A. Harmanci

发表

Architecture of the human regulatory network derived from ENCODE data

David Z. Chen, Kevin Y. Yip, Timothy E. Reddy, 2012, Nature.

AlleleSeq: analysis of allele-specific expression and binding in a network framework

M. Gerstein, M. Rubin, A. Abyzov, 2011, Molecular systems biology.

An Integrated Encyclopedia of DNA Elements in the Human Genome

Raymond K. Auerbach, William Stafford Noble, Stephen C. J. Parker, 2012, Nature.

SVFX: a machine learning framework to quantify the pathogenicity of structural variants

M. Gerstein, A. Harmanci, Sushant Kumar, 2019, Genome Biology.

Integrative Annotation of Variants from 1092 Humans: Application to Cancer Genomics

Gabor T. Marth, Uday S. Evani, H. Kang, 2013, Science.

Comparative Analysis of the Transcriptome across Distant Species

Peter J. Bickel, Raymond K. Auerbach, Peter J. Park, 2014, Nature.

Data Sanitization to Reduce Private Information Leakage from Functional Genomics

Prashant S. Emani, Charlotte M. Brannon, M. Gerstein, 2020, Cell.

When Biology Gets Personal: Hidden Challenges of Privacy and Ethics in Biological Big Data

S. Brenner, Erman Ayday, Haixu Tang, 2018, Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing.

Sensitive information leakage from functional genomics data: Theoretical quantifications & practical file formats for privacy preservation

Molly E. Green, M. Gerstein, Fábio C. P. Navarro, 2018 .

Quantification of private information leakage from phenotype-genotype data: linking attacks

M. Gerstein, A. Harmanci, 2016, Nature Methods.

Pan-cancer analysis of whole genomes

Steven J. M. Jones, Nuno A. Fonseca, Icgc, 2020, Nature.

PARTS: Probabilistic Alignment for RNA joinT Secondary structure prediction

D. Mathews, Gaurav Sharma, A. Harmanci, 2008, Nucleic acids research.

Stochastic sampling of the RNA structural alignment space

D. Mathews, Gaurav Sharma, A. Harmanci, 2009, Nucleic acids research.

Enhanced Transcriptome Maps from Multiple Mouse Tissues Reveal Evolutionary Constraint in Gene Expression for Thousands of Genes

M. Gerstein, Andrea Tanzer, S. Balasubramanian, 2014, bioRxiv.

Enhanced transcriptome maps from multiple mouse tissues reveal evolutionary constraint in gene expression

Dmitri D. Pervouchine, Michael A. Beer, M. Gerstein, 2014, Nature Communications.

Proposed social and technological solutions to issues of data privacy in personal genomics

M. Gerstein, D. Greenbaum, A. Harmanci, 2014, 2014 IEEE International Symposium on Ethics in Science, Technology and Engineering.

A uniform survey of allele-specific binding and expression over 1000-Genomes-Project individuals

M. Gerstein, A. Abyzov, L. Regan, 2016, Nature Communications.

EpiSAFARI: sensitive detection of valleys in epigenetic signals for enhancing annotations of functional elements

A. Harmanci, A. Harmanci, V. Gopalakrishnan, 2019, Bioinformatics.

SVFX: a machine learning framework to quantify the pathogenicity of structural variants

M. Gerstein, A. Harmanci, Sushant Kumar, 2019, bioRxiv.

Combined burden and functional impact tests for cancer driver discovery using DriverPower

Nuno A. Fonseca, Gary D Bader, Benjamin J. Raphael, 2020, Nature Communications.

Privacy-Aware Kinship Inference in Admixed Populations using Projection on Reference Panels

A. Harmanci, Xiaoqian Jiang, Miran Kim, 2022, bioRxiv.

Integrative pathway enrichment analysis of multivariate omics data

Nuno A. Fonseca, Gary D Bader, Benjamin J. Raphael, 2020, Nature Communications.

Identification of novel fusion transcripts in meningioma

D. Wheeler, A. Harmanci, Akash J. Patel, 2020, Journal of Neuro-Oncology.

Cancer LncRNA Census reveals evidence for deep functional conservation of long noncoding RNAs in tumorigenesis

Nuno A. Fonseca, Gary D Bader, Benjamin J. Raphael, 2020, Communications Biology.

Pathway and network analysis of more than 2500 whole cancer genomes

Nuno A. Fonseca, Icgc, Gary D Bader, 2020, Nature Communications.

Cross-Talk Between Histone Methyltransferases and Demethylases Regulate REST Transcription During Neurogenesis

A. Harmanci, Shavali Shaik, Lei Guo, 2022, Frontiers in Oncology.

SHiMMer: Privacy-Aware Alignment of Genomic Sequences with Secure and E cient Hidden Markov Model Evaluation

A. Harmanci, Miran Kim, Yongsoo Song, 2021 .

Ultra-Fast Homomorphic Encryption Models enable Secure Outsourcing of Genotype Imputation

Jung Hee Cheon, Lucila Ohno-Machado, Nicolas Gama, 2020, bioRxiv.

Federated generalized linear mixed models for collaborative genome-wide association studies

A. Harmanci, Wentao Li, Han Chen, 2022, iScience.

Identification of functional immune and neuronal tumor cells in glioma

Jochen F. Meyer, Xiaolong Jiang, A. Harmanci, 2022, bioRxiv.

Identification of functional immune and neuronal tumor cells in glioma

Jochen F. Meyer, Xiaolong Jiang, A. Harmanci, 2022, bioRxiv.

Epigenetic and Signaling Determinants of Blood-Brain Barrier-Regulatory Genetic Networks

Peeyush Kumar, N. Tandon, A. Harmanci, 2022 .

XCVATR: detection and characterization of variant impact on the Embeddings of single -cell and bulk RNA-sequencing samples

A. Harmanci, A. Harmanci, Tiemo J. Klisch, 2022, BMC genomics.

Identification of functional immune and neuronal tumour cells in glioma

Jochen F. Meyer, Xiaolong Jiang, A. Harmanci, 2022, bioRxiv.

An integrated map of genetic variation from 1,092 human genomes

Kenny Q. Ye, Mauricio O. Carneiro, Francisco M. De La Vega, 2012, Nature.

HDAC inhibitors elicit metabolic reprogramming by targeting super-enhancers in glioblastoma models.

P. Canoll, A. Harmanci, Junfei Zhao, 2020, The Journal of clinical investigation.

Analyses of non-coding somatic drivers in 2,658 cancer whole genomes

Jun Yu, Chen Hong, Ken Chen, 2020, Nature.

Patterns of somatic structural variation in human cancer genomes

Nuno A. Fonseca, Gary D Bader, Benjamin J. Raphael, 2020, Nature.

CaSpER identifies and visualizes CNV events by integrative analysis of single-cell or bulk RNA-sequencing data

A. Harmanci, Xiaobo Zhou, Akdes Serin Harmanci, 2020, Nature Communications.

Passenger Mutations in More Than 2,500 Cancer Genomes: Overall Molecular Functional Impact and Consequences

Lucas Lochovsky, Jakob Skou Pedersen, Calvin Wing Yiu Chan, 2020, Cell.

EpiSAFARI: sensitive detection of valleys in epigenetic signals for enhancing annotations of functional elements

Vidya Gopalakrishnan, Arif Harmanci, Akdes Serin Harmancı, 2019, bioRxiv.

Detecting and Annotating Rare Variants

A. Harmanci, A. Harmanci, Jiemin Chen, 2019, Encyclopedia of Bioinformatics and Computational Biology.

Retrospective evaluation of whole exome and genome mutation calls in 746 cancer samples

Nuno A. Fonseca, Gary D Bader, Benjamin J. Raphael, 2020, Nature Communications.

Centers for Mendelian Genomics: A decade of facilitating gene discovery

Jeffrey M. Weiss, Ryan L. Collins, Jack M. Fu, 2021, medRxiv.

Integrative pathway enrichment analysis of multivariate omics data

Nuno A. Fonseca, Gary D Bader, Benjamin J. Raphael, 2018, bioRxiv.

REST promotes ETS1‐dependent vascular growth in medulloblastoma

A. Harmanci, Feng Wang, Shavali Shaik, 2021, Molecular oncology.

Analysis of sensitive information leakage in functional genomics signal profiles through genomic deletions

M. Gerstein, A. Harmanci, 2018, Nature Communications.

An integrative ENCODE resource for cancer genomics

Jie Xu, Lucas Lochovsky, Donghoon Lee, 2019, Nature Communications.

MUSIC: identification of enriched regions in ChIP-Seq experiments using a mappability-corrected multiscale signal processing framework

Mark Gerstein, Arif Harmanci, Joel Rozowsky, 2014, Genome Biology.

Passenger mutations in 2500 cancer genomes: Overall molecular functional impact and consequences

Lucas Lochovsky, Jakob Skou Pedersen, Calvin Wing Yiu Chan, 2018, bioRxiv.

VAT: a computational framework to functionally annotate variants in personal genomes within a cloud-computing environment

Mark Gerstein, David Z. Chen, Michael Snyder, 2012, Bioinform..

SVAT: Secure outsourcing of variant annotation and genotype aggregation

A. Harmanci, Xiaoqian Jiang, Miran Kim, 2021, bioRxiv.

HaploHide: A Data Hiding Framework for Privacy Enhanced Sharing of Personal Genetic Data

Xiaoqian Jiang, Degui Zhi, Arif Harmanci, 2019, bioRxiv.

Private information leakage from functional genomics data: Quantification with calibration experiments and reduction via data sanitization protocols

Mark Gerstein, Gamze Gürsoy, J. Seth Strattan, 2018, bioRxiv.

Efficient pairwise RNA structure prediction using probabilistic alignment constraints in Dynalign

Gaurav Sharma, David H. Mathews, Arif Ozgun Harmanci, 2007, BMC Bioinformatics.

Whole-genome sequencing of phenotypically distinct inflammatory breast cancers reveals similar genomic alterations to non-inflammatory breast cancers

M. Gerstein, W. Woodward, L. Pusztai, 2021, Genome medicine.

Perspectives on ENCODE

Xintao Wei, Christopher B. Burge, Jason Liu, 2020, Nature.

Even heterozygous loss of CDKN2A/B greatly accelerates recurrence in aggressive meningioma

Vicky L Brandt, A. Harmanci, A. Harmanci, 2023, Acta Neuropathologica.

scRegulocity: Detection of local RNA velocity patterns in embeddings of single cell RNA-Seq data

A. Harmanci, Akash J. Patel, Xiaobo Zhou, 2021, bioRxiv.

XCVATR: Characterization of Variant Impact on the Embeddings of Single -Cell and Bulk RNA-Sequencing Samples

A. Harmanci, Akash J. Patel, A. Harmanci, 2021, bioRxiv.

CaSpER: Identification, visualization and integrative analysis of CNV events in multiscale resolution using single-cell or bulk RNA sequencing data

Xiaobo Zhou, Arif Harmanci, Akdes Serin Harmancı, 2018, bioRxiv.

CaSpER identifies and visualizes CNV events by integrative analysis of single-cell or bulk RNA-sequencing data

Akdes Serin Harmanci, Arif O. Harmanci, Xiaobo Zhou, 2020, Nature Communications.

Inference of Clonal Copy Number Alterations from RNASequencing Data

A. Harmanci, A. Harmanci, Xiaobo Zhou, 2020 .

iDASH secure genome analysis competition 2018: blockchain genomic data access logging, homomorphic encryption on GWAS, and DNA segment searching

Xiaoqian Jiang, Lucila Ohno-Machado, Lei Wang, 2020, BMC Medical Genomics.

Author Correction: Integrative pathway enrichment analysis of multivariate omics data

Nuno A. Fonseca, Gary D Bader, Benjamin J. Raphael, 2020, Nature Communications.

Comprehensive molecular characterization of mitochondrial genomes in human cancers

Nuno A. Fonseca, Gary D Bader, Benjamin J. Raphael, 2017, bioRxiv.

Author Correction: Pan-cancer analysis of whole genomes

Nuno A. Fonseca, Gary D Bader, Benjamin J. Raphael, 2023, Nature.

TurboFold: Iterative probabilistic estimation of secondary structures for multiple RNA sequences

Gaurav Sharma, David H. Mathews, Arif Ozgun Harmanci, 2011, BMC Bioinformatics.

Multiple approaches converge on three biological subtypes of meningioma and extract new insights from published studies.

A. Harmanci, Akash J. Patel, A. Harmanci, 2022, Science advances.

Sex differences in oncogenic mutational processes

Nuno A. Fonseca, Gary D Bader, Benjamin J. Raphael, 2019, Nature Communications.

Patient-Derived Orthotopic Xenograft (PDOX) Mouse Models of Primary and Recurrent Meningioma

C. Keller, A. Harmanci, Akash J. Patel, 2020, Cancers.

Targeted gene expression profiling predicts meningioma outcomes and radiotherapy responses

Mark W. Youngblood, Jacob S. Young, Sybren L. N. Maas, 2021, Research square.

Racial and Socioeconomic Disparities in Patients With Meningioma: A Retrospective Cohort Study

A. Harmanci, Akash J. Patel, A. Harmanci, 2021, Neurosurgery.

The evolving privacy and security concerns for genomic data analysis and sharing as observed from the iDASH competition

L. Ohno-Machado, Xiaofeng Wang, A. Harmanci, 2022, J. Am. Medical Informatics Assoc..

SCOR: A secure international informatics infrastructure to investigate COVID-19

Fabian Prasser, Hua Xu, Adam Wilcox, 2020, J. Am. Medical Informatics Assoc..

Open Imputation Server provides secure Imputation services with provable genomic privacy

K. Lauter, A. Harmanci, Yongsoo Song, 2021, bioRxiv.

Abstract 1279: Passenger mutation landscape in cancer genomes

Calvin Wing Yiu Chan, Patrick D. McGillivray, M. Gerstein, 2018, Bioinformatics and Systems Biology.

Integrated clinical genomic analysis reveals xenobiotic metabolic genes are downregulated in meningiomas of current smokers

A. Harmanci, A. Harmanci, Eric A. Goethe, 2023, Journal of Neuro-Oncology.

Iterative estimation of structures of multiple RNA homologs: Turbofold

Gaurav Sharma, David H. Mathews, Arif Ozgun Harmanci, 2011, 2011 IEEE International Conference on Acoustics, Speech and Signal Processing (ICASSP).

Toward Turbo Decoding of RNA Secondary Structure

Gaurav Sharma, David H. Mathews, Arif Ozgun Harmanci, 2007, 2007 IEEE International Conference on Acoustics, Speech and Signal Processing - ICASSP '07.

A deep learning system accurately classifies primary and metastatic cancers using passenger mutation patterns

Nuno A. Fonseca, Benjamin J. Raphael, Allison P. Heath, 2020, Nature Communications.

Analyses of non-coding somatic drivers in 2,658 cancer whole genomes

Nuno A. Fonseca, Gary D Bader, Benjamin J. Raphael, 2020, Nature.

Apr 27, 2021 Pathway and network analysis of more than 2500

Nuno A. Fonseca, Gary D Bader, Calvin Wing Yiu Chan, 2020 .

Analysis of sensitive information leakage in functional genomics signal profiles through genomic deletions

Mark Gerstein, Arif Harmanci, M. Gerstein, 2018, Nature Communications.

When Biology Gets Personal: Hidden Challenges of Privacy and Ethics in Biological Big Data

S. Brenner, Erman Ayday, Haixu Tang, 2018, Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing.

Establishing And Maintaining The Blood-Brain Barrier: Epigenetic And Signaling Determinants

N. Tandon, A. Harmanci, P. Dash, 2023, bioRxiv.

Enhancing Fairness in Disease Prediction by Optimizing Multiple Domain Adversarial Networks

A. Harmanci, Hongchang Gao, Kai Zhang, 2023, bioRxiv.

Evaluation of vicinity-based hidden Markov models for genotype imputation

A. Harmanci, Xiaoqian Jiang, Miran Kim, 2021, bioRxiv.

Targeted gene expression profiling predicts meningioma outcomes and radiotherapy responses

Mark W. Youngblood, Jacob S. Young, Sybren L. N. Maas, 2023, Research square.

Comparative Analysis of the Transcriptome across Distant Species

Dmitri D. Pervouchine, Gennifer E. Merrihew, Benjamin W. Booth, 2014, Nature.

Integrative Annotation of Variants from 1092 Humans: Application to Cancer Genomics

Gabor T. Marth, Uday S. Evani, H. Kang, 2013, Science.

Probabilistic structural alignment of RNA sequences

Gaurav Sharma, David H. Mathews, D. Mathews, 2008, 2008 IEEE International Conference on Acoustics, Speech and Signal Processing.

Identifying Unfolding Pathways of G Protein-Coupled Receptor Protein Structures

A. Harmanci, 2008 .

Quantification of private information leakage from phenotype-genotype data: linking attacks

M. Gerstein, A. Harmanci, 2016, Nature Methods.