Publications

Journal Articles

Kempton CE, Weber KS, Johnson SM. Method to increase undergraduate laboratory student confidence in performing independent research. Journal of Microbiology & Biology Eudcation. 2017 Apr.

Weber KS, Jensen JL, Johnson SM. Anticipation of personal genomics data enhances interest and learning environment in genomics and molecular biology undergraduate courses. PLoS One. 2015 Aug;10(8):e0133486. <website>

Kempton CE, Heninger JR, Johnson SM. Reproducibility and Consistency of In Vitro Nucleosome Reconstitutions Demonstrated by Invitrosome Isolation and Sequencing. PLoS One. 2014 Aug;9(8):e103752. <website>

Locke G, Haberman D, Johnson SM, Morozov AV. Global remodeling of nucleosome positions in C. elegans. BMC Genomics. 2013 Apr;14:284. <website>

Kundaje A, Kyriazopoulou-Panagiotopoulou S, Libbrecht M, Smith CL, Raha D, Winters EE, Johnson SM, Snyder MP, Batzoglou S, Sidow A. Ubiquitous heterogeneity and asymmetry of the chromatin environment at regulatory elements. Genome Research. 2012 Sep;22:1735-1747. <website>

Valouev A, Johnson SM, Boyd SD, Smith CL, Fire AZ, Sidow A. Determinants of nucleosome organization in primary human cells. Nature. 2011 Jun;474:516-520. <website>

Johnson SM. Painting a perspective on the landscape of nucleosome positioning. Journal of Biomolecular Structure and Dynamics. 2010 Jun;27(6):795-802. <website>

Valouev A, Ichikawa J, Tonthat T, Stuart J, Ranade S, Peckham H, Zeng K, Malek JA, Costa G, McKernan K, et al. A high-resolution, nucleosome position map of C. elegans reveals a lack of universal sequence-dictated positioning. Genome Research. 2008 May;18:1051-1063. <website>

Johnson SM, Tan FJ, McCullough HL, Riordan DP, Fire AZ. Flexibility and constraint in the nucleosome core landscape of Caenorhabditis elegans chromatin. Genome Research. 2006 Oct;16:1505-1516. <website>

Moreno-Herrero F, Seidel R, Johnson SM, Fire A, Dekker NH. Structural analysis of hyperperiodic DNA from Caenorhabditis elegans. Nucleic Acids Research. 2006 May;34:3057-3066. <website>

Esquela-Kerscher A, Johnson SM, Bai L, Saito K, Partridge J, Reinert KL, Slack FJ. Post-embryonic expression of C. elegans microRNAs belonging to the lin-4 and let-7 families in the hypodermis and the reproductive system. Developmental Dynamics. 2005 Oct;234:868-877. <website>

Johnson SM, Grosshans H, Shingara J, Byrom M, Jarvis R, Cheng A, Labourier E, Reinert KL, Brown D, Slack FJ. RAS is regulated by the let-7 microRNA family. Cell. 2005 Mar;120:635-647. <website>

Lin S, Johnson SM, Abraham M, Vella MC, Pasquinelli A, Gamberi C, Gottlieb E, Slack FJ. The C. elegans hunchback homolog, hbl-1 controls temporal patterning and is a probable microRNA target. Developmental Cell. 2003 May;4:639-650. <website>

Johnson SM, Lin S, Slack FJ. The time of appearance of the C. elegans let-7 microRNA is transcriptionally controlled utilizing a temporal regulatory element in its promoter. Developmental Biology. 2003 May;259:364-379. <website>

Ma X, Husain T, Peng H, Lin S, Mironenko O, Maun N, Johnson SM, Tuck D, Berliner N, Krause DS, et al. Development of a murine hematopoietic progenitor complementary DNA microarray using a subtracted complementary DNA library. Blood. 2002 Aug;100:833-844. <website>

Database

Snyder M, Raha D, Johnson SM, Winters EE, Sidow A, Weng Z, Smith C, Lacroute P, Cayting P, Kundaje A. Nucleosome Position by MNase-seq from ENCODE/Stanford/BYU. 2011 Jul. <website>

Presentations

Johnson SM. Nucleosome Positioning. Invited lecture, Department of Microbiology and Biochemistry, Rutgers University. Piscataway, New Jersey. 2015 .

Johnson SM. Nucleosome Positioning, Meta-Shapes and Transgene Expression. Invited seminar, Department of Molecular Biology and Biochemistry, Rutgers University. Piscataway, New Jersey. 2015 .

Johnson SM. Chromatin Architecture, Meta-Shapes and Transgene Expression. Invited seminar, MCDB Genetics Training Grant Seminar, Yale University. New Haven, CT. 2014 .

Johnson SM. Chromatin Patterns, Meta-Shapes and Transgene Expression. Invited Seminar: Biology Department Summer Seminar, San Diego State University. San Diego, CA. 2013 .

Johnson SM. Evaluating, Defining and Applying Sequence-Directed Nucleosome Positioning. Invited Seminar: Center for NanoBiotechnology and Life Sciences Research, Alabama State University. Montgomery, Alabama. 2013 .

Johnson SM. Unraveling The Patterns That Turn On Genes. Research Revolution '13. Orem, UT. 2013 .

Johnson SM. Nucleosome Organization and Positioning: From human Cells to C. elegans. The 2013 Southwest Regional Meeting of the Society for Developmental Biology. University of Utah, Salt Lake City, UT. 2013 .

Johnson SM. Nucleosome Organization and Positioning in Human Cells. 5th Annual GeneExpression Systems-Epigenomics, Sequencing & SNiPomics 2012 meeting. Harvard Medical School, Boston, Massachusetts. 2012 .

Johnson SM. Keynote Address: Chromatin Architecture-Turning On and Off Genes. 6th Annual Biotechnology Symposium. Mesa, Arizona. 2012 .

Johnson SM. Gene Therapy-Turning On and Off Genes. Research Revolution '12. Orem, Utah. 2012 .

Johnson SM. Chromatin Architecture, Nucleosome Positioning and Gene Regulation. Invited Seminar: Department of Physics and Biophysics Graduate Program Symposium, The Ohio State University. Columbus, Ohio. 2012 .

Johnson SM. Nucleosome Organization in Primary Human Cells. Keystone Symposia/Histone Code: Fact or Fiction?. Midway, UT. 2011 .

Johnson SM. Chromatin Architecture and Nucleosome Organization in Primary Human Cells. CTE Seminar Series. Mesa, Arizona. 2010 .

Johnson SM. Epigenetics, Chromatin Architecture and Nucleosome Positioning. Current Topics in Molecular Life Sciences Seminar. Provo, UT. 2010 .

Johnson SM, Valouev A, Boyd S, Smith C, Sidow A, Fire A. Genome-wide Mapping and Analysis of Nucleosome Positions in Multiple Human Tissues. Albany 2009: 16th Conversation, SUNY Albany. Albany, NY. 2009 .

Johnson SM. Contrasting methods of gene regulation: from small RNAs to the chromatin landscape. Invited Nobel Week Seminar: Department of Oncology. Stockholm, Sweden. 2006 .