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Vineet Bafna
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Displaying results 1-10 of
14
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Method
:
OMKar automates genome karyotyping using optical maps to identify constitutional abnormalities
Siavash Raeisi Dehkordi
,
Zhaoyang Jia
,
Joey Estabrook
,
Jen Hauenstein
,
Neil Miller
,
Naz Güleray-Lafci
,
Jürgen Neesen
,
Alex Hastie
,
Alka Chaubey
,
Andy Wing Chun Pang
,
Paul Dremsek
,
and
Vineet Bafna
Genome Res.
December 2025
35
:
2671
-
2681
;
Published in Advance
November 14, 2025
,
doi:
10.1101/gr.280536.125
Abstract
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Method
:
CoRAL accurately resolves extrachromosomal DNA genome structures with long-read sequencing
Kaiyuan Zhu
,
Matthew G. Jones
,
Jens Luebeck
,
Xinxin Bu
,
Hyerim Yi
,
King L. Hung
,
Ivy Tsz-Lo Wong
,
Shu Zhang
,
Paul S. Mischel
,
Howard Y. Chang
,
and
Vineet Bafna
Genome Res.
September 2024
34
:
1344
-
1354
;
Published in Advance
July 9, 2024
,
doi:
10.1101/gr.279131.124
Abstract
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Method
:
Targeted genotyping of variable number tandem repeats with adVNTR
Mehrdad Bakhtiari
,
Sharona Shleizer-Burko
,
Melissa Gymrek
,
Vikas Bansal
,
and
Vineet Bafna
Genome Res.
November 2018
28
:
1709
-
1719
;
Published in Advance
October 23, 2018
,
doi:
10.1101/gr.235119.118
Abstract
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Method
:
HapCUT2: robust and accurate haplotype assembly for diverse sequencing technologies
Peter Edge
,
Vineet Bafna
,
and
Vikas Bansal
Genome Res.
May 2017
27
:
801
-
812
;
Published in Advance
December 9, 2016
,
doi:
10.1101/gr.213462.116
Abstract
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Method
:
Amplification and thrifty single-molecule sequencing of recurrent somatic structural variations
Anand Patel
,
Richard Schwab
,
Yu-Tsueng Liu
,
and
Vineet Bafna
Genome Res.
February 2014
24
:
318
-
328
;
Published in Advance
December 4, 2013
,
doi:
10.1101/gr.161497.113
Abstract
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Research
:
Global DNA hypomethylation coupled to repressive chromatin domain formation and gene silencing in breast cancer
Gary C. Hon
,
R. David Hawkins
,
Otavia L. Caballero
,
Christine Lo
,
Ryan Lister
,
Mattia Pelizzola
,
Armand Valsesia
,
Zhen Ye
,
Samantha Kuan
,
Lee E. Edsall
,
Anamaria Aranha Camargo
,
Brian J. Stevenson
,
Joseph R. Ecker
,
Vineet Bafna
,
Robert L. Strausberg
,
Andrew J. Simpson
,
and
Bing Ren
Genome Res.
February 2012
22
:
246
-
258
;
Published in Advance
December 7, 2011
,
doi:
10.1101/gr.125872.111
Abstract
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Methods
:
Sequence and structural variation in a human genome uncovered by short-read, massively parallel ligation sequencing using two-base encoding
Kevin Judd McKernan
,
Heather E. Peckham
,
Gina L. Costa
,
Stephen F. McLaughlin
,
Yutao Fu
,
Eric F. Tsung
,
Christopher R. Clouser
,
Cisyla Duncan
,
Jeffrey K. Ichikawa
,
Clarence C. Lee
,
Zheng Zhang
,
Swati S. Ranade
,
Eileen T. Dimalanta
,
Fiona C. Hyland
,
Tanya D. Sokolsky
,
Lei Zhang
,
Andrew Sheridan
,
Haoning Fu
,
Cynthia L. Hendrickson
,
Bin Li
,
Lev Kotler
,
Jeremy R. Stuart
,
Joel A. Malek
,
Jonathan M. Manning
,
Alena A. Antipova
,
Damon S. Perez
,
Michael P. Moore
,
Kathleen C. Hayashibara
,
Michael R. Lyons
,
Robert E. Beaudoin
,
Brittany E. Coleman
,
Michael W. Laptewicz
,
Adam E. Sannicandro
,
Michael D. Rhodes
,
Rajesh K. Gottimukkala
,
Shan Yang
,
Vineet Bafna
,
Ali Bashir
,
Andrew MacBride
,
Can Alkan
,
Jeffrey M. Kidd
,
Evan E. Eichler
,
Martin G. Reese
,
Francisco M. De La Vega
,
and
Alan P. Blanchard
Genome Res.
September 2009
19
:
1527
-
1541
;
Published in Advance
June 22, 2009
,
doi:
10.1101/gr.091868.109
Abstract
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Methods
:
An MCMC algorithm for haplotype assembly from whole-genome sequence data
Vikas Bansal
,
Aaron L. Halpern
,
Nelson Axelrod
,
and
Vineet Bafna
Genome Res.
August 2008
18
:
1336
-
1346
;
doi:
10.1101/gr.077065.108
Abstract
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Methods
:
Comparative proteogenomics: Combining mass spectrometry and comparative genomics to analyze multiple genomes
Nitin Gupta
,
Jamal Benhamida
,
Vipul Bhargava
,
Daniel Goodman
,
Elisabeth Kain
,
Ian Kerman
,
Ngan Nguyen
,
Noah Ollikainen
,
Jesse Rodriguez
,
Jian Wang
,
Mary S. Lipton
,
Margaret Romine
,
Vineet Bafna
,
Richard D. Smith
,
and
Pavel A. Pevzner
Genome Res.
July 2008
18
:
1133
-
1142
;
Published in Advance
April 21, 2008
,
doi:
10.1101/gr.074344.107
Abstract
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Methods
:
Whole proteome analysis of post-translational modifications: Applications of mass-spectrometry for proteogenomic annotation
Nitin Gupta
,
Stephen Tanner
,
Navdeep Jaitly
,
Joshua N. Adkins
,
Mary Lipton
,
Robert Edwards
,
Margaret Romine
,
Andrei Osterman
,
Vineet Bafna
,
Richard D. Smith
,
and
Pavel A. Pevzner
Genome Res.
September 2007
17
:
1362
-
1377
;
Published in Advance
August 9, 2007
,
doi:
10.1101/gr.6427907
Abstract
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Single-cell gene signature scoring
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Short tandem repeat genotyping using long reads
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