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

137 entries « 1 of 7 »
1.

Eric Y. Lin Paul C Adamson, Sung-Min Ha

Using a public database of Neisseria gonorrhoeae genomes to detect mutations associated with zoliflodacin resistance Journal Article

In: Journal of Antimicrobial Chemotherapy, (dkab262), 2021.

Abstract | Links | BibTeX

2.

D. A. Vaughn, Maggiora

Modulation of attention and stress with arousal: The mental and physical effects of riding a motorcycle Journal Article

In: Brain Research, 1752 (147203), 2021.

Abstract | Links | BibTeX

3.

Perri, Angela R; Mitchell, Kieren J.; Mouton, Alice and

Dire wolves were the last of an ancient New World canid lineage Journal Article

In: Nature, 2021.

Abstract | Links | BibTeX

4.

Eagleman, David M.; Vaughn, Don A.

The Defensive Activation theory: dreaming as a mechanism to prevent takeover of the visual cortex Journal Article

In: bioRxiv , 2020.

Abstract | Links | BibTeX

5.

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

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

Abstract | Links | BibTeX

6.

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

In: Reproductive Sciences, 2020.

Abstract | Links | BibTeX

7.

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

In: GigaScience, 9 (1), 2020.

Abstract | Links | BibTeX

8.

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

In: Evolutionary Applications, 2019.

Abstract | Links | BibTeX

9.

Galmozzi, Andrea; Kok, Bernard P.; Kim, Arthur S.; Montenegro-Burke, J. Rafael; 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

In: 2019.

Abstract | Links | BibTeX

10.

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

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

In: eLife, 2019.

Abstract | Links | BibTeX

11.

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

In: Proc Natl Acad Sci U S A. , 2019.

Abstract | Links | BibTeX

12.

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

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

Abstract | Links | BibTeX

13.

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

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

Abstract | Links | BibTeX

14.

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

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

Abstract | Links | BibTeX

15.

Sammy Pontrelli,; and Shao Thing Teoh Riley C. B. Fricke,; 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

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

Abstract | Links | BibTeX

16.

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

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

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

Abstract | Links | BibTeX

17.

Sammy Pontrelli,; 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

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

Abstract | Links | BibTeX

18.

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

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

Abstract | Links | BibTeX

19.

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

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

Abstract | Links | BibTeX

20.

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

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

Abstract | Links | BibTeX

137 entries « 1 of 7 »

137 entries « 1 of 3 »

2021

Eric Y. Lin Paul C Adamson, Sung-Min Ha

Using a public database of Neisseria gonorrhoeae genomes to detect mutations associated with zoliflodacin resistance Journal Article

In: Journal of Antimicrobial Chemotherapy, (dkab262), 2021.

Abstract | Links | BibTeX | Tags: Antimicrobial resistance

D. A. Vaughn, Maggiora

Modulation of attention and stress with arousal: The mental and physical effects of riding a motorcycle Journal Article

In: Brain Research, 1752 (147203), 2021.

Abstract | Links | BibTeX | Tags: arousal., Modulation, stress

Perri, Angela R; Mitchell, Kieren J.; Mouton, Alice and

Dire wolves were the last of an ancient New World canid lineage Journal Article

In: Nature, 2021.

Abstract | Links | BibTeX | Tags: Evolutionary genetics, Palaeontology, Phylogenetics, Speciation

2020

Eagleman, David M.; Vaughn, Don A.

The Defensive Activation theory: dreaming as a mechanism to prevent takeover of the visual cortex Journal Article

In: bioRxiv , 2020.

Abstract | Links | BibTeX | Tags: REM, visual cortex

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

In: 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

In: 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

In: 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

In: 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, J. Rafael; 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

In: 2019.

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

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

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

In: 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

In: 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

In: 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

In: 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

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

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

2018

Sammy Pontrelli,; and Shao Thing Teoh Riley C. B. Fricke,; 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

In: 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., M. Bruce

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

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

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

Sammy Pontrelli,; 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

In: 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

In: 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

In: 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

In: 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

In: Immunity, 48 (4), pp. 812–830, 2018.

Links | BibTeX | Tags:

Ricketts, Christopher J; Cubas, Aguirre A De; 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

In: 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

In: 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

In: 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

In: 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

In: 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

In: 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

In: 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

In: 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

In: 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

In: 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

In: 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

In: 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

In: 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

In: 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

In: 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

In: 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

In: 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

In: 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

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

Links | BibTeX | Tags:

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

In: 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

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

Links | BibTeX | Tags:

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

In: 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

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

Links | BibTeX | Tags:

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

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

Links | BibTeX | Tags:

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

In: Structure, 26 (5), pp. 759–766, 2018.

Links | BibTeX | Tags:

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

In: 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

In: 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

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

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