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Research

Integrating short-read and long-read single-cell RNA sequencing for comprehensive transcriptome profiling in mouse retina

  • Meng Wang
  • Yumei Li
  • Jun Wang
  • Soo Hwan Oh
  • Yexuan Cao
  • Rui Chen
  • First Published March 6, 2025
Method

CodonBERT large language model for mRNA vaccines

  • Sizhen Li
  • Saeed Moayedpour
  • Ruijiang Li
  • Michael Bailey
  • Saleh Riahi
  • Lorenzo Kogler-Anele Milad Miladi Jacob Miner Fabien Pertuy Dinghai Zheng Jun Wang Akshay Balsubramani Khang Tran Minnie Zacharia Monica Wu Xiaobo Gu Ryan Clinton Carla Asquith Joseph Skaleski Lianne Boeglin Sudha Chivukula Anusha Dias Tod Strugnell
  • ... [+18 authors] ...,
  • Fernando Ulloa Montoya
  • Vikram Agarwal
  • Ziv Bar-Joseph
  • Sven Jager
  • First Published July 1, 2024
Research

Caenorhabditis nematode" > Genetic exchange with an outcrossing sister species causes severe genome-wide dysregulation in a selfing Caenorhabditis nematode

  • Dongying Xie
  • Pohao Ye
  • Yiming Ma
  • Yongbin Li
  • Xiao Liu
  • Peter Sarkies
  • Zhongying Zhao
  • First Published November 9, 2022
In memoriam

C. Thomas Caskey (1938–2022)

  • Richard A. Gibbs
  • Aravinda Chakravarti
  • Evan E. Eichler
  • Eric D. Green
  • Richard M. Myers
  • Anne C. Ferguson-Smith
  • Kateryna D. Makova
  • Hillary E. Sussman
  • First Published February 17, 2022
In memoriam

Deborah A. Nickerson (1954 –2021)

  • Aravinda Chakravarti
  • Evan E. Eichler
  • Richard A. Gibbs
  • Eric D. Green
  • Richard M. Myers
  • Hillary E. Sussman
  • First Published January 24, 2022
Research

RET regulatory code is disrupted in Hirschsprung disease" > A multi-enhancer RET regulatory code is disrupted in Hirschsprung disease

  • Sumantra Chatterjee
  • Kameko M. Karasaki
  • Lauren E. Fries
  • Ashish Kapoor
  • Aravinda Chakravarti
  • First Published November 15, 2021
Method

Sequence-based correction of barcode bias in massively parallel reporter assays

  • Dongwon Lee
  • Ashish Kapoor
  • Changhee Lee
  • Michael Mudgett
  • Michael A. Beer
  • Aravinda Chakravarti
  • First Published July 20, 2021
Method

Predicting unrecognized enhancer-mediated genome topology by an ensemble machine learning model

  • Li Tang
  • Matthew C. Hill
  • Jun Wang
  • Jianxin Wang
  • James F. Martin
  • Min Li
  • First Published November 12, 2020
Method

Efficient and unique cobarcoding of second-generation sequencing reads from long DNA molecules enabling cost-effective and accurate sequencing, haplotyping, and de novo assembly

  • Ou Wang
  • Robert Chin
  • Xiaofang Cheng
  • Michelle Ka Yan Wu
  • Qing Mao
  • Jingbo Tang Yuhui Sun Ellis Anderson Han K. Lam Dan Chen Yujun Zhou Linying Wang Fei Fan Yan Zou Yinlong Xie Rebecca Yu Zhang Snezana Drmanac Darlene Nguyen Chongjun Xu Christian Villarosa Scott Gablenz Nina Barua Staci Nguyen Wenlan Tian Jia Sophie Liu Jingwan Wang Xiao Liu Xiaojuan Qi Ao Chen He Wang Yuliang Dong Wenwei Zhang Andrei Alexeev Huanming Yang Jian Wang
  • ... [+30 authors] ...,
  • Karsten Kristiansen
  • Xun Xu
  • Radoje Drmanac
  • Brock A. Peters
  • First Published April 2, 2019
Method

cis-regulatory elements, their cognate transcription factors, and regulatory DNA sequence variants" > Human cardiac cis-regulatory elements, their cognate transcription factors, and regulatory DNA sequence variants

  • Dongwon Lee
  • Ashish Kapoor
  • Alexias Safi
  • Lingyun Song
  • Marc K. Halushka
  • Gregory E. Crawford
  • Aravinda Chakravarti
  • First Published August 23, 2018
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