An evaluation of using mutual information for selection of acoustic-features representation of phonemes for speech recognition. - Mohamed Kamal Omar; Ken Chen 001; Mark Hasegawa-Johnson; Yigal Brandman (INTERSPEECH, 2002)

Prosody dependent speech recognition with explicit duration modelling at intonational phrase boundaries. - Ken Chen 001; Sarah Borys; Mark Hasegawa-Johnson; Jennifer Cole 001 (INTERSPEECH, 2003)

An automatic prosody labeling system using ANN-based syntactic-prosodic model and GMM-based acoustic-prosodic model. - Ken Chen 001; Mark Hasegawa-Johnson; Aaron Cohen (ICASSP (1), 2004)

Modeling pronunciation variation using artificial neural networks for English spontaneous speech. - Ken Chen 001; Mark Hasegawa-Johnson (INTERSPEECH, 2004)

Automatic recognition of pitch movements using multilayer perceptron and time-Delay Recursive neural network. - Sung-Suk Kim; Mark Hasegawa-Johnson; Ken Chen 001 (IEEE Signal Process. Lett., 2004)

Landmark-Based Speech Recognition: Report of the 2004 Johns Hopkins Summer Workshop. - Mark Hasegawa-Johnson; James Baker; Sarah Borys; Ken Chen 001; Emily Coogan; Steven Greenberg; Amit Juneja; Katrin Kirchhoff; Karen Livescu; Srividya Mohan; Jennifer Muller; M. Kemal Sönmez; et al. (ICASSP (1), 2005)

Simultaneous recognition of words and prosody in the Boston University Radio Speech Corpus. - Mark Hasegawa-Johnson; Ken Chen 001; Jennifer Cole 001; Sarah Borys; Sung-Suk Kim; Aaron Cohen; Tong Zhang 005; Jeung-Yoon Choi; Heejin Kim; Taejin Yoon (Speech Commun., 2005)

Computational Analysis and Prediction of the Binding Motif and Protein Interacting Partners of the Abl SH3 Domain. - Tingjun Hou; Ken Chen 001; William A. McLaughlin; Benzhuo Lu; Wei Wang 051 (PLoS Comput. Biol., 2006)

Prosody dependent speech recognition on radio news corpus of American English. - Ken Chen 001; Mark Hasegawa-Johnson; Aaron Cohen; Sarah Borys; Sung-Suk Kim; Jennifer Cole 001; Jeung-Yoon Choi (IEEE Trans. Speech Audio Process., 2006)

On the detection of functionally coherent groups of protein domains with an extension to protein annotation. - William A. McLaughlin; Ken Chen 001; Tingjun Hou; Wei Wang 051 (BMC Bioinform., 2007)

VarScan: variant detection in massively parallel sequencing of individual and pooled samples. - Daniel C. Koboldt; Ken Chen 001; Todd Wylie; David E. Larson; Michael D. McLellan; Elaine R. Mardis; George M. Weinstock; Richard K. Wilson; Li Ding (Bioinform., 2009)

CMDS: a population-based method for identifying recurrent DNA copy number aberrations in cancer from high-resolution data. - Qunyuan Zhang; Li Ding; David E. Larson; Daniel C. Koboldt; Michael D. McLellan; Ken Chen 001; Xiaoqi Shi; Aldi T. Kraja; Elaine R. Mardis; Richard K. Wilson; Ingrid B. Borecki; Michael A. Province (Bioinform., 2010)

BreakFusion: targeted assembly-based identification of gene fusions in whole transcriptome paired-end sequencing data. - Ken Chen 001; John W. Wallis; Cyriac Kandoth; Joelle M. Kalicki-Veizer; Karen L. Mungall; Andrew J. Mungall; Steven J. M. Jones; Marco A. Marra; Timothy J. Ley; Elaine R. Mardis; Richard K. Wilson; John N. Weinstein; et al. (Bioinform., 2012)

SomaticSniper: identification of somatic point mutations in whole genome sequencing data. - David E. Larson; Christopher C. Harris; Ken Chen 001; Daniel C. Koboldt; Travis E. Abbott; David J. Dooling; Timothy J. Ley; Elaine R. Mardis; Richard K. Wilson; Li Ding (Bioinform., 2012)

Informatics Infrastructure for Routine Personalized Medicine. - Elmer V. Bernstam; Ken Chen 001; Hua Xu 001; Funda Meric-Bernstam (AMIA, 2013)

Integrated genotyping of structural variation. - Xian Fan; Luay Nakhleh; Ken Chen 001 (GlobalSIP, 2013)

Bias from removing read duplication in ultra-deep sequencing experiments. - Wanding Zhou; Tenghui Chen; Hao Zhao; Agda Karina Eterovic; Funda Meric-Bernstam; Gordon B. Mills; Ken Chen 001 (Bioinform., 2014)

Towards accurate characterization of clonal heterogeneity based on structural variation. - Xian Fan; Wanding Zhou; Zechen Chong; Luay Nakhleh; Ken Chen 001 (BMC Bioinform., 2014)

Research on Collaborative Visualization Application of Dynamic Monitoring Figure Spot. - Ken Chen 001; Ping Liao; Fang Wang 020; Yuchuan Wang; Pengfei Xiao (Smart Graphics, 2015)

Genome Modeling System: A Knowledge Management Platform for Genomics. - Malachi Griffith; Obi L. Griffith; Scott M. Smith; Avinash Ramu; Matthew B. Callaway; Anthony M. Brummett; Michael J. Kiwala; Adam C. Coffman; Allison A. Regier; Benjamin J. Oberkfell; Gabriel E. Sanderson; Thomas P. Mooney; et al. (PLoS Comput. Biol., 2015)

BreakPoint Surveyor: a pipeline for structural variant visualization. - Matthew A. Wyczalkowski; Kristine M. Wylie; Song Cao; Michael D. McLellan; Jennifer Flynn; Mo Huang; Kai Ye 001; Xian Fan; Ken Chen 001; Michael C. Wendl; Li Ding (Bioinform., 2017)

SCMarker: Ab initio marker selection for single cell transcriptome profiling. - Fang Wang 020; Shaoheng Liang; Tapsi Kumar; Nicholas Navin; Ken Chen 001 (PLoS Comput. Biol., 2019)

Stratified Test Alleviates Batch Effects in Single-Cell Data. - Shaoheng Liang; Qingnan Liang; Rui Chen 013; Ken Chen 001 (AlCoB, 2020)

Single-cell manifold-preserving feature selection for detecting rare cell populations. - Shaoheng Liang; Vakul Mohanty; Jinzhuang Dou; Qi Miao; Yuefan Huang; Muharrem Müftüoglu; Li Ding; Weiyi Peng; Ken Chen 001 (Nat. Comput. Sci., 2021)

Publisher Correction: Single-cell manifold-preserving feature selection for detecting rare cell populations. - Shaoheng Liang; Vakul Mohanty; Jinzhuang Dou; Qi Miao; Yuefan Huang; Muharrem Müftüoglu; Li Ding; Weiyi Peng; Ken Chen 001 (Nat. Comput. Sci., 2021)

Stratified Test Accurately Identifies Differentially Expressed Genes Under Batch Effects in Single-Cell Data. - Shaoheng Liang; Qingnan Liang; Rui Chen 013; Ken Chen 001 (IEEE ACM Trans. Comput. Biol. Bioinform., 2021)

Sensei: how many samples to tell a change in cell type abundance? - Shaoheng Liang; Jason Willis; Jinzhuang Dou; Vakul Mohanty; Yuefan Huang; Eduardo Vilar; Ken Chen 001 (BMC Bioinform., 2022)

KCLab at Chemotimelines 2024: End-to-end system for chemotherapy timeline extraction - Subtask2. - Yukun Tan; Merve Dede; Ken Chen 001 (ClinicalNLP@NAACL, 2024)

Forecasting acute kidney injury and resource utilization in ICU patients using longitudinal, multimodal models. - Yukun Tan; Merve Dede; Vakul Mohanty; Jinzhuang Dou; Holly Hill; Elmer V. Bernstam; Ken Chen 001 (J. Biomed. Informatics, 2024)