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Method: Graph-based deep reinforcement learning for haplotype assembly with Ralphi

Enzo Battistella,
Anant Maheshwari,
Barış Ekim,
Bonnie Berger,
and Victoria Popic

Genome Res. December 2025 35: 2617-2625; Published in Advance November 14, 2025, doi:10.1101/gr.280569.125

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Editorial: RECOMB 2025 Special Issue

Sriram Sankararaman and
Bonnie Berger

Genome Res. December 2025 35: v-vi; doi:10.1101/gr.281664.125

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Method: Secure discovery of genetic relatives across large-scale and distributed genomic data sets

Matthew M. Hong,
David Froelicher,
Ricky Magner,
Victoria Popic,
Bonnie Berger,
and Hyunghoon Cho

Genome Res. September 2024 34: 1312-1323; Published in Advance August 7, 2024, doi:10.1101/gr.279057.124

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Editorial: Innovations in computational biology: RECOMB 2024 Special Issue

Jian Ma and
Bonnie Berger

Genome Res. September 2024 34: vii-viii; doi:10.1101/gr.280036.124

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Method: Assessing transcriptomic reidentification risks using discriminative sequence models

Shuvom Sadhuka,
Daniel Fridman,
Bonnie Berger,
and Hyunghoon Cho

Genome Res. July 2023 33: 1101-1112; Published in Advance August 4, 2023, doi:10.1101/gr.277699.123

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Method: Efficient mapping of accurate long reads in minimizer space with mapquik

Bariş Ekim,
Kristoffer Sahlin,
Paul Medvedev,
Bonnie Berger,
and Rayan Chikhi

Genome Res. July 2023 33: 1188-1197; Published in Advance June 30, 2023, doi:10.1101/gr.277679.123

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Method: Efficient minimizer orders for large values of k using minimum decycling sets

David Pellow,
Lianrong Pu,
Bariş Ekim,
Lior Kotlar,
Bonnie Berger,
Ron Shamir,
and Yaron Orenstein

Genome Res. July 2023 33: 1154-1161; Published in Advance August 9, 2023, doi:10.1101/gr.277644.123

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Method: Structure-based whole-genome realignment reveals many novel noncoding RNAs

Sebastian Will,
Michael Yu,
and Bonnie Berger

Genome Res. June 2013 23: 1018-1027; Published in Advance January 7, 2013, doi:10.1101/gr.137091.111

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Research: Unusually effective microRNA targeting within repeat-rich coding regions of mammalian mRNAs

Michael Schnall-Levin,
Olivia S. Rissland,
Wendy K. Johnston,
Norbert Perrimon,
David P. Bartel,
and Bonnie Berger

Genome Res. September 2011 21: 1395-1403; Published in Advance June 17, 2011, doi:10.1101/gr.121210.111

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Methods: Inference of RhoGAP/GTPase regulation using single-cell morphological data from a combinatorial RNAi screen

Oaz Nir,
Chris Bakal,
Norbert Perrimon,
and Bonnie Berger

Genome Res. March 2010 20: 372-380; Published in Advance February 9, 2010, doi:10.1101/gr.100248.109

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