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

116 entries « 2 of 3 »

2017

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.

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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.

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Cloez, Bertrand; Dessalles, Renaud; Genadot, Alexandre; Malrieu, Florent; Marguet, Aline; Yvinec, Romain

Probabilistic and piecewise deterministic models in biology Journal Article

ESAIM: Proceedings and Surveys, 60 , pp. 225–245, 2017.

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Mangul, Serghei; Martin, Lana S; Hoffmann, Alexander; Pellegrini, Matteo; Eskin, Eleazar

Addressing the digital divide in contemporary biology: lessons from teaching UNIX Journal Article

Trends in biotechnology, 35 (10), pp. 901–903, 2017.

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Gang, Spencer S; Castelletto, Michelle L; Bryant, Astra S; Yang, Emily; Mancuso, Nicholas; Lopez, Jacqueline B; Pellegrini, Matteo; Hallem, Elissa A

Targeted mutagenesis in a human-parasitic nematode Journal Article

PLoS pathogens, 13 (10), pp. e1006675, 2017.

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Patel, Sanjeet; Bonora, Giancarlo; Sahakyan, Anna; Kim, Rachel; Chronis, Constantinos; Langerman, Justin; Fitz-Gibbon, Sorel T; Rubbi, Liudmilla; Skelton, Rhys JP; Ardehali, Reza; others,

Human embryonic stem cells do not change their X inactivation status during differentiation Journal Article

Cell reports, 18 (1), pp. 54–67, 2017.

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Mack, Julia J; Mosqueiro, Thiago S; Archer, Brian J; Jones, William M; Sunshine, Hannah; Faas, Guido C; Briot, Anais; Aragón, Raquel L; Su, Trent; Romay, Milagros C; others,

NOTCH1 is a mechanosensor in adult arteries Journal Article

Nature communications, 8 (1), pp. 1620, 2017.

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Zhen, Ying; Harrigan, Ryan J; Ruegg, Kristen C; Anderson, Eric C; Ng, Thomas C; Lao, Sirena; Lohmueller, Kirk E; Smith, Thomas B

Genomic divergence across ecological gradients in the Central African rainforest songbird (A ndropadus virens) Journal Article

Molecular ecology, 26 (19), pp. 4966–4977, 2017.

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Thompson, Michael J; others,

An epigenetic aging clock for dogs and wolves Journal Article

Aging (Albany NY), 9 (3), pp. 1055, 2017.

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Scumpia, Philip O; Botten, Giovanni A; Norman, Joshua S; Kelly-Scumpia, Kindra M; Spreafico, Roberto; Ruccia, Amber R; Purbey, Prabhat K; Thomas, Brandon J; Modlin, Robert L; Smale, Stephen T

Opposing roles of Toll-like receptor and cytosolic DNA-STING signaling pathways for Staphylococcus aureus cutaneous host defense Journal Article

PLoS pathogens, 13 (7), pp. e1006496, 2017.

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Huang, Chengyang; Su, Trent; Xue, Yong; Cheng, Chen; Lay, Fides D; McKee, Robin A; Li, Meiyang; Vashisht, Ajay A; Wohlschlegel, James; Novitch, Bennett G; others,

Cbx3 maintains lineage specificity during neural differentiation Journal Article

Genes & development, 31 (3), pp. 241–246, 2017.

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Mognol, Giuliana P; Spreafico, Roberto; Wong, Victor; Scott-Browne, James P; Togher, Susan; Hoffmann, Alexander; Hogan, Patrick G; Rao, Anjana; Trifari, Sara

Exhaustion-associated regulatory regions in CD8+ tumor-infiltrating T cells Journal Article

Proceedings of the National Academy of Sciences, 114 (13), pp. E2776–E2785, 2017.

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Cheng, Christine S; Behar, Marcelo S; Suryawanshi, Gajendra W; Feldman, Kristyn E; Spreafico, Roberto; Hoffmann, Alexander

Sequential rather than coincident molecular mechanisms govern the combinatorial control logic underlying pathogen-responsive gene expression programs Journal Article

Cell systems, 4 (3), pp. 330, 2017.

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Neves, Lauren T; Douglass, Stephen; Spreafico, Roberto; Venkataramanan, Srivats; Kress, Tracy L; Johnson, Tracy L

The histone variant H2A. Z promotes efficient cotranscriptional splicing in S. cerevisiae Journal Article

Genes & development, 31 (7), pp. 702–717, 2017.

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Cheng, Christine S; Behar, Marcelo S; Suryawanshi, Gajendra W; Feldman, Kristyn E; Spreafico, Roberto; Hoffmann, Alexander

Iterative modeling reveals evidence of sequential transcriptional control mechanisms Journal Article

Cell systems, 4 (3), pp. 330–343, 2017.

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Xi, Haibin; Fujiwara, Wakana; Gonzalez, Karen; Jan, Majib; Liebscher, Simone; Handel, Ben Van; Schenke-Layland, Katja; Pyle, April D

In vivo human somitogenesis guides somite development from hPSCs Journal Article

Cell reports, 18 (6), pp. 1573–1585, 2017.

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Le, Thuc M; Poddar, Soumya; Capri, Joseph R; Abt, Evan R; Kim, Woosuk; Wei, Liu; Uong, Nhu T; Cheng, Chloe M; Braas, Daniel; Nikanjam, Mina; others,

ATR inhibition facilitates targeting of leukemia dependence on convergent nucleotide biosynthetic pathways Journal Article

Nature communications, 8 (1), pp. 241, 2017.

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Ding, Yi; Ploper, Diego; Sosa, Eric A; Colozza, Gabriele; Moriyama, Yuki; Benitez, Maria DJ; Zhang, Kelvin; Merkurjev, Daria; Robertis, Edward De M

Spemann organizer transcriptome induction by early beta-catenin, Wnt, Nodal, and Siamois signals in Xenopus laevis Journal Article

Proceedings of the National Academy of Sciences, 114 (15), pp. E3081–E3090, 2017.

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Hovelson, Daniel H; Liu, Chia-Jen; Wang, Yugang; Kang, Qing; Henderson, James; Gursky, Amy; Brockman, Scott; Ramnath, Nithya; Krauss, John C; Talpaz, Moshe; others,

Rapid, ultra low coverage copy number profiling of cell-free DNA as a precision oncology screening strategy Journal Article

Oncotarget, 8 (52), pp. 89848, 2017.

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Stires, Hillary; Heckler, Mary M; Fu, Xiaoyong; Li, Zhao; Grasso, Catherine S; Quist, Michael J; Lewis, Joseph A; Klimach, Uwe; Zwart, Alan; Mahajan, Akanksha; others,

Integrated molecular analysis of Tamoxifen-resistant invasive lobular breast cancer cells identifies MAPK and GRM/mGluR signaling as therapeutic vulnerabilities Journal Article

Molecular and cellular endocrinology, 2017.

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Fitz-Gibbon, Sorel T; Hipp, Andrew L; Pham, Kasey K; Manos, Paul S; Sork, Victoria L

Phylogenomic inferences from reference-mapped and de novo assembled short-read sequence data using RADseq sequencing of California white oaks (Quercus section Quercus) Journal Article

Genome, 60 (9), pp. 743–755, 2017.

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Shi, Huwenbo; Mancuso, Nicholas; Spendlove, Sarah; Pasaniuc, Bogdan

Local genetic correlation gives insights into the shared genetic architecture of complex traits Journal Article

The American Journal of Human Genetics, 101 (5), pp. 737–751, 2017.

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Hellwege, Jacklyn N; Jeff, Janina M; Wise, Lauren A; Gallagher, Scott C; Wellons, Melissa; Hartmann, Katherine E; Jones, Sarah F; Torstenson, Eric S; Dickinson, Scott; Ruiz-Narváez, Edward A; others,

A multi-stage genome-wide association study of uterine fibroids in African Americans Journal Article

Human genetics, 136 (10), pp. 1363–1373, 2017.

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Brown, Robert; Kichaev, Gleb; Mancuso, Nicholas; Boocock, James; Pasaniuc, Bogdan

Enhanced methods to detect haplotypic effects on gene expression Journal Article

Bioinformatics, 33 (15), pp. 2307–2313, 2017.

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Mancuso, Nicholas; Shi, Huwenbo; Goddard, Pagé; Kichaev, Gleb; Gusev, Alexander; Pasaniuc, Bogdan

Integrating gene expression with summary association statistics to identify genes associated with 30 complex traits Journal Article

The American Journal of Human Genetics, 100 (3), pp. 473–487, 2017.

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2016

Weinstein, Michael M; Kang, Taekyu; Lachman, Ralph S; Bamshad, Michael; Nickerson, Deborah A; Krakow, Deborah; Cohn, Daniel H

Somatic mosaicism for a lethal TRPV4 mutation results in non-lethal metatropic dysplasia Journal Article

American Journal of Medical Genetics Part A, 170 (12), pp. 3298–3302, 2016.

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Pradhan, Suman K; Su, Trent; Yen, Linda; Jacquet, Karine; Huang, Chengyang; Cote, Jacques; Kurdistani, Siavash K; Carey, Michael F

EP400 deposits H3. 3 into promoters and enhancers during gene activation Journal Article

Molecular cell, 61 (1), pp. 27–38, 2016.

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Xu, Heng-hao; Su, Trent; Xue, Yong

Histone H3 N-terminal acetylation sites especially K14 are important for rDNA silencing and aging Journal Article

Scientific reports, 6 , pp. 21900, 2016.

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Wang, Wenyuan; Org, Tonis; Montel-Hagen, Amélie; Pioli, Peter D; Duan, Dan; Israely, Edo; Malkin, Daniel; Su, Trent; Flach, Johanna; Kurdistani, Siavash K; others,

MEF2C protects bone marrow B-lymphoid progenitors during stress haematopoiesis Journal Article

Nature communications, 7 , pp. 12376, 2016.

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Chai, Yang D; Zhang, Lifeng; Yang, Yan; Su, Trent; Charugundla, Prashant; Ai, Jiye; Messadi, Diana; Wong, David T; Hu, Shen

Discovery of potential serum protein biomarkers for lymph node metastasis in oral cancer Journal Article

Head & neck, 38 (1), pp. 118–125, 2016.

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Pradhan, Suman K; Su, Trent; Yen, Linda; Jacquet, Karine; Huang, Chengyang; Cote, Jacques; Kurdistani, Siavash K; Carey, Michael F

EP400 deposits H3. 3 into promoters and enhancers during gene activation Journal Article

Molecular cell, 61 (1), pp. 27–38, 2016.

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Shi, Baochen; Wu, Tingxi; McLean, Jeffrey; Edlund, Anna; Young, Youngik; He, Xuesong; Lv, Hongyang; Zhou, Xuedong; Shi, Wenyuan; Li, Huiying; others,

The denture-associated oral microbiome in health and stomatitis Journal Article

mSphere, 1 (6), pp. e00215–16, 2016.

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Shi, Baochen; Bangayan, Nathanael J; Curd, Emily; Taylor, Patricia A; Gallo, Richard L; Leung, Donald YM; Li, Huiying

The skin microbiome is different in pediatric versus adult atopic dermatitis Journal Article

Journal of Allergy and Clinical Immunology, 138 (4), pp. 1233–1236, 2016.

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Barnard, Emma; Shi, Baochen; Kang, Dezhi; Craft, Noah; Li, Huiying

The balance of metagenomic elements shapes the skin microbiome in acne and health Journal Article

Scientific reports, 6 , pp. 39491, 2016.

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Mitchell, Simon; Vargas, Jesse; Hoffmann, Alexander

Signaling via the NF$kappa$B system Journal Article

Wiley Interdisciplinary Reviews: Systems Biology and Medicine, 8 (3), pp. 227–241, 2016.

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Kang, Eun Yong; Martin, Lisa; Mangul, Serghei; Isvilanonda, Warin; Zou, Jennifer; Ben-David, Eyal; Han, Buhm; Lusis, Aldons J; Shifman, Sagiv; Eskin, Eleazar

Discovering SNPs Regulating Human Gene Expression Using Allele Specific Expression from RNA-Seq Data Journal Article

Genetics, pp. genetics–115, 2016.

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Mangul, Serghei; Yang, Harry Taegyun; Hormozdiari, Farhad; Tseng, Elizabeth; Zelikovsky, Alex; Eskin, Eleazar

Hapiso: An accurate method for the haplotype-specific isoforms reconstruction from long single-molecule reads Inproceedings

International Symposium on Bioinformatics Research and Applications, pp. 80–92, Springer 2016.

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Artyomenko, Alexander; Wu, Nicholas C; Mangul, Serghei; Eskin, Eleazar; Sun, Ren; Zelikovsky, Alex

Long single-molecule reads can resolve the complexity of the Influenza virus composed of rare, closely related mutant variants Inproceedings

International Conference on Research in Computational Molecular Biology, pp. 164–175, Springer 2016.

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Lay, Fides D; Liang, Gangning

Rethinking demethylating agents in epigenetic cancer therapy Journal Article

Journal of Molecular Pharmaceutics & Organic Process Research, 2016.

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Charlet, Jessica; Duymich, Christopher E; Lay, Fides D; Mundbjerg, Kamilla; Sørensen, Karina Dalsgaard; Liang, Gangning; Jones, Peter A

Bivalent regions of cytosine methylation and H3K27 acetylation suggest an active role for DNA methylation at enhancers Journal Article

Molecular cell, 62 (3), pp. 422–431, 2016.

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Schokrpur, Shiruyeh; Hu, Junhui; Moughon, Diana L; Liu, Peijun; Lin, Lucia C; Hermann, Kip; Mangul, Serghei; Guan, Wei; Pellegrini, Matteo; Xu, Hua; others,

CRISPR-mediated VHL knockout generates an improved model for metastatic renal cell carcinoma Journal Article

Scientific reports, 6 , pp. 29032, 2016.

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Hoban, Megan D; Lumaquin, Dianne; Kuo, Caroline Y; Romero, Zulema; Long, Joseph D; Ho, Michelle; Young, Courtney S; Mojadidi, Michelle; Fitz-Gibbon, Sorel T; Cooper, Aaron R; others,

CRISPR/Cas9-mediated correction of the sickle mutation in human CD34+ cells Journal Article

Molecular Therapy, 24 (9), pp. 1561–1569, 2016.

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Robinson, Jacqueline A; Vecchyo, Diego Ortega-Del; Fan, Zhenxin; Kim, Bernard Y; Marsden, Clare D; Lohmueller, Kirk E; Wayne, Robert K; others,

Genomic flatlining in the endangered island fox Journal Article

Current Biology, 26 (9), pp. 1183–1189, 2016.

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Langousis, Gerasimos; Shimogawa, Michelle M; Saada, Edwin A; Vashisht, Ajay A; Spreafico, Roberto; Nager, Andrew R; Barshop, William D; Nachury, Maxence V; Wohlschlegel, James A; Hill, Kent L

Loss of the BBSome perturbs endocytic trafficking and disrupts virulence of Trypanosoma brucei Journal Article

Proceedings of the National Academy of Sciences, 113 (3), pp. 632–637, 2016.

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Sosa, Rebecca A; Zarrinpar, Ali; Rossetti, Maura; Lassman, Charles R; Naini, Bita V; Datta, Nakul; Rao, Ping; Harre, Nicholas; Zheng, Ying; Spreafico, Roberto; others,

Early cytokine signatures of ischemia/reperfusion injury in human orthotopic liver transplantation Journal Article

JCI insight, 1 (20), 2016.

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Rossetti, Maura; Spreafico, Roberto; Consolaro, Alessandro; Leong, Jing Yao; Chua, Camillus; Massa, Margherita; Saidin, Suzan; Magni-Manzoni, Silvia; Arkachaisri, Thaschawee; Wallace, Carol A; others,

TCR repertoire sequencing identifies synovial Treg cell clonotypes in the bloodstream during active inflammation in human arthritis Journal Article

Annals of the rheumatic diseases, pp. annrheumdis–2015, 2016.

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Traller, Jesse C; Cokus, Shawn J; Lopez, David Adrian; Gaidarenko, Olga; Smith, Sarah R; McCrow, John P; Gallaher, Sean D; Podell, Sheila; Thompson, Michael J; Cook, Orna; others,

Genome and methylome of the oleaginous diatom Cyclotella cryptica reveal genetic flexibility toward a high lipid phenotype Journal Article

Biotechnology for biofuels, 9 (1), pp. 258, 2016.

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Koh, Wonshill; Li, Wei; Ni, Ying; Mislick, Kayla; Agatisa-Boyle, Brendan; Merkurjev, Daria; Lusis, Aldons J; Tang, WH Wilson

Profiling in Lamin Mutated Dilated Cardiomyopathy Mouse Model Using RNA Sequence Analysis Journal Article

Journal of Cardiac Failure, 22 (8), pp. S86, 2016.

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Shin, Daniel Sanghoon; Zaretsky, Jesse M; Escuin-Ordinas, Helena; Garcia-Diaz, Angel; Hu-Lieskovan, Siwen; Kalbasi, Anusha; Grasso, Catherine S; Hugo, Willy; Sandoval, Salemiz; Torrejon, Davis Y; others,

Primary resistance to PD-1 blockade mediated by JAK$1/2$ mutations Journal Article

Cancer discovery, pp. CD–16, 2016.

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Koch, Ilana Janowitz; Clark, Michelle M; Thompson, Michael J; Deere-Machemer, Kerry A; Wang, Jun; Duarte, Lionel; Gnanadesikan, Gitanjali E; McCoy, Eskender L; Rubbi, Liudmilla; Stahler, Daniel R; others,

The concerted impact of domestication and transposon insertions on methylation patterns between dogs and grey wolves Journal Article

Molecular ecology, 25 (8), pp. 1838–1855, 2016.

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116 entries « 2 of 3 »