Katherine Rothamel

Title(s), Cellular and Molecular Medicine
SchoolVc-health Sciences-schools
Address9500 Gilman Drive #
La Jolla CA 92093
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    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.
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    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. Decoding protein-RNA interactions using CLIP-based methodologies. Nat Rev Genet. 2024 Jul 09. Xiang JS, Schafer DM, Rothamel KL, Yeo GW. PMID: 38982239.
      View in: PubMed   Mentions:
    2. Mudskipper detects combinatorial RNA binding protein interactions in multiplexed CLIP data. Cell Genom. 2024 Jun 25; 100603. Her H, Rothamel KL, Nguyen GG, Boyle EA, Yeo GW. PMID: 38955188.
      View in: PubMed   Mentions:    Fields:    Translation:HumansCells
    3. Protocol to process crosslinking and immunoprecipitation data into annotated binding sites. STAR Protoc. 2024 Jun 21; 5(2):103040. Xu S, Nguyen GG, Naritomi JT, Kopalle HM, Yee BA, Rothamel KL, Boyle EA, Yeo GW. PMID: 38669139; PMCID: PMC11066461.
      View in: PubMed   Mentions:    Fields:    Translation:HumansCells
    4. A super-enhancer-regulated RNA-binding protein cascade drives pancreatic cancer. Nat Commun. 2023 09 06; 14(1):5195. Antal CE, Oh TG, Aigner S, Luo EC, Yee BA, Campos T, Tiriac H, Rothamel KL, Cheng Z, Jiao H, Wang A, Hah N, Lenkiewicz E, Lumibao JC, Truitt ML, Estepa G, Banayo E, Bashi S, Esparza E, Munoz RM, Diedrich JK, Sodir NM, Mueller JR, Fraser CR, Borazanci E, Propper D, Von Hoff DD, Liddle C, Yu RT, Atkins AR, Han H, Lowy AM, Barrett MT, Engle DD, Evan GI, Yeo GW, Downes M, Evans RM. PMID: 37673892; PMCID: PMC10482938.
      View in: PubMed   Mentions: 1     Fields:    Translation:AnimalsCells
    5. HydRA: Deep-learning models for predicting RNA-binding capacity from protein interaction association context and protein sequence. Mol Cell. 2023 07 20; 83(14):2595-2611.e11. Jin W, Brannan KW, Kapeli K, Park SS, Tan HQ, Gosztyla ML, Mujumdar M, Ahdout J, Henroid B, Rothamel K, Xiang JS, Wong L, Yeo GW. PMID: 37421941.
      View in: PubMed   Mentions: 3     Fields:    Translation:HumansAnimalsCells
    6. Large-scale map of RNA binding protein interactomes across the mRNA life-cycle. bioRxiv. 2023 Jun 08. Street L, Rothamel K, Brannan K, Jin W, Bokor B, Dong K, Rhine K, Madrigal A, Al-Azzam N, Kim JK, Ma Y, Abdou A, Wolin E, Doron-Mandel E, Ahdout J, Mujumdar M, Jovanovic M, Yeo GW. PMID: 37333282; PMCID: PMC10274859.
      View in: PubMed   Mentions:
    7. Proteomic discovery of chemical probes that perturb protein complexes in human cells. Mol Cell. 2023 05 18; 83(10):1725-1742.e12. Lazear MR, Remsberg JR, Jaeger MG, Rothamel K, Her HL, DeMeester KE, Njomen E, Hogg SJ, Rahman J, Whitby LR, Won SJ, Schafroth MA, Ogasawara D, Yokoyama M, Lindsey GL, Li H, Germain J, Barbas S, Vaughan J, Hanigan TW, Vartabedian VF, Reinhardt CJ, Dix MM, Koo SJ, Heo I, Teijaro JR, Simon GM, Ghosh B, Abdel-Wahab O, Ahn K, Saghatelian A, Melillo B, Schreiber SL, Yeo GW, Cravatt BF. PMID: 37084731; PMCID: PMC10198961.
      View in: PubMed   Mentions: 11     Fields:    Translation:Humans
    8. Discovery and functional interrogation of SARS-CoV-2 protein-RNA interactions. Res Sq. 2022 Mar 17. Xiang JS, Mueller JR, Luo EC, Yee BA, Schafer D, Schmok JC, Tan FE, Rothamel K, McVicar RN, Kwong EM, Croker BA, Jones KL, Her HL, Chen CY, Vu AQ, Jin W, Park SS, Le P, Brannan KW, Kofman ER, Li Y, Tankka AT, Dong KD, Song Y, Clark AE, Carlin AF, Van Nostrand EL, Leibel SL, Yeo GW. PMID: 35313591; PMCID: PMC8936114.
      View in: PubMed   Mentions:
    9. Discovery and functional interrogation of SARS-CoV-2 protein-RNA interactions. bioRxiv. 2022 Feb 23. Xiang JS, Mueller JR, Luo EC, Yee BA, Schafer D, Schmok JC, Tan FE, Rothamel K, McVicar RN, Kwong EM, Jones KL, Her HL, Chen CY, Vu AQ, Jin W, Park SS, Le P, Brannan KW, Kofman ER, Li Y, Tankka AT, Dong KD, Song Y, Carlin AF, Van Nostrand EL, Leibel SL, Yeo GW. PMID: 35233578; PMCID: PMC8887137.
      View in: PubMed   Mentions: 1  
    10. RNA Binding Proteins as Pioneer Determinants of Infection: Protective, Proviral, or Both? Viruses. 2021 10 28; 13(11). Lisy S, Rothamel K, Ascano M. PMID: 34834978; PMCID: PMC8625426.
      View in: PubMed   Mentions: 5     Fields:    Translation:HumansCells
    11. ELAVL1 primarily couples mRNA stability with the 3' UTRs of interferon-stimulated genes. Cell Rep. 2021 05 25; 35(8):109178. Rothamel K, Arcos S, Kim B, Reasoner C, Lisy S, Mukherjee N, Ascano M. PMID: 34038724; PMCID: PMC8225249.
      View in: PubMed   Mentions: 24     Fields:    Translation:Humans
    12. Viral crosslinking and solid-phase purification enables discovery of ribonucleoprotein complexes on incoming RNA virus genomes. Nat Protoc. 2021 01; 16(1):516-531. Kim B, Arcos S, Rothamel K, Ascano M. PMID: 33268883; PMCID: PMC8489533.
      View in: PubMed   Mentions: 8     Fields:    Translation:HumansCells
    13. Discovery of Widespread Host Protein Interactions with the Pre-replicated Genome of CHIKV Using VIR-CLASP. Mol Cell. 2020 05 21; 78(4):624-640.e7. Kim B, Arcos S, Rothamel K, Jian J, Rose KL, McDonald WH, Bian Y, Reasoner S, Barrows NJ, Bradrick S, Garcia-Blanco MA, Ascano M. PMID: 32380061; PMCID: PMC7263428.
      View in: PubMed   Mentions: 47     Fields:    Translation:HumansAnimalsCells
    14. Publisher Correction: Small molecule inhibition of cGAS reduces interferon expression in primary macrophages from autoimmune mice. Nat Commun. 2017 11 23; 8(1):1827. Vincent J, Adura C, Gao P, Luz A, Lama L, Asano Y, Okamoto R, Imaeda T, Aida J, Rothamel K, Gogakos T, Steinberg J, Reasoner S, Aso K, Tuschl T, Patel DJ, Glickman JF, Ascano M. PMID: 29170402; PMCID: PMC5700994.
      View in: PubMed   Mentions: 1     Fields:    
    15. Small molecule inhibition of cGAS reduces interferon expression in primary macrophages from autoimmune mice. Nat Commun. 2017 09 29; 8(1):750. Vincent J, Adura C, Gao P, Luz A, Lama L, Asano Y, Okamoto R, Imaeda T, Aida J, Rothamel K, Gogakos T, Steinberg J, Reasoner S, Aso K, Tuschl T, Patel DJ, Glickman JF, Ascano M. PMID: 28963528; PMCID: PMC5622107.
      View in: PubMed   Mentions: 136     Fields:    Translation:AnimalsCells
    16. Parsing the Interferon Transcriptional Network and Its Disease Associations. Cell. 2016 Jan 28; 164(3):564-78. Mostafavi S, Yoshida H, Moodley D, LeBoité H, Rothamel K, Raj T, Ye CJ, Chevrier N, Zhang SY, Feng T, Lee M, Casanova JL, Clark JD, Hegen M, Telliez JB, Hacohen N, De Jager PL, Regev A, Mathis D, Benoist C, Immunological Genome Project Consortium. PMID: 26824662; PMCID: PMC4743492.
      View in: PubMed   Mentions: 143     Fields:    Translation:HumansAnimalsCells
    17. Gene expression during the generation and activation of mouse neutrophils: implication of novel functional and regulatory pathways. PLoS One. 2014; 9(10):e108553. Ericson JA, Duffau P, Yasuda K, Ortiz-Lopez A, Rothamel K, Rifkin IR, Monach PA, ImmGen Consortium. PMID: 25279834; PMCID: PMC4184787.
      View in: PubMed   Mentions: 50     Fields:    Translation:AnimalsCells
    18. The transcriptional landscape of αβ T cell differentiation. Nat Immunol. 2013 Jun; 14(6):619-32. Mingueneau M, Kreslavsky T, Gray D, Heng T, Cruse R, Ericson J, Bendall S, Spitzer MH, Nolan GP, Kobayashi K, von Boehmer H, Mathis D, Benoist C, Immunological Genome Consortium, Best AJ, Knell J, Goldrath A, Joic V, Koller D, Shay T, Regev A, Cohen N, Brennan P, Brenner M, Kim F, Nageswara Rao T, Wagers A, Heng T, Ericson J, Rothamel K, Ortiz-Lopez A, Mathis D, Benoist C, Bezman NA, Sun JC, Min-Oo G, Kim CC, Lanier LL, Miller J, Brown B, Merad M, Gautier EL, Jakubzick C, Randolph GJ, Monach P, Blair DA, Dustin ML, Shinton SA, Hardy RR, Laidlaw D, Collins J, Gazit R, Rossi DJ, Malhotra N, Sylvia K, Kang J, Kreslavsky T, Fletcher A, Elpek K, Bellemare-Pelletier A, Malhotra D, Turley S. PMID: 23644507; PMCID: PMC3660436.
      View in: PubMed   Mentions: 155     Fields:    Translation:AnimalsCells
    19. Identification of transcriptional regulators in the mouse immune system. Nat Immunol. 2013 Jun; 14(6):633-43. Jojic V, Shay T, Sylvia K, Zuk O, Sun X, Kang J, Regev A, Koller D, Immunological Genome Project Consortium, Best AJ, Knell J, Goldrath A, Joic V, Koller D, Shay T, Regev A, Cohen N, Brennan P, Brenner M, Kim F, Rao TN, Wagers A, Heng T, Ericson J, Rothamel K, Ortiz-Lopez A, Mathis D, Benoist C, Bezman NA, Sun JC, Min-Oo G, Kim CC, Lanier LL, Miller J, Brown B, Merad M, Gautier EL, Jakubzick C, Randolph GJ, Monach P, Blair DA, Dustin ML, Shinton SA, Hardy RR, Laidlaw D, Collins J, Gazit R, Rossi DJ, Malhotra N, Sylvia K, Kang J, Kreslavsky T, Fletcher A, Elpek K, Bellemarte-Pelletier A, Malhotra D, Turley S. PMID: 23624555; PMCID: PMC3690947.
      View in: PubMed   Mentions: 113     Fields:    Translation:HumansAnimalsCells
    20. Conservation and divergence in the transcriptional programs of the human and mouse immune systems. Proc Natl Acad Sci U S A. 2013 Feb 19; 110(8):2946-51. Shay T, Jojic V, Zuk O, Rothamel K, Puyraimond-Zemmour D, Feng T, Wakamatsu E, Benoist C, Koller D, Regev A, ImmGen Consortium. PMID: 23382184; PMCID: PMC3581886.
      View in: PubMed   Mentions: 176     Fields:    Translation:HumansAnimalsCells
    21. A common polymorphism near PER1 and the timing of human behavioral rhythms. Ann Neurol. 2012 Sep; 72(3):324-34. Lim AS, Chang AM, Shulman JM, Raj T, Chibnik LB, Cain SW, Rothamel K, Benoist C, Myers AJ, Czeisler CA, Buchman AS, Bennett DA, Duffy JF, Saper CB, De Jager PL. PMID: 23034908; PMCID: PMC3464954.
      View in: PubMed   Mentions: 18     Fields:    Translation:HumansCells
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