Selected Publications

A complete bibliography can be found at either PubMed or Google Scholar.

* denotes equal contribution, ^# corresponding author

Recent Pre-prints

Georgolopoulos G, Iwata M, Psatha N, Nishida A, Som T, Yiangou M, Stamatoyannopoulos JA, Vierstra J^# (2020). Chromatin dynamics during hematopoiesis reveal discrete regulatory modules instructing differentiation. bioRxiv.

Vierstra J^#, Lazar J, Sandstrom R, Halow J, Lee K, Bates D, Diegel M, Dunn D, Neri F, Haugen E, Rynes E, Reynolds A, Nelson J, Johnson A, Frerker M, Buckley M, Kaul R, Meuleman W, Stamatoyannopoulos JA^# (2020). Global reference mapping of human transcription factor footprints. Nature, 583(7818):729–736. Pre-print (Supplementary website)

Georgolopoulos G, Iwata M, Psatha N, Yiangou M, Vierstra J^# (2019). Unbiased phenotypic identification of functionally distinct hematopoietic progenitors. J Biol Res (Thessalon), 26(4).

Vierstra J^# and Stamatoyannopoulos JA (2016). Genomic footprinting. Nat Methods. 13(3):213–221. Perspective.

He X, Tillo D, Vierstra J, Syed KS, Deng C, Ray JG, Stamatoyannopoulos JA, Fitzgerald PC, Vinson C (2015). Methylated cytosines mutate to transcription factor binding sites that drive tetrapod evolution. Genome Biol Evol, 7(11):3155-69.
Maurano MT, Haugen E, Sandstrom R, Vierstra J, Shafer T and Stamatoyannopoulos JA (2015). Large-scale identification of functional variants impacting human transcription factor occupancy in vivo. Nat Genetics, 47(12):1393-401.
*Vierstra J, *Reik A, Chang KH, Stehling-Sun S, Zhou YY, Hinkley SJ, Paschon DE, Zhang L, Psatha N, Bendana YR, O’Neill CM, Song AH, Mich A, Liu P-Q, Lee G, Bauer DE, Holmes MC, Orkin SH, Papayannopoulou T, Stamatoyannopoulos G, Rebar EJ, Gregory PD, Urnov FD, Stamatoyannopoulos JA (2015). Functional footprinting of regulatory DNA. Nat Methods, 12(10):927-930.

Mouse ENCODE Project Consortium, *Yue F, *Cheng Y, *Breschi A, *Vierstra J, *Wu W, *Ryba T, *Ma Z, *Davis C, *Pope BD, *Shen Y et al. (2014). An integrated and comparative encyclopedia of DNA elements in the mouse genome. Nature, 515(7527):365-370.
Vierstra J, Rynes E, Sandstrom R, Thurman RE et al. (2014). Mouse regulatory DNA landscapes reveal global principles of cis-regulatory evolution. Science, 346(6212):1007-1012.
Vierstra J, Wang H, John S, Sandstrom R, Stamatoyannopoulos JA. (2014). Coupling transcription factor occupancy to nucleosome architecture with DNase-FLASH. Nat Methods, 11(1):66–72.

*Neph S, *Vierstra J, *Stergachis AB, *Reynolds AP, Haugen E, Vernot B, Thurman RE, John S, Sandstrom R, Johnson AK, Maurano MT, Humbert R, Rynes E, Wang H, Vong S, Lee K, Bates D, Diegel M, Roach V, Dunn D, Neri J, Schafer A, Hansen RS, Kutyavin T, Giste E, Weaver M, Canfield T, Sabo P, Zhang M, Balasundaram G, Byron R, MacCoss MJ, Akey JM, Bender MA, Groudine M, Kaul R, Stamatoyannopoulos JA. (2012). An expansive human regulatory lexicon encoded in transcription factor footprints. Nature, 489(7414):83-90.
Thurman RE, Rynes E, Humbert R, Vierstra J, Maurano MT, Haugen E, Sheffield NC, Stergachis AB, Wang H, Vernot B, Garg K, John S, Sandstrom R, Bates D, Boatman L, Canfield TK, Diegel M, Dunn D, Ebersol AK, Frum T, Giste E, Johnson AK, Johnson EM, Kutyavin T, Lajoie B, Lee BK, Lee K, London D, Lotakis D, Neph S, Neri F, Nguyen ED, Qu H, Reynolds AP, Roach V, Safi A, Sanchez ME, Sanyal A, Shafer A, Simon JM, Song L, Vong S, Weaver M, Yan Y, Zhang Z, Zhang Z, Lenhard B, Tewari M, Dorschner MO, Hansen RS, Navas PA, Stamatoyannopoulos G, Iyer VR, Lieb JD, Sunyaev SR, Akey JM, Sabo PJ, Kaul R, Furey TS, Dekker J, Crawford GE, Stamatoyannopoulos JA.(2012). The accessible chromatin landscape of the human genome. Nature, 489(7414):75-82.