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LUKAS SIMON

TitleAssistant Professor
InstitutionBaylor College of Medicine
DepartmentDepartment of Biochemistry and Molecular Pharmacology
AddressOne Baylor Plaza
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    Other Positions
    TitleAssistant Professor
    InstitutionBaylor College of Medicine
    DepartmentTherapeutic Innovation Center
    DivisionTherapeutic Innovation Center


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    Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Faculty can login to make corrections and additions.
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    PMC Citations indicate the number of times the publication was cited by articles in PubMed Central, and the Altmetric score represents citations in news articles and social media. (Note that publications are often cited in additional ways that are not shown here.) Fields are based on how the National Library of Medicine (NLM) classifies the publication's journal and might not represent the specific topic of the publication. Translation tags are based on the publication type and the MeSH terms NLM assigns to the publication. Some publications (especially newer ones and publications not in PubMed) might not yet be assigned Field or Translation tags.) Click a Field or Translation tag to filter the publications.
    1. Wang W, Cai Q, Liu Y, Nie L, Lee HH, Yan F, Fei Y, Yao Y, Li Y, Tan L, Lorenzi PL, Wang YN, Yao J, Chen Z, McIntosh J, Yu CT, Jain P, Jiang V, Vargas J, Li X, Zhang T, Li S, Santos D, Thirumurthi S, Seeley EH, Simon LM, Flowers CR, Ok CY, Wang ML. TCA cycle mode switch determines the fate of pirtobrutinib-tolerant persister cells in mantle cell lymphoma. Blood. 2025 07 23. PMID: 40700581.
      Citations:    Fields:    
    2. Seasock MJ, Shafiquzzaman M, Ruiz-Echartea ME, Kanchi RS, Tran BT, Simon LM, Meyer MD, Erice PA, Lotlikar SL, Wenlock SC, Ochsner SA, Enright A, Carisey AF, Romero F, Rosas IO, King KY, McKenna NJ, Coarfa C, Rodriguez A, Seasock MJ, Shafiquzzaman M, Ruiz-Echartea ME, Kanchi RS, Tran BT, Simon LM, Meyer MD, Erice PA, Lotlikar SL, Wenlock SC, Ochsner SA, Enright A, Carisey AF, Romero F, Rosas IO, King KY, McKenna NJ, Coarfa C, Rodriguez A, Shafiquzzaman M, Tran BT, Lotlikar SL, Coarfa C, Rodriguez A. Let-7 restrains an oncogenic circuit in AT2 cells to prevent fibrogenic cell intermediates in pulmonary fibrosis. bioRxiv. 2025 Feb 11. PMID: 38826218; PMCID: PMC11142151.
      Citations:    
    3. Henke DM, Renwick A, Zoeller JR, Meena JK, Neill NJ, Bowling EA, Meerbrey KL, Westbrook TF, Simon LM. Bio-primed machine learning to enhance discovery of relevant biomarkers. NPJ Precis Oncol. 2025 Feb 06; 9(1):39. PMID: 39915634; PMCID: PMC11802771.
      Citations: 4     
    4. Liu A, Citu C, Enduru N, Chen X, Manuel AM, Sinha T, Gorski D, Fernandes BS, Yu M, Schulz PE, Simon LM, Soto C, Zhao Z, Liu A, Citu C, Enduru N, Chen X, Manuel AM, Sinha T, Gorski D, Fernandes BS, Yu M, Schulz PE, Simon LM, Soto C, Zhao Z. Single-nucleus multiomics reveals the disrupted regulatory programs in three brain regions of sporadic early-onset Alzheimer's disease. bioRxiv. 2024 Jun 29. PMID: 38979371; PMCID: PMC11230393.
      Citations:    
    5. Dai Y, Itai T, Pei G, Yan F, Chu Y, Jiang X, Weinberg SM, Mukhopadhyay N, Marazita ML, Simon LM, Jia P, Zhao Z. DeepFace: Deep-learning-based framework to contextualize orofacial-cleft-related variants during human embryonic craniofacial development. HGG Adv. 2024 Jul 18; 5(3):100322. PMID: 38944832; PMCID: PMC11262157.
      Citations:    
    6. Palit S, Shrestha AK, Thapa S, L Grimm S, Coarfa C, Theis F, Simon LM, Shivanna B. Leveraging Integrated RNA Sequencing to Decipher Adrenomedullin's Protective Mechanisms in Experimental Bronchopulmonary Dysplasia. Genes (Basel). 2024 Jun 19; 15(6). PMID: 38927741; PMCID: PMC11202456.
      Citations: 1     Fields:    Translation:HumansAnimalsCells
    7. Itai T, Yan F, Liu A, Dai Y, Iwaya C, Curtis SW, Leslie EJ, Simon LM, Jia P, Chen X, Iwata J, Zhao Z. Investigating gene functions and single-cell expression profiles of de novo variants in orofacial clefts. HGG Adv. 2024 Jul 18; 5(3):100313. PMID: 38807368; PMCID: PMC11318074.
      Citations:    
    8. Dai Y, Itai T, Pei G, Yan F, Chu Y, Jiang X, Weinberg SM, Mukhopadhyay N, Marazita ML, Simon LM, Jia P, Zhao Z. DeepFace: Deep-learning-based framework to contextualize orofacial-cleft-related variants during human embryonic craniofacial development. HGG Adv. 2024 Jul 18; 5(3):100312. PMID: 38796699; PMCID: PMC11193024.
      Citations:    
    9. Yan F, Jiang V, Jordan A, Che Y, Liu Y, Cai Q, Xue Y, Li Y, McIntosh J, Chen Z, Vargas J, Nie L, Yao Y, Lee HH, Wang W, Bigcal JR, Badillo M, Meena J, Flowers C, Zhou J, Zhao Z, Simon LM, Wang M. The HSP90-MYC-CDK9 network drives therapeutic resistance in mantle cell lymphoma. Exp Hematol Oncol. 2024 Feb 07; 13(1):14. PMID: 38326887; PMCID: PMC10848414.
      Citations: 2     
    10. Yan F, Suzuki A, Iwaya C, Pei G, Chen X, Yoshioka H, Yu M, Simon LM, Iwata J, Zhao Z. Single-cell multiomics decodes regulatory programs for mouse secondary palate development. Nat Commun. 2024 Jan 27; 15(1):821. PMID: 38280850; PMCID: PMC10821874.
      Citations:    
    11. Simon LM, Flocco C, Burkart F, Methner A, Henke D, Rauer L, M?ller CL, Vogel J, Quaisser C, Overmann J, Simon S. Microbial fingerprints reveal interaction between museum objects, curators, and visitors. iScience. 2023 Sep 15; 26(9):107578. PMID: 37664629; PMCID: PMC10469763.
      Citations:    
    12. Wang M, Deng W, Samuels DC, Zhao Z, Simon LM. MitoTrace: A Computational Framework for Analyzing Mitochondrial Variation in Single-Cell RNA Sequencing Data. Genes (Basel). 2023 06 04; 14(6). PMID: 37372402; PMCID: PMC10298143.
      Citations:    
    13. Pei G, Yan F, Simon LM, Dai Y, Jia P, Zhao Z. deCS: A Tool for Systematic Cell Type Annotations of Single-cell RNA Sequencing Data among Human Tissues. Genomics Proteomics Bioinformatics. 2023 04; 21(2):370-384. PMID: 35470070; PMCID: PMC10626171.
      Citations:    
    14. Yan F, Zhao Z, Simon LM. EmptyNN: A neural network based on positive and unlabeled learning to remove cell-free droplets and recover lost cells in scRNA-seq data. Patterns (N Y). 2021 Aug 13; 2(8):100311. PMID: 34430929; PMCID: PMC8369248.
      Citations:    
    15. Jeong HH, Jia J, Dai Y, Simon LM, Zhao Z. Investigating Cellular Trajectories in the Severity of COVID-19 and Their Transcriptional Programs Using Machine Learning Approaches. Genes (Basel). 2021 04 24; 12(5). PMID: 33923155; PMCID: PMC8145325.
      Citations:    
    16. Bowling EA, Wang JH, Gong F, Wu W, Neill NJ, Kim IS, Tyagi S, Orellana M, Kurley SJ, Chung HC, Hsu TY, Dubrulle J, Saltzman AB, Li H, Meena JK, Canlas GM, Chamakuri S, Singh S, Simon LM, Olson CM, Dobrolecki LE, Lewis MT, Zhang B, Golding I, Rosen JM, Young DW, Malovannaya A, Stossi F, Miles G, Ellis MJ, Yu L, Buonamici S, Lin CY, Karlin KL, Zhang XH, Westbrook TF, Dominguez-Vida?a R. Spliceosome-targeted therapies trigger an antiviral immune response in triple-negative breast cancer. Cell. 2021 01 21; 184(2):384-403.e21. PMID: 33450205; PMCID: PMC8635244.
      Citations: 28     Fields:    Translation:HumansAnimalsCells
    17. Hulstaert E, Morlion A, Avila Cobos F, Verniers K, Nuytens J, Vanden Eynde E, Yigit N, Anckaert J, Geerts A, Hindryckx P, Jacques P, Brusselle G, Bracke KR, Maes T, Malfait T, Derveaux T, Ninclaus V, Van Cauwenbergh C, Roelens K, Roets E, Hemelsoet D, Tilleman K, Brochez L, Kuersten S, Simon LM, Karg S, Kautzky-Willers A, Leutner M, N?hammer C, Slaby O, Prins RW, Koster J, Lefever S, Schroth GP, Vandesompele J, Mestdagh P. Charting Extracellular Transcriptomes in The Human Biofluid RNA Atlas. Cell Rep. 2020 12 29; 33(13):108552. PMID: 33378673.
      Citations:    
    18. Simon LM, Yan F, Zhao Z. DrivAER: Identification of driving transcriptional programs in single-cell RNA sequencing data. Gigascience. 2020 12 10; 9(12). PMID: 33301553; PMCID: PMC7727875.
      Citations:    
    19. Pei G, Wang YY, Simon LM, Dai Y, Zhao Z, Jia P. Gene expression imputation and cell-type deconvolution in human brain with spatiotemporal precision and its implications for brain-related disorders. Genome Res. 2021 01; 31(1):146-158. PMID: 33272935; PMCID: PMC7849392.
      Citations:    
    20. Strunz M, Simon LM, Ansari M, Kathiriya JJ, Angelidis I, Mayr CH, Tsidiridis G, Lange M, Mattner LF, Yee M, Ogar P, Sengupta A, Kukhtevich I, Schneider R, Zhao Z, Voss C, Stoeger T, Neumann JHL, Hilgendorff A, Behr J, O'Reilly M, Lehmann M, Burgstaller G, Königshoff M, Chapman HA, Theis FJ, Schiller HB, Simon LM, Tsidiridis G, Lange M, Kukhtevich I, Schneider R, Behr J, Lehmann M, K?nigshoff M, Theis FJ. Alveolar regeneration through a Krt8+ transitional stem cell state that persists in human lung fibrosis. Nat Commun. 2020 07 16; 11(1):3559. PMID: 32678092; PMCID: PMC7366678.
      Citations: 80     Fields:    Translation:HumansAnimalsCells
    21. Rondina MT, Voora D, Simon LM, Schwertz H, Harper JF, Lee O, Bhatlekar SC, Li Q, Eustes AS, Montenont E, Campbell RA, Tolley ND, Kosaka Y, Weyrich AS, Bray PF, Rowley JW. Longitudinal RNA-Seq Analysis of the Repeatability of Gene Expression and Splicing in Human Platelets Identifies a Platelet SELP Splice QTL. Circ Res. 2020 02 14; 126(4):501-516. PMID: 31852401; PMCID: PMC7323475.
      Citations:    
    22. Sethunath V, Hu H, De Angelis C, Veeraraghavan J, Qin L, Wang N, Wang T, Fu X, Nardone A, Pereira R, Nanda S, Griffith OL, Tsimelzon A, Shaw C, Chamness GC, Reis-Filho JS, Weigelt B, Heiser LM, Hilsenbeck SG, Huang S, Rimawi MF, Gray JW, Osborne CK, Schiff R, Simon LM. Targeting the Mevalonate Pathway to Overcome Acquired Anti-HER2 Treatment Resistance in Breast Cancer. Mol Cancer Res. 2019 11; 17(11):2318-2330. PMID: 31420371; PMCID: PMC6825570.
      Citations: 19     Fields:    Translation:HumansCells
    23. Schiller HB, Montoro DT, Simon LM, Rawlins EL, Meyer KB, Strunz M, Vieira Braga FA, Timens W, Koppelman GH, Budinger GRS, Burgess JK, Waghray A, van den Berge M, Theis FJ, Regev A, Kaminski N, Rajagopal J, Teichmann SA, Misharin AV, Nawijn MC. The Human Lung Cell Atlas: A High-Resolution Reference Map of the Human Lung in Health and Disease. Am J Respir Cell Mol Biol. 2019 07; 61(1):31-41. PMID: 30995076; PMCID: PMC6604220.
      Citations:    
    24. Vieira Braga FA, Kar G, Berg M, Carpaij OA, Polanski K, Simon LM, Brouwer S, Gomes T, Hesse L, Jiang J, Fasouli ES, Efremova M, Vento-Tormo R, Talavera-L?pez C, Jonker MR, Affleck K, Palit S, Strzelecka PM, Firth HV, Mahbubani KT, Cvejic A, Meyer KB, Saeb-Parsy K, Luinge M, Brandsma CA, Timens W, Angelidis I, Strunz M, Koppelman GH, van Oosterhout AJ, Schiller HB, Theis FJ, van den Berge M, Nawijn MC, Teichmann SA. A cellular census of human lungs identifies novel cell states in health and in asthma. Nat Med. 2019 07; 25(7):1153-1163. PMID: 31209336.
      Citations:    
    25. Angelidis I, Simon LM, Fernandez IE, Strunz M, Mayr CH, Greiffo FR, Tsitsiridis G, Ansari M, Graf E, Strom TM, Nagendran M, Desai T, Eickelberg O, Mann M, Theis FJ, Schiller HB. An atlas of the aging lung mapped by single cell transcriptomics and deep tissue proteomics. Nat Commun. 2019 02 27; 10(1):963. PMID: 30814501; PMCID: PMC6393476.
      Citations:    
    26. Neelakantan D, Zhou H, Oliphant MUJ, Zhang X, Henke DM, Shaw CA, Wu MF, Hilsenbeck SG, White LD, Lewis MT, Ford HL, Simon LM. Publisher Correction: EMT cells increase breast cancer metastasis via paracrine GLI activation in neighbouring tumour cells. Nat Commun. 2018 11 12; 9(1):4720. PMID: 30420638; PMCID: PMC6232083.
      Citations: 3     Fields:    
    27. Tricoci P, Neely M, Whitley MJ, Edelstein LC, Simon LM, Shaw C, Fortina P, Moliterno DJ, Armstrong PW, Aylward P, White H, Van de Werf F, Jennings LK, Wallentin L, Held C, Harrington RA, Mahaffey KW, Bray PF. Effects of genetic variation in protease activated receptor 4 after an acute coronary syndrome: Analysis from the TRACER trial. Blood Cells Mol Dis. 2018 09; 72:37-43. PMID: 30055940; PMCID: PMC6097632.
      Citations: 5     Fields:    Translation:Humans
    28. Neelakantan D, Zhou H, Oliphant MUJ, Zhang X, Henke DM, Shaw CA, Wu MF, Hilsenbeck SG, White LD, Lewis MT, Ford HL, Simon LM. EMT cells increase breast cancer metastasis via paracrine GLI activation in neighbouring tumour cells. Nat Commun. 2017 06 12; 8:15773. PMID: 28604738; PMCID: PMC5472791.
      Citations: 71     Fields:    Translation:HumansAnimalsCells
    29. Zou S, Teixeira AM, Kostadima M, Astle WJ, Radhakrishnan A, Simon LM, Truman L, Fang JS, Hwa J, Zhang PX, van der Harst P, Bray PF, Ouwehand WH, Frontini M, Krause DS. SNP in human ARHGEF3 promoter is associated with DNase hypersensitivity, transcript level and platelet function, and Arhgef3 KO mice have increased mean platelet volume. PLoS One. 2017; 12(5):e0178095. PMID: 28542600; PMCID: PMC5441597.
      Citations:    
    30. Saxena K, Simon LM, Zeng XL, Blutt SE, Crawford SE, Sastri NP, Karandikar UC, Ajami NJ, Zachos NC, Kovbasnjuk O, Donowitz M, Conner ME, Shaw CA, Estes MK. A paradox of transcriptional and functional innate interferon responses of human intestinal enteroids to enteric virus infection. Proc Natl Acad Sci U S A. 2017 01 24; 114(4):E570-E579. PMID: 28069942; PMCID: PMC5278484.
      Citations: 62     Fields:    Translation:HumansAnimalsCells
    31. Chaudhury A, Cheema S, Fachini JM, Kongchan N, Lu G, Simon LM, Wang T, Mao S, Rosen DG, Ittmann MM, Hilsenbeck SG, Shaw CA, Neilson JR. CELF1 is a central node in post-transcriptional regulatory programmes underlying EMT. Nat Commun. 2016 11 21; 7:13362. PMID: 27869122; PMCID: PMC5121338.
      Citations: 31     Fields:    Translation:HumansAnimalsCells
    32. Simon LM, Chen ES, Edelstein LC, Kong X, Bhatlekar S, Rigoutsos I, Bray PF, Shaw CA. Integrative Multi-omic Analysis of Human Platelet eQTLs Reveals Alternative Start Site in Mitofusin 2. Am J Hum Genet. 2016 05 05; 98(5):883-897. PMID: 27132591; PMCID: PMC4863560.
      Citations: 15     Fields:    Translation:HumansCells
    33. Hsu TY, Simon LM, Neill NJ, Marcotte R, Sayad A, Bland CS, Echeverria GV, Sun T, Kurley SJ, Tyagi S, Karlin KL, Hartman JD, Renwick A, Scorsone K, Bernardi RJ, Skinner SO, Jain A, Orellana M, Lagisetti C, Golding I, Jung SY, Neilson JR, Zhang XH, Cooper TA, Webb TR, Neel BG, Shaw CA, Westbrook TF, Dominguez-Vida?a R. The spliceosome is a therapeutic vulnerability in MYC-driven cancer. Nature. 2015 Sep 17; 525(7569):384-8. PMID: 26331541; PMCID: PMC4831063.
      Citations: 211     Fields:    Translation:HumansAnimalsCells
    34. Edelstein LC, Simon LM, Lindsay CR, Kong X, Tourdot BE, Chen ES, Ma L, Coughlin S, Nieman M, Holinstat M, Shaw CA, Bray PF, Teruel-Montoya R. Common variants in the human platelet PAR4 thrombin receptor alter platelet function and differ by race. Blood. 2014 Nov 27; 124(23):3450-8. PMID: 25293779; PMCID: PMC4246040.
      Citations: 48     Fields:    Translation:HumansCells
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