Publications - Revision history

MBeer at 05:53, 9 November 2025

2025-11-09T05:53:02Z

MBeer at 05:52, 9 November 2025

2025-11-09T05:52:26Z

MBeer at 05:51, 9 November 2025

2025-11-09T05:51:04Z

MBeer at 15:19, 1 August 2024

2024-08-01T15:19:38Z

MBeer at 15:18, 1 August 2024

2024-08-01T15:18:24Z

MBeer at 01:36, 23 July 2024

2024-07-23T01:36:41Z

MBeer at 06:11, 28 May 2024

2024-05-28T06:11:02Z

MBeer at 12:42, 4 April 2024

2024-04-04T12:42:53Z

MBeer at 19:46, 8 August 2023

2023-08-08T19:46:47Z

MBeer at 19:46, 8 August 2023

2023-08-08T19:46:25Z

← Older revision		Revision as of 05:53, 9 November 2025
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−	Full publication list on '''[https://scholar.google.com/citations?hl=en&user=9aH8_eEAAAAJ google scholar]''' or ''https://orcid.org/0000-0001-9955-3809 Orcid'''.	+	Full publication list on '''[https://scholar.google.com/citations?hl=en&user=9aH8_eEAAAAJ google scholar]''' or '''[https://orcid.org/0000-0001-9955-3809 Orcid]'''. My student '''[https://beerlab.org/dissertations PhD dissertations]'''.
−	My student '''[https://beerlab.org/dissertations PhD dissertations]'''.

	* '''[https://genome.cshlp.org/content/34/5/680 Machine learning identifies activation of RUNX/AP-1 as drivers of mesenchymal and fibrotic regulatory programs in gastric cancer.]''' Razavi-Mohseni M, et al. Genome Research 2024 '''[https://beerlab.org/papers/gr.278565.123.full.pdf pdf]'''		* '''[https://genome.cshlp.org/content/34/5/680 Machine learning identifies activation of RUNX/AP-1 as drivers of mesenchymal and fibrotic regulatory programs in gastric cancer.]''' Razavi-Mohseni M, et al. Genome Research 2024 '''[https://beerlab.org/papers/gr.278565.123.full.pdf pdf]'''

← Older revision		Revision as of 05:52, 9 November 2025
Line 1:		Line 1:
	Full publication list on '''[https://scholar.google.com/citations?hl=en&user=9aH8_eEAAAAJ google scholar]''' or ''https://orcid.org/0000-0001-9955-3809 Orcid'''.		Full publication list on '''[https://scholar.google.com/citations?hl=en&user=9aH8_eEAAAAJ google scholar]''' or ''https://orcid.org/0000-0001-9955-3809 Orcid'''.
		+	My student '''[https://beerlab.org/dissertations PhD dissertations]'''.

	* '''[https://genome.cshlp.org/content/34/5/680 Machine learning identifies activation of RUNX/AP-1 as drivers of mesenchymal and fibrotic regulatory programs in gastric cancer.]''' Razavi-Mohseni M, et al. Genome Research 2024 '''[https://beerlab.org/papers/gr.278565.123.full.pdf pdf]'''		* '''[https://genome.cshlp.org/content/34/5/680 Machine learning identifies activation of RUNX/AP-1 as drivers of mesenchymal and fibrotic regulatory programs in gastric cancer.]''' Razavi-Mohseni M, et al. Genome Research 2024 '''[https://beerlab.org/papers/gr.278565.123.full.pdf pdf]'''

← Older revision		Revision as of 05:51, 9 November 2025
Line 1:		Line 1:
−	Full publication list on '''[https://scholar.google.com/citations?hl=en&user=9aH8_eEAAAAJ google scholar]'''.	+	Full publication list on '''[https://scholar.google.com/citations?hl=en&user=9aH8_eEAAAAJ google scholar]''' or ''https://orcid.org/0000-0001-9955-3809 Orcid'''.

	* '''[https://genome.cshlp.org/content/34/5/680 Machine learning identifies activation of RUNX/AP-1 as drivers of mesenchymal and fibrotic regulatory programs in gastric cancer.]''' Razavi-Mohseni M, et al. Genome Research 2024 '''[https://beerlab.org/papers/gr.278565.123.full.pdf pdf]'''		* '''[https://genome.cshlp.org/content/34/5/680 Machine learning identifies activation of RUNX/AP-1 as drivers of mesenchymal and fibrotic regulatory programs in gastric cancer.]''' Razavi-Mohseni M, et al. Genome Research 2024 '''[https://beerlab.org/papers/gr.278565.123.full.pdf pdf]'''

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 * '''[https://genome.cshlp.org/content/34/5/680 Machine learning identifies activation of RUNX/AP-1 as drivers of mesenchymal and fibrotic regulatory programs in gastric cancer.]''' Razavi-Mohseni M, et al. Genome Research 2024 '''[https://beerlab.org/papers/gr.278565.123.full.pdf pdf]'''
-* '''https://www.nature.com/articles/s41467-024-50708-z Gapped-kmer sequence modeling robustly identifies regulatory vocabularies and distal enhancers conserved between evolutionarily distant mammals.]''' Oh JW and Beer MA. Nature Communications 2024.
+* '''[https://www.nature.com/articles/s41467-024-50708-z Gapped-kmer sequence modeling robustly identifies regulatory vocabularies and distal enhancers conserved between evolutionarily distant mammals.]''' Oh JW and Beer MA. Nature Communications 2024.
 * '''[https://rdcu.be/dhCoG Dynamic network-guided CRISPRi screen identifies CTCF-loop-constrained nonlinear enhancer gene regulatory activity during cell state transitions.]''' Luo R, et al. Nature Genetics 2023 '''[https://beerlab.org/papers/2023%20NG.pdf pdf]'''

← Older revision		Revision as of 15:18, 1 August 2024
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	* '''[https://genome.cshlp.org/content/34/5/680 Machine learning identifies activation of RUNX/AP-1 as drivers of mesenchymal and fibrotic regulatory programs in gastric cancer.]''' Razavi-Mohseni M, et al. Genome Research 2024 '''[https://beerlab.org/papers/gr.278565.123.full.pdf pdf]'''		* '''[https://genome.cshlp.org/content/34/5/680 Machine learning identifies activation of RUNX/AP-1 as drivers of mesenchymal and fibrotic regulatory programs in gastric cancer.]''' Razavi-Mohseni M, et al. Genome Research 2024 '''[https://beerlab.org/papers/gr.278565.123.full.pdf pdf]'''
		+
		+	* '''https://www.nature.com/articles/s41467-024-50708-z Gapped-kmer sequence modeling robustly identifies regulatory vocabularies and distal enhancers conserved between evolutionarily distant mammals.]''' Oh JW and Beer MA. Nature Communications 2024.

	* '''[https://rdcu.be/dhCoG Dynamic network-guided CRISPRi screen identifies CTCF-loop-constrained nonlinear enhancer gene regulatory activity during cell state transitions.]''' Luo R, et al. Nature Genetics 2023 '''[https://beerlab.org/papers/2023%20NG.pdf pdf]'''		* '''[https://rdcu.be/dhCoG Dynamic network-guided CRISPRi screen identifies CTCF-loop-constrained nonlinear enhancer gene regulatory activity during cell state transitions.]''' Luo R, et al. Nature Genetics 2023 '''[https://beerlab.org/papers/2023%20NG.pdf pdf]'''

@@ Line 1: / Line 1: @@
 Full publication list on '''[https://scholar.google.com/citations?hl=en&user=9aH8_eEAAAAJ google scholar]'''.
-* '''[https://genome.cshlp.org/content/early/2024/05/21/gr.278565.123.abstract Machine learning identifies activation of RUNX/AP-1 as drivers of mesenchymal and fibrotic regulatory programs in gastric cancer.]''' Razavi-Mohseni M, et al. Genome Research 2024 '''[https://beerlab.org/papers/gr.278565.123.full.pdf pdf]'''
+* '''[https://genome.cshlp.org/content/34/5/680 Machine learning identifies activation of RUNX/AP-1 as drivers of mesenchymal and fibrotic regulatory programs in gastric cancer.]''' Razavi-Mohseni M, et al. Genome Research 2024 '''[https://beerlab.org/papers/gr.278565.123.full.pdf pdf]'''
 * '''[https://rdcu.be/dhCoG Dynamic network-guided CRISPRi screen identifies CTCF-loop-constrained nonlinear enhancer gene regulatory activity during cell state transitions.]''' Luo R, et al. Nature Genetics 2023 '''[https://beerlab.org/papers/2023%20NG.pdf pdf]'''

← Older revision		Revision as of 06:11, 28 May 2024
Line 1:		Line 1:
	Full publication list on '''[https://scholar.google.com/citations?hl=en&user=9aH8_eEAAAAJ google scholar]'''.		Full publication list on '''[https://scholar.google.com/citations?hl=en&user=9aH8_eEAAAAJ google scholar]'''.
		+
		+	* '''[https://genome.cshlp.org/content/early/2024/05/21/gr.278565.123.abstract Machine learning identifies activation of RUNX/AP-1 as drivers of mesenchymal and fibrotic regulatory programs in gastric cancer.]''' Razavi-Mohseni M, et al. Genome Research 2024 '''[https://beerlab.org/papers/gr.278565.123.full.pdf pdf]'''

	* '''[https://rdcu.be/dhCoG Dynamic network-guided CRISPRi screen identifies CTCF-loop-constrained nonlinear enhancer gene regulatory activity during cell state transitions.]''' Luo R, et al. Nature Genetics 2023 '''[https://beerlab.org/papers/2023%20NG.pdf pdf]'''		* '''[https://rdcu.be/dhCoG Dynamic network-guided CRISPRi screen identifies CTCF-loop-constrained nonlinear enhancer gene regulatory activity during cell state transitions.]''' Luo R, et al. Nature Genetics 2023 '''[https://beerlab.org/papers/2023%20NG.pdf pdf]'''

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 * '''[http://elifesciences.org/content/5/e11613v1 Epigenomic landscapes of retinal rods and cones.]''' Mo, A, Luo, C, Davis, FP, Mukamel, EA, Henry, GL, Nery JR, Urich, MA, Picard, S, Lister, R, Eddy, SR, Beer, MA, Ecker, JR, and Nathans, J. eLife 2016.
-* '''[http://www.nature.com/ng/journal/vaop/ncurrent/full/ng.3331.html A method to predict the impact of regulatory variants from DNA sequence.]''' Lee D, Gorkin DU, Baker M, Strober BJ, Asoni AL, McCallion AS, Beer, MA. Nature Genetics 2015.
+* '''[https://www.nature.com/articles/ng.3331 A method to predict the impact of regulatory variants from DNA sequence.]''' Lee D, Gorkin DU, Baker M, Strober BJ, Asoni AL, McCallion AS, Beer, MA. Nature Genetics 2015.
 * '''[http://www.ncbi.nlm.nih.gov/pubmed/25582907 Enhanced transcriptome maps from multiple mouse tissues reveal evolutionary constraint in gene expression.]''' Pervouchine DD, Djebali S, Breschi A, Davis CA, Barja PP, Dobin, A, Tanzer A, Lagarde J, Zaleski C, See L-H, Fastuca M, Drenkow J, Wang H, Bussotti G, Pei B, Balasubramanian S, Monlong J, Harmanci A, Gerstein M, Beer MA, Notredame C, Guigó R, Gingeras TR. Nat. Comm 2015.