Publications
Below is the list of our publications. You can sort the table by the Year column if you'd like to view by publication date.
These publication list is retrieved automatically from my Google Scholar profile. There is a possibility that Google's automated compilation algorithm falsely detects someone else's paper as mine (20240808: I don't see any false items at the moment).
| Title | Cited by | Year |
|---|---|---|
| Functional significance of macrophage-derived exosomes in inflammation and pain MK McDonald, Y Tian, RA Qureshi, M Gormley, A Ertel, R Gao, EA Lopez, ...PAIN® 155 (8), 1527-1539, 2014 | 324 | 2014 |
| MicroRNA modulation in complex regional pain syndrome IA Orlova, GM Alexander, RA Qureshi, A Sacan, A Graziano, JE Barrett, ...Journal of translational medicine 9, 1-11, 2011 | 183 | 2011 |
| CellTrack: an open-source software for cell tracking and motility analysis A Sacan, H Ferhatosmanoglu, H CoskunBioinformatics 24 (14), 1647-1649, 2008 | 138 | 2008 |
| Comparing the yeast retrograde response and NF‐κB stress responses: implications for aging V Srinivasan, A Kriete, A Sacan, S Michal JazwinskiAging cell 9 (6), 933-941, 2010 | 82 | 2010 |
| Automated wound identification system based on image segmentation and artificial neural networks B Song, A Sacan2012 IEEE International Conference on bioinformatics and biomedicine, 1-4, 2012 | 79 | 2012 |
| Applications and limitations of in silico models in drug discovery A Sacan, S Ekins, S KortagereBioinformatics and drug discovery, 87-124, 2012 | 59 | 2012 |
| Analgesic response to intravenous ketamine is linked to a circulating microRNA signature in female patients with complex regional pain syndrome SR Douglas, BB Shenoda, RA Qureshi, A Sacan, GM Alexander, ...The Journal of Pain 16 (9), 814-824, 2015 | 52 | 2015 |
| A novel method for the normalization of microRNA RT-PCR data R Qureshi, A SacanBMC medical genomics 6, 1-13, 2013 | 51 | 2013 |
| Regulation of proinflammatory genes by the circulating microRNA hsa-miR-939 MK McDonald, S Ramanathan, A Touati, Y Zhou, RU Thanawala, ...Scientific reports 6 (1), 30976, 2016 | 45 | 2016 |
| Exosome microRNA signatures in patients with complex regional pain syndrome undergoing plasma exchange S Ramanathan, SR Douglas, GM Alexander, BB Shenoda, JE Barrett, ...Journal of translational medicine 17, 1-12, 2019 | 44 | 2019 |
| Inflammation potentiates miR-939 expression and packaging into small extracellular vesicles S Ramanathan, BB Shenoda, Z Lin, GM Alexander, A Huppert, A Sacan, ...Journal of extracellular vesicles 8 (1), 1650595, 2019 | 41 | 2019 |
| LFM-Pro: a tool for detecting significant local structural sites in proteins A Sacan, O Ozturk, H Ferhatosmanoglu, Y WangBioinformatics 23 (6), 709-716, 2007 | 39 | 2007 |
| Circulating microRNA signatures in rodent models of pain RA Qureshi, Y Tian, MK McDonald, KE Capasso, SR Douglas, R Gao, ...Molecular neurobiology 53, 3416-3427, 2016 | 38 | 2016 |
| Integrated search and alignment of protein structures A Sacan, IH Toroslu, H FerhatosmanogluBioinformatics 24 (24), 2872-2879, 2008 | 34 | 2008 |
| Xist attenuates acute inflammatory response by female cells BB Shenoda, S Ramanathan, R Gupta, Y Tian, R Jean-Toussaint, ...Cellular and Molecular Life Sciences 78, 299-316, 2021 | 31 | 2021 |
| Effect of histone deacetylase inhibitor JNJ-26481585 in pain KE Capasso, MT Manners, RA Quershi, Y Tian, R Gao, H Hu, JE Barrett, ...Journal of molecular neuroscience 55, 570-578, 2015 | 31 | 2015 |
| Weighted set enrichment of gene expression data R Qureshi, A SacanBMC systems biology 7, 1-11, 2013 | 30 | 2013 |
| Proteome characterization of small extracellular vesicles from spared nerve injury model of neuropathic pain R Jean-Toussaint, Y Tian, AD Chaudhuri, NJ Haughey, A Sacan, SK AjitJournal of proteomics 211, 103540, 2020 | 27 | 2020 |
| Therapeutic and prophylactic effects of macrophage-derived small extracellular vesicles in the attenuation of inflammatory pain R Jean-Toussaint, Z Lin, Y Tian, R Gupta, R Pande, X Luo, H Hu, A Sacan, ...Brain, behavior, and immunity 94, 210-224, 2021 | 23 | 2021 |
| Data simulation and regulatory network reconstruction from time-series microarray data using stepwise multiple linear regression Y Zhou, R Qureshi, A SacanNetwork Modeling Analysis in Health Informatics and Bioinformatics 1, 3-17, 2012 | 20 | 2012 |
| Smolign: a spatial motifs-based protein multiple structural alignment method H Sun, A Sacan, H Ferhatosmanoglu, Y WangIEEE/ACM Transactions on Computational Biology and Bioinformatics 9 (1), 249-261, 2011 | 20 | 2011 |
| Differential RNA packaging into small extracellular vesicles by neurons and astrocytes X Luo, R Jean-Toussaint, A Sacan, SK AjitCell Communication and Signaling 19, 1-15, 2021 | 19 | 2021 |
| Protein surface representation and analysis by dimension reduction H Yang, R Qureshi, A SacanProteome Science 10, 1-13, 2012 | 18 | 2012 |
| Computer and Information Sciences: Proceedings of the 25th International Symposium on Computer and Information Sciences E Gelenbe, R Lent, G Sakellari, A Sacan, H Toroslu, A YaziciSpringer Science & Business Media, 2010 | 15 | 2010 |
| Comparison of feature-based and image registration-based retrieval of image data using multidimensional data access methods S Arslan, A Yazıcı, A Sacan, IH Toroslu, E AcarData & knowledge engineering 86, 124-145, 2013 | 12 | 2013 |
| Content based searching of gene expression databases using binary fingerprints of differential expression profiles F Bell, A Sacan2012 7th International Symposium on Health Informatics and Bioinformatics …, 2012 | 12 | 2012 |
| Approximate similarity search in genomic sequence databases using landmark-guided embedding A Sacan, IH TorosluFirst International Workshop on Similarity Search and Applications (sisap …, 2008 | 12 | 2008 |
| Investigation of data-driven optical neuromonitoring approach during general anesthesia with sevoflurane G Hernandez-Meza, M Izzetoglu, A Sacan, M Green, K IzzetogluNeurophotonics 4 (4), 041408-041408, 2017 | 11 | 2017 |
| UniAlign: protein structure alignment meets evolution C Zhao, A SacanBioinformatics 31 (19), 3139-3146, 2015 | 11 | 2015 |
| Sequence alignment reveals possible MAPK docking motifs on HIV proteins P Evans, A Sacan, L Ungar, A TozerenPLoS One 5 (1), e8942, 2010 | 11 | 2010 |
| Secondary bitmap indexes with vertical and horizontal partitioning G Canahuate, T Apaydin, A Sacan, H FerhatosmanogluProceedings of the 12th International Conference on Extending Database …, 2009 | 11 | 2009 |
| Circulating microRNAs from the mouse tibia fracture model reflect the signature from patients with complex regional pain syndrome JR Wickman, X Luo, W Li, R Jean-Toussaint, P Sahbaie, A Sacan, ...Pain reports 6 (3), e950, 2021 | 9 | 2021 |
| Prediction of HIV-1 and human protein interactions based on a novel evolution-aware structure alignment method C Zhao, A SacanProceedings of the International Conference on Bioinformatics …, 2013 | 8 | 2013 |
| Amino acid substitution matrices based on 4-body Delaunay contact profiles A Sacan, IH Toroslu2007 IEEE 7th International Symposium on BioInformatics and BioEngineering …, 2007 | 8 | 2007 |
| Hiv1-human protein-protein interaction prediction based on interface architecture similarity C Zhao, Y Zang, W Quan, X Hu, A Sacan2017 IEEE International Conference on Bioinformatics and Biomedicine (BIBM …, 2017 | 6 | 2017 |
| MicroarrayDesigner: an online search tool and repository for near-optimal microarray experimental designs A Sacan, N Ferhatosmanoglu, H FerhatosmanogluBMC bioinformatics 10, 1-6, 2009 | 5 | 2009 |
| Reconstruction of gene regulatory networks by stepwise multiple linear regression from time-series microarray data Y Zhou, R Qureshi, A Sacan2012 7th International Symposium on Health Informatics and Bioinformatics, 76-81, 2012 | 4 | 2012 |
| Comparison of multidimensional data access methods for feature-based image retrieval S Arslan, A Saçan, E Açar, IH Toroslu, A Yazıcı2010 20th International Conference on Pattern Recognition, 3260-3263, 2010 | 4 | 2010 |
| Methods of diagnosing and treating chronic pain S Ajit, A Sacan, G Alexander, RJ Schwartzman, M McDonaldUS Patent App. 14/783,766, 2016 | 3 | 2016 |
| Meta-analysis of protein structural alignment J Havrilla, A Sacan2012 IEEE International Conference on Bioinformatics and Biomedicine …, 2012 | 3 | 2012 |
| Online education experiences: information technologies certificate program at METU E Yükseltürk, A Yazici, A Sacan, Ö KayaProceedings of the fifteenth annual conference on Innovation and technology …, 2010 | 3 | 2010 |
| Development of parallel forms of a brief smell identification test useful for longitudinal testing ST Moein, A Sacan, K Pourrezaei, CH Yan, JH Turner, R Sharetts, ...Behavior Research Methods 56 (3), 1449-1458, 2024 | 2 | 2024 |
| Functional significance of macrophage-derived exosomes in inflammation and pain (vol 155, pg 1527, 2014) MK McDonald, Y Tian, RA Qureshi, M Gormley, A Ertel, R Gao, AE Lopez, ...Pain 163 (2), E383-E384, 2022 | 2 | 2022 |
| Analysis of paired miRNA-mRNA microarray expression data using a stepwise multiple linear regression model Y Zhou, R Qureshi, A SacanBioinformatics Research and Applications: 13th International Symposium …, 2017 | 2 | 2017 |
| A weighted hypergeometric statistic for the enrichment of gene sets R Qureshi, A Sacan2012 IEEE International Conference on Bioinformatics and Biomedicine, 1-6, 2012 | 2 | 2012 |
| Protein structure visualization by dimension reduction and texture mapping H Yang, R Qureshi, A Sacan2011 IEEE International Conference on Bioinformatics and Biomedicine, 437-442, 2011 | 2 | 2011 |
| Gene signature reveals decreased SOX10-dependent transcripts in malignant cells from immune checkpoint inhibitor-resistant cutaneous melanomas TJ Purwin, S Caksa, A Sacan, C Capparelli, AE AplinIscience 26 (9), 2023 | 1 | 2023 |
| Small Extracellular Vesicles From Spared Nerve Injury Model and Sham Control Mice Differentially Regulate Gene Expression in Primary Microglia X Luo, R Jean-Toussaint, Y Tian, SV Balashov, A Sacan, SK AjitThe journal of pain 24 (9), 1570-1581, 2023 | 1 | 2023 |
| BioDB: Integration of biological knowledgebases J Gerhart, A Sacan2011 IEEE International Conference on Bioinformatics and Biomedicine …, 2011 | 1 | 2011 |
| Distance-based indexing of residue contacts for protein structure retrieval and alignment A Sacan, IH Toroslu, H Ferhatosmanoglu2008 8th IEEE International Conference on BioInformatics and BioEngineering, 1-7, 2008 | 1 | 2008 |
| Comparing the yeast retrograde response and NF-jB stress responses: implications for aging V Srinivasan, A Kriete, A Sacan, SM JazwinskiAging Cell 9 (6), 933-9, 0 | 1 | |
| GPC2 directed CAR T cells are efficacious against fusion-positive and fusion-negative rhabdomyosarcomas R Shraim, PM Schuerch, AM Giudice, KL Conkrite, AK Weiner, ...Cancer Research 84 (6_Supplement), 1090-1090, 2024 | 2024 | |
| Inflammatory pain resolution by mouse serum-derived small extracellular vesicles Z Lin, X Luo, JR Wickman, D Reddy, R Pande, Y Tian, V Triana, J Lee, ...bioRxiv, 2024 | 2024 | |
| Locus folding mechanisms determine modes of antigen receptor gene assembly BM Allyn, KE Hayer, C Oyeniran, V Nganga, K Lee, B Mishra, A Sacan, ...Journal of Experimental Medicine 221 (2), e20230985, 2024 | 2024 | |
| Environmentally-mediated selection parallels population divergence across a chimpanzee subspecies contact zone MW Mitchell, W Alexander, DV Mitchell, AH Freedman, J Dordel, ...bioRxiv, 2024.07. 26.605171, 2024 | 2024 | |
| IMMUNOTAR-Integrative prioritization of cell surface targets for cancer immunotherapy R Shraim, B Mooney, KL Conkrite, AK Weiner, GB Morin, PH Sorensen, ...bioRxiv, 2024.06. 04.597422, 2024 | 2024 | |
| Immune Regulation By Small Extracellular Vesicles In Attenuating Inflammatory Pain X Luo, A Sacan, S AjitThe Journal of Pain 24 (4), 14, 2023 | 2023 | |
| Abstract A009: Proteogenomic prioritization of immunotherapeutic targets in rhabdomyosarcoma nominate MEGF10 for preclinical development R Shraim, AK Weiner, KL Conkrite, AB Radaoui, JM Maris, YP Mosse, ...Clinical Cancer Research 28 (18_Supplement), A009-A009, 2022 | 2022 | |
| Small extracellular vesicles induced gene expression changes in microglia X Luo, R Jean‐Toussaint, A Sacan, S AjitThe FASEB Journal 36, 2022 | 2022 | |
| 15 Reconstruction of Regulatory Networks from Microarray Data Y Zhou, R Qureshi, F Bell, A SacanMicroarray Image and Data Analysis: Theory and Practice, 401, 2018 | 2018 | |
| Exosome mediated intercellular communication in chronic pain R Jean-Toussaint, M McDonald, A Sacan, S AjitJOURNAL OF NEUROIMMUNE PHARMACOLOGY 12, S30-S30, 2017 | 2017 | |
| Unfolding the Protein Surface for Pattern Matching H Yang, C Zhao, A SacanBioinformatics Research and Applications: 13th International Symposium …, 2017 | 2017 | |
| Content-based search of gene expression databases using binary fingerprints of differential expression profiles F Bell, A SacanNetwork Modeling Analysis in Health Informatics and Bioinformatics 4, 1-10, 2015 | 2015 | |
| Methods of Diagnosing Neuropathic Pain S Ajit, A Sacan, G Alexander, RJ SchwartzmanUS Patent App. 14/117,735, 2014 | 2014 | |
| PDBCirclePlot: A Novel Visualization Method for Protein Structures F Bell, C Zhao, A SacanarXiv preprint arXiv:1402.5323, 2014 | 2014 | |
| Similarity search in protein sequence databases using metric access methods A Cetintas, A Sacan, İH Toroslu | 2013 | |
| Proceedings of the 25th International Conference on Scientific and Statistical Database Management A Szalay, T Budavari, M Balazinska, A Meliou, A SacanACM, 2013 | 2013 | |
| SSDBM 2013: proceedings of the 25th International Conference on Scientific and Statistical Database Management: July 29-31, 2013, Baltimore, Maryland M Balazinska, AS Szalay, T Budavari, A Meliou, A SaçanACM, 2013 | 2013 | |
| Proteomics & Bioinformatics J Havrilla, A SaçanJ Proteomics 6 (8), 171-175, 2013 | 2013 | |
| Letting all have a say: A novel method for microRNA RT-PCR normalization R Qureshi, A SacanProceedings of the International Conference on Bioinformatics …, 2011 | 2011 | |
| 2009 24th International Symposium on Computer and Information Sciences, ISCIS 2009: Preface FT Yarman Vural, İH Toroslu, T Can, P Karagöz, A Saçan | 2009 | |
| 2009 24th International Symposium on Computer and Information Sciences T Can, P Senkul, A SaçanMiddle East, 2009 | 2009 | |
| 2009 24th International Symposium on Computer and Information Sciences, ISCIS 2009: Preface FY Vural, A Yazici, H Toroslu, T Can, P Şenkul, A Saçan2009 24th International Symposium on Computer and Information Sciences …, 2009 | 2009 | |
| Similarity search and analysis of protein sequences and structures: A residue contacts based approach A SaçanMiddle East Technical University, 2008 | 2008 | |
| Automated data discovery in similarity score queries F Altiparmak, AS Tosun, H Ferhatosmanoglu, A SacanDatabase Systems for Advanced Applications: 13th International Conference …, 2008 | 2008 | |
| Prediction of Cysteine Bridges using Sequence Alignments A Sacan | 2004 | |
| JNJ-26481585 KE Capasso, MT Manners, RA Quershi, Y Tian, R Gao, H Hu, JE Barrett, ... | ||
| Original Reports SR Douglas, BB Shenoda, RA Qureshi, A Sacan, GM Alexander, ... | ||
| Tmaptool3D–T1ρ processing tool C Bayas, G Pednekar, G Krishnamoorthy, A Sacan | ||
| HI-BI-BI 2012 Program Committee A Sacan, A Qabaja, A Policriti, B Dasgupta, C Zhang, CK Kwoh, CY Chen, ... |