Classifying the Post-duplication Fate of Paralogous Genes
20th RECOMB satellite conference on comparative genomics

Authors: Kalhor, Reza, Beslon, Guillaume, Lafond, Manuel, Scornavacca, Celine

Source: Lecture notes in computer science. 13883:1-18

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Spatial and temporal organization of the genome: Current state and future aims of the 4D nucleome project

Authors: Dekker, Job, Alber, Frank, Aufmkolk, Sarah, Beliveau, Brian J., Bruneau, Benoit G., Belmont, Andrew S., Bintu, Lacramioara, Boettiger, Alistair, Calandrelli, Riccardo, Disteche, Christine M., Gilbert, David M., Gregor, Thomas, Hansen, Anders S., Huang, Bo, Huangfu, Danwei, Kalhor, Reza, Leslie, Christina S., Li, Wenbo, Li, Yun, Ma, Jian, Noble, William S., Park, Peter J., Phillips-Cremins, Jennifer E., Pollard, Katherine S., Rafelski, Susanne M., Ren, Bing, Ruan, Yijun, Shav-Tal, Yaron, Shen, Yin, Shendure, Jay, Shu, Xiaokun, Strambio-De-Castillia, Caterina, Vertii, Anastassiia, Zhang, Huaiying, Zhong, Sheng

Source: Molecular cell. 83(15):2624-2640

Availability: http://explore.bl.uk/primo_library/libweb/action/display.do?tabs=detailsTab&gathStatTab=true&ct=display&fn=search&doc=ETOCvdc_100194885251.0x000001&indx=1&recIds=ETOCvdc_100194885251.0x000001

Quantitative fate mapping: A general framework for analyzing progenitor state dynamics via retrospective lineage barcoding

Authors: Fang, Weixiang, Bell, Claire M., Sapirstein, Abel, Asami, Soichiro, Leeper, Kathleen, Zack, Donald J., Ji, Hongkai, Kalhor, Reza

Source: In Cell 23 November 2022 185(24):4604-4620

Recording Temporal Signals with Minutes Resolution Using Enzymatic DNA Synthesis

Authors: Bhan, Namita, Callisto, Alec, Strutz, Jonathan, Glaser, Joshua, Kalhor, Reza, Boyden, Edward S., Church, George, Kording, Konrad, Tyo, Keith E. J.

Source: Journal of the American Chemical Society. 143(40):16630-16640

Availability: http://explore.bl.uk/primo_library/libweb/action/display.do?tabs=detailsTab&gathStatTab=true&ct=display&fn=search&doc=ETOCRN627799170&indx=1&recIds=ETOCRN627799170

Rosetta Brains: A Strategy for Molecularly-Annotated Connectomics

Authors: Marblestone, Adam H, Daugharthy, Evan R, Kalhor, Reza, Peikon, Ian D, Kebschull, Justus M, Shipman, Seth L, Mishchenko, Yuriy, Lee, Je Hyuk, Kording, Konrad P, Boyden, Edward S, Zador, Anthony M, Church, George M

Subject Terms: Quantitative Biology - Neurons and Cognition

Access URL: http://arxiv.org/abs/1404.5103

Physical Principles for Scalable Neural Recording

Authors: Marblestone, Adam H., Zamft, Bradley M., Maguire, Yael G., Shapiro, Mikhail G., Cybulski, Thaddeus R., Glaser, Joshua I., Amodei, Dario, Stranges, P. Benjamin, Kalhor, Reza, Dalrymple, David A., Seo, Dongjin, Alon, Elad, Maharbiz, Michel M., Carmena, Jose M., Rabaey, Jan M., Boyden, Edward S., Church, George M., Kording, Konrad P.

Subject Terms: Quantitative Biology - Neurons and Cognition, Physics - Biological Physics

Access URL: http://arxiv.org/abs/1306.5709

A Rigorous Framework to Classify the Postduplication Fate of Paralogous Genes.

Authors: Kalhor, Reza¹ (AUTHOR) Reza.Kalhor@USherbrooke.ca, Beslon, Guillaume² (AUTHOR), Lafond, Manuel¹ (AUTHOR), Scornavacca, Celine³ (AUTHOR)

Source: Journal of Computational Biology. Sep2024, Vol. 31 Issue 9, p815-833. 19p.

Subject Terms: *CHROMOSOME duplication, *GENES, *CLASSIFICATION, *DEFINITIONS

Developmental barcoding of whole mouse via homing CRISPR

Authors: Kalhor, Reza, Kalhor, Kian, Mejia, Leo, Leeper, Kathleen, Graveline, Amanda, Mali, Prashant, Church, George M.

Source: Science, 2018 Aug . 361(6405), 893-893.

Access URL: https://www.jstor.org/stable/26505251

Terminator-free template-independent enzymatic DNA synthesis for digital information storage

Authors: Lee, Henry, Kalhor, Reza, Goela, Naveen, Bolot, Jean, Church, George

Source: Nature communications. 10(1):1-12

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Temporal recording of mammalian development and precancer

Authors: Islam, Mirazul, Yang, Yilin, Simmons, Alan J., Shah, Vishal M., Musale, Krushna Pavan, Xu, Yanwen, Tasneem, Naila, Chen, Zhengyi, Trinh, Linh T., Molina, Paola, Ramirez-Solano, Marisol A., Sadien, Iannish D., Dou, Jinzhuang, Rolong, Andrea, Chen, Ken, Magnuson, Mark A., Rathmell, Jeffrey C., Macara, Ian G., Winton, Douglas J., Liu, Qi, Zafar, Hamim, Kalhor, Reza, Church, George M., Shrubsole, Martha J., Coffey, Robert J., Lau, Ken S.

Source: Nature; October 2024, Vol. 634 Issue: 8036 p1187-1195, 9p

Conserved forkhead dimerization motif controls DNA replication timing and spatial organization of chromosomes in S. cerevisiae

Authors: Ostrow, A. Zachary, Kalhor, Reza, Gan, Yan, Villwock, Sandra K., Linke, Christian, Barberis, Matteo, Chen, Lin, Aparicio, Oscar M.

Source: Proceedings of the National Academy of Sciences of the United States of America, 2017 Mar . 114(12), E2411-E2419.

Access URL: https://www.jstor.org/stable/26480212

Population-based 3D genome structure analysis reveals driving forces in spatial genome organization

Authors: Tjong, Harianto, Li, Wenyuan, Kalhor, Reza, Dai, Chao, Hao, Shengli, Gong, Ke, Zhou, Yonggang, Li, Haochen, Zhou, Xianghong Jasmine, Le Gros, Mark A., Larabell, Carolyn A., Chen, Lin, Alber, Frank

Source: Proceedings of the National Academy of Sciences of the United States of America, 2016 Mar . 113(12), E1663-E1672.

Access URL: https://www.jstor.org/stable/26468794

Multi-target CRISPR for high-throughput studies of double-strand break repair and genetic barcoding at endogenous sites

Authors: Marin-Gonzalez, Alberto, Zou, Roger S., Dveirin, Rachel, Liu, Yang, Shen, Leo, Luo, Jay, Kalhor, Reza, Ha, Taekjip

Source: Biophysical journal. 121(S1):447a-448a

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Multiplexing Cas9 activity with multi-target CRISPR

Authors: Marin-Gonzalez, Alberto, Zou, Roger, Liu, Yang, Shen, Leo, Dveirin, Rachel, Luo, Jay, Kalhor, Reza, Ha, Taekjip

Source: Biophysical journal. 122(S1):307a-307a

Availability: http://explore.bl.uk/primo_library/libweb/action/display.do?tabs=detailsTab&gathStatTab=true&ct=display&fn=search&doc=ETOCvdc_100185960088.0x000001&indx=1&recIds=ETOCvdc_100185960088.0x000001

Highly Multiplexed Subcellular RNA Sequencing in Situ

Authors: Lee, Je Hyuk, Daugharthy, Evan R., Scheiman, Jonathan, Kalhor, Reza, Yang, Joyce L., Ferrante, Thomas C., Terry, Richard, Jeanty, Sauveur S. F., Li, Chao, Amamoto, Ryoji, Peters, Derek T., Turczyk, Brian M., Marblestone, Adam H., Inverso, Samuel A., Bernard, Amy, Mali, Prashant, Rios, Xavier, Aach, John, Church, George M.

Source: Science, 2014 Mar . 343(6177), 1360-1363.

Access URL: http://www.jstor.org/stable/24743483

Crystal Structure of NFAT Bound to the HIV-1 LTR Tandem κB Enhancer Element

Authors: Bates, Darren L., Barthel, Kristen K.B., Wu, Yongqing, Kalhor, Reza, Stroud, James C., Giffin, Michael J., Chen, Lin

Source: In Structure 7 May 2008 16(5):684-694

Genome-wide chromosome conformation capture

Tethered Conformation Capture

Genome-Wide Chromosome Conformation Capture

Homozygous Missense Mutation in Fibulin-5 in an Iranian Autosomal Recessive Cutis Laxa Pedigree and Associated Haplotype

Authors: Elahi, Elahe ^*, Kalhor, Reza, Banihosseini, Setareh S., Torabi, Noorossadat, Pour-Jafari, Hamid, Houshmand, Massoud, Amini, Seyed S.H., Ramezani, Ahmad, Loeys, Bart

Source: In Journal of Investigative Dermatology July 2006 126(7):1506-1509