Ammal Abbasi • UCSD Profiles (original) (raw)

  1. HRProfiler Detects Homologous Recombination Deficiency in Breast and Ovarian Cancers Using Whole-Genome and Whole-Exome Sequencing Data. Cancer Res. 2025 Jul 02; 85(13):2504-2513. Abbasi A, Steele CD, Bergstrom EN, Khandekar A, Farswan A, McKay RR, Pillay N, Alexandrov LB. PMID: 40327608; PMCID: PMC12214882.
    View in: PubMed Mentions: 2 Fields:
    Translation:Humans
  2. Identification and Validation of a Previously Missed Mutational Signature in Colorectal Cancer. bioRxiv. 2025 Jun 07. Kazachkova M, Otlu B, Díaz-Gay M, Abbasi A, Moody S, Perdomo S, Wedge DC, Brennan P, Stratton MR, Alexandrov LB. PMID: 40661437; PMCID: PMC12258970.
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  3. Geographic and age variations in mutational processes in colorectal cancer. Nature. 2025 Jul; 643(8070):230-240. Díaz-Gay M, Dos Santos W, Moody S, Kazachkova M, Abbasi A, Steele CD, Vangara R, Senkin S, Wang J, Fitzgerald S, Bergstrom EN, Khandekar A, Otlu B, Abedi-Ardekani B, de Carvalho AC, Cattiaux T, Penha RCC, Gaborieau V, Chopard P, Carreira C, Cheema S, Latimer C, Teague JW, Mukeriya A, Zaridze D, Cox R, Albert M, Phouthavongsy L, Gallinger S, Malekzadeh R, Niavarani A, Miladinov M, Eric K, Milosavljevic S, Sangrajrang S, Curado MP, Aguiar S, Reis RM, Reis MT, Romagnolo LG, Guimarães DP, Holcatova I, Kalvach J, Vaccaro CA, Piñero TA, Swiatkowska B, Lissowska J, Roszkowska-Purska K, Huertas-Salgado A, Shibata T, Shiba S, Sangkhathat S, Chitapanarux T, Roshandel G, Ashton-Prolla P, Damin DC, de Oliveira FH, Humphreys L, Lawley TD, Perdomo S, Stratton MR, Brennan P, Alexandrov LB. PMID: 40267983; PMCID: PMC12221974.
    View in: PubMed Mentions: 28 Fields:
    Translation:Humans
  4. The complexity of tobacco smoke-induced mutagenesis in head and neck cancer. Nat Genet. 2025 Apr; 57(4):884-896. Torrens L, Moody S, de Carvalho AC, Kazachkova M, Abedi-Ardekani B, Cheema S, Senkin S, Cattiaux T, Cortez Cardoso Penha R, Atkins JR, Gaborieau V, Chopard P, Carreira C, Abbasi A, Bergstrom EN, Vangara R, Wang J, Fitzgerald S, Latimer C, Diaz-Gay M, Jones D, Teague J, Ribeiro Pinto F, Kowalski LP, Polesel J, Giudici F, de Oliveira JC, Lagiou P, Lagiou A, Vilensky M, Mates D, Mates IN, Arantes LM, Reis R, Podesta JRV, von Zeidler SV, Holcatova I, Curado MP, Canova C, Fabianova E, Rodríguez-Urrego PA, Humphreys L, Alexandrov LB, Brennan P, Stratton MR, Perdomo S. PMID: 40164736; PMCID: PMC11985354.
    View in: PubMed Mentions: 9 Fields:
    Translation:Humans
  5. Geographic and age-related variations in mutational processes in colorectal cancer. medRxiv. 2025 Feb 21. Díaz-Gay M, Dos Santos W, Moody S, Kazachkova M, Abbasi A, Steele CD, Vangara R, Senkin S, Wang J, Fitzgerald S, Bergstrom EN, Khandekar A, Otlu B, Abedi-Ardekani B, de Carvalho AC, Cattiaux T, Penha RCC, Gaborieau V, Chopard P, Carreira C, Cheema S, Latimer C, Teague JW, Mukeriya A, Zaridze D, Cox R, Albert M, Phouthavongsy L, Gallinger S, Malekzadeh R, Niavarani A, Miladinov M, Eric K, Milosavljevic S, Sangrajrang S, Curado MP, Aguiar S, Reis RM, Reis MT, Romagnolo LG, Guimarães DP, Holcatova I, Kalvach J, Vaccaro CA, Piñero TA, Swiatkowska B, Lissowska J, Roszkowska-Purska K, Huertas-Salgado A, Shibata T, Shiba S, Sangkhathat S, Chitapanarux T, Roshandel G, Ashton-Prolla P, Damin DC, de Oliveira FH, Humphreys L, Lawley TD, Perdomo S, Stratton MR, Brennan P, Alexandrov LB. PMID: 40034755; PMCID: PMC11875255.
    View in: PubMed Mentions:
  6. Deep Learning Artificial Intelligence Predicts Homologous Recombination Deficiency and Platinum Response From Histologic Slides. J Clin Oncol. 2024 Oct 20; 42(30):3550-3560. Bergstrom EN, Abbasi A, Díaz-Gay M, Galland L, Ladoire S, Lippman SM, Alexandrov LB. PMID: 39083703; PMCID: PMC11469627.
    View in: PubMed Mentions: 23 Fields:
    Translation:Humans
  7. Detecting HRD in whole-genome and whole-exome sequenced breast and ovarian cancers. medRxiv. 2024 Jul 14. Abbasi A, Steele CD, Bergstrom EN, Khandekar A, Farswan A, Mckay RR, Pillay N, Alexandrov LB. PMID: 39040162; PMCID: PMC11261949.
    View in: PubMed Mentions:
  8. The Complexity of Tobacco Smoke-Induced Mutagenesis in Head and Neck Cancer. medRxiv. 2024 Apr 17. Torrens L, Moody S, de Carvalho AC, Kazachkova M, Abedi-Ardekani B, Cheema S, Senkin S, Cattiaux T, Cortez Cardoso Penha R, Atkins JR, Gaborieau V, Chopard P, Carreira C, Abbasi A, Bergstrom EN, Vangara R, Wang J, Fitzgerald S, Latimer C, Diaz-Gay M, Jones D, Teague J, Ribeiro Pinto F, Kowalski LP, Polesel J, Giudici F, de Oliveira JC, Lagiou P, Lagiou A, Vilensky M, Mates D, Mates IN, Arantes LM, Reis R, Podesta JRV, von Zeidler SV, Holcatova I, Curado MP, Canova C, Fabianova E, Rodríguez-Urrego PA, Humphreys L, Alexandrov LB, Brennan P, Stratton MR, Perdomo S. PMID: 38699364; PMCID: PMC11065003.
    View in: PubMed Mentions:
  9. Therapy-induced APOBEC3A drives evolution of persistent cancer cells. Nature. 2023 08; 620(7973):393-401. Isozaki H, Sakhtemani R, Abbasi A, Nikpour N, Stanzione M, Oh S, Langenbucher A, Monroe S, Su W, Cabanos HF, Siddiqui FM, Phan N, Jalili P, Timonina D, Bilton S, Gomez-Caraballo M, Archibald HL, Nangia V, Dionne K, Riley A, Lawlor M, Banwait MK, Cobb RG, Zou L, Dyson NJ, Ott CJ, Benes C, Getz G, Chan CS, Shaw AT, Gainor JF, Lin JJ, Sequist LV, Piotrowska Z, Yeap BY, Engelman JA, Lee JJ, Maruvka YE, Buisson R, Lawrence MS, Hata AN. PMID: 37407818; PMCID: PMC10804446.
    View in: PubMed Mentions: 78 Fields:
    Translation:Humans
  10. Chromosomal fragile site breakage by EBV-encoded EBNA1 at clustered repeats. Nature. 2023 04; 616(7957):504-509. Li JSZ, Abbasi A, Kim DH, Lippman SM, Alexandrov LB, Cleveland DW. PMID: 37046091; PMCID: PMC10328181.
    View in: PubMed Mentions: 39 Fields:
    Translation:HumansCells
  11. Visualizing and exploring patterns of large mutational events with SigProfilerMatrixGenerator. bioRxiv. 2023 Feb 04. Khandekar A, Vangara R, Barnes M, Díaz-Gay M, Abbasi A, Bergstrom EN, Steele CD, Pillay N, Alexandrov LB. PMID: 36778452; PMCID: PMC9915726.
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  12. Signatures of copy number alterations in human cancer. Nature. 2022 06; 606(7916):984-991. Steele CD, Abbasi A, Islam SMA, Bowes AL, Khandekar A, Haase K, Hames-Fathi S, Ajayi D, Verfaillie A, Dhami P, McLatchie A, Lechner M, Light N, Shlien A, Malkin D, Feber A, Proszek P, Lesluyes T, Mertens F, Flanagan AM, Tarabichi M, Van Loo P, Alexandrov LB, Pillay N. PMID: 35705804; PMCID: PMC9242861.
    View in: PubMed Mentions: 262 Fields:
    Translation:Humans
  13. Unwinding the mutational signatures of a DNA topoisomerase enzyme. Nature. 2022 02; 602(7898):580-581. Abbasi A, Alexandrov LB. PMID: 35140368.
    View in: PubMed Mentions: 1 Fields:
  14. Significance and limitations of the use of next-generation sequencing technologies for detecting mutational signatures. DNA Repair (Amst). 2021 Nov; 107:103200. Abbasi A, Alexandrov LB. PMID: 34411908; PMCID: PMC9478565.
    View in: PubMed Mentions: 29 Fields:
    Translation:Humans

This graph shows the number and percent of publications by field. Fields are based on how the National Library of Medicine (NLM) classifies the publications' journals and might not represent the specific topics of the publications. Note that an individual publication can be assigned to more than one field. As a result, the publication counts in this graph might add up to more than the number of publications the person has written. To see the data as text, click here.

This graph shows the number and percent of publications by field. Fields are based on how the National Library of Medicine (NLM) classifies the publications' journals and might not represent the specific topics of the publications. Note that an individual publication can be assigned to more than one field. As a result, the publication counts in this graph might add up to more than the number of publications the person has written. To see the data as text, click here.

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