ME; Amar D; Montgomery S; Snyder MP; Walsh MJ; Sealfon SC; MoTrPAC Study Group
Journal article: CELL METABOLISM. 2024;36(6):1411-1429.e10

The mitochondrial multi-omic response to exercise training across rat tissues.

Amar D; Gay NR; Jimenez-Morales D; Jean Beltran PM; Ramaker ME; Raja AN; Zhao B; Sun Y; Marwaha S; Gaul DA; Hershman SG; Ferrasse A; Xia A; Lanza I; Fernández FM; Montgomery SB; Hevener AL; Ashley EA; Walsh MJ; Sparks LM; Burant CF; Rector RS; Thyfault J; Wheeler MT; Goodpaster BH; Coen PM; Schenk S; Bodine SC; Lindholm ME; MoTrPAC Study Group
Journal article: NATURE. 2024;629(8010):174-183

Temporal dynamics of the multi-omic response to endurance exercise training.

MoTrPAC Study Group; Lead Analysts; MoTrPAC Study Group
Journal article: NATURE METABOLISM. 2024;6(5):963-979

Sexual dimorphism and the multi-omic response to exercise training in rat subcutaneous white adipose tissue.

Many GM; Sanford JA; Sagendorf TJ; Hou Z; Nigro P; Whytock KL; Amar D; Caputo T; Gay NR; Gaul DA; Hirshman MF; Jimenez-Morales D; Lindholm ME; Muehlbauer MJ; Vamvini M; Bergman BC; Fernández FM; Goodyear LJ; Hevener AL; Ortlund EA; Sparks LM; Xia A; Adkins JN; Bodine SC; Newgard CB; Schenk S; MoTrPAC Study Group
Article: ISCIENCE. 2024;27(1):108638

Remodeling of the human skeletal muscle proteome found after long-term endurance training but not after strength training.

Emanuelsson EB; Arif M; Reitzner SM; Perez S; Lindholm ME; Mardinoglu A; Daub C; Sundberg CJ; Chapman MA
Article: AGING CELL. 2024;23(1):e13859

Exercise is associated with younger methylome and transcriptome profiles in human skeletal muscle.

Voisin S; Seale K; Jacques M; Landen S; Harvey NR; Haupt LM; Griffiths LR; Ashton KJ; Coffey VG; Thompson J-LM; Doering TM; Lindholm ME; Walsh C; Davison G; Irwin R; McBride C; Hansson O; Asplund O; Heikkinen AE; Piirilä P; Pietiläinen KH; Ollikainen M; Blocquiaux S; Thomis M; Coletta DK; Sharples AP; Eynon N
Article: ANTIOXIDANTS. 2023;12(12):2043

Comparing the Blood Response to Hyperbaric Oxygen with High-Intensity Interval Training-A Crossover Study in Healthy Volunteers.

Kjellberg A; Lindholm ME; Zheng X; Liwenborg L; Rodriguez-Wallberg KA; Catrina S-B; Lindholm P
Article: CIRCULATION-GENOMIC AND PRECISION MEDICINE. 2021;14(6):e003419

Mono- and Biallelic Protein-Truncating Variants in Alpha-Actinin 2 Cause Cardiomyopathy Through Distinct Mechanisms.

Lindholm ME; Jimenez-Morales D; Zhu H; Seo K; Amar D; Zhao C; Raja A; Madhvani R; Abramowitz S; Espenel C; Sutton S; Caleshu C; Berry GJ; Motonaga KS; Dunn K; Platt J; Ashley EA; Wheeler MT
Article: NATURE COMMUNICATIONS. 2021;12(1):3471

Time trajectories in the transcriptomic response to exercise - a meta-analysis.

Amar D; Lindholm ME; Norrbom J; Wheeler MT; Rivas MA; Ashley EA
Article: MEDICINE & SCIENCE IN SPORTS & EXERCISE. 2020;52(8):1679-1690

Exercise Induces Different Molecular Responses in Trained and Untrained Human Muscle.

Moberg M; Lindholm ME; Reitzner SM; Ekblom B; Sundberg C-J; Psilander N
Article: JOURNAL OF CACHEXIA SARCOPENIA AND MUSCLE. 2020;11(4):887-898

An epigenetic clock for human skeletal muscle.

Voisin S; Harvey NR; Haupt LM; Griffiths LR; Ashton KJ; Coffey VG; Doering TM; Thompson J-LM; Benedict C; Cedernaes J; Lindholm ME; Craig JM; Rowlands DS; Sharples AP; Horvath S; Eynon N
Article: CELL REPORTS. 2020;31(12):107808

Skeletal Muscle Transcriptomic Comparison between Long-Term Trained and Untrained Men and Women.

Chapman MA; Arif M; Emanuelsson EB; Reitzner SM; Lindholm ME; Mardinoglu A; Sundberg CJ
Article: CONTEMPORARY CLINICAL TRIALS COMMUNICATIONS. 2018;10:148-153

Metabolic and functional changes in transgender individuals following cross-sex hormone treatment: Design and methods of the GEnder Dysphoria Treatment in Sweden (GETS) study.

Wiik A; Andersson DP; Brismar TB; Chanpen S; Dhejne C; Ekström TJ; Flanagan JN; Holmberg M; Kere J; Lilja M; Lindholm ME; Lundberg TR; Maret E; Melin M; Olsson SM; Rullman E; Wåhlén K; Arver S; Gustafsson T
Article: NATURE COMMUNICATIONS. 2018;9(1):1612

Medical relevance of protein-truncating variants across 337,205 individuals in the UK Biobank study.

DeBoever C; Tanigawa Y; Lindholm ME; McInnes G; Lavertu A; Ingelsson E; Chang C; Ashley EA; Bustamante CD; Daly MJ; Rivas MA
Article: PLOS GENETICS. 2016;12(9):e1006294

The Impact of Endurance Training on Human Skeletal Muscle Memory, Global Isoform Expression and Novel Transcripts.

Lindholm ME; Giacomello S; Werne Solnestam B; Fischer H; Huss M; Kjellqvist S; Sundberg CJ
Article: EXPERIMENTAL PHYSIOLOGY. 2016;101(1):28-32

Skeletal muscle hypoxia-inducible factor-1 and exercise.

Lindholm ME; Rundqvist H
Article: BMC GENOMICS. 2015;16(1):475

The human cardiac and skeletal muscle proteomes defined by transcriptomics and antibody-based profiling.

Lindskog C; Linné J; Fagerberg L; Hallström BM; Sundberg CJ; Lindholm M; Huss M; Kampf C; Choi H; Liem DA; Ping P; Väremo L; Mardinoglu A; Nielsen J; Larsson E; Pontén F; Uhlén M
Article: EPIGENETICS. 2014;9(12):1557-1569

An integrative analysis reveals coordinated reprogramming of the epigenome and the transcriptome in human skeletal muscle after training.

Lindholm ME; Marabita F; Gomez-Cabrero D; Rundqvist H; Ekström TJ; Tegnér J; Sundberg CJ
Article: FASEB JOURNAL. 2014;28(10):4571-4581

The human skeletal muscle transcriptome: sex differences, alternative splicing, and tissue homogeneity assessed with RNA sequencing.

Lindholm ME; Huss M; Solnestam BW; Kjellqvist S; Lundeberg J; Sundberg CJ
Article: AMERICAN JOURNAL OF PHYSIOLOGY-REGULATORY, INTEGRATIVE AND COMPARATIVE PHYSIOLOGY. 2014;307(3):R248-R255

Negative regulation of HIF in skeletal muscle of elite endurance athletes: a tentative mechanism promoting oxidative metabolism.

Lindholm ME; Fischer H; Poellinger L; Johnson RS; Gustafsson T; Sundberg CJ; Rundqvist H
Article: EPIGENETICS. 2013;8(3):333-346

An evaluation of analysis pipelines for DNA methylation profiling using the Illumina HumanMethylation450 BeadChip platform.

Marabita F; Almgren M; Lindholm ME; Ruhrmann S; Fagerström-Billai F; Jagodic M; Sundberg CJ; Ekström TJ; Teschendorff AE; Tegnér J; Gomez-Cabrero D
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All other publications

Preprint: BIORXIV. 2023;BIORXIV

Multi-omic identification of key transcriptional regulatory programs during endurance exercise training.

Smith GR; Zhao B; Lindholm ME; Raja A; Viggars M; Pincas H; Gay NR; Sun Y; Ge Y; Nair VD; Sanford JA; Amper MAS; Vasoya M; Smith KS; Montgomery S; Zaslavsky E; Bodine SC; Esser KA; Walsh MJ; Snyder MP; MoTrPAC Study Group
Preprint: BIORXIV. 2023;BIORXIV

Sexual dimorphism and the multi-omic response to exercise training in rat subcutaneous white adipose tissue.

Many GM; Sanford JA; Sagendorf TJ; Hou Z; Nigro P; Whytock K; Amar D; Caputo T; Gay NR; Gaul DA; Hirshman M; Jimenez-Morales D; Lindholm ME; Muehlbauer MJ; Vamvini M; Bergman B; Fern Ndez FM; Goodyear LJ; Ortlund EA; Sparks LM; Xia A; Adkins JN; Bodine SC; Newgard CB; Schenk S; MoTrPAC Study Group
Preprint: BIORXIV. 2023;BIORXIV

The mitochondrial multi-omic response to exercise training across tissues.

Amar D; Gay NR; Jimenez-Morales D; Beltran PMJ; Ramaker ME; Raja AN; Zhao B; Sun Y; Marwaha S; Gaul D; Hershman SG; Xia A; Lanza I; Fernandez FM; Montgomery SB; Hevener AL; Ashley EA; Walsh MJ; Sparks LM; Burant CF; Rector RS; Thyfault J; Wheeler MT; Goodpaster BH; Coen PM; Schenk S; Bodine SC; Lindholm ME; MoTrPAC Study Group
Preprint: BIORXIV. 2022

Exercise is associated with younger methylome and transcriptome profiles in human skeletal muscle

Voisin S; Seale K; Jacques M; Landen S; Harvey NR; Haupt LM; Griffiths LR; Ashton KJ; Coffey VG; Thompson J-LM; Doering TM; Lindholm ME; Walsh C; Davison G; Irwin R; McBride C; Hansson O; Asplund O; Heikkinen AE; Piirilä P; Pietiläinen KH; Ollikainen M; Blocquiaux S; Thomis M; Coletta DK; Sharples AP; Eynon N
Preprint: BIORXIV. 2022

Temporal dynamics of the multi-omic response to endurance exercise training across tissues

Group MS; Amar D; Gay NR; Beltran PMJ; Adkins JN; Armenteros JJA; Ashley E; Avila-Pacheco J; Bae D; Bararpour N; Burant C; Clish C; Cutter G; Dasari S; Dennis C; Evans CR; Fernández FM; Gaul D; Ge Y; Gerszten R; Goodyear LJ; Hou Z; Ilkayeva O; Ivanova AA; Jimenez-Morales D; Kachman MT; Keshishian H; Kraus WE; Lanza IR; Li J; Lindholm ME; Lira AC; Many GM; Marwaha S; Miller ME; Muehlbauer MJ; Nair KS; Nair VD; Raja AN; Newgard C; Ortlund EA; Piehowski PD; Presby DM; Qian W-J; Rooney JL; Sanford JA; Savage E; Sealfon SC; Smith GR; Smith KS; Steep A; Stowe CL; Sun Y; Tracy R; Vetr NG; Walsh MJ; Wu S; Zhang T; Zhao B; Zhen J; Albertson BG; Amper MAS; Balci AT; Bamman M; Barton ER; Bergman B; Bessesen D; Booth F; Bouverat B; Buford TW; Caputo T; Chambers TL; Chavez C; Chikina M; Chiu R; Cicha M; Coen PM; Cooper D; Cornell E; Dalton KP; De Sousa LO; Farrar R; Gadde K; Gagne N; Goodpaster BH; Gritsenko MA; Guevara K; Haddad F; Hansen JR; Harris M; Hastie T; Hennig KM; Hershman SG; Hevener A; Hirshman MF; Hsu F-C; Huffman KM; Hung C-J; Hutchinson-Bunch C; Jackson BE; Jankowski C; Jin CA; Johannsen NM; Ke BG; Kohrt WM; Kramer KS; Leeuwenburgh C; Lessard SJ; Lester B; Liu X; Lu C-J; Makarewicz NS; Maner-Smith KM; Mani; Marjanovic N; Marshall A; May S; Melanson E; Monroe ME; Moore RJ; Moore S; Moreau KL; Mundorff CC; Musi N; Nachun D; Nestor MD; Newton RL; Nicklas B; Nigro P; Nudelman G; Pahor M; Pearce C; Petyuk VA; Pincas H; Powers S; Radom-Aizik S; Ramachandran K; Ramaker ME; Ramos I; Rankinen T; Raskind A; Rasmussen BB; Ravussin E; Rector RS; Rejeski WJ; Richards C; Rirak S; Robbins JM; Rubenstein AB; Ruf-Zamojski F; Rushing S; Sagendorf TJ; Samdarshi M; Schauer IE; Schwartz R; Seenarine N; Soni T; Sparks LM; Teng C; Thalacker-Mercer A; Thyfault J; Tibshirani R; Trappe S; Trappe TA; Uppal K; Vangeti S; Vasoya M; Volpi E; Vornholt A; Walkup MP; Williams J; Xia A; Yan Z; Yu X; Zang C; Zaslavsky E; Zebarjadi N; Bodine SC; Carr S; Esser K; Montgomery SB; Schenk S; Snyder MP; Wheeler MT
Conference publication: ACTA PHYSIOLOGICA. 2022;236:57

Do muscles have memory?Molecular effects of training, detraining and retraining

Lindholm ME
Preprint: BIORXIV. 2020

Mono- and bi-allelic protein truncating variants in alpha-actinin 2 cause cardiomyopathy through distinct mechanisms

Lindholm M; Jimenez-Morales D; Zhu H; Seo K; Amar D; Zhao C; Raja A; Madhvani R; Espenel C; Sutton S; Caleshu C; Berry G; Motonaga K; Dunn K; Platt J; Ashley E; Wheeler M
Conference publication: CIRCULATION. 2020;142(Suppl_3)

Abstract 14355: Mono- and Biallelic Structural Variants in Alpha-actinin 2 Cause Contractile Dysfunction and Cardiomyopathy in Humans

Lindholm ME; Zhu H; Seo K; Jimenez-Morales D; Zhao C; Ashley EA; Wheeler MT
Review: CELL. 2020;181(7):1464-1474

Molecular Transducers of Physical Activity Consortium (MoTrPAC): Mapping the Dynamic Responses to Exercise.

Sanford JA; Nogiec CD; Lindholm ME; Adkins JN; Amar D; Dasari S; Drugan JK; Fernández FM; Radom-Aizik S; Schenk S; Snyder MP; Tracy RP; Vanderboom P; Trappe S; Walsh MJ; Molecular Transducers of Physical Activity Consort
Conference publication: CIRCULATION. 2020;142

Mono- and Biallelic Structural Variants in Alpha-actinin 2 Cause Contractile Dysfunction and Cardiomyopathy in Humans

Lindholm ME; Zhu H; Seo K; Jimenez-Morales D; Zhao C; Ashley EA; Wheeler MT
Preprint: BIORXIV. 2019

Differential response trajectories to acute exercise in blood and muscle

Amar D; Lindholm M; Norrbom J; Wheeler M; Rivas M; Ashley E
Preprint: BIORXIV. 2019

An epigenetic clock for human skeletal muscle

Voisin S; Harvey NR; Haupt LM; Griffiths LR; Ashton KJ; Coffey VG; Doering TM; Thompson JM; Benedict C; Cedernaes J; Lindholm ME; Craig JM; Rowlands DS; Sharples AP; Horvath S; Eynon N
Conference publication: JOURNAL OF THE AMERICAN COLLEGE OF CARDIOLOGY. 2019;73(9):1027

NOVEL ALPHA-ACTININ 2 MUTATIONS ARE ASSOCIATED WITH CARDIOMYOPATHY AND HYPERTROPHY IN HUMAN CARDIAC TISSUE AND IPSC-DERIVED CARDIOMYOCYTES

Lindholm M; Zhu H; Huang Y; Ashley EA; Wheeler M
Conference publication: EUROPEAN JOURNAL OF HUMAN GENETICS. 2019;27:1310

Structural variants in Alpha-actinin 2 are associated with cardiomyopathy and hypertrophy in human cardiac tissue and iPSC-derived cardiomyocytes

Lindholm ME; Zhu H; Huang Y; Ashley EA; Wheeler M
Preprint: SSRN ELECTRONIC JOURNAL. 2019

Differential Response Trajectories to Acute Exercise in Blood and Muscle

Amar D; Lindholm ME; Norrbom J; Wheeler MT; Rivas M; Ashley EA
Conference publication: FASEB JOURNAL. 2016;30

Endurance Training Alters Expression of Over 3000 Isoforms and 34 Novel Transcripts in Human Skeletal Muscle

Lindholm M; Giacomello S; Solnestam BW; Fischer H; Kjellqvist S; Huss M; Sundberg CJ
Thesis / dissertation: 2015

The search for human skeletal muscle memory : exercise effects on the transcriptome and epigenome

Lindholm, Maléne
Conference publication: ACTA PHYSIOLOGICA. 2014;211:38

The human skeletal muscle transcriptome - sex differences, alternative splicing and tissue homogeneity assessed with RNA sequencing

Lindholm ME; Huss M; Solnestam BW; Kjellqvist S; Lundeberg J; Sundberg CJ
Conference publication: FASEB JOURNAL. 2013;27(S1):1134.1

Endurance training changes the DNA methylation pattern in human skeletal muscle

Lindholm ME; Marabita F; Gomez‐Cabrero D; Fischer H; Tegnér J; Sundberg CJ
Conference publication: FASEB JOURNAL. 2012;26:533.3

Human skeletal muscle histone modifications in response to six weeks of endurance training

Ydfors M; Lindholm M; Sundberg CJ
Conference publication: FASEB JOURNAL. 2012;26:1086.11

Variation of global mRNA expression in biopsies from the same human muscle

Sundberg CJB; Lindholm M; Solnestam BW; Lundberg J; Fischer H
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Grants

Exercise-induced cardiac adaptation in hypertrophic cardiomyopathy

National Heart Lung and Blood Institute

1 July 2022 - 30 June 2024
Genome-scale mechanisms of adaptation in long-term exercise trained humans – skeletal muscle and adipose tissue crosstalk assessed through spatial transcriptomics analysis

Swedish Research Council

1 January 2019 - 31 December 2021

Employments

Affiliated to Research, Department of Physiology and Pharmacology, Karolinska Institutet, 2023-2026

Degrees and Education

Degree Of Doctor Of Philosophy, Department of Physiology and Pharmacology, Karolinska Institutet, 2015
Master Of Medical Science, Karolinska Institutet, 2009

About me

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