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Replication timing alterations in leukemia affect clinically relevant chromosome domains.

Rivera-Mulia JC, Sasaki T, Trevilla-Garcia C, Nakamichi N, Knapp DJHF, Hammond CA, Chang BH, Tyner JW, Devidas M, Zimmerman J, Klein KN, Somasundaram V, Druker BJ, Gruber TA, Koren A, Eaves CJ, Gilbert DM.

Blood Adv. 2019 Nov 12;3(21):3201-3213. doi: 10.1182/bloodadvances.2019000641.


Amygdala Arginine Vasopressin Modulates Chronic Ethanol Withdrawal Anxiety-Like Behavior in the Social Interaction Task.

Harper KM, Knapp DJ, Butler RK, Cook CA, Criswell HE, Stuber GD, Breese GR.

Alcohol Clin Exp Res. 2019 Oct;43(10):2134-2143. doi: 10.1111/acer.14163. Epub 2019 Aug 23.


Discovery of a CD10-negative B-progenitor in human fetal life identifies unique ontogeny-related developmental programs.

O'Byrne S, Elliott N, Rice S, Buck G, Fordham N, Garnett C, Godfrey L, Crump NT, Wright G, Inglott S, Hua P, Psaila B, Povinelli B, Knapp DJHF, Agraz-Doblas A, Bueno C, Varela I, Bennett P, Koohy H, Watt SM, Karadimitris A, Mead AJ, Ancliff P, Vyas P, Menendez P, Milne TA, Roberts I, Roy A.

Blood. 2019 Sep 26;134(13):1059-1071. doi: 10.1182/blood.2019001289. Epub 2019 Aug 5.


Addendum: Precise tuning of gene expression levels in mammalian cells.

Michaels YS, Barnkob MB, Barbosa H, Baeumler TA, Thompson MK, Andre V, Colin-York H, Fritzsche M, Gileadi U, Sheppard HM, Knapp DJHF, Milne TA, Cerundolo V, Fulga TA.

Nat Commun. 2019 Jun 10;10(1):2622. doi: 10.1038/s41467-019-10615-0.


Decoupling tRNA promoter and processing activities enables specific Pol-II Cas9 guide RNA expression.

Knapp DJHF, Michaels YS, Jamilly M, Ferry QRV, Barbosa H, Milne TA, Fulga TA.

Nat Commun. 2019 Apr 2;10(1):1490. doi: 10.1038/s41467-019-09148-3.


Precise tuning of gene expression levels in mammalian cells.

Michaels YS, Barnkob MB, Barbosa H, Baeumler TA, Thompson MK, Andre V, Colin-York H, Fritzsche M, Gileadi U, Sheppard HM, Knapp DJHF, Milne TA, Cerundolo V, Fulga TA.

Nat Commun. 2019 Feb 18;10(1):818. doi: 10.1038/s41467-019-08777-y.


A topological view of human CD34+ cell state trajectories from integrated single-cell output and proteomic data.

Knapp DJHF, Hammond CA, Wang F, Aghaeepour N, Miller PH, Beer PA, Pellacani D, VanInsberghe M, Hansen C, Bendall SC, Nolan GP, Eaves CJ.

Blood. 2019 Feb 28;133(9):927-939. doi: 10.1182/blood-2018-10-878025. Epub 2019 Jan 8.


Vasopressin and alcohol: a multifaceted relationship.

Harper KM, Knapp DJ, Criswell HE, Breese GR.

Psychopharmacology (Berl). 2018 Dec;235(12):3363-3379. doi: 10.1007/s00213-018-5099-x. Epub 2018 Nov 3. Review.


UM171 Enhances Lentiviral Gene Transfer and Recovery of Primitive Human Hematopoietic Cells.

Ngom M, Imren S, Maetzig T, Adair JE, Knapp DJHF, Chagraoui J, Fares I, Bordeleau ME, Sauvageau G, Leboulch P, Eaves C, Humphries RK.

Mol Ther Methods Clin Dev. 2018 Jul 5;10:156-164. doi: 10.1016/j.omtm.2018.06.009. eCollection 2018 Sep 21.


High-Resolution Single-Cell DNA Methylation Measurements Reveal Epigenetically Distinct Hematopoietic Stem Cell Subpopulations.

Hui T, Cao Q, Wegrzyn-Woltosz J, O'Neill K, Hammond CA, Knapp DJHF, Laks E, Moksa M, Aparicio S, Eaves CJ, Karsan A, Hirst M.

Stem Cell Reports. 2018 Aug 14;11(2):578-592. doi: 10.1016/j.stemcr.2018.07.003. Epub 2018 Aug 2.


Comparative effects of stressors on behavioral and neuroimmune responses of fawn-hooded (FH/Wjd) and Wistar rats: Implications for models of depression.

Knapp DJ, Harper KM, Melton J, Breese G.

J Neuroimmunol. 2018 Sep 15;322:74-80. doi: 10.1016/j.jneuroim.2018.06.015. Epub 2018 Jun 27.


GateFinder: projection-based gating strategy optimization for flow and mass cytometry.

Aghaeepour N, Simonds EF, Knapp DJHF, Bruggner RV, Sachs K, Culos A, Gherardini PF, Samusik N, Fragiadakis GK, Bendall SC, Gaudilliere B, Angst MS, Eaves CJ, Weiss WA, Fantl WJ, Nolan GP.

Bioinformatics. 2018 Dec 1;34(23):4131-4133. doi: 10.1093/bioinformatics/bty430.


Single-cell analysis identifies a CD33+ subset of human cord blood cells with high regenerative potential.

Knapp DJHF, Hammond CA, Hui T, van Loenhout MTJ, Wang F, Aghaeepour N, Miller PH, Moksa M, Rabu GM, Beer PA, Pellacani D, Humphries RK, Hansen C, Hirst M, Eaves CJ.

Nat Cell Biol. 2018 Jun;20(6):710-720. doi: 10.1038/s41556-018-0104-5. Epub 2018 May 25.


Differential effects of single versus repeated minocycline administration-Lack of significant interaction with chronic alcohol history.

Harper KM, Knapp DJ, Park MA, Breese GR.

Pharmacol Biochem Behav. 2018 May;168:33-42. doi: 10.1016/j.pbb.2018.03.007. Epub 2018 Mar 20.


A multiplexable TALE-based binary expression system for in vivo cellular interaction studies.

Toegel M, Azzam G, Lee EY, Knapp DJHF, Tan Y, Fa M, Fulga TA.

Nat Commun. 2017 Nov 21;8(1):1663. doi: 10.1038/s41467-017-01592-3.


Mass Cytometric Analysis Reveals Viable Activated Caspase-3+ Luminal Progenitors in the Normal Adult Human Mammary Gland.

Knapp DJHF, Kannan N, Pellacani D, Eaves CJ.

Cell Rep. 2017 Oct 24;21(4):1116-1126. doi: 10.1016/j.celrep.2017.09.096.


Conflict Resolution Styles as Mediators of Female Child Sexual Abuse Experience and Heterosexual Couple Relationship Satisfaction and Stability in Adulthood.

Knapp AE, Knapp DJ, Brown CC, Larson JH.

J Child Sex Abus. 2017 Jan;26(1):58-77. doi: 10.1080/10538712.2016.1262931.


Analysis of parameters that affect human hematopoietic cell outputs in mutant c-kit-immunodeficient mice.

Miller PH, Rabu G, MacAldaz M, Knapp DJ, Cheung AM, Dhillon K, Nakamichi N, Beer PA, Shultz LD, Humphries RK, Eaves CJ.

Exp Hematol. 2017 Apr;48:41-49. doi: 10.1016/j.exphem.2016.12.012. Epub 2017 Jan 11.


Dissociation of Survival, Proliferation, and State Control in Human Hematopoietic Stem Cells.

Knapp DJ, Hammond CA, Miller PH, Rabu GM, Beer PA, Ricicova M, Lecault V, Da Costa D, VanInsberghe M, Cheung AM, Pellacani D, Piret J, Hansen C, Eaves CJ.

Stem Cell Reports. 2017 Jan 10;8(1):152-162. doi: 10.1016/j.stemcr.2016.12.003.


A mouse model for chronic pain-induced increase in ethanol consumption.

Butler RK, Knapp DJ, Ulici V, Longobardi L, Loeser RF, Breese GR.

Pain. 2017 Mar;158(3):457-462. doi: 10.1097/j.pain.0000000000000780.


Nucleosome Density ChIP-Seq Identifies Distinct Chromatin Modification Signatures Associated with MNase Accessibility.

Lorzadeh A, Bilenky M, Hammond C, Knapp DJHF, Li L, Miller PH, Carles A, Heravi-Moussavi A, Gakkhar S, Moksa M, Eaves CJ, Hirst M.

Cell Rep. 2016 Nov 15;17(8):2112-2124. doi: 10.1016/j.celrep.2016.10.055.


Analysis of Normal Human Mammary Epigenomes Reveals Cell-Specific Active Enhancer States and Associated Transcription Factor Networks.

Pellacani D, Bilenky M, Kannan N, Heravi-Moussavi A, Knapp DJHF, Gakkhar S, Moksa M, Carles A, Moore R, Mungall AJ, Marra MA, Jones SJM, Aparicio S, Hirst M, Eaves CJ.

Cell Rep. 2016 Nov 15;17(8):2060-2074. doi: 10.1016/j.celrep.2016.10.058.


Distinct signaling programs control human hematopoietic stem cell survival and proliferation.

Knapp DJ, Hammond CA, Aghaeepour N, Miller PH, Pellacani D, Beer PA, Sachs K, Qiao W, Wang W, Humphries RK, Sauvageau G, Zandstra PW, Bendall SC, Nolan GP, Hansen C, Eaves CJ.

Blood. 2017 Jan 19;129(3):307-318. doi: 10.1182/blood-2016-09-740654. Epub 2016 Nov 8.


Age-related differences in anxiety-like behavior and amygdalar CCL2 responsiveness to stress following alcohol withdrawal in male Wistar rats.

Harper KM, Knapp DJ, Park MA, Breese GR.

Psychopharmacology (Berl). 2017 Jan;234(1):79-88. doi: 10.1007/s00213-016-4439-y. Epub 2016 Sep 24.


Hematopoietic Stem Cells Are the Major Source of Multilineage Hematopoiesis in Adult Animals.

Sawai CM, Babovic S, Upadhaya S, Knapp DJHF, Lavin Y, Lau CM, Goloborodko A, Feng J, Fujisaki J, Ding L, Mirny LA, Merad M, Eaves CJ, Reizis B.

Immunity. 2016 Sep 20;45(3):597-609. doi: 10.1016/j.immuni.2016.08.007. Epub 2016 Aug 30.


Quantitation of Human Cells that Produce Neutrophils and Platelets in Vivo Obtained from Normal Donors Treated with Granulocyte Colony-Stimulating Factor and/or Plerixafor.

Miller PH, Nakamichi N, Knapp DJHF, Rabu G, Schultz KR, Jones DM, Couban S, Eaves CJ.

Biol Blood Marrow Transplant. 2016 Nov;22(11):1945-1952. doi: 10.1016/j.bbmt.2016.07.023. Epub 2016 Aug 2.


Stress and Withdrawal from Chronic Ethanol Induce Selective Changes in Neuroimmune mRNAs in Differing Brain Sites.

Knapp DJ, Harper KM, Whitman BA, Zimomra Z, Breese GR.

Brain Sci. 2016 Jul 27;6(3). pii: E25. doi: 10.3390/brainsci6030025.


Persistent adaptation by chronic alcohol is facilitated by neuroimmune activation linked to stress and CRF.

Breese GR, Knapp DJ.

Alcohol. 2016 May;52:9-23. doi: 10.1016/j.alcohol.2016.01.005. Epub 2016 Feb 24. Review.


Early production of human neutrophils and platelets posttransplant is severely compromised by growth factor exposure.

Miller PH, Knapp DJ, Beer PA, MacAldaz M, Rabu G, Cheung AM, Wei L, Eaves CJ.

Exp Hematol. 2016 Jul;44(7):635-40. doi: 10.1016/j.exphem.2016.04.003. Epub 2016 Apr 16.


The Use of Perinatal 6-Hydroxydopamine to Produce a Rodent Model of Lesch-Nyhan Disease.

Knapp DJ, Breese GR.

Curr Top Behav Neurosci. 2016;29:265-277. doi: 10.1007/7854_2016_444. Review.


Withdrawal from Chronic Alcohol Induces a Unique CCL2 mRNA Increase in Adolescent But Not Adult Brain--Relationship to Blood Alcohol Levels and Seizures.

Harper KM, Knapp DJ, Breese GR.

Alcohol Clin Exp Res. 2015 Dec;39(12):2375-85. doi: 10.1111/acer.12898. Epub 2015 Nov 11.


Mercury Emission Ratios from Coal-Fired Power Plants in the Southeastern United States during NOMADSS.

Ambrose JL, Gratz LE, Jaffe DA, Campos T, Flocke FM, Knapp DJ, Stechman DM, Stell M, Weinheimer AJ, Cantrell CA, Mauldin RL 3rd.

Environ Sci Technol. 2015 Sep 1;49(17):10389-97. doi: 10.1021/acs.est.5b01755. Epub 2015 Aug 13.


Dominant-negative IKAROS enhances IL-3-stimulated signaling in wild-type but not BCR-ABL1(+) mouse BA/F3 cells.

von Palffy S, Bulaeva E, Babovic S, Kannan N, Knapp DJ, Wei L, Eaves CJ, Beer PA.

Exp Hematol. 2015 Jul;43(7):514-23.e1-2. doi: 10.1016/j.exphem.2015.04.004. Epub 2015 May 4.


DNA barcoding reveals diverse growth kinetics of human breast tumour subclones in serially passaged xenografts.

Nguyen LV, Cox CL, Eirew P, Knapp DJ, Pellacani D, Kannan N, Carles A, Moksa M, Balani S, Shah S, Hirst M, Aparicio S, Eaves CJ.

Nat Commun. 2014 Dec 23;5:5871. doi: 10.1038/ncomms6871.


A dominant-negative isoform of IKAROS expands primitive normal human hematopoietic cells.

Beer PA, Knapp DJ, Kannan N, Miller PH, Babovic S, Bulaeva E, Aghaeepour N, Rabu G, Rostamirad S, Shih K, Wei L, Eaves CJ.

Stem Cell Reports. 2014 Nov 11;3(5):841-57. doi: 10.1016/j.stemcr.2014.09.006. Epub 2014 Oct 11.


Disruption of IKAROS activity in primitive chronic-phase CML cells mimics myeloid disease progression.

Beer PA, Knapp DJ, Miller PH, Kannan N, Sloma I, Heel K, Babovic S, Bulaeva E, Rabu G, Terry J, Druker BJ, Loriaux MM, Loeb KR, Radich JP, Erber WN, Eaves CJ.

Blood. 2015 Jan 15;125(3):504-15. doi: 10.1182/blood-2014-06-581173. Epub 2014 Nov 4.


Cord blood expansion. Pyrimidoindole derivatives are agonists of human hematopoietic stem cell self-renewal.

Fares I, Chagraoui J, Gareau Y, Gingras S, Ruel R, Mayotte N, Csaszar E, Knapp DJ, Miller P, Ngom M, Imren S, Roy DC, Watts KL, Kiem HP, Herrington R, Iscove NN, Humphries RK, Eaves CJ, Cohen S, Marinier A, Zandstra PW, Sauvageau G.

Science. 2014 Sep 19;345(6203):1509-12. doi: 10.1126/science.1256337.


"Deep" sequencing accuracy and reproducibility using Roche/454 technology for inferring co-receptor usage in HIV-1.

Knapp DJ, McGovern RA, Poon AF, Zhong X, Chan D, Swenson LC, Dong W, Harrigan PR.

PLoS One. 2014 Jun 24;9(6):e99508. doi: 10.1371/journal.pone.0099508. eCollection 2014.


Distinct stromal cell factor combinations can separately control hematopoietic stem cell survival, proliferation, and self-renewal.

Wohrer S, Knapp DJ, Copley MR, Benz C, Kent DG, Rowe K, Babovic S, Mader H, Oostendorp RA, Eaves CJ.

Cell Rep. 2014 Jun 26;7(6):1956-67. doi: 10.1016/j.celrep.2014.05.014. Epub 2014 Jun 6.


Limited evolution of inferred HIV-1 tropism while viremia is undetectable during standard HAART therapy.

Lee GQ, Dong W, Mo T, Knapp DJ, Brumme CJ, Woods CK, Kanters S, Yip B, Harrigan PR.

PLoS One. 2014 Jun 6;9(6):e99000. doi: 10.1371/journal.pone.0099000. eCollection 2014.


Postherpetic neuralgia: case study of class 4 laser therapy intervention.

Knapp DJ.

Clin J Pain. 2013 Oct;29(10):e6-9. doi: 10.1097/AJP.0b013e31828b8ef8.


Control of the hematopoietic stem cell state.

Knapp DJ, Eaves CJ.

Cell Res. 2014 Jan;24(1):3-4. doi: 10.1038/cr.2013.139. Epub 2013 Oct 8.


Analysis of the clonal growth and differentiation dynamics of primitive barcoded human cord blood cells in NSG mice.

Cheung AM, Nguyen LV, Carles A, Beer P, Miller PH, Knapp DJ, Dhillon K, Hirst M, Eaves CJ.

Blood. 2013 Oct 31;122(18):3129-37. doi: 10.1182/blood-2013-06-508432. Epub 2013 Sep 12.


Developmental changes in the in vitro activated regenerative activity of primitive mammary epithelial cells.

Makarem M, Kannan N, Nguyen LV, Knapp DJ, Balani S, Prater MD, Stingl J, Raouf A, Nemirovsky O, Eirew P, Eaves CJ.

PLoS Biol. 2013;11(8):e1001630. doi: 10.1371/journal.pbio.1001630. Epub 2013 Aug 13.


The cytokine mRNA increase induced by withdrawal from chronic ethanol in the sterile environment of brain is mediated by CRF and HMGB1 release.

Whitman BA, Knapp DJ, Werner DF, Crews FT, Breese GR.

Alcohol Clin Exp Res. 2013 Dec;37(12):2086-97. doi: 10.1111/acer.12189. Epub 2013 Jul 29.


The Lin28b-let-7-Hmga2 axis determines the higher self-renewal potential of fetal haematopoietic stem cells.

Copley MR, Babovic S, Benz C, Knapp DJ, Beer PA, Kent DG, Wohrer S, Treloar DQ, Day C, Rowe K, Mader H, Kuchenbauer F, Humphries RK, Eaves CJ.

Nat Cell Biol. 2013 Aug;15(8):916-25. doi: 10.1038/ncb2783. Epub 2013 Jun 30.


Heterogeneity in hematopoietic stem cell populations: implications for transplantation.

Miller PH, Knapp DJ, Eaves CJ.

Curr Opin Hematol. 2013 Jul;20(4):257-64. doi: 10.1097/MOH.0b013e328360aaf6. Review.


Enhanced normal short-term human myelopoiesis in mice engineered to express human-specific myeloid growth factors.

Miller PH, Cheung AM, Beer PA, Knapp DJ, Dhillon K, Rabu G, Rostamirad S, Humphries RK, Eaves CJ.

Blood. 2013 Jan 31;121(5):e1-4. doi: 10.1182/blood-2012-09-456566. Epub 2012 Dec 11.


Factors influencing the sensitivity and specificity of conventional sequencing in human immunodeficiency virus type 1 tropism testing.

Knapp DJ, McGovern RA, Dong W, Poon AF, Swenson LC, Zhong X, Woods CK, Harrigan PR.

J Clin Microbiol. 2013 Feb;51(2):444-51. doi: 10.1128/JCM.00739-12. Epub 2012 Nov 21.


Correlates of protective cellular immunity revealed by analysis of population-level immune escape pathways in HIV-1.

Carlson JM, Brumme CJ, Martin E, Listgarten J, Brockman MA, Le AQ, Chui CK, Cotton LA, Knapp DJ, Riddler SA, Haubrich R, Nelson G, Pfeifer N, Deziel CE, Heckerman D, Apps R, Carrington M, Mallal S, Harrigan PR, John M, Brumme ZL; International HIV Adaptation Collaborative.

J Virol. 2012 Dec;86(24):13202-16. doi: 10.1128/JVI.01998-12. Epub 2012 Oct 10.

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