H. Yalamanchili

发表

PolyA-miner: accurate assessment of differential alternative poly-adenylation from 3′Seq data using vector projections and non-negative matrix factorization

H. Zoghbi, Zhandong Liu, E. Wagner, 2020, Nucleic acids research.

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

H. Zoghbi, Zhandong Liu, Ying-Wooi Wan, 2018, Nature Communications.

Inferring gene regulatory networks by integrating ChIP-seq/chip and transcriptome data via LASSO-type regularization methods.

Junwen Wang, J. Qin, Yaohua Hu, 2014, Methods.

Inference of Gene-Phenotype Associations via Protein-Protein Interaction and Orthology

Mulin Jun Li, Wing-Fu Lai, Hari Krishna Yalamanchili, 2013, PloS one.

Title Inference of gene-phenotype associations via protein-proteininteraction and orthology

R. Lovell-Badge, M. J. Li, Panwen Wang, 2013 .

Bayesian detection of embryonic gene expression onset in C. elegans

Kenny Q. Ye, Xiaodan Fan, Zhongying Zhao, 2015, The Annals of Applied Statistics.

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

H. Zoghbi, Zhandong Liu, H. Orr, 2018, Cell reports.

Partial loss of CFIm25 causes learning deficits and aberrant neuronal alternative polyadenylation

H. Zoghbi, Alexander B. Saltzman, M. Leng, 2020, eLife.

Partial loss of CFIm25 causes aberrant alternative polyadenylation and learning deficits

H. Zoghbi, Alexander B. Saltzman, M. Leng, 2019, bioRxiv.

Integrated analysis of the aging brain transcriptome and proteome in tauopathy

Zhandong Liu, N. Seyfried, J. Shulman, 2020, Molecular neurodegeneration.

Integrated analysis of the aging brain transcriptome and proteome in tauopathy

Zhandong Liu, N. Seyfried, J. Shulman, 2020, bioRxiv.

Comparative and quantitative proteomics reveal the adaptive strategies of oyster larvae to ocean acidification

V. Thiyagarajan, H. Yalamanchili, Q. Quan, 2015, Proteomics.

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

D. Bennett, Zhandong Liu, A. Levey, 2019, Alzheimer's & Dementia.

Bias toward long gene misregulation in synaptic disorders can be an artefact of amplification-based methods

H. Zoghbi, Zhandong Liu, Ying-Wooi Wan, 2017, bioRxiv.

Sex-specific epigenetic development in the mouse hypothalamic arcuate nucleus pinpoints human genomic regions associated with body mass index

Chathura Gunasekara, C. Coarfa, Yumei Li, 2022, Science advances.

PolyAMiner-Bulk: A Machine Learning Based Bioinformatics Algorithm to Infer and Decode Alternative Polyadenylation Dynamics from bulk RNA-seq data

Zhandong Liu, E. Wagner, H. Yalamanchili, 2023, bioRxiv.

Extensive cryptic splicing upon loss of RBM17 and TDP43 in neurodegeneration models.

Joshua J. White, Zhandong Liu, H. Zoghbi, 2016, Human molecular genetics.

A novel neural response algorithm for protein function prediction

Junwen Wang, Quan-Wu Xiao, Hari Krishna Yalamanchili, 2012, BMC Systems Biology.

NRProF: Neural response based protein function prediction algorithm

Junwen Wang, Quan-Wu Xiao, Hari Krishna Yalamanchili, 2011, 2011 IEEE International Conference on Systems Biology (ISB).

PGC-1α senses the CBC of pre-mRNA to dictate the fate of promoter-proximally paused RNAPII.

Geoffrey M. Nelson, L. Maquat, Xavier Rambout, 2023, Molecular cell.

Shu Yang, Michael Q. Zhang, Pak Chung Sham, 2011, Bioinform..

Disruption of MeCP2–TCF20 complex underlies distinct neurodevelopmental disorders

H. Zoghbi, A. Burlingame, Zhandong Liu, 2022, Proceedings of the National Academy of Sciences.

Forniceal deep brain stimulation induces gene expression and splicing changes that promote neurogenesis and plasticity

H. Zoghbi, Zhandong Liu, Ying-Wooi Wan, 2018, eLife.

BAYESIAN DETECTION OF EMBRYONIC GENE EXPRESSION

Zhongying Zhao, H. Yalamanchili, Junwen Wang, 2015 .

DDGni: Dynamic delay gene-network inference from high-temporal data using gapped local alignment

Bin Yan, Francis Y. L. Chin, Zhongying Zhao, 2014, Bioinform..

Identifying structural repeats in proteins using graph centrality measures

Ruchi Jain, Hari Krishna Yalamanchili, Nita Parekh, 2009, 2009 World Congress on Nature & Biologically Inspired Computing (NaBIC).

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

Zhandong Liu, Hari Krishna Yalamanchili, Hyun-Hwan Jeong, 2018, PSB.

SpliceNet: recovering splicing isoform-specific differential gene networks from RNA-Seq data of normal and diseased samples

Hari Krishna Yalamanchili, Panwen Wang, Panwen Wang, 2014, Nucleic acids research.

Alternative polyadenylation alters protein dosage by switching between intronic and 3′UTR sites

Vicky L Brandt, Kimara L. Targoff, J. Rosenfeld, 2023, Science advances.

Emerging roles of alternative cleavage and polyadenylation (APA) in human disease

H. Yalamanchili, H. Karmouty-quintana, A. Guha, 2021, Journal of cellular physiology.

A computational pipeline to infer alternative poly-adenylation from 3' sequencing data.

Zhandong Liu, E. Wagner, Nathan D. Elrod, 2021, Methods in enzymology.

The Current Status and Challenges in Computational Analysis of Genomic Big Data

Bin Yan, Junwen Wang, Jing Qin, 2015, Big Data Res..

Acacetin causes a frequency- and use-dependent blockade of hKv1.5 channels by binding to the S6 domain.

Hari Krishna Yalamanchili, Hung-Fat Tse, Panwen Wang, 2011, Journal of molecular and cellular cardiology.

A Comprehensive and Integrative Approach to MeCP2 Disease Transcriptomics

Zhandong Liu, Ying-Wooi Wan, R. Al-ouran, 2023, International journal of molecular sciences.

MECP2pedia: A Comprehensive Transcriptome Portal for MECP2 Disease Research

Zhandong Liu, Ying-Wooi Wan, R. Al-ouran, 2021, bioRxiv.

Dual targeting of brain region‐specific kinases potentiates neurological rescue in Spinocerebellar ataxia type 1

Maxime W. C. Rousseaux, Zhandong Liu, H. Zoghbi, 2021, The EMBO journal.

Transcriptional Regulation by ATOH1 and its Target SPDEF in the Intestine

Zhandong Liu, Z. Li, Ying-Wooi Wan, 2016, Cellular and molecular gastroenterology and hepatology.

Cleavage stimulating factor 64 depletion mitigates cardiac fibrosis through alternative polyadenylation.

R. Thandavarayan, K. Youker, H. Yalamanchili, 2022, Biochemical and biophysical research communications.

Application and design considerations for 3'-end sequencing using click-chemistry.

Zhandong Liu, Hari Krishna Yalamanchili, Nathan D Elrod, 2021, Methods in enzymology.

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

Zhandong Liu, Hari Krishna Yalamanchili, Zhandong Liu, 2017, Current protocols in bioinformatics.

NCOR1/2 loss of function impairs memory through a novel GABAergic hypothalamus–CA3 projection

Zhandong Liu, Ying-Wooi Wan, J. Morton, 2018, Nature Neuroscience.

NUDT21 alters glioma migration through differential alternative polyadenylation of LAMC1

E. Wagner, Nathan D. Elrod, Kai-Lieh Huang, 2023, Journal of Neuro-Oncology.

Graph Spectral Approach for Identifying Protein Domains

Hari Krishna Yalamanchili, Nita Parekh, H. Yalamanchili, 2009, BICoB.

The epigenetic response of mouse brown adipose tissue to cold stress: histone proteoform, DNA methylation, and RNA expression

N. McKenna, S. Ochsner, H. Yalamanchili, 2023, bioRxiv.

Forniceal deep brain stimulation induces gene expression and splicing changes that promote neurogenesis and plasticity

H. Zoghbi, Ying-Wooi Wan, Jianrong Tang, 2018, eLife.

SF3B1-dependent alternative splicing is critical for maintaining endometrial homeostasis and the establishment of pregnancy

H. Yalamanchili, R. Kommagani, S. Chadchan, 2023, bioRxiv.

Author Correction: Loss of function of NCOR1 and NCOR2 impairs memory through a novel GABAergic hypothalamus–CA3 projection

Ying-Wooi Wan, J. Morton, X. Hou, 2019, Nature Neuroscience.

brain stimulation induces gene expression and splicing changes that promote 2 neurogenesis and plasticity 3 4

H. Zoghbi, Ying-Wooi Wan, Jianrong Tang, 2018 .

NCOR1/2 loss of function impairs memory through a novel GABAergic hypothalamus–CA3 projection

Zhandong, Ying-Wooi Wan, Gong, 2019 .

PolyAMiner-Bulk is a deep learning-based algorithm that decodes alternative polyadenylation dynamics from bulk RNA-seq data

H. Yalamanchili, V. Jonnakuti, Zhandong Liu, 2024, Cell Reports Methods.

Differential effects of MATR3 variants on its cryptic splicing repression function

U. Pandey, H. Yalamanchili, Sukhleen Kour, 2023, bioRxiv.

CPSF3 inhibition blocks pancreatic cancer cell proliferation through disruption of core histone mRNA processing

H. Yalamanchili, Michael E. Feigin, Jianmin Wang, 2024, RNA.