Our Collaboratory Fellows have published papers on a variety of research topics, stemming from Collaboratory-supported collaborations across campus.

Find us on Google Scholar: https://scholar.google.com/citations?user=XN6DdggAAAAJ&hl=en

132 entries « 1 of 7 »
1. Bhat, Kruttika; Saki, Mohammad; Vlashi, Erina; Cheng, Fei; Duhachek-Muggy, Sara; Alli, Claudia; Yu, Garrett; Medina, Paul; He, Ling; Damoiseaux, Robert; Pellegrini, Matteo; Zemke, Nathan R; Nghiemphu, Phioanh Leia; Cloughesy, Timothy F; Liau, Linda M; Kornblum, Harley I; Pajonk, Frank: The dopamine receptor antagonist trifluoperazine prevents phenotype conversion and improves survival in mouse models of glioblastoma. In: Proceedings of the National Academy of Sciences , 32358191 , 2020. (Type: Journal Article | Abstract | Links | BibTeX)
2. Neal, Adam S; Nunez, Miguel; Lai, Tiffany; Tosevska, Anela; Morselli, Marco; Amneus, Malaika; Zakhour, Mae; Moatamed, Neda A; Pellegrini, Matteo; Memarzadeh, Sanaz: Expression of Stromal Progesterone Receptor and Differential Methylation Patterns in the Endometrium May Correlate with Response to Progesterone Therapy in Endometrial Complex Atypical Hyperplasia.. In: Reproductive Sciences, 2020. (Type: Journal Article | Abstract | Links | BibTeX)
3. Brito, Jaqueline J; Mosqueiro, Thiago; Rotman, Jeremy; Xue, Victor; Chapski, Douglas J; la Hoz, Juan De; Matias, Paulo; Martin, Lana S; Zelikovsky, Alex; Pellegrini, Matteo; Mangul, Serghei: Telescope: an interactive tool for managing large-scale analysis from mobile devices. In: GigaScience, 9 (1), 2020. (Type: Journal Article | Abstract | Links | BibTeX)
4. Lozano‐Huntelman, Natalie Ann; Singh, Nina; Valencia, Alondra; Mira, Portia; Sakayan, Maral; Boucher, Ian; Tang, Sharon; Brennan, Kelley; Gianvecchio, Crystal; Fitz‐Gibbon, Sorel; Yeh, Pamela: Evolution of Antibiotic Cross‐resistance and Collateral Sensitivity in Staphylococcus Epidermidis Using the Mutant Prevention Concentration and the Mutant Selection Window. In: Evolutionary Applications, 2019. (Type: Journal Article | Abstract | Links | BibTeX)
5. Galmozzi, Andrea; Kok, Bernard P; Kim, Arthur S; Montenegro-Burke, Rafael J; Lee, Jae Y; Spreafico, Roberto; Mosure, Sarah; Albert, Verena; Cintron-Colon, Rigo; Godio, Cristina; Webb, William R; Conti, Bruno; Solt, Laura A; Kojetin, Douglas; Parker, Christopher G; Peluso, John J; Pru, James K; Siuzdak, Gary; Cravatt, Benjamin F; Saez, Enrique: PGRMC2 is an intracellular haem chaperone critical for adipocyte function. In: 2019. (Type: Journal Article | Abstract | Links | BibTeX)
6. Kurmangaliyev, Yerbol Z; Yoo, Juyoun; LoCascio, Samuel A; Zipursky, Lawrence S: Modular transcriptional programs separately define axon and dendrite connectivity.. In: eLife, 2019. (Type: Journal Article | Abstract | Links | BibTeX)
7. Bulterys, P L; Toesca, I J; Norris, M H; Maloy, J P; Fitz-Gibbon, S T; France, B; Toffig, B; Morselli, M; Somprasong, N; Pellegrini, M; Schweizer, H P; Tuanyok, A; Damoiseaux, R; French, C T; Miller, J F: An in situ high-throughput screen identifies inhibitors of intracellular Burkholderia pseudomallei with therapeutic efficacy.. In: Proc Natl Acad Sci U S A. , 2019. (Type: Journal Article | Abstract | Links | BibTeX)
8. Romero, Zulema; Lomova, Anastasia; Said, Suzanne; Miggelbrink, Alexandra; Kuo, Caroline Y; Campo-Fernandez, Beatriz; D.Hoban, Megan; E.Masiuk, Katelyn; N.Clark, Danielle; Long, Joseph; M.Sanchez, Julie; MiriamVelez, ; Miyahira, Eric; Zhang, Ruixue; Brown, Devin; Wang, Xiaoyan; Z.Kurmangaliyev, Yerbol; P.Hollis, Roger; B.Kohn., Donald: Editing the Sickle Cell Disease Mutation in Human Hematopoietic Stem Cells: Comparison of Endonucleases and Homologous Donor Templates.. In: Molecular Therapy, 27 (8), pp. 1389-1406, 2019. (Type: Journal Article | Abstract | Links | BibTeX)
9. Cantarella, S; Carnevali, D; Morselli, M; Conti, A; Pellegrini, M; Montanini, B; Dieci, G: Alu RNA Modulates the Expression of Cell Cycle Genes in Human Fibroblasts.. In: Int J Mol Sci. , 20 (13), 2019. (Type: Journal Article | Abstract | Links | BibTeX)
10. Leung CS, ; Douglass SM, ; Morselli M, ; Obusan MB, ; Pavlyukov MS, ; Pellegrini M, ; TL., Johnson: H3K36 Methylation and the Chromodomain Protein Eaf3 Are Required for Proper Cotranscriptional Spliceosome Assembly.. In: Cell Rep. , 27 (13), pp. 3760-3769, 2019. (Type: Journal Article | Abstract | Links | BibTeX)
11. Pontrelli Sammy, ; Riley C. B. Fricke and Shao Thing Teoh, ; Walter A. Laviña, ; Sastia Prama Putri, ; Sorel Fitz-Gibbon, ; Matthew Chung, ; Matteo Pellegrini, ; Eiichiro Fukusaki, ; Liao, James C: Metabolic repair through emergence of new pathways in Escherichia coli. In: Nature Chemical Biology, 14 (11), pp. 1005–1009, 2018. (Type: Journal Article | Abstract | Links | BibTeX)
12. Eagleman, Sarah L; Vaughn, Don A; Drover, David R; Drover, Caitlin M; Cohen, Mark S; Ouellette, Nicholas T; MacIver., Bruce M: Do Complexity Measures of Frontal EEG Distinguish Loss of Consciousness in Geriatric Patients Under Anesthesia?. In: Frontiers in neuroscience, 12 , pp. 645, 2018. (Type: Journal Article | Abstract | Links | BibTeX)
13. Pontrelli Sammy, ; Riley C. B. Fricke, ; Memon, Sana Subhan; Sakurai, Sastia ; Prama Putri, ; Sorel Fitz-Gibbon, ; Matthew Chung, ; Hsin-Yi Wu, : Directed strain evolution restructures metabolism for 1-butanol production in minimal media. In: Metabolic Engineering, 49 , pp. 153-163, 2018. (Type: Journal Article | Abstract | Links | BibTeX)
14. Camacho, J; Truong, L; Kurt, Z; Chen, YW ; Morselli, M; Gutierrez, G; Pellegrini, M; Yang, X; Allard, P: The Memory of Environmental Chemical Exposure in C. elegans Is Dependent on the Jumonji Demethylases jmjd-2 and jmjd-3/utx-1.. In: Cell Rep., 23 (8), pp. 2392-2404, 2018. (Type: Journal Article | Abstract | Links | BibTeX)
15. Sarin, Sumeet; Zuniga-Sanchez, Elizabeth; Z.Kurmangaliyev, Yerbol; Cousins, Henry; Patel, Mili; Hernandez, Jeanette; X.Zhang, Kelvin; A.Samuel, Melanie; Morey, Marta; R.Sanes, Joshua; Zipursky, Lawrence: Role for Wnt Signaling in Retinal Neuropil Development: Analysis via RNA-Seq and In Vivo Somatic CRISPR Mutagenesis. In: Neuron, 98 (1), pp. 109-126, 2018. (Type: Journal Article | Abstract | Links | BibTeX)
16. S, Ziyad; JD, Riordan; AM, Cavanaugh; T, Su; GE, Hernandez; G, Hilfenhaus; M, Morselli; K, Huynh; K, Wang; JN, Chen; AJ, Dupuy; ML., Iruela-Arispe: A Forward Genetic Screen Targeting the Endothelium Reveals a Regulatory Role for the Lipid Kinase Pi4ka in Myelo- and Erythropoiesis.. In: Cell Rep. , 22 (5), pp. 1211-1224, 2018. (Type: Journal Article | Abstract | Links | BibTeX)
17. Thorsson, Vésteinn; Gibbs, David L; Brown, Scott D; Wolf, Denise; Bortone, Dante S; Yang, Tai-Hsien Ou; Porta-Pardo, Eduard; Gao, Galen F; Plaisier, Christopher L; Eddy, James A; others, : The immune landscape of cancer. In: Immunity, 48 (4), pp. 812–830, 2018. (Type: Journal Article | Links | BibTeX)
18. Ricketts, Christopher J; Cubas, Aguirre De A; Fan, Huihui; Smith, Christof C; Lang, Martin; Reznik, Ed; Bowlby, Reanne; Gibb, Ewan A; Akbani, Rehan; Beroukhim, Rameen; others, : The Cancer Genome Atlas Comprehensive Molecular Characterization of Renal Cell Carcinoma. In: Cell reports, 23 (1), pp. 313–326, 2018. (Type: Journal Article | Links | BibTeX)
19. Listgarten, Jennifer; Weinstein, Michael M; Kleinstiver, Benjamin P; Sousa, Alexander A; Joung, Keith J; Crawford, Jake; Gao, Kevin; Hoang, Luong; Elibol, Melih; Doench, John G; others, : Prediction of off-target activities for the end-to-end design of CRISPR guide RNAs. In: Nature Biomedical Engineering, 2 (1), pp. 38, 2018. (Type: Journal Article | Links | BibTeX)
20. Shi, Baochen; Leung, Donald YM; Taylor, Patricia A; Li, Huiying: Methicillin-Resistant Staphylococcus aureus Colonization Is Associated with Decreased Skin Commensal Bacteria in Atopic Dermatitis.. In: The Journal of investigative dermatology, 2018. (Type: Journal Article | Links | BibTeX)
132 entries « 1 of 7 »

132 entries « 1 of 3 »

2020

Bhat, Kruttika; Saki, Mohammad; Vlashi, Erina; Cheng, Fei; Duhachek-Muggy, Sara; Alli, Claudia; Yu, Garrett; Medina, Paul; He, Ling; Damoiseaux, Robert; Pellegrini, Matteo; Zemke, Nathan R; Nghiemphu, Phioanh Leia; Cloughesy, Timothy F; Liau, Linda M; Kornblum, Harley I; Pajonk, Frank

The dopamine receptor antagonist trifluoperazine prevents phenotype conversion and improves survival in mouse models of glioblastoma Journal Article

Proceedings of the National Academy of Sciences , 32358191 , 2020.

Abstract | Links | BibTeX | Tags: dedifferentiation; dopamine receptor antagonist; glioblastoma; glioma-initiating cells; radiation

Neal, Adam S; Nunez, Miguel; Lai, Tiffany; Tosevska, Anela; Morselli, Marco; Amneus, Malaika; Zakhour, Mae; Moatamed, Neda A; Pellegrini, Matteo; Memarzadeh, Sanaz

Expression of Stromal Progesterone Receptor and Differential Methylation Patterns in the Endometrium May Correlate with Response to Progesterone Therapy in Endometrial Complex Atypical Hyperplasia. Journal Article

Reproductive Sciences, 2020.

Abstract | Links | BibTeX | Tags: Biomarker, Endometrial hyperplasia, Hormonal therapy, Progesterone receptor, Progesterone therapy

Brito, Jaqueline J; Mosqueiro, Thiago; Rotman, Jeremy; Xue, Victor; Chapski, Douglas J; la Hoz, Juan De; Matias, Paulo; Martin, Lana S; Zelikovsky, Alex; Pellegrini, Matteo; Mangul, Serghei

Telescope: an interactive tool for managing large-scale analysis from mobile devices Journal Article

GigaScience, 9 (1), 2020.

Abstract | Links | BibTeX | Tags: DAG, directed acyclic graph, Graphical User Interface, GUI, Research Computing, Secure Shell, SGE, Sun Grid Engine, telescopes, VDI

2019

Lozano‐Huntelman, Natalie Ann; Singh, Nina; Valencia, Alondra; Mira, Portia; Sakayan, Maral; Boucher, Ian; Tang, Sharon; Brennan, Kelley; Gianvecchio, Crystal; Fitz‐Gibbon, Sorel; Yeh, Pamela

Evolution of Antibiotic Cross‐resistance and Collateral Sensitivity in Staphylococcus Epidermidis Using the Mutant Prevention Concentration and the Mutant Selection Window Journal Article

Evolutionary Applications, 2019.

Abstract | Links | BibTeX | Tags: antibiotic resistance, antimicrobial, bacterial evolution, correlated traits, susceptible

Galmozzi, Andrea; Kok, Bernard P; Kim, Arthur S; Montenegro-Burke, Rafael J; Lee, Jae Y; Spreafico, Roberto; Mosure, Sarah; Albert, Verena; Cintron-Colon, Rigo; Godio, Cristina; Webb, William R; Conti, Bruno; Solt, Laura A; Kojetin, Douglas; Parker, Christopher G; Peluso, John J; Pru, James K; Siuzdak, Gary; Cravatt, Benjamin F; Saez, Enrique

PGRMC2 is an intracellular haem chaperone critical for adipocyte function Journal Article

2019.

Abstract | Links | BibTeX | Tags: adipocytes, cytotoxic, gene, haem, haemoproteins, intracellular, molecules, proteins, signalling, thermogenesis

Kurmangaliyev, Yerbol Z; Yoo, Juyoun; LoCascio, Samuel A; Zipursky, Lawrence S

Modular transcriptional programs separately define axon and dendrite connectivity. Journal Article

eLife, 2019.

Abstract | Links | BibTeX | Tags: D. melanogaster; genetics; genomics; neuronal connectivity; neuroscience; single-cell sequencing; transcriptional programs

Bulterys, P L; Toesca, I J; Norris, M H; Maloy, J P; Fitz-Gibbon, S T; France, B; Toffig, B; Morselli, M; Somprasong, N; Pellegrini, M; Schweizer, H P; Tuanyok, A; Damoiseaux, R; French, C T; Miller, J F

An in situ high-throughput screen identifies inhibitors of intracellular Burkholderia pseudomallei with therapeutic efficacy. Journal Article

Proc Natl Acad Sci U S A. , 2019.

Abstract | Links | BibTeX | Tags: Burkholderia pseudomallei; drug discovery; melioidosis; small molecule; type 6 secretion system

Romero, Zulema; Lomova, Anastasia; Said, Suzanne; Miggelbrink, Alexandra; Kuo, Caroline Y; Campo-Fernandez, Beatriz; D.Hoban, Megan; E.Masiuk, Katelyn; N.Clark, Danielle; Long, Joseph; M.Sanchez, Julie; MiriamVelez, ; Miyahira, Eric; Zhang, Ruixue; Brown, Devin; Wang, Xiaoyan; Z.Kurmangaliyev, Yerbol; P.Hollis, Roger; B.Kohn., Donald

Editing the Sickle Cell Disease Mutation in Human Hematopoietic Stem Cells: Comparison of Endonucleases and Homologous Donor Templates. Journal Article

Molecular Therapy, 27 (8), pp. 1389-1406, 2019.

Abstract | Links | BibTeX | Tags: CRISPR/Cas9; adeno-associated virus 6; gene editing; hematopoietic stem cells; homologous recombination; non-homologous end joining; sickle cell disease; zinc finger nuclease

Cantarella, S; Carnevali, D; Morselli, M; Conti, A; Pellegrini, M; Montanini, B; Dieci, G

Alu RNA Modulates the Expression of Cell Cycle Genes in Human Fibroblasts. Journal Article

Int J Mol Sci. , 20 (13), 2019.

Abstract | Links | BibTeX | Tags: Alu retrotransposons; cell cycle; non-coding RNA

Leung CS, ; Douglass SM, ; Morselli M, ; Obusan MB, ; Pavlyukov MS, ; Pellegrini M, ; TL., Johnson

H3K36 Methylation and the Chromodomain Protein Eaf3 Are Required for Proper Cotranscriptional Spliceosome Assembly. Journal Article

Cell Rep. , 27 (13), pp. 3760-3769, 2019.

Abstract | Links | BibTeX | Tags: Eaf3; H3K36; Set2; chromatin; cotranscriptional splicing; methylation

2018

Pontrelli Sammy, ; Riley C. B. Fricke and Shao Thing Teoh, ; Walter A. Laviña, ; Sastia Prama Putri, ; Sorel Fitz-Gibbon, ; Matthew Chung, ; Matteo Pellegrini, ; Eiichiro Fukusaki, ; Liao, James C

Metabolic repair through emergence of new pathways in Escherichia coli Journal Article

Nature Chemical Biology, 14 (11), pp. 1005–1009, 2018.

Abstract | Links | BibTeX | Tags: e.coli, metabolic repair

Eagleman, Sarah L; Vaughn, Don A; Drover, David R; Drover, Caitlin M; Cohen, Mark S; Ouellette, Nicholas T; MacIver., Bruce M

Do Complexity Measures of Frontal EEG Distinguish Loss of Consciousness in Geriatric Patients Under Anesthesia? Journal Article

Frontiers in neuroscience, 12 , pp. 645, 2018.

Abstract | Links | BibTeX | Tags: anesthesia, electroencephalogram, entropy, geriatric, multiscale

Pontrelli Sammy, ; Riley C. B. Fricke, ; Memon, Sana Subhan; Sakurai, Sastia ; Prama Putri, ; Sorel Fitz-Gibbon, ; Matthew Chung, ; Hsin-Yi Wu,

Directed strain evolution restructures metabolism for 1-butanol production in minimal media Journal Article

Metabolic Engineering, 49 , pp. 153-163, 2018.

Abstract | Links | BibTeX | Tags: butanol, metabolomics, proteomics

Camacho, J; Truong, L; Kurt, Z; Chen, YW ; Morselli, M; Gutierrez, G; Pellegrini, M; Yang, X; Allard, P

The Memory of Environmental Chemical Exposure in C. elegans Is Dependent on the Jumonji Demethylases jmjd-2 and jmjd-3/utx-1. Journal Article

Cell Rep., 23 (8), pp. 2392-2404, 2018.

Abstract | Links | BibTeX | Tags: Bisphenol A; C. elegans; epigenetic; histone demethylase; reproductive function; transgenerational inheritance

Sarin, Sumeet; Zuniga-Sanchez, Elizabeth; Z.Kurmangaliyev, Yerbol; Cousins, Henry; Patel, Mili; Hernandez, Jeanette; X.Zhang, Kelvin; A.Samuel, Melanie; Morey, Marta; R.Sanes, Joshua; Zipursky, Lawrence

Role for Wnt Signaling in Retinal Neuropil Development: Analysis via RNA-Seq and In Vivo Somatic CRISPR Mutagenesis Journal Article

Neuron, 98 (1), pp. 109-126, 2018.

Abstract | Links | BibTeX | Tags: Fzd4; Fzd5; OPL; Ryk; Wnt5; bipolars; neuron; photoreceptors; retina; synapse

S, Ziyad; JD, Riordan; AM, Cavanaugh; T, Su; GE, Hernandez; G, Hilfenhaus; M, Morselli; K, Huynh; K, Wang; JN, Chen; AJ, Dupuy; ML., Iruela-Arispe

A Forward Genetic Screen Targeting the Endothelium Reveals a Regulatory Role for the Lipid Kinase Pi4ka in Myelo- and Erythropoiesis. Journal Article

Cell Rep. , 22 (5), pp. 1211-1224, 2018.

Abstract | Links | BibTeX | Tags: Akt; Erk; PI4KAP2; Pi4ka; erythropoiesis; hematopoiesis; hemogenic endothelium; leukemia; lipid kinase; myelopoiesis

Thorsson, Vésteinn; Gibbs, David L; Brown, Scott D; Wolf, Denise; Bortone, Dante S; Yang, Tai-Hsien Ou; Porta-Pardo, Eduard; Gao, Galen F; Plaisier, Christopher L; Eddy, James A; others,

The immune landscape of cancer Journal Article

Immunity, 48 (4), pp. 812–830, 2018.

Links | BibTeX | Tags:

Ricketts, Christopher J; Cubas, Aguirre De A; Fan, Huihui; Smith, Christof C; Lang, Martin; Reznik, Ed; Bowlby, Reanne; Gibb, Ewan A; Akbani, Rehan; Beroukhim, Rameen; others,

The Cancer Genome Atlas Comprehensive Molecular Characterization of Renal Cell Carcinoma Journal Article

Cell reports, 23 (1), pp. 313–326, 2018.

Links | BibTeX | Tags:

Listgarten, Jennifer; Weinstein, Michael M; Kleinstiver, Benjamin P; Sousa, Alexander A; Joung, Keith J; Crawford, Jake; Gao, Kevin; Hoang, Luong; Elibol, Melih; Doench, John G; others,

Prediction of off-target activities for the end-to-end design of CRISPR guide RNAs Journal Article

Nature Biomedical Engineering, 2 (1), pp. 38, 2018.

Links | BibTeX | Tags: CRISPR

Shi, Baochen; Leung, Donald YM; Taylor, Patricia A; Li, Huiying

Methicillin-Resistant Staphylococcus aureus Colonization Is Associated with Decreased Skin Commensal Bacteria in Atopic Dermatitis. Journal Article

The Journal of investigative dermatology, 2018.

Links | BibTeX | Tags: bacteria

Fraser, Devaughn; Mouton, Alice; Serieys, Laurel EK; Cole, Steve; Carver, Scott; Vandewoude, Sue; Lappin, Michael; Riley, Seth PD; Wayne, Robert

Genome-wide expression reveals multiple systemic effects associated with detection of anticoagulant poisons in bobcats (Lynx rufus) Journal Article

Molecular ecology, 27 (5), pp. 1170–1187, 2018.

Links | BibTeX | Tags: GWAS

Ziyad, Safiyyah; Riordan, Jesse D; Cavanaugh, Ann M; Su, Trent; Hernandez, Gloria E; Hilfenhaus, Georg; Morselli, Marco; Huynh, Kristine; Wang, Kevin; Chen, Jau-Nian; others,

A Forward Genetic Screen Targeting the Endothelium Reveals a Regulatory Role for the Lipid Kinase Pi4ka in Myelo-and Erythropoiesis Journal Article

Cell reports, 22 (5), pp. 1211–1224, 2018.

Links | BibTeX | Tags: cancer, gene mutation, leukemia, RNA-seq

Ko, Albert; Venkatesan, Natarajan; Chatoff, Jenna; Morselli, Marco; Fishbein, Gregory; Bomont, Pascale; Pellegrini, Matteo; Wang, Marilene; Srivatsan, Eri

GAN gene exon 8 SNP is related to gigaxonin expression and increased expression of e-cadherin in head and neck cancer Miscellaneous

2018.

Links | BibTeX | Tags:

Khalid, Aysha B; Slayden, Alexandria V; Kumpati, Jerusha; Perry, Chanel D; Berryhill, Stuart B; Crawford, Julie A; Fatima, Iram; Morselli, Marco; Pellegrini, Matteo; Miranda-Carboni, Gustavo A; others,

GATA4 represses RANKL via multiple long-range enhancers to regulate osteoclast differentiation Journal Article

Bone, 2018.

Links | BibTeX | Tags:

Borgognone, Alessandra; Castanera, Raul; Morselli, Marco; López-Varas, Leticia; Rubbi, Liudmilla; Pisabarro, Antonio G; Pellegrini, Matteo; Ramirez, Lucia

Transposon-associated epigenetic silencing during Pleurotus ostreatus life cycle Journal Article

DNA Research, 2018.

Links | BibTeX | Tags:

Mitchell, Simon; Roy, Koushik; Zangle, Thomas A; Hoffmann, Alexander

Nongenetic origins of cell-to-cell variability in B lymphocyte proliferation Journal Article

Proceedings of the National Academy of Sciences, 115 (12), pp. E2888–E2897, 2018.

Links | BibTeX | Tags:

Roy, Koushik; Shokhirev, Maxim Nikolaievich; Mitchell, Simon; Hoffmann, Alexander

Deriving Quantitative Cell Biological Information from Dye-Dilution Lymphocyte Proliferation Experiments Incollection

B Cell Receptor Signaling, pp. 81–94, Springer, 2018.

Links | BibTeX | Tags:

Gangalum, Rajendra K; Kim, Dongjae; Kashyap, Raj K; Mangul, Serghei; Zhou, Xinkai; Elashoff, David; Bhat, Suraj

Spatial Analysis of Single Fiber Cells of the Developing Ocular Lens Reveals Regulated Heterogeneity of Gene Expression Journal Article

Available at SSRN 3205412, 2018.

Links | BibTeX | Tags:

Mangul, Serghei; Martin, Lana S; Eskin, Eleazar

Involving undergraduates in genomics research to narrow the education--research gap Journal Article

Nature biotechnology, 36 (4), pp. 369, 2018.

Links | BibTeX | Tags: education, training

Lay, Fides D; Kelly, Theresa K; Jones, Peter A

Nucleosome Occupancy and Methylome Sequencing (NOMe-seq) Incollection

DNA Methylation Protocols, pp. 267–284, Springer, 2018.

Links | BibTeX | Tags:

Miao, Jianwei; Pryor, Alan; Yang, Yongsoo; Rana, Arjun; Gallagher-Jones, Marcus; Zhou, Jihan; Lo, Yuan Hung; Rodriguez, Jose A; Chiu, Wah

GENFIRE: from Precisely Localizing Single Atoms in Materials to High Resolution 3D Imaging of Cellular Structures Journal Article

Microscopy and Microanalysis, 24 (S1), pp. 1446–1447, 2018.

Links | BibTeX | Tags:

Pryor, Alan; Rana, Arjun; Xu, Rui; Rodriguez, Jose A; Yang, Yongsoo; Gallagher-Jones, Marcus; Jiang, Huaidong; Kanhaiya, Krishan; Nathanson, Michael; Park, Jae Hyun; others,

Single-shot 3D coherent diffractive imaging of core-shell nanoparticles with elemental specificity Journal Article

Scientific reports, 8 (1), pp. 8284, 2018.

Links | BibTeX | Tags:

Lo, Yuan Hung; Zhao, Lingrong; Gallagher-Jones, Marcus; Rana, Arjun; Lodico, Jared; Xiao, Weikun; Regan, BC; Miao, Jianwei

In situ coherent diffractive imaging Journal Article

Nature communications, 9 (1), pp. 1826, 2018.

Links | BibTeX | Tags:

Park, Shuin; Ranjbarvazirj, Sara; Lay, Fides D; Zhao, Peng; Miller, Mark J; Dhaliwal, Jasmeet S; Huertas-Vazquez, Adriana; Wu, Xiuju; Qiao, Rong; Soffer, Justin M; others,

Genetic Regulation of Fibroblast Activation and Proliferation in Cardiac Fibrosis Journal Article

Circulation, pp. CIRCULATIONAHA–118, 2018.

Links | BibTeX | Tags:

Cheng, Lucy; Marinelli, Laura J; Grosset, Noel; Fitz-Gibbon, Sorel T; Bowman, Charles A; Dang, Brian Q; Russell, Daniel A; Jacobs-Sera, Deborah; Shi, Baochen; Pellegrini, Matteo; others,

Complete genomic sequences of Propionibacterium freudenreichii phages from Swiss cheese reveal greater diversity than Cutibacterium (formerly Propionibacterium) acnes phages Journal Article

BMC microbiology, 18 (1), pp. 19, 2018.

Links | BibTeX | Tags: bacteria

Vaughn, Don A; van Deen, Welmoed K; Kerr, Wesley T; Meyer, Travis R; Bertozzi, Andrea L; Hommes, Daniel W; Cohen, Mark Steven

Using insurance claims to predict and improve hospitalizations and biologics use in members with inflammatory bowel diseases Journal Article

Journal of biomedical informatics, 81 , pp. 93–101, 2018.

Links | BibTeX | Tags:

Loohuis, Loes Olde M; Mangul, Serghei; Ori, Anil PS; Jospin, Guillaume; Koslicki, David; Yang, Harry Taegyun; Wu, Timothy; Boks, Marco P; Lomen-Hoerth, Catherine; Wiedau-Pazos, Martina; others,

Transcriptome analysis in whole blood reveals increased microbial diversity in schizophrenia Journal Article

Translational psychiatry, 8 (1), pp. 96, 2018.

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Mangul, Serghei; Yang, Harry Taegyun; Strauli, Nicolas; Gruhl, Franziska; Porath, Hagit T; Hsieh, Kevin; Chen, Linus; Daley, Timothy; Christenson, Stephanie; Wesolowska-Andersen, Agata; others,

ROP: Dumpster Diving in RNA-sequencing to find the source of 1 trillion reads across diverse adult human tissues Journal Article

Genome biology, 19 (1), pp. 36, 2018.

Links | BibTeX | Tags:

Vaughn, Don A; Savjani, Ricky R; Cohen, Mark Steven; Eagleman, David M

Empathic neural responses predict group allegiance Journal Article

Frontiers in Human Neuroscience, 12 , pp. 302, 2018.

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Shirali, Aditya S; Romay, Milagros C; McDonald, Austin I; Su, Trent; Steel, Michelle E; Iruela-Arispe, Luisa M

A multi-step transcriptional cascade underlies vascular regeneration in vivo Journal Article

Scientific reports, 8 (1), pp. 5430, 2018.

Links | BibTeX | Tags: endothelial growth, Galaxy, gene expression, RNA-seq, wound repair

Gallagher-Jones, Marcus; Glynn, Calina; Boyer, David R; Martynowycz, Michael W; Hernandez, Evelyn; Miao, Jennifer; Zee, Chih-Te; Novikova, Irina V; Goldschmidt, Lukasz; McFarlane, Heather T; others,

Sub-ångström cryo-EM structure of a prion protofibril reveals a polar clasp Journal Article

Nature structural & molecular biology, 25 (2), pp. 131, 2018.

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Buckner, Janet C; Ellingson, Ryan; Gold, David A; Jones, Terry L; Jacobs, David K

Mitogenomics supports an unexpected taxonomic relationship for the extinct diving duck Chendytes lawi and definitively places the extinct Labrador Duck Journal Article

Molecular phylogenetics and evolution, 122 , pp. 102–109, 2018.

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Hattne, Johan; Shi, Dan; Glynn, Calina; Zee, Chih-Te; Gallagher-Jones, Marcus; Martynowycz, Michael W; Rodriguez, Jose A; Gonen, Tamir

Analysis of global and site-specific radiation damage in cryo-EM Journal Article

Structure, 26 (5), pp. 759–766, 2018.

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McDonald, Austin I; Shirali, Aditya S; Aragón, Raquel L; Ma, Feiyang; Hernandez, Gloria E; Vaughn, Don A; Mack, Julia J; Lim, Tiffany Y; Sunshine, Hannah; Zhao, Peng; others,

Endothelial regeneration of large vessels is a biphasic process driven by local cells with distinct proliferative capacities Journal Article

Cell stem cell, 23 (2), pp. 210–225, 2018.

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Merkurjev, Daria; Hong, Wan-Ting; Iida, Kei; Oomoto, Ikumi; Goldie, Belinda J; Yamaguti, Hitoshi; Ohara, Takayuki; Kawaguchi, Shin-ya; Hirano, Tomoo; Martin, Kelsey C; others,

Synaptic N 6-methyladenosine (m 6 A) epitranscriptome reveals functional partitioning of localized transcripts Journal Article

Nature neuroscience, pp. 1, 2018.

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Gallaher, Sean D; Fitz-Gibbon, Sorel T; Strenkert, Daniela; Purvine, Samuel O; Pellegrini, Matteo; Merchant, Sabeeha S

High-throughput sequencing of the chloroplast and mitochondrion of Chlamydomonas reinhardtii to generate improved de novo assemblies, analyze expression patterns and transcript speciation, and evaluate diversity among laboratory strains and wild isolates Journal Article

The Plant Journal, 93 (3), pp. 545–565, 2018.

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Kuo, Caroline Y; Long, Joseph D; Campo-Fernandez, Beatriz; de Oliveira, Satiro; Cooper, Aaron R; Romero, Zulema; Hoban, Megan D; Joglekar, Alok V; Lill, Georgia R; Kaufman, Michael L; others,

Site-Specific Gene Editing of Human Hematopoietic Stem Cells for X-Linked Hyper-IgM Syndrome Journal Article

Cell reports, 23 (9), pp. 2606–2616, 2018.

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Gusev, Alexander; Mancuso, Nicholas; Won, Hyejung; Kousi, Maria; Finucane, Hilary K; Reshef, Yakir; Song, Lingyun; Safi, Alexias; McCarroll, Steven; Neale, Benjamin M; others,

Transcriptome-wide association study of schizophrenia and chromatin activity yields mechanistic disease insights Journal Article

Nature genetics, 50 (4), pp. 538, 2018.

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Fejzo, Marlena S; Sazonova, Olga V; Sathirapongsasuti, Fah J; Hallgr'imsdóttir, Ingileif B; Vacic, Vladimir; MacGibbon, Kimber W; Schoenberg, Frederic P; Mancuso, Nicholas; Slamon, Dennis J; Mullin, Patrick M

Placenta and appetite genes GDF15 and IGFBP7 are associated with hyperemesis gravidarum Journal Article

Nature communications, 9 (1), pp. 1178, 2018.

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Garrett, Matthew; Sperry, Jantzen; Braas, Daniel; Yan, Weihong; Le, Thuc M; Mottahedeh, Jack; Ludwig, Kirsten; Eskin, Ascia; Qin, Yue; Levy, Rachelle; others,

Metabolic characterization of isocitrate dehydrogenase (IDH) mutant and IDH wildtype gliomaspheres uncovers cell type-specific vulnerabilities Journal Article

Cancer & metabolism, 6 (1), pp. 4, 2018.

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