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Matthew N. McCall, Ph.D., M.H.S.

Matthew N. McCall, Ph.D., M.H.S.

he/him/his

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Office (585) 273-3177

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About Me

In 2010, I received a PhD in Biostatistics and an MHS in Bioinformatics from the Johns Hopkins School of Public Health under the supervision of Dr. Rafael Irizarry. From 2010 to 2014, I worked as a Postdoctoral Fellow at the University of Rochester Medical Center under the mentorship of Drs. Anthony...
In 2010, I received a PhD in Biostatistics and an MHS in Bioinformatics from the Johns Hopkins School of Public Health under the supervision of Dr. Rafael Irizarry. From 2010 to 2014, I worked as a Postdoctoral Fellow at the University of Rochester Medical Center under the mentorship of Drs. Anthony Almudevar and Hartmut Land. In the fall of 2014, I accepted a position as an Assistant Professor in the Department of Biostatistics and Computational Biology with a joint appointment in the Department of Biomedical Genetics at the University of Rochester Medical Center.

Faculty Appointments

Associate Professor - Department of Biostatistics and Computational Biology (SMD)

Associate Professor - Department of Biomedical Genetics (SMD) - Joint

Credentials

Education

MHS | Johns Hopkins Bloomberg School of Public Health. Bioinformatics. 2010

PhD | Johns Hopkins Bloomberg School of Public Health. Biostatistics. 2010

BS | University of Michigan. Statistics. 2004

Research

My research interests are in statistical genomics, systems biology, and bioinformatics. Currently, I am focusing on: (1) developing methods to estimate gene regulatory networks involved in cancer from perturbation experiments, (2) examining the effect of cellular composition on tissue-level gene exp...
My research interests are in statistical genomics, systems biology, and bioinformatics. Currently, I am focusing on: (1) developing methods to estimate gene regulatory networks involved in cancer from perturbation experiments, (2) examining the effect of cellular composition on tissue-level gene expression, (3) tackling within-subject genomic heterogeneity, focusing on predicting recurrence of hepatocellular carcinoma after liver transplantation, and (4) developing methods for preprocessing and analysis of genomic data.

Publications

Journal Articles

Circadian rhythms of macrophages are altered by the acidic tumor microenvironment.

Knudsen-Clark AM, Mwangi D, Cazarin J, Morris K, Baker C, Hablitz LM, McCall MN, Kim M, Altman BJ

EMBO reports.. 2024 October 16 Epub 10/16/2024.

Exon Skipping-based Subtyping of Colorectal Cancers.

Ambeskovic A, McCall MN, Woodsmith J, Juhl H, Land H

Gastroenterology.. 2024 August 22 Epub 08/22/2024.

Circadian rhythms of macrophages are altered by the acidic pH of the tumor microenvironment.

Knudsen-Clark AM, Mwangi D, Cazarin J, Hablitz LM, Kim M, Altman BJ

bioRxiv : the preprint server for biology.. 2024 July 24 Epub 07/24/2024.

miRglmm: a generalized linear mixed model of isomiR-level counts improves estimation of miRNA-level differential expression and uncovers variable differential expression between isomiRs.

Baran AM, Patil AH, Aparicio-Puerta E, Halushka MK, McCall MN

bioRxiv : the preprint server for biology.. 2024 July 18 Epub 07/18/2024.

Smad4 restricts injury-provoked biliary proliferation and carcinogenesis.

Alexander WB, Wang W, Hill MA, O'Dell MR, Ruffolo LI, Guo B, Jackson KM, Ullman N, Friedland SC, McCall MN, Patel A, Figueroa-Guilliani N, Georger M, Belt BA, Whitney-Miller CL, Linehan DC, Murphy PJ, Hezel AF

Disease models & mechanisms.. 2024 June 117 (6)Epub 02/28/2024.

Patterns of Unwanted Biological and Technical Expression Variation Among 49 Human Tissues.

Nieuwenhuis TO, Giles HH, Arking JVA, Patil AH, Shi W, McCall MN, Halushka MK

Laboratory investigation; a journal of technical methods and pathology.. 2024 June 104 (6):102069. Epub 04/24/2024.

A model-based hierarchical Bayesian approach to Sholl analysis.

VonKaenel E, Feidler A, Lowery R, Andersh K, Love T, Majewska A, McCall MN

Bioinformatics.. 2024 March 2940 (4)Epub 1900 01 01.

Brooklyn plots to identify co-expression dysregulation in single cell sequencing.

Patil AH, McCall MN, Halushka MK

NAR genomics and bioinformatics.. 2024 March 6 (1):lqad112. Epub 01/11/2024.

Developmental Ethanol Exposure Impacts Purkinje Cells but Not Microglia in the Young Adult Cerebellum.

Cealie MY, Douglas JC, Swan HK, Vonkaenel ED, McCall MN, Drew PD, Majewska AK

Cells.. 2024 February 2313 (5)Epub 02/23/2024.

Cortical microglia dynamics are conserved during voluntary wheel running.

Strohm AO, O'Connor TN, Oldfield S, Young S, Hammond C, McCall M, Dirksen RT, Majewska AK

Journal of applied physiology.. 2024 January 1136 (1):89-108. Epub 11/16/2023.

Patterns of unwanted biological and technical expression variation across 49 human tissues.

Nieuwenhuis TO, Giles HH, McCall MN, Halushka MK

bioRxiv : the preprint server for biology.. 2023 March 12 Epub 03/12/2023.

A Model-Based Hierarchical Bayesian Approach to Sholl Analysis.

Vonkaenel E, Feidler A, Lowery R, Andersh K, Love T, Majewska A, Mccall MN

bioRxiv : the preprint server for biology.. 2023 January 23 Epub 01/23/2023.

Developmental ethanol exposure has minimal impact on cerebellar microglial dynamics, morphology, and interactions with Purkinje cells during adolescence.

Cealie MY, Douglas JC, Le LHD, Vonkaenel ED, McCall MN, Drew PD, Majewska AK

Frontiers in neuroscience.. 2023 17 :1176581. Epub 05/05/2023.

Protocol to use TopNet for gene regulatory network modeling using gene expression data from perturbation experiments.

McMurray HR, Stern HA, Ambeskovic A, Land H, McCall MN

STAR protocols.. 2022 December 163 (4):101737. Epub 09/30/2022.

A curated human cellular microRNAome based on 196 primary cell types.

Patil AH, Baran A, Brehm ZP, McCall MN, Halushka MK

GigaScience.. 2022 August 2511 Epub 1900 01 01.

Gestational and lactational exposure to 2,3,7,8-tetrachlorodibenzo-p-dioxin primes cortical microglia to tissue injury.

Lowery RL, Latchney SE, Peer RP, Lamantia CE, Lordy KA, Opanashuk LA, McCall M, Majewska AK

Brain, behavior, and immunity.. 2022 March 101 :288-303. Epub 01/19/2022.

Gene network modeling via TopNet reveals functional dependencies between diverse tumor-critical mediator genes.

McMurray HR, Ambeskovic A, Newman LA, Aldersley J, Balakrishnan V, Smith B, Stern HA, Land H, McCall MN

Cell reports.. 2021 December 2137 (12):110136. Epub 1900 01 01.

A systems genomics approach uncovers molecular associates of RSV severity.

McCall MN, Chu CY, Wang L, Benoodt L, Thakar J, Corbett A, Holden-Wiltse J, Slaunwhite C, Grier A, Gill SR, Falsey AR, Topham DJ, Caserta MT, Walsh EE, Qiu X, Mariani TJ

PLoS computational biology.. 2021 December 17 (12):e1009617. Epub 12/28/2021.

Tissue, age, sex, and disease patterns of matrisome expression in GTEx transcriptome data.

Nieuwenhuis TO, Rosenberg AZ, McCall MN, Halushka MK

Scientific reports.. 2021 November 311 (1):21549. Epub 11/03/2021.

FNDC-1-mediated mitophagy and ATFS-1 coordinate to protect against hypoxia-reoxygenation.

Lim Y, Berry B, Viteri S, McCall M, Park EC, Rongo C, Brookes PS, Nehrke K

Autophagy.. 2021 November 17 (11):3389-3401. Epub 01/19/2021.

The effect of air pollution on the transcriptomics of the immune response to respiratory infection.

Croft DP, Burton DS, Nagel DJ, Bhattacharya S, Falsey AR, Georas SN, Hopke PK, Johnston CJ, Kottmann RM, Litonjua AA, Mariani TJ, Rich DQ, Thevenet-Morrison K, Thurston SW, Utell MJ, McCall MN

Scientific reports.. 2021 September 3011 (1):19436. Epub 09/30/2021.

The role of P2Y12 in the kinetics of microglial self-renewal and maturation in the adult visual cortex in vivo.

Mendes M, Le L, Atlas J, Brehm Z, Ladron-de-Guevara A, Matei E, Lamantia C, McCall M, Majewska AK

eLife.. 2021 July 1210 Epub 07/12/2021.

Airway Gene Expression Correlates of Respiratory Syncytial Virus Disease Severity and Microbiome Composition in Infants.

Chu CY, Qiu X, McCall MN, Wang L, Corbett A, Holden-Wiltse J, Slaunwhite C, Grier A, Gill SR, Pryhuber GS, Falsey AR, Topham DJ, Caserta MT, Walsh EE, Mariani TJ

The Journal of infectious diseases.. 2021 May 20223 (9):1639-1649. Epub 1900 01 01.

Single cell RNA-seq analysis of the flexor digitorum brevis mouse myofibers.

Verma RX, Kannan S, Lin BL, Fomchenko KM, Nieuwenhuis TO, Patil AH, Lukban C, Yang X, Fox-Talbot K, McCall MN, Kwon C, Kass DA, Rosenberg AZ, Halushka MK

Skeletal muscle. 2021 May 1711 (1):13. Epub 05/17/2021.

Autoregressive modeling and diagnostics for qPCR amplification.

Hsu B, Sherina V, McCall MN

Bioinformatics.. 2021 April 136 (22-23):5386-5391. Epub 1900 01 01.

Airway gene-expression classifiers for respiratory syncytial virus (RSV) disease severity in infants.

Wang L, Chu CY, McCall MN, Slaunwhite C, Holden-Wiltse J, Corbett A, Falsey AR, Topham DJ, Caserta MT, Mariani TJ, Walsh EE, Qiu X

BMC medical genomics.. 2021 February 2514 (1):57. Epub 02/25/2021.

The effect of tissue composition on gene co-expression.

Zhang Y, Cuerdo J, Halushka MK, McCall MN

Briefings in bioinformatics. 2021 January 1822 (1):127-139. Epub 1900 01 01.

Acute 2,3,7,8-Tetrachlorodibenzo-p-dioxin exposure in adult mice does not alter the morphology or inflammatory response of cortical microglia.

Lowery RL, Latchney SE, Peer RP, Lamantia CE, Opanashuk L, McCall M, Majewska AK

Neuroscience letters.. 2021 January 18742 :135516. Epub 11/20/2020.

Spatial Proteomic Approach to Characterize Skeletal Muscle Myofibers.

Fomchenko KM, Walsh EM, Yang X, Verma RX, Lin BL, Nieuwenhuis TO, Patil AH, Fox-Talbot K, McCall MN, Kass DA, Rosenberg AZ, Halushka MK

Journal of proteome research.. 2021 January 120 (1):888-894. Epub 11/30/2020.

Multiple imputation and direct estimation for qPCR data with non-detects.

Sherina V, McMurray HR, Powers W, Land H, Love TMT, McCall MN

BMC bioinformatics.. 2020 November 2621 (1):545. Epub 11/26/2020.

Consistent RNA sequencing contamination in GTEx and other data sets.

Nieuwenhuis TO, Yang SY, Verma RX, Pillalamarri V, Arking DE, Rosenberg AZ, McCall MN, Halushka MK

Nature communications.. 2020 April 2211 (1):1933. Epub 04/22/2020.

Cardioprotection by the mitochondrial unfolded protein response requires ATF5.

Wang YT, Lim Y, McCall MN, Huang KT, Haynes CM, Nehrke K, Brookes PS

American journal of physiology. Heart and circulatory physiology.. 2019 August 1317 (2):H472-H478. Epub 07/05/2019.

Aims, Study Design, and Enrollment Results From the Assessing Predictors of Infant Respiratory Syncytial Virus Effects and Severity Study.

Walsh EE, Mariani TJ, Chu C, Grier A, Gill SR, Qiu X, Wang L, Holden-Wiltse J, Corbett A, Thakar J, Benoodt L, McCall MN, Topham DJ, Falsey AR, Caserta MT

JMIR research protocols.. 2019 June 68 (6):e12907. Epub 06/06/2019.

Identification of the novel Ido1 imprinted locus and its potential epigenetic role in pregnancy loss.

Spinelli P, Latchney SE, Reed JM, Fields A, Baier BS, Lu X, McCall MN, Murphy SP, Mak W, Susiarjo M

Human molecular genetics.. 2019 February 1528 (4):662-674. Epub 1900 01 01.

Systematic exploration of cell morphological phenotypes associated with a transcriptomic query.

Nassiri I, McCall MN

Nucleic acids research.. 2018 November 246 (19):e116. Epub 1900 01 01.

and Mutations Cause Cholangiocyte- and Hepatocyte-Derived Cholangiocarcinoma.

Hill MA, Alexander WB, Guo B, Kato Y, Patra KC, O'Dell MR, McCall MN, Whitney-Miller CL, Bardeesy N, Hezel AF

Cancer research.. 2018 August 1578 (16):4445-4451. Epub 06/05/2018.

xMD-miRNA-seq to generate near in vivo miRNA expression estimates in colon epithelial cells.

Rosenberg AZ, Wright C, Fox-Talbot K, Rajpurohit A, Williams C, Porter C, Kovbasnjuk O, McCall MN, Shin JH, Halushka MK

Scientific reports.. 2018 June 288 (1):9783. Epub 06/28/2018.

Big Strides in Cellular MicroRNA Expression.

Halushka MK, Fromm B, Peterson KJ, McCall MN

Trends in genetics : TIG.. 2018 March 34 (3):165-167. Epub 01/18/2018.

Toward the human cellular microRNAome.

McCall MN, Kim MS, Adil M, Patil AH, Lu Y, Mitchell CJ, Leal-Rojas P, Xu J, Kumar M, Dawson VL, Dawson TM, Baras AS, Rosenberg AZ, Arking DE, Burns KH, Pandey A, Halushka MK

Genome research.. 2017 October 27 (10):1769-1781. Epub 09/06/2017.

A four gene signature predictive of recurrent prostate cancer.

Komisarof J, McCall M, Newman L, Bshara W, Mohler JL, Morrison C, Land H

Oncotarget.. 2017 January 108 (2):3430-3440. Epub 1900 01 01.

Complex Sources of Variation in Tissue Expression Data: Analysis of the GTEx Lung Transcriptome.

McCall MN, Illei PB, Halushka MK

American journal of human genetics.. 2016 September 199 (3):624-635. Epub 1900 01 01.

A microRNA biomarker of hepatocellular carcinoma recurrence following liver transplantation accounting for within-patient heterogeneity.

Xie QY, Almudevar A, Whitney-Miller CL, Barry CT, McCall MN

BMC medical genomics.. 2016 April 89 :18. Epub 04/08/2016.

A benchmark for microRNA quantification algorithms using the OpenArray platform.

McCall MN, Baras AS, Crits-Christoph A, Ingersoll R, McAlexander MA, Witwer KW, Halushka MK

BMC bioinformatics.. 2016 March 2217 :138. Epub 03/22/2016.

Integrating High-Dimensional Transcriptomics and Image Analysis Tools into Early Safety Screening: Proof of Concept for a New Early Drug Development Strategy.

Verbist BM, Verheyen GR, Vervoort L, Crabbe M, Beerens D, Bosmans C, Jaensch S, Osselaer S, Talloen W, Van den Wyngaert I, Van Hecke G, Wuyts D, , Van Goethem F, Göhlmann HW

Chemical research in toxicology.. 2015 October 1928 (10):1914-25. Epub 09/15/2015.

Using transcriptomics to guide lead optimization in drug discovery projects: Lessons learned from the QSTAR project.

Verbist B, Klambauer G, Vervoort L, Talloen W, , Shkedy Z, Thas O, Bender A, Göhlmann HW, Hochreiter S

Drug discovery today.. 2015 May 20 (5):505-13. Epub 01/10/2015.

Connecting gene expression data from connectivity map and in silico target predictions for small molecule mechanism-of-action analysis.

Ravindranath AC, Perualila-Tan N, Kasim A, Drakakis G, Liggi S, Brewerton SC, Mason D, Bodkin MJ, Evans DA, Bhagwat A, Talloen W, Göhlmann HW, Qstar Consortium , Shkedy Z, Bender A

Molecular bioSystems.. 2015 January 11 (1):86-96. Epub 09/25/2014.

On non-detects in qPCR data.

McCall MN, McMurray H, Land H, Almudevar A

Bioinformatics.. 2014 August 1530 (16):2310-6. Epub 04/23/2014.

Lessons from miR-143/145: the importance of cell-type localization of miRNAs.

Kent OA, McCall MN, Cornish TC, Halushka MK

Nucleic acids research.. 2014 July 42 (12):7528-38. Epub 05/29/2014.

The Gene Expression Barcode 3.0: improved data processing and mining tools.

McCall MN, Jaffee HA, Zelisko SJ, Sinha N, Hooiveld G, Irizarry RA, Zilliox MJ

Nucleic acids research.. 2014 January 42 (Database issue):D938-43. Epub 11/22/2013.

A critical evaluation of microRNA biomarkers in non-neoplastic disease.

Haider BA, Baras AS, McCall MN, Hertel JA, Cornish TC, Halushka MK

PloS one.. 2014 9 (2):e89565. Epub 02/26/2014.

ChIP-PED enhances the analysis of ChIP-seq and ChIP-chip data.

Wu G, Yustein JT, McCall MN, Zilliox M, Irizarry RA, Zeller K, Dang CV, Ji H

Bioinformatics.. 2013 May 129 (9):1182-9. Epub 03/01/2013.

Estimation of Gene Regulatory Networks.

McCall MN

Postdoc journal : a journal of postdoctoral research and postdoctoral affairs.. 2013 January 1 (1):60-69. Epub 1900 01 01.

On the underlying assumptions of threshold Boolean networks as a model for genetic regulatory network behavior.

Tran V, McCall MN, McMurray HR, Almudevar A

Frontiers in genetics.. 2013 4 :263. Epub 12/11/2013.

fRMA ST: frozen robust multiarray analysis for Affymetrix Exon and Gene ST arrays.

McCall MN, Jaffee HA, Irizarry RA

Bioinformatics.. 2012 December 128 (23):3153-4. Epub 10/07/2012.

Gene expression anti-profiles as a basis for accurate universal cancer signatures.

Bravo HC, Pihur V, McCall M, Irizarry RA, Leek JT

BMC bioinformatics.. 2012 October 2213 :272. Epub 10/22/2012.

Affymetrix GeneChip microarray preprocessing for multivariate analyses.

McCall MN, Almudevar A

Briefings in bioinformatics. 2012 September 13 (5):536-46. Epub 12/30/2011.

Micro RNA expression profiles as adjunctive data to assess the risk of hepatocellular carcinoma recurrence after liver transplantation.

Barry CT, D'Souza M, McCall M, Safadjou S, Ryan C, Kashyap R, Marroquin C, Orloff M, Almudevar A, Godfrey TE

American journal of transplantation : official journal of the American Society of Transplantation and the American Society of Transplant Surgeons.. 2012 February 12 (2):428-37. Epub 10/18/2011.

MicroRNA profiling of diverse endothelial cell types.

McCall MN, Kent OA, Yu J, Fox-Talbot K, Zaiman AL, Halushka MK

BMC medical genomics.. 2011 November 24 :78. Epub 11/02/2011.

Fitting Boolean networks from steady state perturbation data.

Almudevar A, McCall MN, McMurray H, Land H

Statistical applications in genetics and molecular biology. 2011 October 510 (1)Epub 10/05/2011.

Thawing Frozen Robust Multi-array Analysis (fRMA).

McCall MN, Irizarry RA

BMC bioinformatics.. 2011 September 1612 :369. Epub 09/16/2011.

Assessing affymetrix GeneChip microarray quality.

McCall MN, Murakami PN, Lukk M, Huber W, Irizarry RA

BMC bioinformatics.. 2011 May 712 :137. Epub 05/07/2011.

The Gene Expression Barcode: leveraging public data repositories to begin cataloging the human and murine transcriptomes.

McCall MN, Uppal K, Jaffee HA, Zilliox MJ, Irizarry RA

Nucleic acids research.. 2011 January 39 (Database issue):D1011-5. Epub 1900 01 01.

The MicroArray Quality Control (MAQC)-II study of common practices for the development and validation of microarray-based predictive models.

Shi L, Campbell G, Jones WD, Campagne F, Wen Z, Walker SJ, Su Z, Chu TM, Goodsaid FM, Pusztai L, Shaughnessy JD, Oberthuer A, Thomas RS, Paules RS, Fielden M, Barlogie B, Chen W, Du P, Fischer M, Furlanello C, Gallas BD, Ge X, Megherbi DB, Symmans WF, Wang MD, Zhang J, Bitter H, Brors B, Bushel PR, Bylesjo M, Chen M, Cheng J, Cheng J, Chou J, Davison TS, Delorenzi M, Deng Y, Devanarayan V, Dix DJ, Dopazo J, Dorff KC, Elloumi F, Fan J, Fan S, Fan X, Fang H, Gonzaludo N, Hess KR, Hong H, Huan J, Irizarry RA, Judson R, Juraeva D, Lababidi S, Lambert CG, Li L, Li Y, Li Z, Lin SM, Liu G, Lobenhofer EK, Luo J, Luo W, McCall MN, Nikolsky Y, Pennello GA, Perkins RG, Philip R, Popovici V, Price ND, Qian F, Scherer A, Shi T, Shi W, Sung J, Thierry-Mieg D, Thierry-Mieg J, Thodima V, Trygg J, Vishnuvajjala L, Wang SJ, Wu J, Wu Y, Xie Q, Yousef WA, Zhang L, Zhang X, Zhong S, Zhou Y, Zhu S, Arasappan D, Bao W, Lucas AB, Berthold F, Brennan RJ, Buness A, Catalano JG, Chang C, Chen R, Cheng Y, Cui J, Czika W, Demichelis F, Deng X, Dosymbekov D, Eils R, Feng Y, Fostel J, Fulmer-Smentek S, Fuscoe JC, Gatto L, Ge W, Goldstein DR, Guo L, Halbert DN, Han J, Harris SC, Hatzis C, Herman D, Huang J, Jensen RV, Jiang R, Johnson CD, Jurman G, Kahlert Y, Khuder SA, Kohl M, Li J, Li L, Li M, Li QZ, Li S, Li Z, Liu J, Liu Y, Liu Z, Meng L, Madera M, Martinez-Murillo F, Medina I, Meehan J, Miclaus K, Moffitt RA, Montaner D, Mukherjee P, Mulligan GJ, Neville P, Nikolskaya T, Ning B, Page GP, Parker J, Parry RM, Peng X, Peterson RL, Phan JH, Quanz B, Ren Y, Riccadonna S, Roter AH, Samuelson FW, Schumacher MM, Shambaugh JD, Shi Q, Shippy R, Si S, Smalter A, Sotiriou C, Soukup M, Staedtler F, Steiner G, Stokes TH, Sun Q, Tan PY, Tang R, Tezak Z, Thorn B, Tsyganova M, Turpaz Y, Vega SC, Visintainer R, von Frese J, Wang C, Wang E, Wang J, Wang W, Westermann F, Willey JC, Woods M, Wu S, Xiao N, Xu J, Xu L, Yang L, Zeng X, Zhang J, Zhang L, Zhang M, Zhao C, Puri RK, Scherf U, Tong W, Wolfinger RD,

Nature biotechnology.. 2010 August 28 (8):827-38. Epub 07/30/2010.

Frozen robust multiarray analysis (fRMA).

McCall MN, Bolstad BM, Irizarry RA

Biostatistics.. 2010 April 11 (2):242-53. Epub 01/22/2010.

Performance evaluation of commercial miRNA expression array platforms.

Sah S, McCall MN, Eveleigh D, Wilson M, Irizarry RA

BMC research notes.. 2010 March 183 :80. Epub 03/18/2010.

Consolidated strategy for the analysis of microarray spike-in data.

McCall MN, Irizarry RA

Nucleic acids research.. 2008 October 36 (17):e108. Epub 08/01/2008.