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

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

114 entries « 1 of 3 »

2018

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

Camacho, Jessica; Truong, Lisa; Kurt, Zeyneb; Chen, Yen-Wei; Morselli, Marco; Gutierrez, Gerardo; Pellegrini, Matteo; Yang, Xia; Allard, Patrick

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 reports, 23 (8), pp. 2392–2404, 2018.

Links | BibTeX | Tags:

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.

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

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.

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

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.

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

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

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

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

Links | BibTeX | Tags:

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.

Links | BibTeX | Tags:

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.

Links | BibTeX | Tags:

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.

Links | BibTeX | Tags:

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.

Links | BibTeX | Tags:

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.

Links | BibTeX | Tags:

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.

Links | BibTeX | Tags:

Feusner, Jamie D; Kerr, Wesley T; Moody, Teena D; Zhang, Aifeng F; Cohen, Mark S; Leow, Alex D; Strober, Michael A; Vaughn, Don A

Cross-diagnostic Prediction of Dimensional Psychiatric Phenotypes in Anorexia Nervosa and Body Dysmorphic Disorder Using Multimodal Neuroimaging and Psychometric Data Incollection

Graphs in Biomedical Image Analysis and Integrating Medical Imaging and Non-Imaging Modalities, pp. 92–99, Springer, 2018.

Links | BibTeX | Tags:

McDonald, Austin I; Shirali, Aditya S; Aragón, Raquel; Ma, Feiyang; Hernandez, Gloria; 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.

Links | BibTeX | Tags:

2017

Wu, Ye Emily; Pan, Lin; Zuo, Yanning; Li, Xinmin; Hong, Weizhe

Detecting activated cell populations using single-cell RNA-seq Journal Article

Neuron, 96 (2), pp. 313–329, 2017.

Links | BibTeX | Tags:

Xue, Yong; Pradhan, Suman K; Sun, Fei; Chronis, Constantinos; Tran, Nancy; Su, Trent; Van, Christopher; Vashisht, Ajay A; Wohlschlegel, James; Peterson, Craig L; others,

Mot1, Ino80C, and NC2 function coordinately to regulate pervasive transcription in yeast and mammals Journal Article

Molecular cell, 67 (4), pp. 594–607, 2017.

Links | BibTeX | Tags:

Olivera-Perez, Henry M; Lam, Larry; Dang, Johnny; Jiang, Weilan; Rodriguez, Fabian; Rigali, Elizabeth; Weitzman, Sarah; Porter, Verna; Rubbi, Liudmilla; Morselli, Marco; others,

Omega-3 fatty acids increase the unfolded protein response and improve amyloid-$beta$ phagocytosis by macrophages of patients with mild cognitive impairment Journal Article

The FASEB Journal, 31 (10), pp. 4359–4369, 2017.

Links | BibTeX | Tags:

Nakano, Haruko; Minami, Itsunari; Braas, Daniel; Pappoe, Herman; Wu, Xiuju; Sagadevan, Addelynn; Vergnes, Laurent; Fu, Kai; Morselli, Marco; Ding, Xueqin; others,

Glucose Inhibits Cardiomyocyte Maturation Through Nucleotide Biosynthesis Journal Article

Circulation Research, 121 (Suppl_1), pp. A346, 2017.

Links | BibTeX | Tags:

Saha, Ashis; Kim, Yungil; Gewirtz, Ariel DH; Jo, Brian; Gao, Chuan; McDowell, Ian C; Engelhardt, Barbara E; Battle, Alexis; ç, Fran; Ardlie, Kristin G; others,

Co-expression networks reveal the tissue-specific regulation of transcription and splicing Journal Article

Genome research, 2017.

Links | BibTeX | Tags:

Neben, Cynthia L; Tuzon, Creighton T; Mao, Xiaojing; Lay, Fides D; Merrill, Amy E

FGFR2 mutations in bent bone dysplasia syndrome activate nucleolar stress and perturb cell fate determination Journal Article

Human molecular genetics, 26 (17), pp. 3253–3270, 2017.

Links | BibTeX | Tags:

Neben, Cynthia L; Lay, Fides D; Mao, Xiaojing; Tuzon, Creighton T; Merrill, Amy E

Ribosome biogenesis is dynamically regulated during osteoblast differentiation Journal Article

Gene, 612 , pp. 29–35, 2017.

Links | BibTeX | Tags:

Helbo, Alexandra Søgaard; Lay, Fides D; Jones, Peter A; Liang, Gangning; æ, Kirsten Grønb

Nucleosome positioning and NDR structure at RNA polymerase III promoters Journal Article

Scientific reports, 7 , pp. 41947, 2017.

Links | BibTeX | Tags:

Luo, Zhifei; Rhie, Suhn Kyong; Lay, Fides D; Farnham, Peggy J

A prostate cancer risk element functions as a repressive loop that regulates HOXA13 Journal Article

Cell reports, 21 (6), pp. 1411–1417, 2017.

Links | BibTeX | Tags:

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

GENFIRE: A generalized Fourier iterative reconstruction algorithm for high-resolution 3D imaging Journal Article

Scientific reports, 7 (1), pp. 10409, 2017.

Links | BibTeX | Tags:

Kim, Yoonhee; Kim, Chan; Kwon, Ou Young; Nam, Daewoong; Kim, Sang Soo; Park, Jae Hyun; Kim, Sunam; Gallagher-Jones, Marcus; Kohmura, Yoshiki; Ishikawa, Tetsuya; others,

Visualization of a Mammalian Mitochondrion by Coherent X-ray Diffractive Imaging Journal Article

Scientific reports, 7 (1), pp. 1850, 2017.

Links | BibTeX | Tags:

Gallagher-Jones, Marcus; Dias, Carlos Sato Baraldi; Pryor, Alan; Bouchmella, Karim; Zhao, Lingrong; Lo, Yuan Hung; Cardoso, Mateus Borba; Shapiro, David; Rodriguez, Jose A; Miao, Jianwei

Correlative cellular ptychography with functionalized nanoparticles at the Fe L-edge Journal Article

Scientific reports, 7 (1), pp. 4757, 2017.

Links | BibTeX | Tags:

Dessalles, Renaud; Fromion, Vincent; Robert, Philippe

A stochastic analysis of autoregulation of gene expression Journal Article

Journal of mathematical biology, 75 (5), pp. 1253–1283, 2017.

Links | BibTeX | Tags:

114 entries « 1 of 3 »