Publications

Selected publications

• Single-cell multi-omics defines the cell-type-specific impact of splicing aberrations in human hematopoietic clonal outgrowths.
  Cortés-López M, Chamely P, Hawkins AG, Stanley RF, Swett AD, Ganesan S, Mouhieddine TH, Dai X, Kluegel L, Chen C, Batta K, Furer N, Vedula RS, Beaulaurier J, Drong AW, Hickey S, Dusaj N, Mullokandov G, Stasiw AM, Su J, Chaligné R, Juul S, Harrington E, Knowles DA, Potenski CJ, Wiseman DH, Tanay A, Shlush L, Lindsley RC, Ghobrial IM, Taylor J, Abdel-Wahab O, Gaiti F, Landau DA.
  Cell Stem Cell. 2023;30(9):1262-1281.e8. doi: 10.1016/j.stem.2023.07.012 · Paper.
• SON is an essential m(6)A target for hematopoietic stem cell fate.
  Luo H, Cortés-López M, Tam CL, Xiao M, Wakiro I, Chu KL, Pierson A, Chan M, Chang K, Yang X, Fecko D, Han G, Ahn EE, Morris QD, Landau DA, Kharas MG.
  Cell Stem Cell. 2023;30(12):1658-1673.e10. doi: 10.1016/j.stem.2023.11.006 · Paper.
• High-throughput mutagenesis identifies mutations and RNA-binding proteins controlling CD19 splicing and CART-19 therapy resistance.
  Cortés-López M, Schulz L, Enculescu M, Paret C, Spiekermann B, Quesnel-Vallières M, Torres-Diz M, Unic S, Busch A, Orekhova A, Kuban M, Mesitov M, Mulorz MM, Shraim R, Kielisch F, Faber J, Barash Y, Thomas-Tikhonenko A, Zarnack K, Legewie S, König J.
  Nat Commun. 2022;13(1):5570. doi: 10.1038/s41467-022-31818-y · Paper.
• Direct long-read RNA sequencing identifies a subset of questionable exitrons likely arising from reverse transcription artifacts.
  Schulz L, Torres-Diz M, Cortés-López M, Hayer KE, Asnani M, Tasian SK, Barash Y, Sotillo E, Zarnack K, König J, Thomas-Tikhonenko A.
  Genome Biol. 2021;22(1):190. doi: 10.1186/s13059-021-02411-1 · Paper.

All publications

2025

• The Somatic Mosaicism across Human Tissues Network.
  Coorens THH, Oh JW, Choi YA, Lim NS, Zhao B, Voshall A, Abyzov A, Antonacci-Fulton L, Aparicio S, Ardlie KG, Bell TJ, Bennett JT, Bernstein BE, Blanchard TG, Boyle AP, Buenrostro JD, Burns KH, Chen F, Chen R, Choudhury S, Doddapaneni HV, Eichler EE, Evrony GD, Faith MA, Fazzio TG, Fulton RS, Garber M, Gehlenborg N, Germer S, Getz G, Gibbs RA, Hernandez RG, Jin F, Korbel JO, Landau DA, Lawson HA, Lennon NJ, Li H, Li Y, Loh PR, Marth G, McConnell MJ, Mills RE, Montgomery SB, Natarajan P, Park PJ, Satija R, Sedlazeck FJ, Shao DD, Shen H, Stergachis AB, Underhill HR, Urban AE, VonDran MW, Walsh CA, Wang T, Wu TP, Zong C, Lee EA, Vaccarino FM.
  Nature. 2025;643(8070):47-59. doi: 10.1038/s41586-025-09096-7 · Paper.

2024

• GoT-Splice protocol for multi-omics profiling of gene expression, cell-surface proteins, mutational status, and RNA splicing in human cells.
  Ganesan S, Cortés-López M, Swett AD, Dai X, Hickey S, Chamely P, Hawkins AG, Juul S, Landau DA, Gaiti F.
  STAR Protoc. 2024;5(2):102966. doi: 10.1016/j.xpro.2024.102966 · Paper.

2023

• Single-cell multi-omics defines the cell-type-specific impact of splicing aberrations in human hematopoietic clonal outgrowths.
  Cortés-López M, Chamely P, Hawkins AG, Stanley RF, Swett AD, Ganesan S, Mouhieddine TH, Dai X, Kluegel L, Chen C, Batta K, Furer N, Vedula RS, Beaulaurier J, Drong AW, Hickey S, Dusaj N, Mullokandov G, Stasiw AM, Su J, Chaligné R, Juul S, Harrington E, Knowles DA, Potenski CJ, Wiseman DH, Tanay A, Shlush L, Lindsley RC, Ghobrial IM, Taylor J, Abdel-Wahab O, Gaiti F, Landau DA.
  Cell Stem Cell. 2023;30(9):1262-1281.e8. doi: 10.1016/j.stem.2023.07.012 · Paper.
• SON is an essential m(6)A target for hematopoietic stem cell fate.
  Luo H, Cortés-López M, Tam CL, Xiao M, Wakiro I, Chu KL, Pierson A, Chan M, Chang K, Yang X, Fecko D, Han G, Ahn EE, Morris QD, Landau DA, Kharas MG.
  Cell Stem Cell. 2023;30(12):1658-1673.e10. doi: 10.1016/j.stem.2023.11.006 · Paper.
• Analysis of RBP expression and binding sites identifies PTBP1 as a regulator of CD19 expression in B-ALL.
  Ziegler N, Cortés-López M, Alt F, Sprang M, Ustjanzew A, Lehmann N, El Malki K, Wingerter A, Russo A, Beck O, Attig S, Roth L, König J, Paret C, Faber J.
  Oncoimmunology. 2023;12(1):2184143. doi: 10.1080/2162402X.2023.2184143 · Paper.

2022

• High-throughput mutagenesis identifies mutations and RNA-binding proteins controlling CD19 splicing and CART-19 therapy resistance.
  Cortés-López M, Schulz L, Enculescu M, Paret C, Spiekermann B, Quesnel-Vallières M, Torres-Diz M, Unic S, Busch A, Orekhova A, Kuban M, Mesitov M, Mulorz MM, Shraim R, Kielisch F, Faber J, Barash Y, Thomas-Tikhonenko A, Zarnack K, Legewie S, König J.
  Nat Commun. 2022;13(1):5570. doi: 10.1038/s41467-022-31818-y · Paper.

2021

• Direct long-read RNA sequencing identifies a subset of questionable exitrons likely arising from reverse transcription artifacts.
  Schulz L, Torres-Diz M, Cortés-López M, Hayer KE, Asnani M, Tasian SK, Barash Y, Sotillo E, Zarnack K, König J, Thomas-Tikhonenko A.
  Genome Biol. 2021;22(1):190. doi: 10.1186/s13059-021-02411-1 · Paper.

2018

• Genome-Wide circRNA Profiling from RNA-seq Data.
  Cooper DA, Cortés-López M, Miura P.
  Methods Mol Biol. 2018;1724:27-41. doi: 10.1007/978-1-4939-7562-4_3 · Paper.
• Decoding a cancer-relevant splicing decision in the RON proto-oncogene using high-throughput mutagenesis.
  Braun S, Enculescu M, Setty ST, Cortés-López M, de Almeida BP, Sutandy FXR, Schulz L, Busch A, Seiler M, Ebersberger S, Barbosa-Morais NL, Legewie S, König J, Zarnack K.
  Nat Commun. 2018;9(1):3315. doi: 10.1038/s41467-018-05748-7 · Paper.
• Global accumulation of circRNAs during aging in Caenorhabditis elegans.
  Cortés-López M, Gruner MR, Cooper DA, Gruner HN, Voda AI, van der Linden AM, Miura P.
  BMC Genomics. 2018;19(1):8. doi: 10.1186/s12864-017-4386-y · Paper.

2017

• Loss of adult skeletal muscle stem cells drives age-related neuromuscular junction degeneration.
  Liu W, Klose A, Forman S, Paris ND, Wei-LaPierre L, Cortés-López M, Tan A, Flaherty M, Miura P, Dirksen RT, Chakkalakal JV.
  Elife. 2017;6. doi: 10.7554/eLife.26464 · Paper.

2016

• CircRNA accumulation in the aging mouse brain.
  Gruner H, Cortés-López M, Cooper DA, Bauer M, Miura P.
  Sci Rep. 2016;6:38907. doi: 10.1038/srep38907 · Paper.
• Emerging Functions of Circular RNAs.
  Cortés-López M, Miura P.
  Yale J Biol Med. 2016;89(4):527-537. Paper.