Hammelman J - Search Results

1

Ranking reprogramming factors for cell differentiation.

Hammelman J, Patel T, Closser M, Wichterle H, Gifford D. Hammelman J, et al. Nat Methods. 2022 Jul;19(7):812-822. doi: 10.1038/s41592-022-01522-2. Epub 2022 Jun 16. Nat Methods. 2022. PMID: 35710610 Free PMC article.

2

Identification of determinants of differential chromatin accessibility through a massively parallel genome-integrated reporter assay.

Hammelman J, Krismer K, Banerjee B, Gifford DK, Sherwood RI. Hammelman J, et al. Genome Res. 2020 Oct;30(10):1468-1480. doi: 10.1101/gr.263228.120. Epub 2020 Sep 24. Genome Res. 2020. PMID: 32973041 Free PMC article.

3

Discovering differential genome sequence activity with interpretable and efficient deep learning.

Hammelman J, Gifford DK. Hammelman J, et al. PLoS Comput Biol. 2021 Aug 9;17(8):e1009282. doi: 10.1371/journal.pcbi.1009282. eCollection 2021 Aug. PLoS Comput Biol. 2021. PMID: 34370721 Free PMC article.

4

An expansion of the non-coding genome and its regulatory potential underlies vertebrate neuronal diversity.

Closser M, Guo Y, Wang P, Patel T, Jang S, Hammelman J, De Nooij JC, Kopunova R, Mazzoni EO, Ruan Y, Gifford DK, Wichterle H. Closser M, et al. Among authors: hammelman j. Neuron. 2022 Jan 5;110(1):70-85.e6. doi: 10.1016/j.neuron.2021.10.014. Epub 2021 Nov 1. Neuron. 2022. PMID: 34727520 Free PMC article.

5

spatzie: an R package for identifying significant transcription factor motif co-enrichment from enhancer-promoter interactions.

Hammelman J, Krismer K, Gifford DK. Hammelman J, et al. Nucleic Acids Res. 2022 May 20;50(9):e52. doi: 10.1093/nar/gkac036. Nucleic Acids Res. 2022. PMID: 35100401 Free PMC article.

6

seqgra: principled selection of neural network architectures for genomics prediction tasks.

Krismer K, Hammelman J, Gifford DK. Krismer K, et al. Among authors: hammelman j. Bioinformatics. 2022 Apr 28;38(9):2381-2388. doi: 10.1093/bioinformatics/btac101. Bioinformatics. 2022. PMID: 35191481 Free PMC article.

7

Transcriptional dynamics of murine motor neuron maturation in vivo and in vitro.

Patel T, Hammelman J, Aziz S, Jang S, Closser M, Michaels TL, Blum JA, Gifford DK, Wichterle H. Patel T, et al. Among authors: hammelman j. Nat Commun. 2022 Sep 15;13(1):5427. doi: 10.1038/s41467-022-33022-4. Nat Commun. 2022. PMID: 36109497 Free PMC article.

8

Major β cell-specific functions of NKX2.2 are mediated via the NK2-specific domain.

Abarinov V, Levine JA, Churchill AJ, Hopwood B, Deiter CS, Guney MA, Wells KL, Schrunk JM, Guo Y, Hammelman J, Gifford DK, Magnuson MA, Wichterle H, Sussel L. Abarinov V, et al. Among authors: hammelman j. Genes Dev. 2023 Jun 1;37(11-12):490-504. doi: 10.1101/gad.350569.123. Epub 2023 Jun 26. Genes Dev. 2023. PMID: 37364986 Free PMC article.

9

Physiological controls of large-scale patterning in planarian regeneration: a molecular and computational perspective on growth and form.

Durant F, Lobo D, Hammelman J, Levin M. Durant F, et al. Among authors: hammelman j. Regeneration (Oxf). 2016 Apr 28;3(2):78-102. doi: 10.1002/reg2.54. eCollection 2016 Apr. Regeneration (Oxf). 2016. PMID: 27499881 Free PMC article.

10

MoCha: Molecular Characterization of Unknown Pathways.

Lobo D, Hammelman J, Levin M. Lobo D, et al. Among authors: hammelman j. J Comput Biol. 2016 Apr;23(4):291-7. doi: 10.1089/cmb.2015.0211. Epub 2016 Mar 7. J Comput Biol. 2016. PMID: 26950055 Free PMC article.

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