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Zachary Thomas Herbert, M.S.

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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. Herbert ZT, Thimmapuram J, Xie S, Kershner JP, Kolling FW, Ringelberg CS, LeClerc A, Alekseyev YO, Fan J, Podnar JW, Stevenson HS, Sommerville G, Gupta S, Berkeley M, Koeman J, Perera A, Scott AR, Grenier JK, Malik J, Ashton JM, Pivarski KL, Wang X, Kuffel G, Mesa TE, Smith AT, Shen J, Takata Y, Volkert TL, Love JA, Zhang Y, Wang J, Xuei X, Adams M, Levine SS. Multisite Evaluation of Next-Generation Methods for Small RNA Quantification. J Biomol Tech. 2020 Jul; 31(2):47-56. PMID: 31966025.
    Citations:    
  2. Li H, Adamopoulos IE, Moulton VR, Stillman IE, Herbert Z, Moon JJ, Sharabi A, Krishfield S, Tsokos MG, Tsokos GC. Systemic lupus erythematosus favors the generation of IL-17 producing double negative T cells. Nat Commun. 2020 06 05; 11(1):2859. PMID: 32503973.
    Citations:    
  3. Podnar JW, Pantano L, Zeller MJ, Kolling FW, Zhang Y, Alekseyev YO, Niece J, Deiderick H, Fan J, Xuei X, Kieleczawa J, Levine SS, Herbert ZT, Adams M. Cross-Site Evaluation of Commercial Sanger Sequencing Chemistries. J Biomol Tech. 2020 May 15. PMID: 32831655.
    Citations:    
  4. Feng Y, Mischler WJ, Gurung AC, Kavanagh TR, Androsov G, Sadow PM, Herbert ZT, Priolo C. Therapeutic Targeting of the Secreted Lysophospholipase D Autotaxin Suppresses Tuberous Sclerosis Complex-Associated Tumorigenesis. Cancer Res. 2020 Jul 01; 80(13):2751-2763. PMID: 32393662.
    Citations:    
  5. Podnar JW, Kolling FW, Zeller MJ, Zhang Y, Thimmapuram J, Alekseyev YO, Deiulio A, Niece J, Deiderick H, Fan J, Xuei X, Pantano L, Levine SS, Herbert ZT, Adams M, Kieleczawa J. Cross Site Evaluation of Sanger Sequencing Dye Chemistries. J Biomol Tech. 2019 Dec; 30(Suppl):S46. PMID: 31896979.
    Citations:    
  6. Oser MG, Sabet AH, Gao W, Chakraborty AA, Schinzel AC, Jennings RB, Fonseca R, Bonal DM, Booker MA, Flaifel A, Novak JS, Christensen CL, Zhang H, Herbert ZT, Tolstorukov MY, Buss EJ, Wong KK, Bronson RT, Nguyen QD, Signoretti S, Kaelin WG. The KDM5A/RBP2 histone demethylase represses NOTCH signaling to sustain neuroendocrine differentiation and promote small cell lung cancer tumorigenesis. Genes Dev. 2019 12 01; 33(23-24):1718-1738. PMID: 31727771.
    Citations:    
  7. Reitman ZJ, Paolella BR, Bergthold G, Pelton K, Becker S, Jones R, Sinai CE, Malkin H, Huang Y, Grimmet L, Herbert ZT, Sun Y, Weatherbee JL, Alberta JA, Daley JF, Rozenblatt-Rosen O, Condurat AL, Qian K, Khadka P, Segal RA, Haas-Kogan D, Filbin MG, Suva ML, Regev A, Stiles CD, Kieran MW, Goumnerova L, Ligon KL, Shalek AK, Bandopadhayay P, Beroukhim R. Mitogenic and progenitor gene programmes in single pilocytic astrocytoma cells. Nat Commun. 2019 08 19; 10(1):3731. PMID: 31427603.
    Citations:    
  8. Jadhav U, Cavazza A, Banerjee KK, Xie H, O'Neill NK, Saenz-Vash V, Herbert Z, Madha S, Orkin SH, Zhai H, Shivdasani RA. Extensive Recovery of Embryonic Enhancer and Gene Memory Stored in Hypomethylated Enhancer DNA. Mol Cell. 2019 05 02; 74(3):542-554.e5. PMID: 30905509.
    Citations:    
  9. Chakraborty AA, Laukka T, Myllykoski M, Ringel AE, Booker MA, Tolstorukov MY, Meng YJ, Meier SR, Jennings RB, Creech AL, Herbert ZT, McBrayer SK, Olenchock BA, Jaffe JD, Haigis MC, Beroukhim R, Signoretti S, Koivunen P, Kaelin WG. Histone demethylase KDM6A directly senses oxygen to control chromatin and cell fate. Science. 2019 03 15; 363(6432):1217-1222. PMID: 30872525.
    Citations:    
  10. Feng X, Guan D, Auen T, Choi JW, Salazar Hernández MA, Lee J, Chun H, Faruk F, Kaplun E, Herbert Z, Copps KD, Ozcan U. IL1R1 is required for celastrol's leptin-sensitization and antiobesity effects. Nat Med. 2019 04; 25(4):575-582. PMID: 30833749.
    Citations:    
  11. Aref AR, Campisi M, Ivanova E, Portell A, Larios D, Piel BP, Mathur N, Zhou C, Coakley RV, Bartels A, Bowden M, Herbert Z, Hill S, Gilhooley S, Carter J, Cañadas I, Thai TC, Kitajima S, Chiono V, Paweletz CP, Barbie DA, Kamm RD, Jenkins RW. 3D microfluidic ex vivo culture of organotypic tumor spheroids to model immune checkpoint blockade. Lab Chip. 2018 10 09; 18(20):3129-3143. PMID: 30183789.
    Citations:    Fields:    Translation:AnimalsCells
  12. da Silva A, Bowden M, Zhang S, Masugi Y, Thorner AR, Herbert ZT, Zhou CW, Brais L, Chan JA, Hodi FS, Rodig S, Ogino S, Kulke MH. Characterization of the Neuroendocrine Tumor Immune Microenvironment. Pancreas. 2018 10; 47(9):1123-1129. PMID: 30153220.
    Citations:    Fields:    
  13. Castaño Z, San Juan BP, Spiegel A, Pant A, DeCristo MJ, Laszewski T, Ubellacker JM, Janssen SR, Dongre A, Reinhardt F, Henderson A, Del Rio AG, Gifford AM, Herbert ZT, Hutchinson JN, Weinberg RA, Chaffer CL, McAllister SS. IL-1ß inflammatory response driven by primary breast cancer prevents metastasis-initiating cell colonization. Nat Cell Biol. 2018 09; 20(9):1084-1097. PMID: 30154549.
    Citations:    Fields:    
  14. Priolo C, Khabibullin D, Reznik E, Filippakis H, Ogórek B, Kavanagh TR, Nijmeh J, Herbert ZT, Asara JM, Kwiatkowski DJ, Wu CL, Henske EP. Impairment of gamma-glutamyl transferase 1 activity in the metabolic pathogenesis of chromophobe renal cell carcinoma. Proc Natl Acad Sci U S A. 2018 07 03; 115(27):E6274-E6282. PMID: 29891694.
    Citations:    Fields:    Translation:HumansCells
  15. Cornwell M, Vangala M, Taing L, Herbert Z, Köster J, Li B, Sun H, Li T, Zhang J, Qiu X, Pun M, Jeselsohn R, Brown M, Liu XS, Long HW. VIPER: Visualization Pipeline for RNA-seq, a Snakemake workflow for efficient and complete RNA-seq analysis. BMC Bioinformatics. 2018 04 12; 19(1):135. PMID: 29649993.
    Citations:    Fields:    Translation:Cells
  16. Herbert ZT, Kershner JP, Butty VL, Thimmapuram J, Choudhari S, Alekseyev YO, Fan J, Podnar JW, Wilcox E, Gipson J, Gillaspy A, Jepsen K, BonDurant SS, Morris K, Berkeley M, LeClerc A, Simpson SD, Sommerville G, Grimmett L, Adams M, Levine SS. Cross-site comparison of ribosomal depletion kits for Illumina RNAseq library construction. BMC Genomics. 2018 Mar 15; 19(1):199. PMID: 29703133.
    Citations:    Fields:    Translation:Humans
  17. Chan S, Sridhar P, Kirchner R, Lock YJ, Herbert Z, Buonamici S, Smith P, Lieberman J, Petrocca F. Basal-A Triple-Negative Breast Cancer Cells Selectively Rely on RNA Splicing for Survival. Mol Cancer Ther. 2017 Dec; 16(12):2849-2861. PMID: 28878028.
    Citations:    Fields:    Translation:HumansCells
  18. Trivedi P, Kumar RK, Iyer A, Boswell S, Gerarduzzi C, Dadhania VP, Herbert Z, Joshi N, Luyendyk JP, Humphreys BD, Vaidya VS. Targeting Phospholipase D4 Attenuates Kidney Fibrosis. J Am Soc Nephrol. 2017 Dec; 28(12):3579-3589. PMID: 28814511.
    Citations:    Fields:    Translation:HumansAnimalsCells
  19. Jadhav U, Saxena M, O'Neill NK, Saadatpour A, Yuan GC, Herbert Z, Murata K, Shivdasani RA. Dynamic Reorganization of Chromatin Accessibility Signatures during Dedifferentiation of Secretory Precursors into Lgr5+ Intestinal Stem Cells. Cell Stem Cell. 2017 07 06; 21(1):65-77.e5. PMID: 28648363.
    Citations: 16     Fields:    Translation:AnimalsCells
  20. Pomerantz MM, Spisák S, Jia L, Cronin AM, Csabai I, Ledet E, Sartor AO, Rainville I, O'Connor EP, Herbert ZT, Szállási Z, Oh WK, Kantoff PW, Garber JE, Schrag D, Kibel AS, Freedman ML. The association between germline BRCA2 variants and sensitivity to platinum-based chemotherapy among men with metastatic prostate cancer. Cancer. 2017 Sep 15; 123(18):3532-3539. PMID: 28608931.
    Citations: 5     Fields:    Translation:Humans
  21. Townsend EC, Murakami MA, Christodoulou A, Christie AL, Köster J, DeSouza TA, Morgan EA, Kallgren SP, Liu H, Wu SC, Plana O, Montero J, Stevenson KE, Rao P, Vadhi R, Andreeff M, Armand P, Ballen KK, Barzaghi-Rinaudo P, Cahill S, Clark RA, Cooke VG, Davids MS, DeAngelo DJ, Dorfman DM, Eaton H, Ebert BL, Etchin J, Firestone B, Fisher DC, Freedman AS, Galinsky IA, Gao H, Garcia JS, Garnache-Ottou F, Graubert TA, Gutierrez A, Halilovic E, Harris MH, Herbert ZT, Horwitz SM, Inghirami G, Intlekofer AM, Ito M, Izraeli S, Jacobsen ED, Jacobson CA, Jeay S, Jeremias I, Kelliher MA, Koch R, Konopleva M, Kopp N, Kornblau SM, Kung AL, Kupper TS, LeBoeuf NR, LaCasce AS, Lees E, Li LS, Look AT, Murakami M, Muschen M, Neuberg D, Ng SY, Odejide OO, Orkin SH, Paquette RR, Place AE, Roderick JE, Ryan JA, Sallan SE, Shoji B, Silverman LB, Soiffer RJ, Steensma DP, Stegmaier K, Stone RM, Tamburini J, Thorner AR, van Hummelen P, Wadleigh M, Wiesmann M, Weng AP, Wuerthner JU, Williams DA, Wollison BM, Lane AA, Letai A, Bertagnolli MM, Ritz J, Brown M, Long H, Aster JC, Shipp MA, Griffin JD, Weinstock DM. The Public Repository of Xenografts Enables Discovery and Randomized Phase II-like Trials in Mice. Cancer Cell. 2016 07 11; 30(1):183. PMID: 27479034.
    Citations: 13     Fields:    
  22. Townsend EC, Murakami MA, Christodoulou A, Christie AL, Köster J, DeSouza TA, Morgan EA, Kallgren SP, Liu H, Wu SC, Plana O, Montero J, Stevenson KE, Rao P, Vadhi R, Andreeff M, Armand P, Ballen KK, Barzaghi-Rinaudo P, Cahill S, Clark RA, Cooke VG, Davids MS, DeAngelo DJ, Dorfman DM, Eaton H, Ebert BL, Etchin J, Firestone B, Fisher DC, Freedman AS, Galinsky IA, Gao H, Garcia JS, Garnache-Ottou F, Graubert TA, Gutierrez A, Halilovic E, Harris MH, Herbert ZT, Horwitz SM, Inghirami G, Intlekofer AM, Ito M, Izraeli S, Jacobsen ED, Jacobson CA, Jeay S, Jeremias I, Kelliher MA, Koch R, Konopleva M, Kopp N, Kornblau SM, Kung AL, Kupper TS, LeBoeuf NR, LaCasce AS, Lees E, Li LS, Look AT, Murakami M, Muschen M, Neuberg D, Ng SY, Odejide OO, Orkin SH, Paquette RR, Place AE, Roderick JE, Ryan JA, Sallan SE, Shoji B, Silverman LB, Soiffer RJ, Steensma DP, Stegmaier K, Stone RM, Tamburini J, Thorner AR, van Hummelen P, Wadleigh M, Wiesmann M, Weng AP, Wuerthner JU, Williams DA, Wollison BM, Lane AA, Letai A, Bertagnolli MM, Ritz J, Brown M, Long H, Aster JC, Shipp MA, Griffin JD, Weinstock DM. The Public Repository of Xenografts Enables Discovery and Randomized Phase II-like Trials in Mice. Cancer Cell. 2016 04 11; 29(4):574-586. PMID: 27070704.
    Citations: 19     Fields:    Translation:HumansAnimalsCells
  23. Spisák S, Lawrenson K, Fu Y, Csabai I, Cottman RT, Seo JH, Haiman C, Han Y, Lenci R, Li Q, Tisza V, Szállási Z, Herbert ZT, Chabot M, Pomerantz M, Solymosi N, Gayther SA, Joung JK, Freedman ML. CAUSEL: an epigenome- and genome-editing pipeline for establishing function of noncoding GWAS variants. Nat Med. 2015 Nov; 21(11):1357-63. PMID: 26398868.
    Citations: 22     Fields:    Translation:HumansCells
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Funded by the NIH National Center for Advancing Translational Sciences through its Clinical and Translational Science Awards Program, grant number UL1TR002541.