C. Sahinalp

发表

The structure and evolution of centromeric transition regions within the human genome

D. Haussler, E. Eichler, J. Bailey, 2004, Nature.

Abstract 3000: Pervasive intra-tumour heterogeneity and subclonal selection across cancer types

Yuan Ji, Ville Mustonen, Salem Malikic, 2018, Molecular and Cellular Biology / Genetics.

Protecting Genomic Data Privacy with Probabilistic Modeling

Sean K. Simmons, B. Berger, C. Sahinalp, 2019, Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing.

Enabling Privacy-Preservi ng GWASs in Heterogeneous Human Populations Graphical Abstract Highlights

Sean K. Simmons, B. Berger, C. Sahinalp, 2016 .

Analysis of the androgen receptor-regulated lncRNA landscape identifies a role for ARLNC1 in prostate cancer progression

John T. Wei, S. Dhanasekaran, A. Chinnaiyan, 2018, Nature Genetics.

The Proteogenomic Landscape of Curable Prostate Cancer.

Natalie S. Fox, A. Lapuk, T. H. van der Kwast, 2019, Cancer cell.

The lncRNA landscape of breast cancer reveals a role for DSCAM-AS1 in breast cancer progression

A. Chinnaiyan, C. Collins, R. Backofen, 2016, Nature Communications.

Spatial genomic heterogeneity within localized, multifocal prostate cancer

Faraz Hach, Robert E Denroche, Neil Fleshner, 2015, Nature Genetics.

The long noncoding RNA landscape of neuroendocrine prostate cancer and its clinical implications

Dong Lin, Cenk Sahinalp, Harrison Tsai, 2018, GigaScience.

Widespread and Functional RNA Circularization in Localized Prostate Cancer

Alain Bergeron, Youri Hoogstrate, Natalie S. Fox, 2019, Cell.

Clonal Evolution and Heterogeneity of Osimertinib Acquired Resistance Mechanisms in EGFR Mutant Lung Cancer

Anna L. Brown, Chuong D. Hoang, A. Panchenko, 2020, Cell reports medicine.

Supplement for ” Enabling Privacy Preserving GWAS in Heterogenous Human Populations ”

Sean K. Simmons, B. Berger, C. Sahinalp, 2015 .

Big data in basic and translational cancer research

E. Ruppin, S. Hannenhalli, C. Sahinalp, 2022, Nature Reviews Cancer.

Proteogenomic Analysis Unveils the HLA Class I-Presented Immunopeptidome in Melanoma and EGFR-Mutant Lung Adenocarcinoma

J. Khan, C. Sahinalp, J. Yang, 2021, Molecular & cellular proteomics : MCP.

Ultra High-Dimensional Nonlinear Feature Selection for Big Biological Data

Avishek Saha, Makoto Yamada, Yi Chang, 2016, IEEE Transactions on Knowledge and Data Engineering.

SRRM4 Drives Neuroendocrine Transdifferentiation of Prostate Adenocarcinoma Under Androgen Receptor Pathway Inhibition.

C. Collins, M. Gleave, Nilgun Donmez, 2017, European urology.

Divergent origins and concerted expansion of two segmental duplications on chromosome 16.

E. Eichler, C. Alkan, E. Tuzun, 2001, The Journal of heredity.

Proteogenomic Analysis Unveils the HLA Class I-Presented Immunopeptidome in Melanoma and EGFR-Mutant Lung Adenocarcinoma

C. Sahinalp, J. Yang, U. Guha, 2020, bioRxiv.

Genomic hallmarks of localized, non-indolent prostate cancer

Alain Bergeron, Colin C. Collins, Mathieu Lupien, 2017, Nature.

HIT'nDRIVE: Patient-specific multi-driver gene prioritization for precision oncology.

Thomas Sauerwald, Gholamreza Haffari, Fabio Vandin, 2017, Genome research.

A community effort to create standards for evaluating tumor subclonal reconstruction

Nathan M. Wilson, Joshua M. Stuart, Christopher M. Lalansingh, 2019, Nature Biotechnology.

Mapping the protein interaction network in methicillin-resistant Staphylococcus aureus.

Artem Cherkasov, Phuong Dao, Farhad Hormozdiari, 2011, Journal of proteome research.

BAP1 haploinsufficiency predicts a distinct immunogenic class of malignant peritoneal mesothelioma

Yuzhuo, Faraz Hach, S. C. Sahinalp, 2019, Genome Medicine.

CYP2C8, CYP2C9 and CYP2C19 characterization using Next Generation Sequencing and Haplotype Analysis: A GeT-RM Collaborative Project.

Neil A. Miller, A. Halpern, D. Nickerson, 2022, The Journal of molecular diagnostics : JMD.

A community effort to create standards for evaluating tumor subclonal reconstruction

Nathan M. Wilson, Ville Mustonen, Salem Malikic, 2019, Nature Biotechnology.

Analysis of the androgen receptor–regulated lncRNA landscape identifies a role for ARLNC1 in prostate cancer progression

John T. Wei, S. Dhanasekaran, A. Chinnaiyan, 2018, Nature Genetics.

Melanoma clonal subline analysis uncovers heterogeneity-driven immunotherapy resistance mechanisms

Howard H. Yang, S. Hannenhalli, C. Sahinalp, 2023, bioRxiv.

Using centroid based nearest neighbor classifier in predicting small molecule activity

Farhad Hormozdiari, Cenk Sahinalp, F. Hormozdiari, 2009 .

CSI-Microbes: Identifying cell-type specific intracellular microbes from single-cell RNA-seq data

Mark D. M. Leiserson, A. Schäffer, E. Ruppin, 2021 .

Combinatorial Algorithms for Strain Level Metagenomic Microbial Detection and Quantification

Yuzhen Ye, Kaiyuan Zhu, Cenk Sahinalp, 2020 .

PRESAGE: PRivacy-preserving gEnetic testing via SoftwAre Guard Extension

Md Momin Al Aziz, Md. Nazmus Sadat, K. Lauter, 2017, BMC Medical Genomics.