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Adam Siepel
Adam Siepel
Simons Center for Quantitative Biology, Cold Spring Harbor Laboratory
Verified email at cshl.edu - Homepage
Title
Cited by
Year
Single-cell transcription mapping of murine and human mammary organoids responses to female hormones
JR Ortiz, SM Lewis, M Ciccone, D Chatterjee, S Henry, A Siepel, ...
Journal of Mammary Gland Biology and Neoplasia 29 (1), 3, 2024
12024
Clonal Lineage Tracing with Somatic Delivery of Recordable Barcodes Reveals Migration Histories of Metastatic Prostate Cancer
RN Serio, A Scheben, B Lu, DV Gargiulo, L Patruno, CL Buckholtz, ...
Cancer Discovery, 2024
2024
Identification of constrained sequence elements across 239 primate genomes
LFK Kuderna, JC Ulirsch, S Rashid, M Ameen, L Sundaram, G Hickey, ...
Nature 625 (7996), 735-742, 2024
112024
DNA-sequence and epigenomic determinants of local rates of transcription elongation
L Liu, Y Zhao, A Siepel
bioRxiv, 2023
2023
Model-based characterization of the equilibrium dynamics of transcription initiation and promoter-proximal pausing in human cells
Y Zhao, L Liu, R Hassett, A Siepel
Nucleic Acids Research 51 (21), e106-e106, 2023
32023
Domain-adaptive neural networks improve supervised machine learning based on simulated population genetic data
Z Mo, A Siepel
PLoS Genetics 19 (11), e1011032, 2023
92023
Utility of AlphaMissense predictions in Asparagine Synthetase deficiency variant classification
SJ Staklinski, A Scheben, A Siepel, MS Kilberg
bioRxiv, 2023
2023
Long-read sequencing reveals rapid evolution of immunity-and cancer-related genes in bats
A Scheben, O Mendivil Ramos, M Kramer, S Goodwin, S Oppenheim, ...
Genome biology and evolution 15 (9), evad148, 2023
20*2023
Teosinte Pollen Drive guides maize diversification and domestication by RNAi
B Berube, E Ernst, J Cahn, B Roche, C de Santis Alves, J Lynn, ...
BioRxiv, 2023
32023
Selective sweeps on different pigmentation genes mediate convergent evolution of island melanism in two incipient bird species
L Campagna, Z Mo, A Siepel, JAC Uy
PLoS Genetics 18 (11), e1010474, 2022
152022
Extreme purifying selection against point mutations in the human genome
N Dukler, MR Mughal, R Ramani, YF Huang, A Siepel
Nature Communications 13 (1), 4312, 2022
252022
RNA Pol II pausing facilitates phased pluripotency transitions by buffering transcription
A Abuhashem, AG Chivu, Y Zhao, EJ Rice, A Siepel, CG Danko, ...
Genes & development 36 (13-14), 770-789, 2022
132022
A multiple alignment workflow shows the effect of repeat masking and parameter tuning on alignment in plants
Y Wu, L Johnson, B Song, C Romay, M Stitzer, A Siepel, E Buckler, ...
The Plant Genome 15 (2), e20204, 2022
72022
A deep-learning approach for inference of selective sweeps from the ancestral recombination graph
HA Hejase, Z Mo, L Campagna, A Siepel
Molecular Biology and Evolution 39 (1), msab332, 2022
34*2022
Deconvolution of expression for nascent RNA-sequencing data (DENR) highlights pre-RNA isoform diversity in human cells
Y Zhao, N Dukler, G Barshad, S Toneyan, CG Danko, A Siepel
Bioinformatics 37 (24), 4727-4736, 2021
72021
ACE: a probabilistic model for characterizing gene-level essentiality in CRISPR screens
ER Hutton, CR Vakoc, A Siepel
Genome Biology 22, 1-25, 2021
62021
Characterizing RNA stability genome-wide through combined analysis of PRO-seq and RNA-seq data
A Blumberg, Y Zhao, YF Huang, N Dukler, EJ Rice, AG Chivu, K Krumholz, ...
BMC biology 19, 1-17, 2021
562021
A multiple genome alignment workflow shows the impact of repeat masking and parameter tuning on alignment of functional regions in plants
Y Wu, L Johnson, B Song, C Romay, M Stitzer, A Siepel, E Buckler, ...
BioRxiv, 2021.06. 01.446647, 2021
22021
Circadian immunity, sunrise time and the seasonality of respiratory infections
Z Mo, A Scheben, J Steinberg, A Siepel, R Martienssen
medRxiv, 2021
12021
Characterization of gene expression signatures for the identification of cellular heterogeneity in the developing mammary gland
S Henry, MC Trousdell, SL Cyrill, Y Zhao, MJ Feigman, JM Bouhuis, ...
Journal of Mammary Gland Biology and Neoplasia 26 (1), 43-66, 2021
132021
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