Publications by authors named "Zhandong Liu"

88Publications

Integrated analysis of the aging brain transcriptome and proteome in tauopathy.

Mol Neurodegener 2020 Sep 29;15(1):56. Epub 2020 Sep 29.

Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA.

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http://dx.doi.org/10.1186/s13024-020-00405-4DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7526226PMC
September 2020

miR760 regulates ATXN1 levels via interaction with its 5' untranslated region.

Genes Dev 2020 Sep 6;34(17-18):1147-1160. Epub 2020 Aug 6.

Program in Integrative Molecular and Biomedical Sciences, Baylor College of Medicine, Houston, Texas 77030, USA.

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http://dx.doi.org/10.1101/gad.339317.120DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7462065PMC
September 2020

GDASC: a GPU parallel-based web server for detecting hidden batch factors.

Bioinformatics 2020 Aug;36(14):4211-4213

Department of Automation and Intelligence Science, College of Artificial Intelligence, Nankai University, 300350 Tianjin, China.

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http://dx.doi.org/10.1093/bioinformatics/btaa427DOI Listing
August 2020

PRIME: a probabilistic imputation method to reduce dropout effects in single-cell RNA sequencing.

Bioinformatics 2020 Jul;36(13):4021-4029

Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital.

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http://dx.doi.org/10.1093/bioinformatics/btaa278DOI Listing
July 2020

Are HHV-6A and HHV-7 Really More Abundant in Alzheimer's Disease?

Neuron 2019 12;104(6):1034-1035

Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX, USA; Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA; Quantitative and Computational Biosciences Program, Baylor College of Medicine, Houston, TX, USA. Electronic address:

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http://dx.doi.org/10.1016/j.neuron.2019.11.009DOI Listing
December 2019

Tau-Mediated Disruption of the Spliceosome Triggers Cryptic RNA Splicing and Neurodegeneration in Alzheimer's Disease.

Cell Rep 2019 10;29(2):301-316.e10

Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Department of Neuroscience, Baylor College of Medicine, Houston, TX 77030, USA; Department of Neurology, Baylor College of Medicine, Houston, TX 77030, USA; Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX 77030, USA. Electronic address:

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http://dx.doi.org/10.1016/j.celrep.2019.08.104DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6919331PMC
October 2019

A Portal to Visualize Transcriptome Profiles in Mouse Models of Neurological Disorders.

Genes (Basel) 2019 09 26;10(10). Epub 2019 Sep 26.

Department of Pediatrics, Baylor College of Medicine, Houston, TX 77030, USA.

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http://dx.doi.org/10.3390/genes10100759DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6826490PMC
September 2019

Using MARRVEL v1.2 for Bioinformatics Analysis of Human Genes and Variant Pathogenicity.

Curr Protoc Bioinformatics 2019 09;67(1):e85

Department of Pediatrics, Jan and Dan Duncan Neurological Research Institute at Texas, Children's Hospital, Houston, Texas.

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http://dx.doi.org/10.1002/cpbi.85DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6750039PMC
September 2019

Navigating MARRVEL, a Web-Based Tool that Integrates Human Genomics and Model Organism Genetics Information.

J Vis Exp 2019 08 15(150). Epub 2019 Aug 15.

Program in Developmental Biology, Baylor College of Medicine; Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital; Department of Molecular and Human Genetics, Baylor College of Medicine; Department of Neuroscience, Baylor College of Medicine;

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http://dx.doi.org/10.3791/59542DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7401700PMC
August 2019

Beta-binomial modeling of CRISPR pooled screen data identifies target genes with greater sensitivity and fewer false negatives.

Genome Res 2019 06 23;29(6):999-1008. Epub 2019 Apr 23.

Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, Texas 77030, USA.

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http://dx.doi.org/10.1101/gr.245571.118DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6581060PMC
June 2019

Metabolomics of mammalian brain reveals regional differences.

BMC Syst Biol 2018 12 21;12(Suppl 8):127. Epub 2018 Dec 21.

Program in Developmental Biology, Baylor College of Medicine, Houston, TX, USA.

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http://dx.doi.org/10.1186/s12918-018-0644-0DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6302375PMC
December 2018

Complement C3aR Inactivation Attenuates Tau Pathology and Reverses an Immune Network Deregulated in Tauopathy Models and Alzheimer's Disease.

Neuron 2018 12 8;100(6):1337-1353.e5. Epub 2018 Nov 8.

Huffington Center on Aging, Baylor College of Medicine, Houston, TX 77030, USA; Integrative Molecular and Biomedical Sciences Program, Baylor College of Medicine, Houston, TX 77030, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX 77030, USA. Electronic address:

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http://dx.doi.org/10.1016/j.neuron.2018.10.031DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6309202PMC
December 2018

RBM17 Interacts with U2SURP and CHERP to Regulate Expression and Splicing of RNA-Processing Proteins.

Cell Rep 2018 10;25(3):726-736.e7

Program in Developmental Biology, Baylor College of Medicine, Houston, TX 77030, USA; Jan and Dan Duncan Neurological Research Institute at Texas Children's Hospital, Houston, TX 77030, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Howard Hughes Medical Institute, Baylor College of Medicine, Houston, TX 77030, USA; Department of Pediatrics, Baylor College of Medicine, Houston, TX 77030, USA; Department of Neuroscience, Baylor College of Medicine, Houston, TX 77030, USA. Electronic address:

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http://dx.doi.org/10.1016/j.celrep.2018.09.041DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6292215PMC
October 2018

Synthesis and biological evaluation of novel tricyclic matrinic derivatives as potential anti-filovirus agents.

Acta Pharm Sin B 2018 Jul 21;8(4):629-638. Epub 2018 Feb 21.

Beijing Key Laboratory of Antimicrobial Agents, Institute of Medicinal Biotechnology, Chinese Academy of Medical Science & Peking Union Medical College, Beijing 10050, China.

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http://dx.doi.org/10.1016/j.apsb.2018.01.006DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6089848PMC
July 2018

Apparent bias toward long gene misregulation in MeCP2 syndromes disappears after controlling for baseline variations.

Nat Commun 2018 08 13;9(1):3225. Epub 2018 Aug 13.

Graduate Program in Quantitative and Computational Biosciences, Baylor College of Medicine, Houston, TX, 77030, USA.

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http://dx.doi.org/10.1038/s41467-018-05627-1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6089998PMC
August 2018

High-Throughput Functional Analysis Distinguishes Pathogenic, Nonpathogenic, and Compensatory Transcriptional Changes in Neurodegeneration.

Cell Syst 2018 07 20;7(1):28-40.e4. Epub 2018 Jun 20.

Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Jan and Dan Duncan Neurological Research Institute at Texas Children's Hospital, Houston, TX 77030, USA. Electronic address:

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http://dx.doi.org/10.1016/j.cels.2018.05.010DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6082401PMC
July 2018

Tau Activates Transposable Elements in Alzheimer's Disease.

Cell Rep 2018 06;23(10):2874-2880

Department of Neuroscience, Baylor College of Medicine, Houston, TX 77030, USA; Jan and Dan Duncan Neurologic Research Institute, Texas Children's Hospital, Houston, TX 77030, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Department of Neurology, Baylor College of Medicine, Houston, TX 77030, USA. Electronic address:

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http://dx.doi.org/10.1016/j.celrep.2018.05.004DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6181645PMC
June 2018

Epigenetic drift of H3K27me3 in aging links glycolysis to healthy longevity in .

Elife 2018 05 29;7. Epub 2018 May 29.

Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Pudong, China.

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http://dx.doi.org/10.7554/eLife.35368DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5991832PMC
May 2018

Genome-wide distribution of linker histone H1.0 is independent of MeCP2.

Nat Neurosci 2018 06 25;21(6):794-798. Epub 2018 May 25.

Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.

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http://dx.doi.org/10.1038/s41593-018-0155-8DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6099063PMC
June 2018

Detecting hidden batch factors through data-adaptive adjustment for biological effects.

Bioinformatics 2018 04;34(7):1141-1147

Graduate Program in Structural and Computational Biology and Molecular Biophysics, Baylor College of Medicine, Houston, TX 77030, USA.

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http://dx.doi.org/10.1093/bioinformatics/btx635DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6454417PMC
April 2018

Simple Assessment of Nitrogen Nutrition Index in Summer Maize by Using Chlorophyll Meter Readings.

Front Plant Sci 2018 19;9:11. Epub 2018 Jan 19.

Key Laboratory of Crop Water Use and Regulation, Ministry of Agriculture, Farmland Irrigation Research Institute, Chinese Academy of Agricultural Sciences, Xinxiang, China.

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http://dx.doi.org/10.3389/fpls.2018.00011DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5780453PMC
January 2018

Otud7a Knockout Mice Recapitulate Many Neurological Features of 15q13.3 Microdeletion Syndrome.

Am J Hum Genet 2018 02;102(2):296-308

Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA; Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX, USA. Electronic address:

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http://dx.doi.org/10.1016/j.ajhg.2018.01.005DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5985472PMC
February 2018

Loss of Capicua alters early T cell development and predisposes mice to T cell lymphoblastic leukemia/lymphoma.

Proc Natl Acad Sci U S A 2018 02 30;115(7):E1511-E1519. Epub 2018 Jan 30.

Jan and Dan Duncan Neurological Research Institute at Texas Children's Hospital, Houston, TX 77030;

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http://dx.doi.org/10.1073/pnas.1716452115DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5816173PMC
February 2018

An ultra-fast and scalable quantification pipeline for transposable elements from next generation sequencing data.

Pac Symp Biocomput 2018 ;23:168-179

Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA, ²Jan and Dan Duncan Neurological Research Institute, Texas Childrens Hospital, Houston, Texas 77030, USA.

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August 2018

The International Conference on Intelligent Biology and Medicine (ICIBM) 2016: summary and innovation in genomics.

BMC Genomics 2017 Oct 3;18(Suppl 6):703. Epub 2017 Oct 3.

Department of Computer Science, The University of Texas at San Antonio, San Antonio, TX, 78249, USA.

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http://dx.doi.org/10.1186/s12864-017-4018-6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5629612PMC
October 2017

The International Conference on Intelligent Biology and Medicine (ICIBM) 2016: from big data to big analytical tools.

BMC Bioinformatics 2017 Oct 3;18(Suppl 11):405. Epub 2017 Oct 3.

Center for Precision Health, School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX, 77030, USA.

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http://dx.doi.org/10.1186/s12859-017-1797-3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5629550PMC
October 2017

Data Analysis Pipeline for RNA-seq Experiments: From Differential Expression to Cryptic Splicing.

Curr Protoc Bioinformatics 2017 09 13;59:11.15.1-11.15.21. Epub 2017 Sep 13.

Bioinformatics Core, Jan and Dan Duncan Neurological Research Institute at Texas Children's Hospital, Houston, Texas.

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http://dx.doi.org/10.1002/cpbi.33DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6373869PMC
September 2017

Disease-related gene module detection based on a multi-label propagation clustering algorithm.

PLoS One 2017 19;12(5):e0178006. Epub 2017 May 19.

Department of Biological Sciences, Northern Illinois University, DeKalb, IL 60115, United States of America.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0178006PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5438150PMC
October 2017

CRISPRcloud: a secure cloud-based pipeline for CRISPR pooled screen deconvolution.

Bioinformatics 2017 Sep;33(18):2963-2965

Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX, USA.

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http://dx.doi.org/10.1093/bioinformatics/btx335DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5870715PMC
September 2017

MARRVEL: Integration of Human and Model Organism Genetic Resources to Facilitate Functional Annotation of the Human Genome.

Am J Hum Genet 2017 Jun 11;100(6):843-853. Epub 2017 May 11.

Program in Developmental Biology, Baylor College of Medicine (BCM), Houston, TX 77030, USA; Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX 77030, USA; Department of Molecular and Human Genetics, BCM, Houston, TX 77030, USA; Howard Hughes Medical Institute, BCM, Houston, TX 77030, USA. Electronic address:

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http://dx.doi.org/10.1016/j.ajhg.2017.04.010DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5670038PMC
June 2017

Comprehensive evaluation of RNA-seq quantification methods for linearity.

BMC Bioinformatics 2017 Mar 22;18(Suppl 4):117. Epub 2017 Mar 22.

Department of Pediatrics-Neurology, Jan and Dan Duncan Neurological Research Institute, Baylor College of Medicine, 1250 Moursund St., Suite 1325, Houston, 77030, TX, USA.

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http://dx.doi.org/10.1186/s12859-017-1526-yDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5374695PMC
March 2017

Serotonin regulation in a rat model of exercise-induced chronic fatigue.

Neuroscience 2017 05 28;349:27-34. Epub 2017 Feb 28.

China Institute of Sports Medicine, 2-A Sidegate, Tiyuguan Road, Dongcheng District, Beijing 100061, China.

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http://dx.doi.org/10.1016/j.neuroscience.2017.02.037DOI Listing
May 2017

Transcriptional Regulation by ATOH1 and its Target SPDEF in the Intestine.

Cell Mol Gastroenterol Hepatol 2017 Jan 21;3(1):51-71. Epub 2016 Oct 21.

Integrative Molecular and Biomedical Sciences Graduate Program, Baylor College of Medicine, Houston, Texas; Division of Medicine, Section of Gastroenterology and Hepatology, Baylor College of Medicine, Houston, Texas.

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https://linkinghub.elsevier.com/retrieve/pii/S2352345X163012
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http://dx.doi.org/10.1016/j.jcmgh.2016.10.001DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5247424PMC
January 2017

Impacts of Steel-Slag-Based Silicate Fertilizer on Soil Acidity and Silicon Availability and Metals-Immobilization in a Paddy Soil.

PLoS One 2016 14;11(12):e0168163. Epub 2016 Dec 14.

Ministry of Agriculture Key Laboratory of Crop Water Use and Regulation, Institute of Farmland Irrigation Research, Chinese Academy of Agricultural Sciences, Xinxiang, China.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0168163PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5156425PMC
July 2017

In situ stabilization of heavy metals in multiple-metal contaminated paddy soil using different steel slag-based silicon fertilizer.

Environ Sci Pollut Res Int 2016 Dec 11;23(23):23638-23647. Epub 2016 Sep 11.

Ministry of Agriculture Key Laboratory of Crop Water Use and Regulation, Institute of Farmland Irrigation Research, Chinese Academy of Agricultural Sciences, Xinxiang, 453002, China.

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http://dx.doi.org/10.1007/s11356-016-7588-yDOI Listing
December 2016

XMRF: an R package to fit Markov Networks to high-throughput genetics data.

BMC Syst Biol 2016 08 26;10 Suppl 3:69. Epub 2016 Aug 26.

Computational and Integrative Biomedical Research Center, Baylor College of Medicine, Houston, Texas, USA.

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http://dx.doi.org/10.1186/s12918-016-0313-0DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5009817PMC
August 2016

Graphical Models via Univariate Exponential Family Distributions.

J Mach Learn Res 2015 Dec;16:3813-3847

Department of Pediatrics-Neurology, Baylor College of Medicine, Houston, TX 77030, USA.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4998206PMC
December 2015

Yield Response of Spring Maize to Inter-Row Subsoiling and Soil Water Deficit in Northern China.

PLoS One 2016 21;11(4):e0153809. Epub 2016 Apr 21.

Key Laboratory of Crop Water Use and Regulation, Ministry of Agriculture, Farmland Irrigation Research Institute, Chinese Academy of Agricultural Sciences, Xinxiang, China.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0153809PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4839663PMC
February 2017

Crowdsourced estimation of cognitive decline and resilience in Alzheimer's disease.

Authors:
Genevera I Allen Nicola Amoroso Catalina Anghel Venkat Balagurusamy Christopher J Bare Derek Beaton Roberto Bellotti David A Bennett Kevin L Boehme Paul C Boutros Laura Caberlotto Cristian Caloian Frederick Campbell Elias Chaibub Neto Yu-Chuan Chang Beibei Chen Chien-Yu Chen Ting-Ying Chien Tim Clark Sudeshna Das Christos Davatzikos Jieyao Deng Donna Dillenberger Richard J B Dobson Qilin Dong Jimit Doshi Denise Duma Rosangela Errico Guray Erus Evan Everett David W Fardo Stephen H Friend Holger Fröhlich Jessica Gan Peter St George-Hyslop Satrajit S Ghosh Enrico Glaab Robert C Green Yuanfang Guan Ming-Yi Hong Chao Huang Jinseub Hwang Joseph Ibrahim Paolo Inglese Anandhi Iyappan Qijia Jiang Yuriko Katsumata John S K Kauwe Arno Klein Dehan Kong Roland Krause Emilie Lalonde Mario Lauria Eunjee Lee Xihui Lin Zhandong Liu Julie Livingstone Benjamin A Logsdon Simon Lovestone Tsung-Wei Ma Ashutosh Malhotra Lara M Mangravite Taylor J Maxwell Emily Merrill John Nagorski Aishwarya Namasivayam Manjari Narayan Mufassra Naz Stephen J Newhouse Thea C Norman Ramil N Nurtdinov Yen-Jen Oyang Yudi Pawitan Shengwen Peng Mette A Peters Stephen R Piccolo Paurush Praveen Corrado Priami Veronica Y Sabelnykova Philipp Senger Xia Shen Andrew Simmons Aristeidis Sotiras Gustavo Stolovitzky Sabina Tangaro Andrea Tateo Yi-An Tung Nicholas J Tustison Erdem Varol George Vradenburg Michael W Weiner Guanghua Xiao Lei Xie Yang Xie Jia Xu Hojin Yang Xiaowei Zhan Yunyun Zhou Fan Zhu Hongtu Zhu Shanfeng Zhu

Alzheimers Dement 2016 06 11;12(6):645-53. Epub 2016 Apr 11.

School of Computer Science, Fudan University, Shanghai, Shanghai, China; Shanghai Key Lab of Intelligent Information Processing, Fudan University, Shanghai, Shanghai, China; Centre for Computational Systems Biology, Fudan University, Shanghai, China.

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http://dx.doi.org/10.1016/j.jalz.2016.02.006DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5474755PMC
June 2016

Reversal of phenotypes in MECP2 duplication mice using genetic rescue or antisense oligonucleotides.

Nature 2015 Dec 25;528(7580):123-6. Epub 2015 Nov 25.

Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA.

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http://dx.doi.org/10.1038/nature16159DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4839300PMC
December 2015

Post-transcriptional regulation of SHANK3 expression by microRNAs related to multiple neuropsychiatric disorders.

Mol Brain 2015 Nov 16;8(1):74. Epub 2015 Nov 16.

Department of Neuroscience and Division of Brain Korea 21 Biomedical Science, College of Medicine, Korea University, Seoul, 136-705, South Korea.

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http://www.molecularbrain.com/content/8/1/74
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http://dx.doi.org/10.1186/s13041-015-0165-3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4647645PMC
November 2015

TCGA2STAT: simple TCGA data access for integrated statistical analysis in R.

Bioinformatics 2016 03 14;32(6):952-4. Epub 2015 Nov 14.

Computational and Integrative Biomedical Research Center, Department of Pediatrics-Neurology, Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Baylor College of Medicine, Houston, TX, USA.

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http://bioinformatics.oxfordjournals.org/content/early/2015/
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http://dx.doi.org/10.1093/bioinformatics/btv677DOI Listing
March 2016

FOXG1 expression shows correlation with neuronal differentiation in cerebellar development, aggressive phenotype in medulloblastomas, and survival in a xenograft model of medulloblastoma.

Hum Pathol 2015 Dec 24;46(12):1859-71. Epub 2015 Aug 24.

Department of Pathology and Immunology, Texas Children's Hospital, Baylor College of Medicine, Houston, TX 77030.

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http://dx.doi.org/10.1016/j.humpath.2015.08.003DOI Listing
December 2015

A drosophila genetic resource of mutants to study mechanisms underlying human genetic diseases.

Cell 2014 Sep;159(1):200-214

Program in Developmental Biology, Baylor College of Medicine (BCM), Houston, TX 77030, USA; Department of Molecular and Human Genetics, BCM, Houston, TX 77030, USA; Jan and Dan Duncan Neurological Research Institute, Houston, TX 77030, USA; Howard Hughes Medical Institute, Houston, TX 77030, USA; Program in Structural and Computational Biology and Molecular Biophysics, BCM, Houston, TX 77030, USA; Department of Neuroscience, BCM, Houston, TX 77030, USA. Electronic address:

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http://dx.doi.org/10.1016/j.cell.2014.09.002DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4298142PMC
September 2014

Serine catabolism regulates mitochondrial redox control during hypoxia.

Cancer Discov 2014 Dec 3;4(12):1406-17. Epub 2014 Sep 3.

Cancer Biology and Genetics Program and Immunology Program, Memorial Sloan Kettering Cancer Center, New York, New York.

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http://dx.doi.org/10.1158/2159-8290.CD-14-0250DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4258153PMC
December 2014

On the reproducibility of TCGA ovarian cancer microRNA profiles.

PLoS One 2014 29;9(1):e87782. Epub 2014 Jan 29.

Department of Pediatrics, Baylor College of Medicine, Houston, Texas, United States of America ; Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, Texas, United States of America ; Computational and Integrative Biomedical Research (CIBR) Center, Baylor College of Medicine, Houston, Texas, United States of America ; Neurological Research Institute, Texas Children's Hospital, Houston, Texas, United States of America.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0087782PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3906208PMC
October 2014

Combinatorial therapy discovery using mixed integer linear programming.

Bioinformatics 2014 May 24;30(10):1456-63. Epub 2014 Jan 24.

Computational and Integrative Biomedical Research Center, Baylor College of Medicine, Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Department of Pediatrics-Neurology, Department of Obstetrics and Gynaecology, Department of Molecular Virology and Microbiology, Baylor College of Medicine, School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA, and Department of Cancer Biology, University of Pennsylvania, Philadelphia, PA 19104, USA.

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http://dx.doi.org/10.1093/bioinformatics/btu046DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4016706PMC
May 2014

A Local Poisson Graphical Model for inferring networks from sequencing data.

IEEE Trans Nanobioscience 2013 Sep 15;12(3):189-98. Epub 2013 Aug 15.

Department of Statistics & Electrical and Computer Engineering, Rice University, Houston, TX 77005, USA.

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http://dx.doi.org/10.1109/TNB.2013.2263838DOI Listing
September 2013

Expression and functional pathway analysis of nuclear receptor NR2F2 in ovarian cancer.

J Clin Endocrinol Metab 2013 Jul 20;98(7):E1152-62. Epub 2013 May 20.

Departments of Obstetrics and Gynecology, The Dan L Duncan Cancer Center, Baylor College of Medicine, The Methodist Hospital, Houston, Texas 77030, USA.

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http://dx.doi.org/10.1210/jc.2013-1081DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3701283PMC
July 2013

Digital sorting of complex tissues for cell type-specific gene expression profiles.

BMC Bioinformatics 2013 Mar 7;14:89. Epub 2013 Mar 7.

Department of Pediatrics, Neurological Research Institute, Baylor College of Medicine, Houston, TX, USA.

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http://dx.doi.org/10.1186/1471-2105-14-89DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3626856PMC
March 2013

Gene expression deconvolution in linear space.

Nat Methods 2011 Dec 28;9(1):8-9; author reply 9. Epub 2011 Dec 28.

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http://dx.doi.org/10.1038/nmeth.1830DOI Listing
December 2011

The Snf1-related kinase, Hunk, is essential for mammary tumor metastasis.

Proc Natl Acad Sci U S A 2009 Sep 28;106(37):15855-60. Epub 2009 Aug 28.

Department of Cancer Biology, Abramson Family Cancer Research Institute, University of Pennsylvania School of Medicine, Philadelphia, PA 19104-6160, USA.

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http://dx.doi.org/10.1073/pnas.0906993106DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2734880PMC
September 2009

Singular value decomposition-based regression identifies activation of endogenous signaling pathways in vivo.

Genome Biol 2008 18;9(12):R180. Epub 2008 Dec 18.

Department of Cancer Biology, Abramson Family Cancer Research Institute, University of Pennsylvania, 421 Curie Blvd, BRB II/III 616, Philadelphia, PA 19104, USA.

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http://dx.doi.org/10.1186/gb-2008-9-12-r180DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2646284PMC
March 2009

Sequence space coverage, entropy of genomes and the potential to detect non-human DNA in human samples.

BMC Genomics 2008 Oct 30;9:509. Epub 2008 Oct 30.

Genomics and Computational Biology Graduate Group, School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.

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http://dx.doi.org/10.1186/1471-2164-9-509DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2628393PMC
October 2008

Asbestos exposure, pleural mesothelioma, and serum osteopontin levels.

N Engl J Med 2005 Oct;353(15):1564-73

Department of Surgery, Wayne State University, Karmanos Cancer Institute, John A. Dingell Veterans Hospital, Detroit, Mich, USA.

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http://dx.doi.org/10.1056/NEJMoa051185DOI Listing
October 2005

In silico and wet-bench identification of nuclear matrix attachment regions.

Methods Mol Med 2005 ;108:439-58

Department of Obstetrics and Gynecology, Center for Molecular Medicine and Genetics, Wayne State University, Detroit, MI, USA.

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http://dx.doi.org/10.1385/1-59259-850-1:439DOI Listing
September 2005

Gene expression profiles predict survival and progression of pleural mesothelioma.

Clin Cancer Res 2004 Feb;10(3):849-59

Thoracic Oncology, Karmanos Cancer Institute, Wayne State University, Detroit, MI 48201, USA.

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http://dx.doi.org/10.1158/1078-0432.ccr-0607-3DOI Listing
February 2004

Determination of fatty acid levels in erythrocyte membranes of patients with chronic fatigue syndrome.

Nutr Neurosci 2003 Dec;6(6):389-92

Department of Neurology, Beijing Friendship Hospital, Affiliated Hospital of Capital University of Medical Science, 95 Yong-an Rd, Beijing 100050, China.

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http://dx.doi.org/10.1080/10284150310001640356DOI Listing
December 2003

Nuclear matrix association of the human beta-globin locus utilizing a novel approach to quantitative real-time PCR.

Nucleic Acids Res 2003 Jun;31(12):3257-66

Department of Obstetrics and Gynecology, Center for Molecular Medicine and Genetics, Wayne State University, Detroit, MI, USA.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC162328PMC
http://dx.doi.org/10.1093/nar/gkg424DOI Listing
June 2003