Publications: Ion Mandoiu

• 2023

• CD8+ T Cell-Dependent Antitumor Activity In Vivo of a Mass Spectrometry-Identified Neoepitope despite Undetectable CD8+ Immunogenicity In Vitro.
  Gillig MA, Brennick CA, George MM, Balsbaugh JL, Shcheglova TV, Mandoiu II, Rosales T, Baker BM, Srivastava PK, Karandikar SH
  Journal of immunology (Baltimore, Md. : 1950) (2023) 211(12):1783-1791 PMC8210748 10.4049/jimmunol.2300356
• GeNeo: A Bioinformatics Toolbox for Genomics-Guided Neoepitope Prediction.
  Al Seesi S, Al-Okaily A, Shcheglova TV, Sherafat E, Alqahtani FH, Hagymasi AT, Kaur A, Srivastava PK, Măndoiu II
  Journal of computational biology : a journal of computational molecular cell biology (2023) 30(4):538-551 10.1089/cmb.2022.0491
• Special Issue: 11th International Computational Advances in Bio and Medical Sciences (ICCABS 2021).
  Bansal MS, Măndoiu II, Moussa M, Patterson M, Rajasekaran S, Skums P, Zelikovsky A
  Journal of computational biology : a journal of computational molecular cell biology (2023) 30(4):363-365 10.1089/cmb.2023.29085.msb

• 2022

• Transcriptomic Responses of Upon Treatments of -Cinnamaldehyde, Carvacrol, and Eugenol.
  Ranjitkar S, Duan JE, Srirattana K, Alqahtani F, Tulman ER, Mandoiu I, Venkitanarayanan K, Tian X
  Frontiers in microbiology (2022) 13:888433 PMC6977290 10.1186/s12864-020-6460-0

• 2021

• Special Issue: 10th International Computational Advances in Bio and Medical Sciences (ICCABS 2020).
  Jha SK, MĂndoiu I, Rajasekaran S, Skums P, Zelikovsky A
  Journal of computational biology : a journal of computational molecular cell biology (2021) 28(11):1033-1034 10.1089/cmb.2021.29048.skj
• Reversion analysis reveals the in vivo immunogenicity of a poorly MHC I-binding cancer neoepitope.
  Ebrahimi-Nik H, Moussa M, Englander RP, Singhaviranon S, Michaux J, Pak H, Miyadera H, Corwin WL, Keller GLJ, Hagymasi AT, Shcheglova TV, Coukos G, Baker BM, Mandoiu II, Bassani-Sternberg M, Srivastava PK
  Nature communications (2021) 12(1):6423 PMC8571378 10.1038/s41467-021-26646-5
• Pipeline for Analyzing Activity of Metabolic Pathways in Planktonic Communities Using Metatranscriptomic Data.
  Rondel FM, Hosseini R, Sahoo B, Knyazev S, Mandric I, Stewart F, Măndoiu II, Pasaniuc B, Porozov Y, Zelikovsky A
  Journal of computational biology : a journal of computational molecular cell biology (2021) 28(8):842-855 PMC8575064 10.1089/cmb.2021.0053
• TNet: Transmission Network Inference Using Within-Host Strain Diversity and its Application to Geographical Tracking of COVID-19 Spread.
  Dhar S, Zhang C, Mandoiu II, Bansal MS
  IEEE/ACM transactions on computational biology and bioinformatics (2021) 19(1):230-242 PMC5850600 10.1109/TCBB.2021.3096455
• SC1: A Tool for Interactive Web-Based Single-Cell RNA-Seq Data Analysis.
  Moussa M, Măndoiu II
  Journal of computational biology : a journal of computational molecular cell biology (2021) 28(8):820-841 10.1089/cmb.2021.0051
• TreeFix-TP: Phylogenetic Error-Correction for Infectious Disease Transmission Network Inference.
  Sledzieski S, Zhang C, Mandoiu I, Bansal MS
  Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing (2021) 26:119-130
• Direct reprogramming of oligodendrocyte precursor cells into GABAergic inhibitory neurons by a single homeodomain transcription factor Dlx2.
  Boshans LL, Soh H, Wood WM, Nolan TM, Mandoiu II, Yanagawa Y, Tzingounis AV, Nishiyama A
  Scientific reports (2021) 11(1):3552 PMC7878775 10.1038/s41598-021-82931-9
• Special Issue: 9th International Computational Advances in Bio and Medical Sciences (ICCABS 2019).
  Mandoiu I, Murali TM, Narasimhan G, Rajasekaran S, Skums P, Zelikovsky A
  Journal of computational biology : a journal of computational molecular cell biology (2021) 28(2):115-116 10.1089/cmb.2021.29034.im
• Complete mitochondrial genome of the water vole, (Cricetidae, Rodentia).
  Alqahtani F, Duckett D, Pirro S, Mandoiu II
  Mitochondrial DNA. Part B, Resources (2021) 5(3):2498-2499 PMC7782294 10.1080/23802359.2020.1780640

• 2020

• Semi-supervised learning for somatic variant calling and peptide identification in personalized cancer immunotherapy.
  Sherafat E, Force J, Măndoiu II
  BMC bioinformatics (2020) 21(Suppl 18):498 PMC7772914 10.1186/s12859-020-03813-x
• An unbiased approach to defining bona fide cancer neoepitopes that elicit immune-mediated cancer rejection.
  Brennick CA, George MM, Moussa MM, Hagymasi AT, Seesi SA, Shcheglova TV, Englander RP, Keller GL, Balsbaugh JL, Baker BM, Schietinger A, Mandoiu II, Srivastava PK
  The Journal of clinical investigation (2020) 131(3): PMC7843235 10.1172/JCI142823
• Sympathetic nervous tone limits the development of myeloid-derived suppressor cells.
  Nevin JT, Moussa M, Corwin WL, Mandoiu II, Srivastava PK
  Science immunology (2020) 5(51): 10.1126/sciimmunol.aay9368
• Eleven grand challenges in single-cell data science.
  Lähnemann D, Köster J, Szczurek E, McCarthy DJ, Hicks SC, Robinson MD, Vallejos CA, Campbell KR, Beerenwinkel N, Mahfouz A, Pinello L, Skums P, Stamatakis A, Attolini CS, Aparicio S, Baaijens J, Balvert M, Barbanson B, Cappuccio A, Corleone G, Dutilh BE, Florescu M, Guryev V, Holmer R, Jahn K, Lobo TJ, Keizer EM, Khatri I, Kielbasa SM, Korbel JO, Kozlov AM, Kuo TH, Lelieveldt BPF, Mandoiu II, Marioni JC, Marschall T, Mölder F, Niknejad A, Raczkowski L, Reinders M, Ridder J, Saliba AE, Somarakis A, Stegle O, Theis FJ, Yang H, Zelikovsky A, McHardy AC, Raphael BJ, Shah SP, Schönhuth A
  Genome biology (2020) 21(1):31 PMC7007675 10.1186/s13059-020-1926-6

• 2019

• Mass spectrometry driven exploration reveals nuances of neoepitope-driven tumor rejection.
  Ebrahimi-Nik H, Michaux J, Corwin WL, Keller GL, Shcheglova T, Pak H, Coukos G, Baker BM, Mandoiu II, Bassani-Sternberg M, Srivastava PK
  JCI insight (2019) 5: PMC6675551 10.1172/jci.insight.129152
• Methylome Dynamics of Bovine Gametes and Early Embryos.
  Duan JE, Jiang ZC, Alqahtani F, Mandoiu I, Dong H, Zheng X, Marjani SL, Chen J, Tian XC
  Frontiers in genetics (2019) 10:512 PMC6546829 10.3389/fgene.2019.00512
• CD91 on dendritic cells governs immunosurveillance of nascent, emerging tumors.
  Sedlacek AL, Younker TP, Zhou YJ, Borghesi L, Shcheglova T, Mandoiu II, Binder RJ
  JCI insight (2019) 4(7): PMC6483634 10.1172/jci.insight.127239
• Locality Sensitive Imputation for Single Cell RNA-Seq Data.
  Moussa M, Măndoiu II
  Journal of computational biology : a journal of computational molecular cell biology (2019) 26(8):822-835 PMC6703247 10.1089/cmb.2018.0236

• 2018

• Dosage Compensation and Gene Expression of the X Chromosome in Sheep.
  Duan JE, Flock K, Jue N, Zhang M, Jones A, Seesi SA, Mandoiu I, Pillai S, Hoffman M, O'Neill R, Zinn S, Govoni K, Reed S, Jiang H, Jiang ZC, Tian XC
  G3 (Bethesda) (2018) 9(1):305-314 (PMC6325915) 10.1534/g3.118.200815
• CircMarker: a fast and accurate algorithm for circular RNA detection.
  Li X, Chu C, Pei J, Măndoiu I, Wu Y
  BMC Genomics (2018) 19(Suppl 6):572 (PMC6101086) 10.1186/s12864-018-4926-0
• Single cell RNA-seq data clustering using TF-IDF based methods.
  Moussa M, Măndoiu II
  BMC Genomics (2018) 19(Suppl 6):569 (PMC6101073) 10.1186/s12864-018-4922-4
• Effects of maternal nutrition on the expression of genomic imprinted genes in ovine fetuses.
  Duan JE, Zhang M, Flock K, Seesi SA, Mandoiu I, Jones A, Johnson E, Pillai S, Hoffman M, McFadden K, Jiang H, Reed S, Govoni K, Zinn S, Jiang Z, Tian XC
  Epigenetics (2018) 13(8):793-807 (PMC6224220) 10.1080/15592294.2018.1503489
• CD11c MHCII GM-CSF-bone marrow-derived dendritic cells act as antigen donor cells and as antigen presenting cells in neoepitope-elicited tumor immunity against a mouse fibrosarcoma.
  Ebrahimi-Nik H, Corwin WL, Shcheglova T, Das Mohapatra A, Mandoiu II, Srivastava PK
  Cancer Immunol. Immunother. (2018) 67(9):1449-1459 (PMC6132860) 10.1007/s00262-018-2202-4
• Draft Genome Sequence of DUP 13076, Which Exhibits Potent Antipathogenic Effects against Serovars Enteritidis, Typhimurium, and Heidelberg.
  Muyyarikkandy MS, Alqahtani FH, Mandoiu I, Amalaradjou MA
  Genome Announc (2018) 6(7): (PMC5814482) 10.1128/genomeA.00065-18
• Draft Genome Sequence of NRRL B-442, a Potential Probiotic Strain.
  Muyyarikkandy MS, Alqahtani FH, Mandoiu I, Amalaradjou MA
  Genome Announc (2018) 6(7): (PMC5814505) 10.1128/genomeA.00046-18

• 2017

• Identification of cancer-specific motifs in mimotope profiles of serum antibody repertoire.
  Gerasimov E, Zelikovsky A, Măndoiu I, Ionov Y
  BMC Bioinformatics (2017) 18(Suppl 8):244 (PMC5471937)
• Fast bootstrapping-based estimation of confidence intervals of expression levels and differential expression from RNA-Seq data.
  Mandric I, Temate-Tiagueu Y, Shcheglova T, Al Seesi S, Zelikovsky A, Mandoiu II
  Bioinformatics (2017) 33(20):3302-3304
• Tumor Control Index as a new tool to assess tumor growth in experimental animals.
  Corwin WL, Ebrahimi-Nik H, Floyd SM, Tavousi P, Mandoiu II, Srivastava PK
  J. Immunol. Methods (2017) 445:71-76

• 2016

• Network-based bioinformatics analysis of spatio-temporal RNA-Seq data reveals transcriptional programs underpinning normal and aberrant retinal development.
  Karunakaran DK, Al Seesi S, Banday AR, Baumgartner M, Olthof A, Lemoine C, Măndoiu II, Kanadia RN
  BMC Genomics (2016) 17 Suppl 5:495 (PMC5009874)
• Inferring metabolic pathway activity levels from RNA-Seq data.
  Temate-Tiagueu Y, Seesi SA, Mathew M, Mandric I, Rodriguez A, Bean K, Cheng Q, Glebova O, Măndoiu I, Lopanik NB, Zelikovsky A
  BMC Genomics (2016) 17 Suppl 5:542 (PMC5009525)

• 2015

• This special issue includes a selection of papers presented at the 2nd IEEE International Conference. Introduction.
  Mandoiu I, Pop M, Rajasekaran S, Spouge JL
  Int J Bioinform Res Appl (2015) 10(4-5):341-4
• Metabolic pathway predictions for metabolomics: a molecular structure matching approach.
  Hamdalla MA, Rajasekaran S, Grant DF, Măndoiu II
  J Chem Inf Model (2015) 55(3):709-18

• 2014

• Minor splicing snRNAs are enriched in the developing mouse CNS and are crucial for survival of differentiating retinal neurons.
  Baumgartner M, Lemoine C, Al Seesi S, Karunakaran DK, Sturrock N, Banday AR, Kilcollins AM, Mandoiu I, Kanadia RN
  Dev Neurobiol (2014) 75(9):895-907
• Replication-dependent histone genes are actively transcribed in differentiating and aging retinal neurons.
  Banday AR, Baumgartner M, Al Seesi S, Karunakaran DK, Venkatesh A, Congdon S, Lemoine C, Kilcollins AM, Mandoiu I, Punzo C, Kanadia RN
  Cell Cycle (2014) 13(16):2526-41 (PMC4614993)
• Bootstrap-based differential gene expression analysis for RNA-Seq data with and without replicates.
  Al Seesi S, Tiagueu YT, Zelikovsky A, Măndoiu II
  BMC Genomics (2014) 15 Suppl 8:S2 (PMC4248812)
• Feature selection and classifier performance on diverse bio- logical datasets.
  Hemphill E, Lindsay J, Lee C, Măndoiu II, Nelson CE
  BMC Bioinformatics (2014) 15 Suppl 1:S4 (PMC4248652)
• Computational framework for next-generation sequencing of heterogeneous viral populations using combinatorial pooling.
  Skums P, Artyomenko A, Glebova O, Ramachandran S, Mandoiu I, Campo DS, Dimitrova Z, Zelikovsky A, Khudyakov Y
  Bioinformatics (2014) 31(5):682-90
• ILP-based maximum likelihood genome scaffolding.
  Lindsay J, Salooti H, Măndoiu I, Zelikovsky A
  BMC Bioinformatics (2014) 15 Suppl 9:S9 (PMC4168704)
• Genomic and bioinformatic profiling of mutational neoepitopes reveals new rules to predict anticancer immunogenicity.
  Duan F, Duitama J, Al Seesi S, Ayres CM, Corcelli SA, Pawashe AP, Blanchard T, McMahon D, Sidney J, Sette A, Baker BM, Mandoiu II, Srivastava PK
  J. Exp. Med. (2014) 211(11):2231-48 (PMC4203949)
• Guest editors' introduction to the special section on bioinformatics research and applications.
  Mandoiu II, Wang J, Zelikovsky A
  IEEE/ACM Trans Comput Biol Bioinform (2014) 10(6):1345-6

• 2013

• Neuraminidase subtyping of avian influenza viruses with PrimerHunter-designed primers and quadruplicate primer pools.
  Huang Y, Khan MI, Khan M, Măndoiu I, Măndoiu II
  PLoS ONE (2013) 8(11):e81842 (PMC3843705)
• In silico enzymatic synthesis of a 400,000 compound biochemical database for nontargeted metabolomics.
  Menikarachchi LC, Hill DW, Hamdalla MA, Mandoiu II, Grant DF
  J Chem Inf Model (2013) 53(9):2483-92 (PMC3819714)
• Reconstruction of viral population structure from next-generation sequencing data using multicommodity flows.
  Skums P, Mancuso N, Artyomenko A, Tork B, Mandoiu I, Khudyakov Y, Zelikovsky A
  BMC Bioinformatics (2013) 14 Suppl 9:S2 (PMC3698000)
• BioSM: metabolomics tool for identifying endogenous mammalian biochemical structures in chemical structure space.
  Hamdalla MA, Mandoiu II, Hill DW, Rajasekaran S, Grant DF
  J Chem Inf Model (2013) 53(3):601-12 (PMC3866231)

• 2012

• Improved transcriptome quantification and reconstruction from RNA-Seq reads using partial annotations.
  Mangul S, Caciula A, Glebova O, Mandoiu I, Zelikovsky A
  In Silico Biol. (Gedrukt) (2012) 11(5-6):251-61
• Reconstructing viral quasispecies from NGS amplicon reads.
  Mancuso N, Tork B, Skums P, Ganova-Raeva L, Măndoiu I, Zelikovsky A
  In Silico Biol. (Gedrukt) (2012) 11(5-6):237-49
• Guest editors' introduction.
  Chen J, Măndoiu I, Sunderraman R, Wang J, Zelikovsky A
  BMC Bioinformatics (2012) 13 Suppl 1:S1 (PMC3382435)
• Area under the curve as a tool to measure kinetics of tumor growth in experimental animals.
  Duan F, Simeone S, Wu R, Grady J, Mandoiu I, Srivastava PK
  J. Immunol. Methods (2012) 382(1-2):224-8
• Towards accurate detection and genotyping of expressed variants from whole transcriptome sequencing data.
  Duitama J, Srivastava PK, Măndoiu II
  BMC Genomics (2012) 13 Suppl 2:S6 (PMC3394419)
• The use of graph matching algorithms to identify biochemical substructures in synthetic chemical compounds: Application to metabolomics.
  Hamdalla M, Grant D, Mandoiu I, Hill D, Rajasekaran S, Ammar R
  IEEE Int Conf Comput Adv Bio Med Sci (2012) 2012: (PMC4593623)

• 2011

• Inferring viral quasispecies spectra from 454 pyrosequencing reads.
  Astrovskaya I, Tork B, Mangul S, Westbrooks K, Măndoiu I, Balfe P, Zelikovsky A
  BMC Bioinformatics (2011) 12 Suppl 6:S1 (PMC3194189)
• Inferring ethnicity from mitochondrial DNA sequence.
  Lee C, Măndoiu II, Nelson CE
  BMC Proc (2011) 5 Suppl 2:S11 (PMC3090759)
• Estimation of alternative splicing isoform frequencies from RNA-Seq data.
  Nicolae M, Mangul S, Măndoiu II, Zelikovsky A
  Algorithms Mol Biol (2011) 6(1):9 (PMC3107792)
• Linkage disequilibrium based genotype calling from low-coverage shotgun sequencing reads.
  Duitama J, Kennedy J, Dinakar S, Hernández Y, Wu Y, Măndoiu II
  BMC Bioinformatics (2011) 12 Suppl 1:S53 (PMC3044311)

• 2010

• Guest Editors' introduction to the special section on bioinformatics research and applications.
  Mandoiu I, Narasimhan G, Pan Y, Zhang Y
  IEEE/ACM Trans Comput Biol Bioinform (2010) 7(4):577-8

• 2009

• Identification of mammalian orthologs using local synteny.
  Jun J, Mandoiu II, Nelson CE
  BMC Genomics (2009) 10:630 (PMC2807883)
• The birth of new genes by RNA- and DNA-mediated duplication during mammalian evolution.
  Jun J, Ryvkin P, Hemphill E, Mandoiu I, Nelson C
  J. Comput. Biol. (2009) 16(10):1429-44
• PrimerHunter: a primer design tool for PCR-based virus subtype identification.
  Duitama J, Kumar DM, Hemphill E, Khan M, Mandoiu II, Nelson CE
  Nucleic Acids Res. (2009) 37(8):2483-92 (PMC2677861)

• 2008

• Genotype error detection using Hidden Markov Models of haplotype diversity.
  Kennedy J, Măndoiu I, Paşaniuc B
  J. Comput. Biol. (2008) 15(9):1155-71
• Guest editors' introduction to the special section on bioinformatics research and applications.
  Mandoiu II, Pan Y, Zelikovsky A
  IEEE/ACM Trans Comput Biol Bioinform (2008) 5(3):321-2
• Highly scalable genotype phasing by entropy minimization.
  Gusev A, Măndoiu II, Paşaniuc B
  IEEE/ACM Trans Comput Biol Bioinform (2008) 5(2):252-61

• 2007

• Highly scalable algorithms for robust string barcoding.
  Dasgupta B, Konwar KM, Mandoiu II, Shvartsman AA
  Int J Bioinform Res Appl (2007) 1(2):145-61
• Highly scalable genotype phasing by entropy minimization.
  Pasaniuc B, Mandoiu I
  Conf Proc IEEE Eng Med Biol Soc (2007) 1:3482-6
• High-throughput SNP genotyping by SBE/SBH.
  Măndoiu II, Prăjescu C
  IEEE Trans Nanobioscience (2007) 6(1):28-35

• 2006

• Exact and approximation algorithms for DNA tag set design.
  Măndoiu II, Trincă D
  J. Comput. Biol. (2006) 13(3):732-44

• 2005

• DNA-BAR: distinguisher selection for DNA barcoding.
  DasGupta B, Konwar KM, Mandoiu II, Shvartsman AA
  Bioinformatics (2005) 21(16):3424-6

• 2004

• Scalable heuristics for design of DNA probe arrays.
  Kahng AB, Măndoiu II, Pevzner PA, Reda S, Zelikovsky AZ
  J. Comput. Biol. (2004) 11(2-3):429-47