Ignacia Echeverria Riesco, PhD

Title(s)Assistant Professor, Bioengineering
SchoolSchool of Pharmacy
Address600 16th Street, #S472
San Francisco CA 94158
PronounsShe/Her/Hers
ORCID ORCID Icon0000-0003-4717-1467 Additional info
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    Johns Hopkins UniversityPhDMolecular Biophysics

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    Using in vivo genetic and physical interaction data for structure determination of protein assemblies
    NIH R35GM151256Aug 8, 2023 - Jun 30, 2028
    Role: Principal Investigator

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    Collapse selected publications
    Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Researchers can login to make corrections and additions, or contact us for help. to make corrections and additions.
    Newest   |   Oldest   |   Most Cited   |   Most Discussed   |   Timeline   |   Field Summary   |   Plain Text
    Altmetrics Details 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. Molecular mechanism of substrate transport by human peroxisomal ABCD3. bioRxiv. 2025 May 27. Gupta M, Khandelwal NK, Seka DJ, Balasubramani SG, Dickinson MS, Myasnikov A, Echeverria I, Stroud RM. PMID: 40501884; PMCID: PMC12154719.
      View in: PubMed   Mentions:
    2. Evolutionary Sequence and Structural Basis for the Epistatic Origins of Drug Resistance in HIV. bioRxiv. 2025 May 02. Biswas A, Choudhuri I, Huang K, Sun Q, Sali A, Echeverria I, Haldane A, Levy RM, Lyumkis D. PMID: 40364913; PMCID: PMC12073831.
      View in: PubMed   Mentions:
    3. Multimodal cell maps as a foundation for structural and functional genomics. Nature. 2025 Apr 09. Schaffer LV, Hu M, Qian G, Moon KM, Pal A, Soni N, Latham AP, Pontano Vaites L, Tsai D, Mattson NM, Licon K, Bachelder R, Cesnik A, Gaur I, Le T, Leineweber W, Palar A, Pulido E, Qin Y, Zhao X, Churas C, Lenkiewicz J, Chen J, Ono K, Pratt D, Zage P, Echeverria I, Sali A, Harper JW, Gygi SP, Foster LJ, Huttlin EL, Lundberg E, Ideker T. PMID: 40205054.
      View in: PubMed   Mentions:    Fields:    
    4. Structural basis of disease mutation and substrate recognition by the human SLC2A9 transporter. Proc Natl Acad Sci U S A. 2025 Feb 18; 122(7):e2418282122. Khandelwal NK, Gupta M, Kumar P, Balasubramani SG, Echeverria I, Stroud RM. PMID: 39937868; PMCID: PMC11848319.
      View in: PubMed   Mentions:    Fields:    Translation:Humans
    5. The molecular architecture of the nuclear basket. Cell. 2024 Sep 19; 187(19):5267-5281.e13. Singh D, Soni N, Hutchings J, Echeverria I, Shaikh F, Duquette M, Suslov S, Li Z, van Eeuwen T, Molloy K, Shi Y, Wang J, Guo Q, Chait BT, Fernandez-Martinez J, Rout MP, Sali A, Villa E. PMID: 39127037; PMCID: PMC11416316.
      View in: PubMed   Mentions: 11     Fields:    Translation:AnimalsCells
    6. Trioxane-based MS-cleavable Cross-linking Mass Spectrometry for Profiling Multimeric Interactions of Cellular Networks. bioRxiv. 2024 Aug 07. Yu C, Novitsky E, Wang X, Echeverria I, Rychnovsky S, Huang L. PMID: 39211111; PMCID: PMC11360931.
      View in: PubMed   Mentions:
    7. The Molecular Architecture of the Nuclear Basket. bioRxiv. 2024 Mar 28. Singh D, Soni N, Hutchings J, Echeverria I, Shaikh F, Duquette M, Suslov S, Li Z, van Eeuwen T, Molloy K, Shi Y, Wang J, Guo Q, Chait BT, Fernandez-Martinez J, Rout MP, Sali A, Villa E. PMID: 38586009; PMCID: PMC10996695.
      View in: PubMed   Mentions:
    8. SARS-CoV-2 variants evolve convergent strategies to remodel the host response. Cell. 2023 10 12; 186(21):4597-4614.e26. Bouhaddou M, Reuschl AK, Polacco BJ, Thorne LG, Ummadi MR, Ye C, Rosales R, Pelin A, Batra J, Jang GM, Xu J, Moen JM, Richards AL, Zhou Y, Harjai B, Stevenson E, Rojc A, Ragazzini R, Whelan MVX, Furnon W, De Lorenzo G, Cowton V, Syed AM, Ciling A, Deutsch N, Pirak D, Dowgier G, Mesner D, Turner JL, McGovern BL, Rodriguez ML, Leiva-Rebollo R, Dunham AS, Zhong X, Eckhardt M, Fossati A, Liotta NF, Kehrer T, Cupic A, Rutkowska M, Mena I, Aslam S, Hoffert A, Foussard H, Olwal CO, Huang W, Zwaka T, Pham J, Lyons M, Donohue L, Griffin A, Nugent R, Holden K, Deans R, Aviles P, Lopez-Martin JA, Jimeno JM, Obernier K, Fabius JM, Soucheray M, Hüttenhain R, Jungreis I, Kellis M, Echeverria I, Verba K, Bonfanti P, Beltrao P, Sharan R, Doudna JA, Martinez-Sobrido L, Patel AH, Palmarini M, Miorin L, White K, Swaney DL, Garcia-Sastre A, Jolly C, Zuliani-Alvarez L, Towers GJ, Krogan NJ. PMID: 37738970; PMCID: PMC10604369.
      View in: PubMed   Mentions: 34     Fields:    
    9. Implications of a multiscale structure of the yeast nuclear pore complex. Mol Cell. 2023 09 21; 83(18):3283-3302.e5. Akey CW, Echeverria I, Ouch C, Nudelman I, Shi Y, Wang J, Chait BT, Sali A, Fernandez-Martinez J, Rout MP. PMID: 37738963; PMCID: PMC10630966.
      View in: PubMed   Mentions: 7     Fields:    Translation:AnimalsCells
    10. Structure and dynamics of the essential endogenous mycobacterial polyketide synthase Pks13. Nat Struct Mol Biol. 2023 03; 30(3):296-308. Kim SK, Dickinson MS, Finer-Moore J, Guan Z, Kaake RM, Echeverria I, Chen J, Pulido EH, Sali A, Krogan NJ, Rosenberg OS, Stroud RM. PMID: 36782050; PMCID: PMC10312659.
      View in: PubMed   Mentions: 12     Fields:    Translation:Cells
    11. The structural basis for HIV-1 Vif antagonism of human APOBEC3G. Nature. 2023 03; 615(7953):728-733. Li YL, Langley CA, Azumaya CM, Echeverria I, Chesarino NM, Emerman M, Cheng Y, Gross JD. PMID: 36754086; PMCID: PMC10033410.
      View in: PubMed   Mentions: 31     Fields:    Translation:HumansAnimalsCells
    12. Integrative structure determination of histones H3 and H4 using genetic interactions. FEBS J. 2023 05; 290(10):2565-2575. Echeverria I, Braberg H, Krogan NJ, Sali A. PMID: 35298864; PMCID: PMC9481981.
      View in: PubMed   Mentions: 1     Fields:    Translation:Animals
    13. From systems to structure - using genetic data to model protein structures. Nat Rev Genet. 2022 06; 23(6):342-354. Braberg H, Echeverria I, Kaake RM, Sali A, Krogan NJ. PMID: 35013567; PMCID: PMC8744059.
      View in: PubMed   Mentions: 11     Fields:    
    14. Comprehensive structure and functional adaptations of the yeast nuclear pore complex. Cell. 2022 01 20; 185(2):361-378.e25. Akey CW, Singh D, Ouch C, Echeverria I, Nudelman I, Varberg JM, Yu Z, Fang F, Shi Y, Wang J, Salzberg D, Song K, Xu C, Gumbart JC, Suslov S, Unruh J, Jaspersen SL, Chait BT, Sali A, Fernandez-Martinez J, Ludtke SJ, Villa E, Rout MP. PMID: 34982960; PMCID: PMC8928745.
      View in: PubMed   Mentions: 74     Fields:    Translation:AnimalsCells
    15. Reversible phosphorylation of cyclin T1 promotes assembly and stability of P-TEFb. Elife. 2021 11 25; 10. Huang F, Nguyen TT, Echeverria I, Rakesh R, Cary DC, Paculova H, Sali A, Weiss A, Peterlin BM, Fujinaga K. PMID: 34821217; PMCID: PMC8648303.
      View in: PubMed   Mentions: 12     Fields:    Translation:HumansCells
    16. Characterization of an A3G-VifHIV-1-CRL5-CBFβ Structure Using a Cross-linking Mass Spectrometry Pipeline for Integrative Modeling of Host-Pathogen Complexes. Mol Cell Proteomics. 2021; 20:100132. Kaake RM, Echeverria I, Kim SJ, Von Dollen J, Chesarino NM, Feng Y, Yu C, Ta H, Chelico L, Huang L, Gross J, Sali A, Krogan NJ. PMID: 34389466; PMCID: PMC8459920.
      View in: PubMed   Mentions: 7     Fields:    
    17. Genetic interaction mapping informs integrative structure determination of protein complexes. Science. 2020 12 11; 370(6522). Braberg H, Echeverria I, Bohn S, Cimermancic P, Shiver A, Alexander R, Xu J, Shales M, Dronamraju R, Jiang S, Dwivedi G, Bogdanoff D, Chaung KK, Hüttenhain R, Wang S, Mavor D, Pellarin R, Schneidman D, Bader JS, Fraser JS, Morris J, Haber JE, Strahl BD, Gross CA, Dai J, Boeke JD, Sali A, Krogan NJ. PMID: 33303586; PMCID: PMC7946025.
      View in: PubMed   Mentions: 12     Fields:    Translation:AnimalsCells
    18. Using Integrative Modeling Platform to compute, validate, and archive a model of a protein complex structure. Protein Sci. 2021 01; 30(1):250-261. Saltzberg DJ, Viswanath S, Echeverria I, Chemmama IE, Webb B, Sali A. PMID: 33166013; PMCID: PMC7737781.
      View in: PubMed   Mentions: 30     Fields:    Translation:Cells
    19. Structural basis of CD4 downregulation by HIV-1 Nef. Nat Struct Mol Biol. 2020 09; 27(9):822-828. Kwon Y, Kaake RM, Echeverria I, Suarez M, Karimian Shamsabadi M, Stoneham C, Ramirez PW, Kress J, Singh R, Sali A, Krogan N, Guatelli J, Jia X. PMID: 32719457; PMCID: PMC7483821.
      View in: PubMed   Mentions: 27     Fields:    Translation:HumansCells
    20. Structural dynamics of the human COP9 signalosome revealed by cross-linking mass spectrometry and integrative modeling. Proc Natl Acad Sci U S A. 2020 02 25; 117(8):4088-4098. Gutierrez C, Chemmama IE, Mao H, Yu C, Echeverria I, Block SA, Rychnovsky SD, Zheng N, Sali A, Huang L. PMID: 32034103; PMCID: PMC7049115.
      View in: PubMed   Mentions: 35     Fields:    Translation:HumansCells
    21. Modeling Biological Complexes Using Integrative Modeling Platform. Methods Mol Biol. 2019; 2022:353-377. Saltzberg D, Greenberg CH, Viswanath S, Chemmama I, Webb B, Pellarin R, Echeverria I, Sali A. PMID: 31396911.
      View in: PubMed   Mentions: 21     Fields:    Translation:Cells
    22. Integrative structure and functional anatomy of a nuclear pore complex. Nature. 2018 03 22; 555(7697):475-482. Kim SJ, Fernandez-Martinez J, Nudelman I, Shi Y, Zhang W, Raveh B, Herricks T, Slaughter BD, Hogan JA, Upla P, Chemmama IE, Pellarin R, Echeverria I, Shivaraju M, Chaudhury AS, Wang J, Williams R, Unruh JR, Greenberg CH, Jacobs EY, Yu Z, de la Cruz MJ, Mironska R, Stokes DL, Aitchison JD, Jarrold MF, Gerton JL, Ludtke SJ, Akey CW, Chait BT, Sali A, Rout MP. PMID: 29539637; PMCID: PMC6022767.
      View in: PubMed   Mentions: 227     Fields:    Translation:AnimalsCells
    23. Regulation of Rvb1/Rvb2 by a Domain within the INO80 Chromatin Remodeling Complex Implicates the Yeast Rvbs as Protein Assembly Chaperones. Cell Rep. 2017 06 06; 19(10):2033-2044. Zhou CY, Stoddard CI, Johnston JB, Trnka MJ, Echeverria I, Palovcak E, Sali A, Burlingame AL, Cheng Y, Narlikar GJ. PMID: 28591576; PMCID: PMC5564220.
      View in: PubMed   Mentions: 28     Fields:    Translation:AnimalsCells
    24. Insights into HIV-1 proviral transcription from integrative structure and dynamics of the Tat:AFF4:P-TEFb:TAR complex. Elife. 2016 10 12; 5. Schulze-Gahmen U, Echeverria I, Stjepanovic G, Bai Y, Lu H, Schneidman-Duhovny D, Doudna JA, Zhou Q, Sali A, Hurley JH. PMID: 27731797; PMCID: PMC5072841.
      View in: PubMed   Mentions: 23     Fields:    Translation:HumansCells
    25. Na+ coordination at the Na2 site of the Na+/I- symporter. Proc Natl Acad Sci U S A. 2016 09 13; 113(37):E5379-88. Ferrandino G, Nicola JP, Sánchez YE, Echeverria I, Liu Y, Amzel LM, Carrasco N. PMID: 27562170; PMCID: PMC5027462.
      View in: PubMed   Mentions: 12     Fields:    Translation:HumansCells
    26. Oncogenic mutations weaken the interactions that stabilize the p110α-p85α heterodimer in phosphatidylinositol 3-kinase α. FEBS J. 2015 Sep; 282(18):3528-42. Echeverria I, Liu Y, Gabelli SB, Amzel LM. PMID: 26122737; PMCID: PMC4573839.
      View in: PubMed   Mentions: 24     Fields:    Translation:HumansCells
    27. The Acetylation Landscape of the H4 Histone Tail: Disentangling the Interplay between the Specific and Cumulative Effects. J Am Chem Soc. 2015 May 20; 137(19):6245-53. Winogradoff D, Echeverria I, Potoyan DA, Papoian GA. PMID: 25905561.
      View in: PubMed   Mentions: 37     Fields:    Translation:Cells
    28. DNA exit ramps are revealed in the binding landscapes obtained from simulations in helical coordinates. PLoS Comput Biol. 2015 Feb; 11(2):e1003980. Echeverria I, Papoian GA. PMID: 25675216; PMCID: PMC4326129.
      View in: PubMed   Mentions: 2     Fields:    Translation:Cells
    29. Concerted dihedral rotations give rise to internal friction in unfolded proteins. J Am Chem Soc. 2014 Jun 18; 136(24):8708-13. Echeverria I, Makarov DE, Papoian GA. PMID: 24844314.
      View in: PubMed   Mentions: 33     Fields:    Translation:Cells
    30. Activation of PI3Kα by physiological effectors and by oncogenic mutations: structural and dynamic effects. Biophys Rev. 2014 Mar 01; 6(1):89-95. Gabelli SB, Echeverria I, Alexander M, Duong-Ly KC, Chaves-Moreira D, Brower ET, Vogelstein B, Amzel LM. PMID: 25309634; PMCID: PMC4192660.
      View in: PubMed   Mentions: 11  
    31. Estimation of free-energy differences from computed work distributions: an application of Jarzynski's equality. J Phys Chem B. 2012 Sep 13; 116(36):10986-95. Echeverria I, Amzel LM. PMID: 22849340.
      View in: PubMed   Mentions: 2     Fields:    Translation:Cells
    32. Disaccharide binding to galectin-1: free energy calculations and molecular recognition mechanism. Biophys J. 2011 May 04; 100(9):2283-92. Echeverria I, Amzel LM. PMID: 21539798; PMCID: PMC3149269.
      View in: PubMed   Mentions: 7     Fields:    Translation:AnimalsCells
    33. Structural insights into maize viviparous14, a key enzyme in the biosynthesis of the phytohormone abscisic acid. Plant Cell. 2010 Sep; 22(9):2970-80. Messing SA, Gabelli SB, Echeverria I, Vogel JT, Guan JC, Tan BC, Klee HJ, McCarty DR, Amzel LM. PMID: 20884803; PMCID: PMC2965545.
      View in: PubMed   Mentions: 72     Fields:    Translation:AnimalsCells
    34. α-Helix peptides designed from EBV-gH protein display higher antigenicity and induction of monocyte apoptosis than the native peptide. Amino Acids. 2010 Nov; 39(5):1507-19. Urquiza M, Melo-Cardenas J, Guevara T, Echeverria I, Rodriguez IC, Vanegas M, Amzel M, Patarroyo ME. PMID: 20473772; PMCID: PMC2963735.
      View in: PubMed   Mentions:    Fields:    Translation:HumansAnimalsCells
    35. Helix propensities calculations for amino acids in alanine based peptides using Jarzynski's equality. Proteins. 2010 Apr; 78(5):1302-10. Echeverria I, Amzel LM. PMID: 20014024.
      View in: PubMed   Mentions: 7     Fields:    Translation:Cells
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