Kendell Clement

Kendell Clement, PhD

Languages spoken: English

Academic Information

Departments Primary - Biomedical Informatics

Academic Office Information

k.clement@utah.edu

Education History

Postdoctoral Fellowship Massachusetts General Hospital
 Postdoctoral Research Fellow
Harvard-MIT Program in Health Sciences and Technology
 PhD
Fellowship Free University
 Fellow
Brigham Young University
 BS
Undergraduate Brigham Young University
 BS

Selected Publications

Journal Article

  1. Ten Hacken E, Gruber M, Hernndez-Snchez M, Hoffmann GB, Baranowski K, Redd RA, Clement K, Livak K, Wu CJ (2023). Generation of mouse models carrying B cell restricted single or multiplexed loss-of-function mutations through CRISPR-Cas9 gene editing. STAR Protoc, 4(4), 102165.
  2. ten Hacken E, Yin S, Redd R, Hernndez Snchez M, Clement K, Hoffmann GB, Regis FF, Witten E, Li S, Neuberg D, Pinello L, Livak KJ, Wu CJ (2022). Loss-of-function lesions impact B-cell development and fitness but are insufficient to drive CLL in mouse models. Blood Adv, 7(16), 4514-4517.
  3. Ten Hacken E, Sewastianik T, Yin S, Hoffmann GB, Gruber M, Clement K, Penter L, Redd RA, Ruthen N, Hergalant S, Sholokhova A, Fell G, Parry EM, Brosus J, Guieze R, Lucas F, Hernndez-Snchez M, Baranowski K, Southard J, Joyal H, Billington L, Regis FFD, Witten E, Uduman M, Knisbacher BA, Li S, Lyu H, Vaisitti T, Deaglio S, Inghirami G, Feugier P, Stilgenbauer S, Tausch E, Davids MS, Getz G, Livak KJ, Bozic I, Neuberg DS, Carrasco RD, Wu CJ (2022). In Vivo Modeling of CLL Transformation to Richter Syndrome Reveals Convergent Evolutionary Paths and Therapeutic Vulnerabilities. Blood Cancer Discov, 4(2), 150-169.
  4. Stevens LE, Peluffo G, Qiu X, Temko D, Fassl A, Li Z, Trinh A, Seehawer M, Jovanovi B, Alekovi M, Wilde CM, Geck RC, Shu S, Kingston NL, Harper NW, Almendro V, Pyke AL, Egri SB, Papanastasiou M, Clement K, Zhou N, Walker S, Salas J, Park SY, Frank DA, Meissner A, Jaffe JD, Sicinski P, Toker A, Michor F, Long HW, Overmoyer BA, Polyak K (2022). JAK-STAT Signaling in Inflammatory Breast Cancer Enables Chemotherapy-Resistant Cell States. Cancer Res, 83(2), 264-284.
  5. Petri K, Zhang W, Ma J, Schmidts A, Lee H, Horng JE, Kim DY, Kurt IC, Clement K, Hsu JY, Pinello L, Maus MV, Joung JK, Yeh JJ (2021). CRISPR prime editing with ribonucleoprotein complexes in zebrafish and primary human cells. Nat Biotechnol, 40(2), 189-193.
  6. Annas GJ, Beisel CL, Clement K, Crisanti A, Francis S, Galardini M, Galizi R, Grnewald J, Immobile G, Khalil AS, Mller R, Pattanayak V, Petri K, Paul L, Pinello L, Simoni A, Taxiarchi C, Joung JK (2021). A Code of Ethics for Gene Drive Research. CRISPR J, 4(1), 19-24.
  7. Kretzmer H, Biran A, Purroy N, Lemvigh CK, Clement K, Gruber M, Gu H, Rassenti L, Mohammad AW, Lesnick C, Slager SL, Braggio E, Shanafelt TD, Kay NE, Fernandes SM, Brown JR, Wang L, Li S, Livak KJ, Neuberg DS, Klages S, Timmermann B, Kipps TJ, Campo E, Gnirke A, Wu CJ, Meissner A (2020). Preneoplastic Alterations Define CLL DNA Methylome and Persist through Disease Progression and Therapy. Blood Cancer Discov, 2(1), 54-69.
  8. Ten Hacken E, Clement K, Li S, Hernndez-Snchez M, Redd R, Wang S, Ruff D, Gruber M, Baranowski K, Jacob J, Flynn J, Jones KW, Neuberg D, Livak KJ, Pinello L, Wu CJ (2020). High throughput single-cell detection of multiplex CRISPR-edited gene modifications. Genome Biol, 21(1), 266.
  9. Bachireddy P, Ennis C, Nguyen VN, Gohil SH, Clement K, Shukla SA, Forman J, Barkas N, Freeman S, Bavli N, Elagina L, Leshchiner I, Mohammad AW, Mathewson ND, Keskin DB, Rassenti LZ, Kipps TJ, Brown JR, Getz G, Ho VT, Gnirke A, Neuberg D, Soiffer RJ, Ritz J, Alyea EP, Kharchenko PV, Wu CJ (2020). Distinct evolutionary paths in chronic lymphocytic leukemia during resistance to the graft-versus-leukemia effect. Sci Transl Med, 12(561).
  10. Zeng J, Wu Y, Ren C, Bonanno J, Shen AH, Shea D, Gehrke JM, Clement K, Luk K, Yao Q, Kim R, Wolfe SA, Manis JP, Pinello L, Joung JK, Bauer DE (2020). Therapeutic base editing of human hematopoietic stem cells. Nat Med, 26(4), 535-541.
  11. Chen H, Lareau C, Andreani T, Vinyard ME, Garcia SP, Clement K, Andrade-Navarro MA, Buenrostro JD, Pinello L (2019). Assessment of computational methods for the analysis of single-cell ATAC-seq data. Genome Biol, 20(1), 241.
  12. Di Stefano B, Luo EC, Haggerty C, Aigner S, Charlton J, Brumbaugh J, Ji F, Rabano Jimnez I, Clowers KJ, Huebner AJ, Clement K, Lipchina I, de Kort MAC, Anselmo A, Pulice J, Gerli MFM, Gu H, Gygi SP, Sadreyev RI, Meissner A, Yeo GW, Hochedlinger K (2019). The RNA Helicase DDX6 Controls Cellular Plasticity by Modulating P-Body Homeostasis. Cell Stem Cell, 25(5), 622-638.e13.
  13. Wu Y, Zeng J, Roscoe BP, Liu P, Yao Q, Lazzarotto CR, Clement K, Cole MA, Luk K, Baricordi C, Shen AH, Ren C, Esrick EB, Manis JP, Dorfman DM, Williams DA, Biffi A, Brugnara C, Biasco L, Brendel C, Pinello L, Tsai SQ, Wolfe SA, Bauer DE (2019). Highly efficient therapeutic gene editing of human hematopoietic stem cells. Nat Med, 25(5), 776-783.
  14. Gaiti F, Chaligne R, Gu H, Brand RM, Kothen-Hill S, Schulman RC, Grigorev K, Risso D, Kim KT, Pastore A, Huang KY, Alonso A, Sheridan C, Omans ND, Biederstedt E, Clement K, Wang L, Felsenfeld JA, Bhavsar EB, Aryee MJ, Allan JN, Furman R, Gnirke A, Wu CJ, Meissner A, Landau DA (2019). Epigenetic evolution and lineage histories of chronic lymphocytic leukaemia. Nature, 569(7757), 576-580.
  15. Clement K, Rees H, Canver MC, Gehrke JM, Farouni R, Hsu JY, Cole MA, Liu DR, Joung JK, Bauer DE, Pinello L (2019). CRISPResso2 provides accurate and rapid genome editing sequence analysis. Nat Biotechnol, 37(3), 224-226.
  16. Kleinstiver BP, Sousa AA, Walton RT, Tak YE, Hsu JY, Clement K, Welch MM, Horng JE, Malagon-Lopez J, Scarf I, Maus MV, Pinello L, Aryee MJ, Joung JK (2019). Engineered CRISPR-Cas12a variants with increased activities and improved targeting ranges for gene, epigenetic and base editing. Nat Biotechnol, 37(3), 276-282.
  17. Hsu JY, Fulco CP, Cole MA, Canver MC, Pellin D, Sher F, Farouni R, Clement K, Guo JA, Biasco L, Orkin SH, Engreitz JM, Lander ES, Joung JK, Bauer DE, Pinello L (2018). CRISPR-SURF: discovering regulatory elements by deconvolution of CRISPR tiling screen data. Nat Methods, 15(12), 992-993.
  18. Zhang Y, Charlton J, Karnik R, Beerman I, Smith ZD, Gu H, Boyle P, Mi X, Clement K, Pop R, Gnirke A, Rossi DJ, Meissner A (2018). Targets and genomic constraints of ectopic Dnmt3b expression. Elife, 7.
  19. Ichida JK, Staats KA, Davis-Dusenbery BN, Clement K, Galloway KE, Babos KN, Shi Y, Son EY, Kiskinis E, Atwater N, Gu H, Gnirke A, Meissner A, Eggan K (2018). Comparative genomic analysis of embryonic, lineage-converted and stem cell-derived motor neurons. Development, 145(22).
  20. Gehrke JM, Cervantes O, Clement MK, Wu Y, Zeng J, Bauer DE, Pinello L, Joung JK (2018). An APOBEC3A-Cas9 base editor with minimized bystander and off-target activities. Nat Biotechnol, 36(10), 977-982.
  21. Di Stefano B, Ueda M, Sabri S, Brumbaugh J, Huebner AJ, Sahakyan A, Clement K, Clowers KJ, Erickson AR, Shioda K, Gygi SP, Gu H, Shioda T, Meissner A, Takashima Y, Plath K, Hochedlinger K (2018). Reduced MEK inhibition preserves genomic stability in naive human embryonic stem cells. Nat Methods, 15(9), 732-740.
  22. Akcakaya P, Bobbin ML, Guo JA, Malagon-Lopez J, Clement K, Garcia SP, Fellows MD, Porritt MJ, Firth MA, Carreras A, Baccega T, Seeliger F, Bjursell M, Tsai SQ, Nguyen NT, Nitsch R, Mayr LM, Pinello L, Bohlooly-Y M, Aryee MJ, Maresca M, Joung JK (2018). In vivo CRISPR editing with no detectable genome-wide off-target mutations. Nature, 561(7723), 416-419.
  23. Schwarz BA, Cetinbas M, Clement K, Walsh RM, Cheloufi S, Gu H, Langkabel J, Kamiya A, Schorle H, Meissner A, Sadreyev RI, Hochedlinger K (2018). Prospective Isolation of Poised iPSC Intermediates Reveals Principles of Cellular Reprogramming. Cell Stem Cell, 23(2), 289-305.e5.
  24. Clement K, Farouni R, Bauer DE, Pinello L (2018). AmpUMI: design and analysis of unique molecular identifiers for deep amplicon sequencing. Bioinformatics, 34(13), i202-i210.
  25. Du P, Pirouz M, Choi J, Huebner AJ, Clement K, Meissner A, Hochedlinger K, Gregory RI (2018). An Intermediate Pluripotent State Controlled by MicroRNAs Is Required for the Naive-to-Primed Stem Cell Transition. Cell Stem Cell, 22(6), 851-864.e5.
  26. Shukla SA, Bachireddy P, Schilling B, Galonska C, Zhan Q, Bango C, Langer R, Lee PC, Gusenleitner D, Keskin DB, Babadi M, Mohammad A, Gnirke A, Clement K, Cartun ZJ, Van Allen EM, Miao D, Huang Y, Snyder A, Merghoub T, Wolchok JD, Garraway LA, Meissner A, Weber JS, Hacohen N, Neuberg D, Potts PR, Murphy GF, Lian CG, Schadendorf D, Hodi FS, Wu CJ (2018). Cancer-Germline Antigen Expression Discriminates Clinical Outcome to CTLA-4 Blockade. Cell, 173(3), 624-633.e8.
  27. Cesana M, Guo MH, Cacchiarelli D, Wahlster L, Barragan J, Doulatov S, Vo LT, Salvatori B, Trapnell C, Clement K, Cahan P, Tsanov KM, Sousa PM, Tazon-Vega B, Bolondi A, Giorgi FM, Califano A, Rinn JL, Meissner A, Hirschhorn JN, Daley GQ (2017). A CLK3-HMGA2 Alternative Splicing Axis Impacts Human Hematopoietic Stem Cell Molecular Identity throughout Development. Cell Stem Cell, 22(4), 575-588.e7.
  28. Charlton J, Downing TL, Smith ZD, Gu H, Clement K, Pop R, Akopian V, Klages S, Santos DP, Tsankov AM, Timmermann B, Ziller MJ, Kiskinis E, Gnirke A, Meissner A (2018). Global delay in nascent strand DNA methylation. Nat Struct Mol Biol, 25(4), 327-332.
  29. Lareau CA, Clement K, Hsu JY, Pattanayak V, Joung JK, Aryee MJ, Pinello L (2018). Response to "Unexpected mutations after CRISPR-Cas9 editing in vivo". Nat Methods, 15(4), 238-239.
  30. Galonska C, Charlton J, Mattei AL, Donaghey J, Clement K, Gu H, Mohammad AW, Stamenova EK, Cacchiarelli D, Klages S, Timmermann B, Cantz T, Schler HR, Gnirke A, Ziller MJ, Meissner A (2018). Genome-wide tracking of dCas9-methyltransferase footprints. Nat Commun, 9(1), 597.
  31. Donaghey J, Thakurela S, Charlton J, Chen JS, Smith ZD, Gu H, Pop R, Clement K, Stamenova EK, Karnik R, Kelley DR, Gifford CA, Cacchiarelli D, Rinn JL, Gnirke A, Ziller MJ, Meissner A (2018). Genetic determinants and epigenetic effects of pioneer-factor occupancy. Nat Genet, 50(2), 250-258.
  32. Smith ZD, Shi J, Gu H, Donaghey J, Clement K, Cacchiarelli D, Gnirke A, Michor F, Meissner A (2017). Epigenetic restriction of extraembryonic lineages mirrors the somatic transition to cancer. Nature, 549(7673), 543-547.
  33. Choi J, Huebner AJ, Clement K, Walsh RM, Savol A, Lin K, Gu H, Di Stefano B, Brumbaugh J, Kim SY, Sharif J, Rose CM, Mohammad A, Odajima J, Charron J, Shioda T, Gnirke A, Gygi S, Koseki H, Sadreyev RI, Xiao A, Meissner A, Hochedlinger K (2017). Prolonged Mek1/2 suppression impairs the developmental potential of embryonic stem cells. Nature, 548(7666), 219-223.
  34. Choi J, Clement K, Huebner AJ, Webster J, Rose CM, Brumbaugh J, Walsh RM, Lee S, Savol A, Etchegaray JP, Gu H, Boyle P, Elling U, Mostoslavsky R, Sadreyev R, Park PJ, Gygi SP, Meissner A, Hochedlinger K (2017). DUSP9 Modulates DNA Hypomethylation in Female Mouse Pluripotent Stem Cells. Cell Stem Cell, 20(5), 706-719.e7.
  35. Choi J, Lee S, Mallard W, Clement K, Tagliazucchi GM, Lim H, Choi IY, Ferrari F, Tsankov AM, Pop R, Lee G, Rinn JL, Meissner A, Park PJ, Hochedlinger K (2015). A comparison of genetically matched cell lines reveals the equivalence of human iPSCs and ESCs. Nat Biotechnol, 33(11), 1173-81.
  36. Liao J, Karnik R, Gu H, Ziller MJ, Clement K, Tsankov AM, Akopian V, Gifford CA, Donaghey J, Galonska C, Pop R, Reyon D, Tsai SQ, Mallard W, Joung JK, Rinn JL, Gnirke A, Meissner A (2015). Targeted disruption of DNMT1, DNMT3A and DNMT3B in human embryonic stem cells. Nat Genet, 47(5), 469-78.
  37. Huh SJ, Clement K, Jee D, Merlini A, Choudhury S, Maruyama R, Yoo R, Chytil A, Boyle P, Ran FA, Moses HL, Barcellos-Hoff MH, Jackson-Grusby L, Meissner A, Polyak K (2015). Age- and pregnancy-associated DNA methylation changes in mammary epithelial cells. Stem Cell Reports, 4(2), 297-311.
  38. Landau DA, Clement K, Ziller MJ, Boyle P, Fan J, Gu H, Stevenson K, Sougnez C, Wang L, Li S, Kotliar D, Zhang W, Ghandi M, Garraway L, Fernandes SM, Livak KJ, Gabriel S, Gnirke A, Lander ES, Brown JR, Neuberg D, Kharchenko PV, Hacohen N, Getz G, Meissner A, Wu CJ (2014). Locally disordered methylation forms the basis of intratumor methylome variation in chronic lymphocytic leukemia. Cancer Cell, 26(6), 813-825.
  39. Li W, Cavelti-Weder C, Zhang Y, Clement K, Donovan S, Gonzalez G, Zhu J, Stemann M, Xu K, Hashimoto T, Yamada T, Nakanishi M, Zhang Y, Zeng S, Gifford D, Meissner A, Weir G, Zhou Q (2014). Long-term persistence and development of induced pancreatic beta cells generated by lineage conversion of acinar cells. Nat Biotechnol, 32(12), 1223-30.
  40. Boyle P, Clement K, Gu H, Smith ZD, Ziller M, Fostel JL, Holmes L, Meldrim J, Kelley F, Gnirke A, Meissner A (2012). Gel-free multiplexed reduced representation bisulfite sequencing for large-scale DNA methylation profiling. Genome Biol, 13(10), R92.
  41. Clement K, Gustafson N, Berbert A, Carroll H, Merris C, Olsen A, Clement M, Snell Q, Allen J, Roper RJ (2009). PathGen: a transitive gene pathway generator. Bioinformatics, 26(3), 423-5.

Review

  1. Clement K, Hsu JY, Canver MC, Joung JK, Pinello L (2019). Technologies and Computational Analysis Strategies for CRISPR Applications. [Review]. Mol Cell, 79(1), 11-29.

Patent

  1. Clement K, Getz G, Landau D, Meissner A, Wu C (2020). Compositions and methods for diagnosing, evaluating and treating cancer. U.S. Patent No. US 10801070. Washington, D.C.:U.S. Patent and Trademark Office.
  2. Clement K, Pinello L (2019). Biologically informed and accurate sequence alignment. U.S. Patent No. US2019/066167. Washington, D.C.:U.S. Patent and Trademark Office.