Publications

Goods Lab

As an interdisciplinary group, we seek to publish in journals that span the broad readership of the problems we address.

Additionally, we support open access publishing practices and try to post our papers on pre-print servers, like biorxiv.

For the most up-to-date list of publications from the lab

Visit Google Scholar

Selected publications

A Composite interaction Score: Prioritizing cell–cell interactions from single-cell RNA-seq with application to pre-menopausal epithelial barriers
Olha Kholod; Hien M. Bui; H.Robert Frost; Brittany A. Goods
Journal of Advanced Research
March 2026
doi
A streamlined and comprehensive protocol for the generation and multi-omic analysis of human monocyte-derived macrophages.
Palmer OG; Perreard L; Kolling Iv FW; Pioli PA; Goods BA
BMC biotechnology
December 29, 2025
doi
Randomized Spatial PCA (RASP): A computationally efficient method for dimensionality reduction of high-resolution spatial transcriptomics data.
Gingerich IK; Goods BA; Frost HR
PLoS computational biology
December 10, 2025
doi
Systematic benchmarking of imaging spatial transcriptomics platforms in FFPE tissues.
Wang H; Huang R; Nelson J; Gao C; Tran M; Yeaton A; Krishna S; Felt K; Pfaff KL; Bowman T et al.
Nature communications
November 20, 2025
doi
Single-cell and spatiotemporal profile of ovulation in the mouse ovary.
Huang R; Kratka CE; Pea J; McCann C; Nelson J; Bryan JP; Zhou LT; Russo DD; Zaniker-Gomez EJ; Gandhi AH et al.
PLoS biology
June 24, 2025
doi
Disrupted MOS signaling alters meiotic cell cycle regulation and the egg transcriptome
Gisela Cairo; Olha Kholod; Olivia Palmer; Sophia Meytin; Brittany A Goods; Soni Lacefield
Reproduction
May 27, 2025
doi
Transcriptomic analysis of whole-staged ovarian follicles reveals stage-specific folliculogenesis signatures in mice
Hannah VanBenschoten; Yu-Ying Chen; Olha Kholod; Daniela D Russo; Alex K Shalek; Francesca E Duncan; Teresa K Woodruff; Brittany A Goods
March 22, 2025
doi
Follicle-intrinsic and spatially distinct molecular programs drive follicle rupture and luteinization during ex vivo mammalian ovulation.
Zaniker EJ; Zhang J; Russo D; Huang R; Suritis K; Drake RS; Barlow-Smith E; Shalek AK; Woodruff TK; Xiao S et al.
Communications biology
October 23, 2024
doi
Maternal SARS-CoV-2 impacts fetal placental macrophage programs and placenta-derived microglial models of neurodevelopment.
Shook LL; Batorsky RE; De Guzman RM; McCrea LT; Brigida SM; Horng JE; Sheridan SD; Kholod O; Cook AM; Li JZ et al.
Journal of neuroinflammation
June 25, 2024
doi
Vitrification preserves follicular transcriptomic dynamics during ex vivo ovulation†.
Zhang J; Russo DD; Wang Y; Zhang Q; Zelinski MB; Shalek AK; Goods BA; Xiao S
Biology of reproduction
September 1, 2023
doi
Organoid co-culture model of the human endometrium in a fully synthetic extracellular matrix enables the study of epithelial-stromal crosstalk.
Gnecco JS; Brown A; Buttrey K; Ives C; Goods BA; Baugh L; Hernandez-Gordillo V; Loring M; Isaacson KB; Griffith LG
Med (New York, N.Y.)
August 1, 2023
doi
An ex vivo ovulation system enables the discovery of novel ovulatory pathways and nonhormonal contraceptive candidates†.
Zhang J; Goods BA; Pattarawat P; Wang Y; Haining T; Zhang Q; Shalek AK; Duncan FE; Woodruff TK; Xiao S
Biology of Reproduction
April 1, 2023
doi
Leveraging an endometrial proteomic and single cell transcriptomics pipeline reveals menstrual cycle and endometriosis-associated molecular profiles
Lauren Baugh*, Brittany A. Goods*, Juan S. Gnecco, Yunbeen Bae, Michael Retchin, Constantine N. Tzouanas, Megan Loring, Keith Issacson, Alex K. Shalek, Douglas Lauffenburger, and Linda Griffith
medRxiv
November 4, 2022
doi
Diverse antiviral IgG effector activities are predicted by unique biophysical antibody features
Cheng HD, Dowell KG, Bailey-Kellogg C, Goods BA, Love JC, Ferrari G, Alter G, Gach J, Forthal DN, Lewis GK, Greene K, Gao H, Montefiori DC, Ackerman ME
Retrovirology
November 4, 2022
Pubmed doi
Single-cell transcriptomics of staged oocytes and somatic cells reveal novel regulators of follicle activation
Chen YY, Russo DD, Drake RS, Duncan FE, Shalek AK, Goods BA+,*, Woodruff TK*.
Reproduction
November 4, 2022
Pubmed doi
Cellular and transcriptional diversity over the course of human lactation.
Sarah K Nyquist, Patricia Gao, Tessa K. J. Haining, Michael R Retchin, Yarden Golan Maor, Riley S Drake, Kellie Kolb, Benjamin E Mead, Nadav Ahituv, Micaela E Martinez, Bonnie Berger, Alex K Shalek, Brittany A Goods.
PNAS
November 13, 2021
doi
Tissue engineered organoid co-culture model of the cycling human endometrium in a fully-defined synthetic extracellular matrix.
Juan S. Gnecco, Alexander Brown, Kira Buttrey, Clara Ives, Britt Goods, Lauren Baugh, Victor Hernandez-Gordillo, Megan Loring, Keith Issacson, Linda G. Griffith.
bioRxiv
September 30, 2021
Pubmed
Vitrification preserves murine ovarian follicular cell transcriptome in a 3D encapsulated in vitro follicle growth system.
Wang Y, Russo DD, Pattarawat P, Zhang Q, Zelinski MB, Shalek AK, Goods BA, Xiao S.
Biol Reprod
September 21, 2021
Pubmed
Divergent Functions of Tissue-Resident and Blood-Derived Macrophages in the Hemorrhagic Brain.
Chang CF, Goods BA, Askenase MH, Beatty HE, Osherov A, DeLong JH, Hammond MD, Massey J, Landreneau M, Love JC, Sansing LH.
Stroke
April 12, 2021
Pubmed
Leukocyte dynamics after intracerebral hemorrhage in a living patient reveal rapid adaptations to tissue milieu
Goods BA*, Askenase MH*, Markarian E, Beatty HE, Drake RS, Fleming I, DeLong JH, Philip NH, Matouk CC, Awad IA, Zuccarello M, Hanley DF, Love JC, Shalek AK, Sansing LH; ICHseq Investigators.
JCI Insight
March 22, 2021
Pubmed
Longitudinal transcriptomics define the stages of myeloid activation in the living human brain after intracerebral hemorrhage
Askenase MH*, Goods BA*, Beatty HE, Steinschneider AF, Velazquez SE, Osherov A, Landreneau MJ, Carroll SL, Tran TB, Avram VS, Drake RS, Gatter GJ, Massey JA, Karuppagounder SS, Ratan RR, Matouk CC, Sheth KN, Ziai WC, Parry-Jones AR, Awad IA, Zuccarello M, Thompson RE, Dawson J, Hanley DF, Love JC, Shalek AK, Sansing LH; MISTIE III Consortium; ICHseq investigators; ICHseq Investigators MISTIE III Investigators
Sci Immunol
February 19, 2021
Pubmed
Single-cell transcriptomic atlas of the human retina identifies cell types associated with age-related macular degeneration.
Menon M, Mohammadi S, Davila-Velderrain J, Goods BA, Cadwell TD, Xing Y, Stemmer-Rachamimov A, Shalek AK, Love JC, Kellis M, Hafler BP.
Nature Communications
October 25, 2019
Pubmed
Profiling human antibody responses by integrated single-cell analysis.
Ogunniyi A, Thomas BA, Politano TJ, Varadarajan N, Landais E, Poignard P, Walker BD, Kwon DS, Love JC.
Vaccine
May 24, 2019
Blood handling and leukocyte isolation methods impact the global transcriptome of immune cells.
Goods BA+, Vahey J, Steinschneider A, Askenase M, Sansing LH, Love JC.
BMC Immunol
October 30, 2018
Pubmed
Erythrocyte efferocytosis modulates macrophages towards recovery after intracerebral hemorrhage.
Chang CG, Goods BA, Askenase MH, Hammond MD, Renfroe SC, Steinschneider AF, Landreneau MJ, Ai Y, Mack M, Sheth K, Greer D, Huttner A, Coman D, Fahmeed Hyder DS, Ghosh S, Rothlin C, Love JC, Sansing LH.
J Clin Invest
December 18, 2017
Pubmed
Functional Differences Between PD-1+ and PD-1– CD4+ Effector T Cells in Healthy Donors and Patients with Glioblastoma Multiforme.
Goods BA*, Lowther DE*, Hernandez AL*, Lucca LE, Lerner BA, Raddassi K, van Dijk D, Duan X, Gunel M, Coric V, Krishnaswamy S, Love JC, Hafler DA.
PLoS One
September 7, 2017
Pubmed
TGF-β1 Modulates Microglial Phenotype and Promotes Recovery after Intracerebral Hemorrhage. J Clin Invest.
Taylor RA, Chang C, Goods BA, Hammond MD, MacGrory B, Ai Y, McCullough LD, Scott E. Kasner SE, Mullen MT, Hafler DA, Love JC, Sansing LH.
J Clin Invest
January 3, 2017
Pubmed
Diversity of Antiviral IgG Effector Activities Observed in HIV-Infected and Vaccinated Subjects.
Huang Y, Ferrari G, Alter G, Forthal DN, Kappes JC, Lewis GK, Love JC, Borate B, Harris L, Greene K, Gao H, Phan TB, Landucci G, Goods BA, Dowell KG, Cheng HD, Bailey-Kellogg C, Montefiori DC, Ackerman ME.
J Immunol
December 15, 2016
Pubmed
PD-1 marks dysfunctional regulatory T cells in malignant gliomas.
Lowther DE*, Goods BA*, Lucca LE*, Lerner BA, Raddassi K, van Dijk D, Hernandez AL, Duan X, Gunel M, Coric V, Krishnaswamy S, Love JC, Hafler DA.
JCI Insight
April 21, 2016
Pubmed
CNS demyelination and enhanced myelin-reactive responses after ipilimumab treatment. Neurology.
Cao Y, Nylander A, Ramanan S, Goods BA, Ponath G, Zabad R, Chiang VL, Vortmeyer AO, Hafler DA, Pitt D.
Neurology
April 19, 2016
Pubmed
Development of a High-Throughput Functional Screen Using Nanowell-Assisted Cell Patterning.
Ozkumur AY*, Goods BA*, Love JC
Small
September 11, 2015
Pubmed
Automated pipeline for rapid production and screening of HIV-specific monoclonal antibodies using pichia pastoris.
Shah KA, Clark JJ, Goods BA, Politano TJ, Mozdzierz NJ, Zimnisky RM, Leeson RL, Love JC, Love KR.
Biotechnol Bioeng
July 31, 2015
Pubmed
Functional inflammatory profiles distinguish myelin-reactive T cells from patients with multiple sclerosis.
Cao Y*, Goods BA*, Raddassi K, Nepom GT, Kwok WW, Love JC, Hafler DA.
Sci Transl Med
May 13, 2015
Pubmed

As an interdisciplinary group, we seek to publish in journals that span the broad readership of the problems we address.

Selected publications

2026

A Composite interaction Score: Prioritizing cell–cell interactions from single-cell RNA-seq with application to pre-menopausal epithelial barriers

2025

A streamlined and comprehensive protocol for the generation and multi-omic analysis of human monocyte-derived macrophages.

Randomized Spatial PCA (RASP): A computationally efficient method for dimensionality reduction of high-resolution spatial transcriptomics data.

Systematic benchmarking of imaging spatial transcriptomics platforms in FFPE tissues.

Single-cell and spatiotemporal profile of ovulation in the mouse ovary.

Disrupted MOS signaling alters meiotic cell cycle regulation and the egg transcriptome

Transcriptomic analysis of whole-staged ovarian follicles reveals stage-specific folliculogenesis signatures in mice

2024

Follicle-intrinsic and spatially distinct molecular programs drive follicle rupture and luteinization during ex vivo mammalian ovulation.

Maternal SARS-CoV-2 impacts fetal placental macrophage programs and placenta-derived microglial models of neurodevelopment.

2023

Vitrification preserves follicular transcriptomic dynamics during ex vivo ovulation†.

Organoid co-culture model of the human endometrium in a fully synthetic extracellular matrix enables the study of epithelial-stromal crosstalk.

An ex vivo ovulation system enables the discovery of novel ovulatory pathways and nonhormonal contraceptive candidates†.

2022

Leveraging an endometrial proteomic and single cell transcriptomics pipeline reveals menstrual cycle and endometriosis-associated molecular profiles

Diverse antiviral IgG effector activities are predicted by unique biophysical antibody features

Single-cell transcriptomics of staged oocytes and somatic cells reveal novel regulators of follicle activation

2021

Cellular and transcriptional diversity over the course of human lactation.

Tissue engineered organoid co-culture model of the cycling human endometrium in a fully-defined synthetic extracellular matrix.

Vitrification preserves murine ovarian follicular cell transcriptome in a 3D encapsulated in vitro follicle growth system.

Divergent Functions of Tissue-Resident and Blood-Derived Macrophages in the Hemorrhagic Brain.

Leukocyte dynamics after intracerebral hemorrhage in a living patient reveal rapid adaptations to tissue milieu

Longitudinal transcriptomics define the stages of myeloid activation in the living human brain after intracerebral hemorrhage

2015-2020

Single-cell transcriptomic atlas of the human retina identifies cell types associated with age-related macular degeneration.

Profiling human antibody responses by integrated single-cell analysis.

Blood handling and leukocyte isolation methods impact the global transcriptome of immune cells.

Erythrocyte efferocytosis modulates macrophages towards recovery after intracerebral hemorrhage.

Functional Differences Between PD-1+ and PD-1– CD4+ Effector T Cells in Healthy Donors and Patients with Glioblastoma Multiforme.

TGF-β1 Modulates Microglial Phenotype and Promotes Recovery after Intracerebral Hemorrhage. J Clin Invest.

Diversity of Antiviral IgG Effector Activities Observed in HIV-Infected and Vaccinated Subjects.

PD-1 marks dysfunctional regulatory T cells in malignant gliomas.

CNS demyelination and enhanced myelin-reactive responses after ipilimumab treatment. Neurology.

Development of a High-Throughput Functional Screen Using Nanowell-Assisted Cell Patterning.

Automated pipeline for rapid production and screening of HIV-specific monoclonal antibodies using pichia pastoris.

Functional inflammatory profiles distinguish myelin-reactive T cells from patients with multiple sclerosis.